Starting phenix.real_space_refine on Thu Mar 21 07:37:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gxw_34363/03_2024/8gxw_34363_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gxw_34363/03_2024/8gxw_34363.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gxw_34363/03_2024/8gxw_34363.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gxw_34363/03_2024/8gxw_34363.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gxw_34363/03_2024/8gxw_34363_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gxw_34363/03_2024/8gxw_34363_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 1 5.21 5 S 104 5.16 5 C 18725 2.51 5 N 5126 2.21 5 O 5568 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 225": "OD1" <-> "OD2" Residue "E PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 29530 Number of models: 1 Model: "" Number of chains: 15 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: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 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: 15.75, per 1000 atoms: 0.53 Number of scatterers: 29530 At special positions: 0 Unit cell: (149.4, 151.06, 173.47, 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 6 15.00 Mg 1 11.99 O 5568 8.00 N 5126 7.00 C 18725 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: 12.02 Conformation dependent library (CDL) restraints added in 5.6 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: 134 helices and 34 sheets defined 42.4% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.60 Creating SS restraints... Processing helix chain 'A' and resid 91 through 97 Processing helix chain 'A' and resid 210 through 214 Processing helix chain 'A' and resid 234 through 244 Processing helix chain 'A' and resid 259 through 271 Proline residue: A 270 - end of helix Processing helix chain 'A' and resid 281 through 284 Processing helix chain 'A' and resid 296 through 315 removed outlier: 3.609A 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 354 through 364 removed outlier: 3.808A pdb=" N ARG A 364 " --> 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 401 Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'A' and resid 433 through 442 Proline residue: A 437 - end of helix removed outlier: 3.571A pdb=" N ASN A 442 " --> pdb=" O TYR A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 471 removed outlier: 4.013A pdb=" N GLU A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ILE A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 475 No H-bonds generated for 'chain 'A' and resid 473 through 475' Processing helix chain 'A' and resid 478 through 493 Processing helix chain 'A' and resid 509 through 532 Processing helix chain 'A' and resid 536 through 539 No H-bonds generated for 'chain 'A' and resid 536 through 539' Processing helix chain 'A' and resid 543 through 553 removed outlier: 3.597A pdb=" N ALA A 551 " --> pdb=" O ILE A 548 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ARG A 552 " --> pdb=" O GLY A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 575 removed outlier: 3.848A pdb=" N PHE A 574 " --> pdb=" O ILE A 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 98 Processing helix chain 'B' and resid 210 through 214 Processing helix chain 'B' and resid 234 through 244 Processing helix chain 'B' and resid 259 through 271 Proline residue: B 270 - end of helix Processing helix chain 'B' and resid 281 through 284 Processing helix chain 'B' and resid 296 through 315 removed outlier: 4.983A pdb=" N ILE B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 4.700A 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 364 removed outlier: 3.832A pdb=" N ARG B 364 " --> pdb=" O ALA B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 402 removed outlier: 3.639A pdb=" N ILE B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 415 Processing helix chain 'B' and resid 432 through 442 Proline residue: B 437 - end of helix Processing helix chain 'B' and resid 447 through 463 Processing helix chain 'B' and resid 465 through 470 Processing helix chain 'B' and resid 478 through 493 Processing helix chain 'B' and resid 509 through 532 Processing helix chain 'B' and resid 536 through 541 Processing helix chain 'B' and resid 543 through 549 Processing helix chain 'B' and resid 551 through 553 No H-bonds generated for 'chain 'B' and resid 551 through 553' Processing helix chain 'B' and resid 559 through 576 removed outlier: 3.863A pdb=" N PHE B 574 " --> pdb=" O ILE B 570 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS B 575 " --> pdb=" O GLN B 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'C' and resid 210 through 214 Processing helix chain 'C' and resid 234 through 244 Processing helix chain 'C' and resid 259 through 271 Proline residue: C 270 - end of helix Processing helix chain 'C' and resid 281 through 284 Processing helix chain 'C' and resid 296 through 315 removed outlier: 3.661A 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 347 through 349 No H-bonds generated for 'chain 'C' and resid 347 through 349' Processing helix chain 'C' and resid 354 through 364 removed outlier: 3.566A 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 399 Processing helix chain 'C' and resid 411 through 415 Processing helix chain 'C' and resid 436 through 442 Processing helix chain 'C' and resid 447 through 471 removed outlier: 4.039A pdb=" N GLU C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 4.128A 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 532 Processing helix chain 'C' and resid 536 through 540 Processing helix chain 'C' and resid 543 through 549 Processing helix chain 'C' and resid 551 through 553 No H-bonds generated for 'chain 'C' and resid 551 through 553' Processing helix chain 'C' and resid 559 through 575 removed outlier: 3.595A pdb=" N GLN C 571 " --> pdb=" O MET C 567 " (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 198 through 210 Processing helix chain 'D' and resid 213 through 216 Processing helix chain 'D' and resid 228 through 249 Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 260 through 274 Processing helix chain 'D' and resid 280 through 282 No H-bonds generated for 'chain 'D' and resid 280 through 282' Processing helix chain 'D' and resid 287 through 297 removed outlier: 4.391A 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 346 Processing helix chain 'D' and resid 362 through 365 No H-bonds generated for 'chain 'D' and resid 362 through 365' Processing helix chain 'D' and resid 375 through 399 removed outlier: 3.916A pdb=" N ALA D 397 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ILE D 398 " --> pdb=" O LYS D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 421 Processing helix chain 'D' and resid 432 through 445 removed outlier: 3.878A 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: 3.765A pdb=" N TRP D 471 " --> pdb=" O GLU D 468 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 88 No H-bonds generated for 'chain 'E' and resid 86 through 88' Processing helix chain 'E' and resid 136 through 140 Processing helix chain 'E' and resid 160 through 170 Processing helix chain 'E' and resid 175 through 178 Processing helix chain 'E' and resid 198 through 210 Processing helix chain 'E' and resid 213 through 216 Processing helix chain 'E' and resid 228 through 249 removed outlier: 3.506A pdb=" N ILE E 232 " --> pdb=" O THR E 228 " (cutoff:3.500A) Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 260 through 274 Processing helix chain 'E' and resid 287 through 297 removed outlier: 3.534A pdb=" N ILE E 294 " --> pdb=" O ASP E 290 " (cutoff:3.500A) removed outlier: 4.922A 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 Processing helix chain 'E' and resid 341 through 345 Processing helix chain 'E' and resid 362 through 364 No H-bonds generated for 'chain 'E' and resid 362 through 364' Processing helix chain 'E' and resid 375 through 399 removed outlier: 3.882A pdb=" N ALA E 397 " --> pdb=" O ARG E 393 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ILE E 398 " --> pdb=" O LYS E 394 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE E 399 " --> pdb=" O LEU E 395 " (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: 3.792A 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 141 Processing helix chain 'F' and resid 160 through 170 Processing helix chain 'F' and resid 175 through 178 No H-bonds generated for 'chain 'F' and resid 175 through 178' Processing helix chain 'F' and resid 198 through 211 Processing helix chain 'F' and resid 214 through 216 No H-bonds generated for 'chain 'F' and resid 214 through 216' Processing helix chain 'F' and resid 229 through 249 removed outlier: 3.619A pdb=" N THR F 234 " --> pdb=" O ARG F 231 " (cutoff:3.500A) Proline residue: F 235 - end of helix removed outlier: 3.546A pdb=" N PHE F 247 " --> pdb=" O TYR F 244 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU F 248 " --> pdb=" O LEU F 245 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N HIS F 249 " --> pdb=" O ALA F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 273 Processing helix chain 'F' and resid 280 through 282 No H-bonds generated for 'chain 'F' and resid 280 through 282' Processing helix chain 'F' and resid 287 through 295 removed outlier: 3.606A pdb=" N ILE F 294 " --> pdb=" O ASP F 290 " (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 360 through 364 removed outlier: 4.290A pdb=" N ASN F 363 " --> pdb=" O ARG F 360 " (cutoff:3.500A) Processing helix chain 'F' and resid 375 through 399 removed outlier: 3.686A 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: 4.008A pdb=" N MET F 445 " --> pdb=" O ALA F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 450 No H-bonds generated for 'chain 'F' and resid 448 through 450' Processing helix chain 'F' and resid 456 through 462 Processing helix chain 'F' and resid 467 through 469 No H-bonds generated for 'chain 'F' and resid 467 through 469' Processing helix chain 'G' and resid 8 through 65 removed outlier: 3.698A pdb=" N GLY G 41 " --> pdb=" O ALA G 37 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ARG G 44 " --> pdb=" O PHE G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 70 No H-bonds generated for 'chain 'G' and resid 67 through 70' 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 123 through 207 removed outlier: 4.213A pdb=" N ARG G 128 " --> pdb=" O LEU G 124 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA G 129 " --> pdb=" O GLU G 125 " (cutoff:3.500A) removed outlier: 5.372A 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 removed outlier: 3.527A pdb=" N GLN H 11 " --> pdb=" O PRO H 7 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLY H 12 " --> pdb=" O GLU H 8 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 38 Processing helix chain 'H' and resid 55 through 63 removed outlier: 6.787A pdb=" N ARG H 61 " --> pdb=" O ARG H 57 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N LEU H 62 " --> pdb=" O ALA H 58 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N MET H 63 " --> pdb=" O VAL H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 82 removed outlier: 3.820A pdb=" N PHE H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN H 82 " --> pdb=" O LYS H 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 77 through 82' Processing helix chain 'H' and resid 86 through 97 Processing helix chain 'I' and resid 82 through 118 removed outlier: 3.512A pdb=" N ARG I 106 " --> pdb=" O LYS I 102 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ASP I 108 " --> pdb=" O MET I 104 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N GLU I 109 " --> pdb=" O ALA I 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 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: 4.518A pdb=" N ALA J 133 " --> pdb=" O PRO J 129 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N LEU J 134 " --> pdb=" O HIS J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 167 through 186 removed outlier: 4.499A pdb=" N ASP J 176 " --> pdb=" O ASP J 172 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ALA J 177 " --> pdb=" O ARG J 173 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N SER J 180 " --> pdb=" O ASP J 176 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS J 181 " --> pdb=" O ALA J 177 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN J 184 " --> pdb=" O SER J 180 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA J 185 " --> pdb=" O LYS J 181 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 118 removed outlier: 3.971A pdb=" N ARG K 106 " --> pdb=" O LYS K 102 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N ASP K 108 " --> pdb=" O MET K 104 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N GLU K 109 " --> pdb=" O ALA K 105 " (cutoff:3.500A) Processing helix chain 'L' and resid 63 through 96 Proline residue: L 95 - end of helix Processing helix chain 'L' and resid 98 through 114 Proline residue: L 101 - end of helix Processing helix chain 'L' and resid 125 through 138 Proline residue: L 129 - end of helix removed outlier: 5.259A pdb=" N ALA L 133 " --> pdb=" O PRO L 129 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N LEU L 134 " --> pdb=" O HIS L 130 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG L 136 " --> pdb=" O GLU L 132 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 186 removed outlier: 5.346A pdb=" N ASP L 176 " --> pdb=" O ASP L 172 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N ALA L 177 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N SER L 180 " --> pdb=" O ASP L 176 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N LYS L 181 " --> pdb=" O ALA L 177 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 3 through 5 removed outlier: 6.373A pdb=" N PHE A 48 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N LEU A 42 " --> pdb=" O THR A 46 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N THR A 46 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N LYS A 17 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ILE A 6 " --> pdb=" O LYS A 17 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 72 through 75 Processing sheet with id= C, first strand: chain 'A' and resid 82 through 84 removed outlier: 4.001A pdb=" N GLY A 82 " --> pdb=" O THR A 285 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL A 250 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ILE A 288 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N TYR A 252 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ASN A 290 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N GLY A 254 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ALA A 377 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N LEU A 322 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N THR A 379 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ALA A 324 " --> pdb=" O THR A 379 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL A 381 " --> pdb=" O ALA A 324 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 117 through 119 Processing sheet with id= E, first strand: chain 'A' and resid 197 through 199 removed outlier: 3.515A pdb=" N ARG A 197 " --> pdb=" O ILE A 369 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LYS A 367 " --> pdb=" O LEU A 199 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 134 through 140 removed outlier: 6.633A pdb=" N ILE A 147 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N THR A 137 " --> pdb=" O HIS A 145 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N HIS A 145 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N PHE A 143 " --> pdb=" O PRO A 139 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 157 through 160 removed outlier: 7.132A pdb=" N VAL A 174 " --> pdb=" O LYS A 158 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 2 through 5 removed outlier: 4.124A pdb=" N ILE B 2 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N PHE B 48 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N LEU B 42 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N THR B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N LYS B 17 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N ILE B 6 " --> pdb=" O LYS B 17 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 72 through 76 Processing sheet with id= J, first strand: chain 'B' and resid 82 through 84 removed outlier: 4.036A pdb=" N GLY B 82 " --> pdb=" O THR B 285 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL B 250 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ILE B 288 " --> pdb=" O VAL B 250 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N TYR B 252 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL B 249 " --> pdb=" O SER B 319 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ALA B 377 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N LEU B 322 " --> pdb=" O ALA B 377 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N THR B 379 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N ALA B 324 " --> pdb=" O THR B 379 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL B 381 " --> pdb=" O ALA B 324 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ALA B 405 " --> pdb=" O ALA B 225 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N TRP B 407 " --> pdb=" O PRO B 227 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 164 through 166 removed outlier: 5.822A pdb=" N ALA B 118 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE B 147 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N THR B 137 " --> pdb=" O HIS B 145 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N HIS B 145 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N PHE B 143 " --> pdb=" O PRO B 139 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 197 through 199 removed outlier: 3.527A pdb=" N ARG B 197 " --> pdb=" O ILE B 369 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LYS B 367 " --> pdb=" O LEU B 199 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 157 through 160 removed outlier: 6.533A pdb=" N VAL B 174 " --> pdb=" O LYS B 158 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 3 through 5 removed outlier: 6.514A pdb=" N PHE C 48 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N LEU C 42 " --> pdb=" O THR C 46 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N THR C 46 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N LYS C 17 " --> pdb=" O ILE C 6 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N ILE C 6 " --> pdb=" O LYS C 17 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 72 through 76 Processing sheet with id= P, first strand: chain 'C' and resid 82 through 84 removed outlier: 4.075A pdb=" N GLY C 82 " --> pdb=" O THR C 285 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL C 250 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N ILE C 288 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TYR C 252 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N ASN C 290 " --> pdb=" O TYR C 252 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLY C 254 " --> pdb=" O ASN C 290 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ALA C 377 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N LEU C 322 " --> pdb=" O ALA C 377 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N THR C 379 " --> pdb=" O LEU C 322 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N ALA C 324 " --> pdb=" O THR C 379 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL C 381 " --> pdb=" O ALA C 324 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL C 384 " --> pdb=" O ILE C 226 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 164 through 166 removed outlier: 5.495A pdb=" N ALA C 118 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE C 147 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N THR C 137 " --> pdb=" O HIS C 145 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N HIS C 145 " --> pdb=" O THR C 137 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 366 through 369 Processing sheet with id= S, first strand: chain 'C' and resid 157 through 160 removed outlier: 6.813A pdb=" N VAL C 174 " --> pdb=" O LYS C 158 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 11 through 15 removed outlier: 6.336A pdb=" N PHE D 20 " --> pdb=" O THR D 12 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ILE D 14 " --> pdb=" O LEU D 18 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LEU D 18 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU D 49 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N GLN D 58 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N VAL D 47 " --> pdb=" O GLN D 58 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N PHE D 60 " --> pdb=" O GLY D 45 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N GLY D 45 " --> pdb=" O PHE D 60 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ASP D 34 " --> pdb=" O LEU D 75 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LEU D 75 " --> pdb=" O ASP D 34 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N LYS D 36 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N VAL D 73 " --> pdb=" O LYS D 36 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 81 through 84 Processing sheet with id= V, first strand: chain 'D' and resid 91 through 93 removed outlier: 3.929A pdb=" N ARG D 91 " --> pdb=" O SER D 217 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N VAL D 218 " --> pdb=" O PHE D 187 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL D 189 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N PHE D 220 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N PHE D 191 " --> pdb=" O PHE D 220 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N HIS D 252 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N VAL D 190 " --> pdb=" O HIS D 252 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU D 254 " --> pdb=" O VAL D 190 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ALA D 192 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ILE D 256 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N SER D 307 " --> pdb=" O VAL D 253 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N VAL D 255 " --> pdb=" O SER D 307 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N THR D 309 " --> pdb=" O VAL D 255 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N LEU D 257 " --> pdb=" O THR D 309 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE D 311 " --> pdb=" O LEU D 257 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 336 through 338 Processing sheet with id= X, first strand: chain 'E' and resid 11 through 15 removed outlier: 6.542A pdb=" N PHE E 20 " --> pdb=" O THR E 12 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ILE E 14 " --> pdb=" O LEU E 18 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N LEU E 18 " --> pdb=" O ILE E 14 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU E 49 " --> pdb=" O VAL E 56 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N GLN E 58 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N VAL E 47 " --> pdb=" O GLN E 58 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU E 77 " --> pdb=" O ILE E 32 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ASP E 34 " --> pdb=" O LEU E 75 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N LEU E 75 " --> pdb=" O ASP E 34 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N LYS E 36 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 5.628A 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 removed outlier: 3.601A pdb=" N LYS E 110 " --> pdb=" O VAL E 84 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 91 through 93 removed outlier: 3.806A pdb=" N ARG E 91 " --> pdb=" O SER E 217 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N VAL E 218 " --> pdb=" O PHE E 187 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N VAL E 189 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N PHE E 220 " --> pdb=" O VAL E 189 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N PHE E 191 " --> pdb=" O PHE E 220 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N HIS E 252 " --> pdb=" O ALA E 188 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N VAL E 190 " --> pdb=" O HIS E 252 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N LEU E 254 " --> pdb=" O VAL E 190 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N ALA E 192 " --> pdb=" O LEU E 254 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ILE E 256 " --> pdb=" O ALA E 192 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N SER E 307 " --> pdb=" O VAL E 253 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N VAL E 255 " --> pdb=" O SER E 307 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N THR E 309 " --> pdb=" O VAL E 255 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N LEU E 257 " --> pdb=" O THR E 309 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE E 311 " --> pdb=" O LEU E 257 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE E 152 " --> pdb=" O LEU E 314 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'F' and resid 11 through 15 removed outlier: 6.440A pdb=" N PHE F 20 " --> pdb=" O THR F 12 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE F 14 " --> pdb=" O LEU F 18 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LEU F 18 " --> pdb=" O ILE F 14 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU F 49 " --> pdb=" O VAL F 56 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLN F 58 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N VAL F 47 " --> pdb=" O GLN F 58 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N ASP F 34 " --> pdb=" O LEU F 75 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N LEU F 75 " --> pdb=" O ASP F 34 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LYS F 36 " --> pdb=" O VAL F 73 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N VAL F 73 " --> pdb=" O LYS F 36 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 81 through 84 Processing sheet with id= AC, first strand: chain 'F' and resid 92 through 94 removed outlier: 7.916A pdb=" N PHE F 93 " --> pdb=" O SER F 217 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N LEU F 219 " --> pdb=" O PHE F 93 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL F 189 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N PHE F 220 " --> pdb=" O VAL F 189 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N PHE F 191 " --> pdb=" O PHE F 220 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ASN F 222 " --> pdb=" O PHE F 191 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ALA F 193 " --> pdb=" O ASN F 222 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N SER F 307 " --> pdb=" O VAL F 253 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N VAL F 255 " --> pdb=" O SER F 307 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N THR F 309 " --> pdb=" O VAL F 255 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N LEU F 257 " --> pdb=" O THR F 309 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ILE F 311 " --> pdb=" O LEU F 257 " (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 'G' and resid 91 through 96 Processing sheet with id= AF, first strand: chain 'H' and resid 19 through 22 removed outlier: 3.534A pdb=" N TYR H 21 " --> pdb=" O VAL H 3 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ASP H 48 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N VAL H 70 " --> pdb=" O VAL H 45 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N VAL H 47 " --> pdb=" O VAL H 70 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU H 72 " --> pdb=" O VAL H 47 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'J' and resid 141 through 144 removed outlier: 7.055A pdb=" N VAL J 155 " --> pdb=" O LYS J 119 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N LEU J 121 " --> pdb=" O ARG J 153 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ARG J 153 " --> pdb=" O LEU J 121 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'L' and resid 141 through 144 removed outlier: 3.509A pdb=" N ALA L 123 " --> pdb=" O GLN L 143 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL L 155 " --> pdb=" O LYS L 119 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LEU L 121 " --> pdb=" O ARG L 153 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ARG L 153 " --> pdb=" O LEU L 121 " (cutoff:3.500A) 1224 hydrogen bonds defined for protein. 3342 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: 10.04 Time building geometry restraints manager: 12.97 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: 9964 1.34 - 1.46: 4874 1.46 - 1.58: 15045 1.58 - 1.69: 8 1.69 - 1.81: 194 Bond restraints: 30085 Sorted by residual: bond pdb=" O3 SO4 A 600 " pdb=" S SO4 A 600 " ideal model delta sigma weight residual 1.499 1.450 0.049 2.00e-02 2.50e+03 5.89e+00 bond pdb=" O4 SO4 A 600 " pdb=" S SO4 A 600 " ideal model delta sigma weight residual 1.499 1.453 0.046 2.00e-02 2.50e+03 5.27e+00 bond pdb=" O2 SO4 A 600 " pdb=" S SO4 A 600 " ideal model delta sigma weight residual 1.498 1.452 0.046 2.00e-02 2.50e+03 5.19e+00 bond pdb=" O1 SO4 A 600 " pdb=" S SO4 A 600 " ideal model delta sigma weight residual 1.498 1.454 0.044 2.00e-02 2.50e+03 4.85e+00 bond pdb=" N MET H 1 " pdb=" CA MET H 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.00e+00 ... (remaining 30080 not shown) Histogram of bond angle deviations from ideal: 99.51 - 107.57: 1232 107.57 - 115.62: 18259 115.62 - 123.68: 20533 123.68 - 131.73: 702 131.73 - 139.78: 42 Bond angle restraints: 40768 Sorted by residual: angle pdb=" N ILE C 402 " pdb=" CA ILE C 402 " pdb=" C ILE C 402 " ideal model delta sigma weight residual 113.71 110.88 2.83 9.50e-01 1.11e+00 8.88e+00 angle pdb=" C3' ATP C 601 " pdb=" C4' ATP C 601 " pdb=" O4' ATP C 601 " ideal model delta sigma weight residual 105.22 101.58 3.64 1.30e+00 5.94e-01 7.85e+00 angle pdb=" N PRO A 420 " pdb=" CA PRO A 420 " pdb=" C PRO A 420 " ideal model delta sigma weight residual 112.10 118.97 -6.87 2.60e+00 1.48e-01 6.98e+00 angle pdb=" N ILE D 325 " pdb=" CA ILE D 325 " pdb=" C ILE D 325 " ideal model delta sigma weight residual 112.35 109.39 2.96 1.20e+00 6.94e-01 6.08e+00 angle pdb=" N VAL D 76 " pdb=" CA VAL D 76 " pdb=" C VAL D 76 " ideal model delta sigma weight residual 111.67 109.38 2.29 9.50e-01 1.11e+00 5.83e+00 ... (remaining 40763 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 16628 17.85 - 35.71: 1354 35.71 - 53.56: 302 53.56 - 71.42: 58 71.42 - 89.27: 30 Dihedral angle restraints: 18372 sinusoidal: 7550 harmonic: 10822 Sorted by residual: dihedral pdb=" CA VAL A 368 " pdb=" C VAL A 368 " pdb=" N ILE A 369 " pdb=" CA ILE A 369 " ideal model delta harmonic sigma weight residual 180.00 155.70 24.30 0 5.00e+00 4.00e-02 2.36e+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 -158.40 -21.60 0 5.00e+00 4.00e-02 1.87e+01 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 -159.11 -20.89 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 18369 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 3848 0.058 - 0.117: 653 0.117 - 0.175: 61 0.175 - 0.234: 0 0.234 - 0.292: 6 Chirality restraints: 4568 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 2.13e+00 chirality pdb=" C2' ATP B 601 " pdb=" C1' ATP B 601 " pdb=" C3' ATP B 601 " pdb=" O2' ATP B 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 B 601 " pdb=" C2' ATP B 601 " pdb=" C4' ATP B 601 " pdb=" O3' ATP B 601 " both_signs ideal model delta sigma weight residual False -2.63 -2.91 0.28 2.00e-01 2.50e+01 1.93e+00 ... (remaining 4565 not shown) Planarity restraints: 5332 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS D 323 " -0.038 5.00e-02 4.00e+02 5.72e-02 5.23e+00 pdb=" N PRO D 324 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO D 324 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 324 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 386 " -0.034 5.00e-02 4.00e+02 5.19e-02 4.31e+00 pdb=" N PRO C 387 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO C 387 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 387 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS F 323 " -0.028 5.00e-02 4.00e+02 4.17e-02 2.78e+00 pdb=" N PRO F 324 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO F 324 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO F 324 " -0.023 5.00e-02 4.00e+02 ... (remaining 5329 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 117 2.45 - 3.07: 20325 3.07 - 3.68: 44631 3.68 - 4.29: 67482 4.29 - 4.90: 113480 Nonbonded interactions: 246035 Sorted by model distance: nonbonded pdb=" OG SER C 235 " pdb="MG MG C 602 " model vdw 1.843 2.170 nonbonded pdb=" O2G ATP C 601 " pdb="MG MG C 602 " model vdw 1.883 2.170 nonbonded pdb=" O MET C 220 " pdb=" OG1 THR C 379 " model vdw 1.952 2.440 nonbonded pdb=" O LYS E 370 " pdb=" OG1 THR E 371 " model vdw 1.955 2.440 nonbonded pdb=" O MET A 220 " pdb=" OG1 THR A 379 " model vdw 1.983 2.440 ... (remaining 246030 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' and resid 1 through 578) 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: 3.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 14.630 Check model and map are aligned: 0.380 Set scattering table: 0.230 Process input model: 78.500 Find NCS groups from input model: 2.030 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:10.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 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 0.086 30085 Z= 0.367 Angle : 0.546 6.868 40768 Z= 0.286 Chirality : 0.044 0.292 4568 Planarity : 0.004 0.057 5332 Dihedral : 14.203 89.274 11454 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.36 % Favored : 97.61 % Rotamer: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.14), residues: 3764 helix: 1.67 (0.13), residues: 1570 sheet: -0.06 (0.22), residues: 552 loop : 0.01 (0.16), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 119 HIS 0.008 0.001 HIS B 283 PHE 0.017 0.002 PHE D 60 TYR 0.016 0.002 TYR E 463 ARG 0.006 0.000 ARG F 210 *********************** 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 798 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 798 time to evaluate : 3.397 Fit side-chains REVERT: A 3 GLN cc_start: 0.7613 (mt0) cc_final: 0.7333 (tm-30) REVERT: A 93 ARG cc_start: 0.7595 (mmp80) cc_final: 0.7230 (mmp80) REVERT: A 133 MET cc_start: 0.7648 (mtp) cc_final: 0.7347 (mtt) REVERT: A 156 ARG cc_start: 0.6628 (mtm110) cc_final: 0.5655 (ttm-80) REVERT: A 296 VAL cc_start: 0.8746 (p) cc_final: 0.8426 (t) REVERT: A 397 GLN cc_start: 0.8469 (mm110) cc_final: 0.8232 (mm110) REVERT: A 491 ARG cc_start: 0.7530 (mmt180) cc_final: 0.6575 (mtm110) REVERT: A 502 GLU cc_start: 0.6514 (mp0) cc_final: 0.6262 (tp30) REVERT: A 524 LYS cc_start: 0.7689 (mmmt) cc_final: 0.7372 (mttm) REVERT: A 527 GLU cc_start: 0.7008 (tt0) cc_final: 0.6583 (pt0) REVERT: B 93 ARG cc_start: 0.7372 (mtm-85) cc_final: 0.7167 (mtm110) REVERT: B 282 MET cc_start: 0.8431 (mmm) cc_final: 0.8210 (tpt) REVERT: B 415 PHE cc_start: 0.7649 (t80) cc_final: 0.7035 (t80) REVERT: B 447 TYR cc_start: 0.7074 (t80) cc_final: 0.6692 (t80) REVERT: B 452 ASP cc_start: 0.6537 (m-30) cc_final: 0.5858 (t70) REVERT: B 456 GLU cc_start: 0.6833 (tp30) cc_final: 0.6299 (tm-30) REVERT: B 477 GLN cc_start: 0.4762 (mt0) cc_final: 0.4411 (pt0) REVERT: B 524 LYS cc_start: 0.5586 (mmmt) cc_final: 0.5355 (ttmt) REVERT: B 527 GLU cc_start: 0.5878 (tt0) cc_final: 0.5593 (tt0) REVERT: C 133 MET cc_start: 0.8049 (mtp) cc_final: 0.7836 (mtp) REVERT: C 152 ASP cc_start: 0.7643 (m-30) cc_final: 0.7245 (p0) REVERT: C 182 LYS cc_start: 0.8171 (mtpt) cc_final: 0.7924 (mttp) REVERT: C 424 TRP cc_start: 0.7882 (p90) cc_final: 0.7266 (p-90) REVERT: C 425 ASN cc_start: 0.8172 (m-40) cc_final: 0.7677 (t0) REVERT: C 527 GLU cc_start: 0.6580 (mm-30) cc_final: 0.6117 (pt0) REVERT: C 548 ILE cc_start: 0.6871 (mt) cc_final: 0.6523 (mt) REVERT: C 567 MET cc_start: 0.7028 (mmm) cc_final: 0.6648 (mmm) REVERT: C 568 LYS cc_start: 0.7113 (mttt) cc_final: 0.6841 (mppt) REVERT: D 34 ASP cc_start: 0.7079 (m-30) cc_final: 0.6839 (m-30) REVERT: D 70 THR cc_start: 0.7621 (p) cc_final: 0.7420 (p) REVERT: D 259 ASP cc_start: 0.6161 (t0) cc_final: 0.5796 (t0) REVERT: D 358 LEU cc_start: 0.8805 (tp) cc_final: 0.8590 (tm) REVERT: D 362 MET cc_start: 0.8712 (ttt) cc_final: 0.8345 (ttp) REVERT: D 388 ASN cc_start: 0.7403 (m-40) cc_final: 0.6941 (t0) REVERT: D 420 ARG cc_start: 0.7050 (mtm-85) cc_final: 0.6833 (mmm160) REVERT: E 5 LYS cc_start: 0.4667 (mttt) cc_final: 0.4388 (ptmt) REVERT: E 81 ARG cc_start: 0.7204 (mtm-85) cc_final: 0.6722 (mtt90) REVERT: E 133 THR cc_start: 0.8549 (p) cc_final: 0.8272 (t) REVERT: E 206 GLN cc_start: 0.7063 (tp40) cc_final: 0.6810 (tp40) REVERT: E 248 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7438 (mm-30) REVERT: E 250 ASP cc_start: 0.7994 (m-30) cc_final: 0.7768 (m-30) REVERT: E 364 ASN cc_start: 0.8192 (t0) cc_final: 0.7963 (t0) REVERT: E 393 ARG cc_start: 0.7245 (ttp-170) cc_final: 0.7015 (ttm170) REVERT: F 5 LYS cc_start: 0.6382 (tttt) cc_final: 0.6053 (ttmt) REVERT: F 36 LYS cc_start: 0.7973 (tttt) cc_final: 0.7768 (ttpp) REVERT: F 50 VAL cc_start: 0.8940 (t) cc_final: 0.8682 (m) REVERT: F 376 LYS cc_start: 0.7930 (tttp) cc_final: 0.7692 (tptt) REVERT: G 9 MET cc_start: 0.7477 (ttp) cc_final: 0.7264 (ptm) REVERT: G 31 LYS cc_start: 0.7629 (tttm) cc_final: 0.7317 (tttp) REVERT: G 44 ARG cc_start: 0.5662 (mtm180) cc_final: 0.5082 (mmp80) REVERT: G 47 MET cc_start: 0.5288 (ptp) cc_final: 0.4137 (ptm) REVERT: G 162 ASN cc_start: 0.7349 (m-40) cc_final: 0.7096 (m-40) REVERT: G 193 ARG cc_start: 0.7336 (mtm-85) cc_final: 0.6472 (mtm110) REVERT: H 68 LEU cc_start: 0.4196 (tt) cc_final: 0.3880 (mp) REVERT: H 87 GLU cc_start: 0.5490 (tm-30) cc_final: 0.5189 (mm-30) REVERT: L 78 GLU cc_start: 0.4726 (mt-10) cc_final: 0.4399 (mp0) outliers start: 0 outliers final: 0 residues processed: 798 average time/residue: 1.7787 time to fit residues: 1606.0807 Evaluate side-chains 446 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 446 time to evaluate : 3.073 ------------------------------------------------------------------------------- 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: 4.9990 chunk 282 optimal weight: 4.9990 chunk 156 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 190 optimal weight: 1.9990 chunk 151 optimal weight: 0.6980 chunk 292 optimal weight: 0.9980 chunk 113 optimal weight: 0.0870 chunk 177 optimal weight: 6.9990 chunk 217 optimal weight: 0.9990 chunk 338 optimal weight: 4.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN A 238 GLN A 316 GLN A 496 GLN B 239 GLN B 397 GLN B 442 ASN C 238 GLN D 166 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 GLN E 23 ASN E 46 GLN E 58 GLN E 338 GLN E 427 GLN E 448 GLN E 458 HIS F 161 ASN F 206 GLN F 262 ASN F 364 ASN F 413 GLN F 425 GLN F 465 GLN G 175 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30085 Z= 0.188 Angle : 0.537 12.639 40768 Z= 0.275 Chirality : 0.043 0.204 4568 Planarity : 0.005 0.050 5332 Dihedral : 5.799 86.599 4248 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.86 % Favored : 98.11 % Rotamer: Outliers : 2.92 % Allowed : 14.04 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.14), residues: 3764 helix: 1.72 (0.13), residues: 1578 sheet: 0.10 (0.22), residues: 566 loop : 0.31 (0.16), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 117 HIS 0.005 0.001 HIS B 283 PHE 0.015 0.001 PHE B 48 TYR 0.015 0.001 TYR B 166 ARG 0.008 0.000 ARG L 138 *********************** 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 545 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 455 time to evaluate : 3.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 ILE cc_start: 0.8043 (OUTLIER) cc_final: 0.7655 (mm) REVERT: A 93 ARG cc_start: 0.7554 (mmp80) cc_final: 0.7352 (mmp80) REVERT: A 133 MET cc_start: 0.7649 (mtp) cc_final: 0.7326 (mtt) REVERT: A 156 ARG cc_start: 0.6620 (mtm110) cc_final: 0.5651 (ttm-80) REVERT: A 261 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7646 (mp0) REVERT: A 374 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7548 (mm-30) REVERT: A 397 GLN cc_start: 0.8287 (mm110) cc_final: 0.7911 (mm110) REVERT: A 423 ASN cc_start: 0.8648 (t0) cc_final: 0.8396 (t0) REVERT: A 491 ARG cc_start: 0.7474 (mmt180) cc_final: 0.6599 (mtm110) REVERT: A 502 GLU cc_start: 0.6588 (mp0) cc_final: 0.6376 (tp30) REVERT: A 524 LYS cc_start: 0.7591 (mmmt) cc_final: 0.7330 (mttm) REVERT: A 538 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.6875 (tt0) REVERT: B 41 ARG cc_start: 0.8621 (ttm170) cc_final: 0.7999 (ttm110) REVERT: B 92 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7378 (mp0) REVERT: B 415 PHE cc_start: 0.7662 (t80) cc_final: 0.7036 (t80) REVERT: B 447 TYR cc_start: 0.6957 (t80) cc_final: 0.6610 (t80) REVERT: B 449 GLU cc_start: 0.5266 (mp0) cc_final: 0.4541 (mp0) REVERT: B 452 ASP cc_start: 0.6723 (m-30) cc_final: 0.5627 (t70) REVERT: B 477 GLN cc_start: 0.4663 (mt0) cc_final: 0.4282 (pt0) REVERT: B 527 GLU cc_start: 0.5880 (tt0) cc_final: 0.5594 (tt0) REVERT: C 53 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7951 (mt-10) REVERT: C 133 MET cc_start: 0.8173 (mtp) cc_final: 0.7846 (mtp) REVERT: C 152 ASP cc_start: 0.7647 (m-30) cc_final: 0.7352 (p0) REVERT: C 182 LYS cc_start: 0.8315 (mtpt) cc_final: 0.8059 (mttp) REVERT: C 260 ASN cc_start: 0.8285 (m-40) cc_final: 0.8032 (m-40) REVERT: C 425 ASN cc_start: 0.8112 (m-40) cc_final: 0.7525 (t0) REVERT: C 527 GLU cc_start: 0.6662 (mm-30) cc_final: 0.6180 (pt0) REVERT: C 567 MET cc_start: 0.7030 (mmm) cc_final: 0.6570 (mmm) REVERT: C 568 LYS cc_start: 0.7018 (mttt) cc_final: 0.6743 (mppt) REVERT: D 26 ASP cc_start: 0.7990 (OUTLIER) cc_final: 0.7528 (m-30) REVERT: D 50 VAL cc_start: 0.8853 (OUTLIER) cc_final: 0.8590 (m) REVERT: D 87 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7464 (mt-10) REVERT: D 275 GLU cc_start: 0.7318 (OUTLIER) cc_final: 0.6744 (mp0) REVERT: D 316 MET cc_start: 0.7685 (OUTLIER) cc_final: 0.7083 (mpp) REVERT: D 362 MET cc_start: 0.8708 (ttt) cc_final: 0.8389 (ttp) REVERT: D 394 LYS cc_start: 0.7952 (OUTLIER) cc_final: 0.7599 (mtpt) REVERT: D 420 ARG cc_start: 0.7055 (mtm-85) cc_final: 0.6836 (mmm160) REVERT: D 452 LYS cc_start: 0.7227 (mmmt) cc_final: 0.6956 (mtpt) REVERT: E 5 LYS cc_start: 0.4811 (mttt) cc_final: 0.4371 (ptmt) REVERT: E 6 LYS cc_start: 0.6949 (ttmm) cc_final: 0.6685 (ttmt) REVERT: E 81 ARG cc_start: 0.7069 (mtm-85) cc_final: 0.6706 (mtt90) REVERT: E 103 LEU cc_start: 0.7797 (mp) cc_final: 0.7545 (mt) REVERT: E 130 PHE cc_start: 0.8106 (OUTLIER) cc_final: 0.6308 (p90) REVERT: E 206 GLN cc_start: 0.7043 (tp40) cc_final: 0.6746 (tp40) REVERT: E 248 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7445 (mm-30) REVERT: E 410 ARG cc_start: 0.6791 (mtm180) cc_final: 0.6512 (ttt180) REVERT: E 445 MET cc_start: 0.7215 (mtp) cc_final: 0.6981 (mtt) REVERT: E 448 GLN cc_start: 0.7497 (tt0) cc_final: 0.7192 (tt0) REVERT: F 5 LYS cc_start: 0.6641 (tttt) cc_final: 0.6214 (ttmt) REVERT: F 7 GLU cc_start: 0.7379 (mm-30) cc_final: 0.7177 (tp30) REVERT: F 36 LYS cc_start: 0.8029 (tttt) cc_final: 0.7825 (ttpp) REVERT: F 41 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.6917 (tmm-80) REVERT: F 61 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.6941 (mt-10) REVERT: F 376 LYS cc_start: 0.7883 (tttp) cc_final: 0.7542 (tppt) REVERT: G 44 ARG cc_start: 0.5664 (mtm180) cc_final: 0.5189 (mmp80) REVERT: G 48 GLU cc_start: 0.5451 (OUTLIER) cc_final: 0.5173 (mp0) REVERT: G 162 ASN cc_start: 0.7416 (m-40) cc_final: 0.7169 (m-40) REVERT: G 193 ARG cc_start: 0.7387 (mtm-85) cc_final: 0.6569 (mtm110) REVERT: H 87 GLU cc_start: 0.5432 (tm-30) cc_final: 0.5206 (mm-30) REVERT: L 78 GLU cc_start: 0.5059 (mt-10) cc_final: 0.4594 (mp0) REVERT: L 132 GLU cc_start: 0.2730 (mm-30) cc_final: 0.2218 (tt0) outliers start: 90 outliers final: 30 residues processed: 514 average time/residue: 1.7344 time to fit residues: 1013.6885 Evaluate side-chains 437 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 392 time to evaluate : 3.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 459 GLN Chi-restraints excluded: chain C residue 547 ARG Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain D residue 394 LYS Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain F residue 41 ARG Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 455 SER Chi-restraints excluded: chain G residue 48 GLU Chi-restraints excluded: chain G residue 156 LYS Chi-restraints excluded: chain G residue 181 GLN Chi-restraints excluded: chain L residue 92 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 188 optimal weight: 0.4980 chunk 105 optimal weight: 6.9990 chunk 281 optimal weight: 0.8980 chunk 230 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 339 optimal weight: 10.0000 chunk 366 optimal weight: 0.9990 chunk 302 optimal weight: 5.9990 chunk 336 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 272 optimal weight: 3.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN A 293 ASN B 397 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 363 ASN D 413 GLN E 363 ASN E 427 GLN E 437 GLN E 465 GLN F 206 GLN ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 364 ASN F 413 GLN F 465 GLN G 10 ASN G 17 GLN H 82 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 30085 Z= 0.370 Angle : 0.654 10.999 40768 Z= 0.336 Chirality : 0.048 0.186 4568 Planarity : 0.006 0.051 5332 Dihedral : 6.296 80.450 4248 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.21 % Favored : 97.77 % Rotamer: Outliers : 3.89 % Allowed : 15.05 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.14), residues: 3764 helix: 1.18 (0.13), residues: 1564 sheet: -0.02 (0.22), residues: 569 loop : 0.18 (0.16), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 187 HIS 0.012 0.002 HIS B 283 PHE 0.022 0.002 PHE A 559 TYR 0.020 0.002 TYR A 304 ARG 0.012 0.001 ARG A 547 *********************** 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 526 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 406 time to evaluate : 3.366 Fit side-chains revert: symmetry clash REVERT: A 2 ILE cc_start: 0.8195 (OUTLIER) cc_final: 0.7776 (mm) REVERT: A 93 ARG cc_start: 0.7537 (mmp80) cc_final: 0.7181 (mmp80) REVERT: A 133 MET cc_start: 0.7579 (mtp) cc_final: 0.7219 (mtt) REVERT: A 257 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7754 (mm-30) REVERT: A 261 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7774 (mp0) REVERT: A 374 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7616 (mm-30) REVERT: A 393 GLU cc_start: 0.6568 (tt0) cc_final: 0.6175 (tp30) REVERT: A 397 GLN cc_start: 0.8485 (mm110) cc_final: 0.8244 (mm110) REVERT: A 433 SER cc_start: 0.8261 (OUTLIER) cc_final: 0.7938 (t) REVERT: A 491 ARG cc_start: 0.7511 (mmt180) cc_final: 0.6674 (mtm110) REVERT: A 502 GLU cc_start: 0.6693 (mp0) cc_final: 0.6469 (tp30) REVERT: A 520 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7831 (mt) REVERT: A 524 LYS cc_start: 0.7601 (mmmt) cc_final: 0.7295 (mttm) REVERT: A 538 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7294 (tm-30) REVERT: B 29 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.8258 (mmtp) REVERT: B 53 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7278 (mp0) REVERT: B 114 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7617 (mp0) REVERT: B 282 MET cc_start: 0.8719 (mmm) cc_final: 0.8234 (tpt) REVERT: B 391 MET cc_start: 0.6846 (mmt) cc_final: 0.6000 (mmp) REVERT: B 449 GLU cc_start: 0.5297 (mp0) cc_final: 0.4639 (mp0) REVERT: B 452 ASP cc_start: 0.6728 (m-30) cc_final: 0.5695 (t70) REVERT: B 477 GLN cc_start: 0.4713 (mt0) cc_final: 0.4194 (pt0) REVERT: B 548 ILE cc_start: 0.6006 (tt) cc_final: 0.5709 (tp) REVERT: B 554 VAL cc_start: 0.5926 (p) cc_final: 0.5316 (m) REVERT: C 53 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.7828 (mt-10) REVERT: C 133 MET cc_start: 0.8150 (mtp) cc_final: 0.7889 (mtp) REVERT: C 152 ASP cc_start: 0.7710 (m-30) cc_final: 0.7429 (p0) REVERT: C 182 LYS cc_start: 0.8417 (mtpt) cc_final: 0.8194 (mttp) REVERT: C 260 ASN cc_start: 0.8356 (m-40) cc_final: 0.8122 (m-40) REVERT: C 425 ASN cc_start: 0.8160 (m-40) cc_final: 0.7582 (t0) REVERT: C 493 ASP cc_start: 0.7636 (m-30) cc_final: 0.7359 (m-30) REVERT: C 557 GLU cc_start: 0.7030 (mp0) cc_final: 0.6648 (tp30) REVERT: C 567 MET cc_start: 0.6924 (mmm) cc_final: 0.6511 (mmm) REVERT: C 568 LYS cc_start: 0.7142 (mttt) cc_final: 0.6740 (mppt) REVERT: D 26 ASP cc_start: 0.8006 (OUTLIER) cc_final: 0.7514 (m-30) REVERT: D 49 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.8146 (tt0) REVERT: D 87 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7575 (mt-10) REVERT: D 109 GLU cc_start: 0.7208 (OUTLIER) cc_final: 0.6499 (mp0) REVERT: D 130 PHE cc_start: 0.8437 (OUTLIER) cc_final: 0.8129 (p90) REVERT: D 275 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.7122 (mp0) REVERT: D 316 MET cc_start: 0.7846 (OUTLIER) cc_final: 0.7228 (mpp) REVERT: D 420 ARG cc_start: 0.7147 (mtm-85) cc_final: 0.6901 (mmm160) REVERT: E 5 LYS cc_start: 0.4912 (mttt) cc_final: 0.4424 (ptmt) REVERT: E 81 ARG cc_start: 0.7197 (mtm-85) cc_final: 0.6713 (mtt180) REVERT: E 103 LEU cc_start: 0.7697 (mp) cc_final: 0.7444 (mt) REVERT: E 206 GLN cc_start: 0.7294 (tp40) cc_final: 0.7064 (tp40) REVERT: E 248 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7584 (mm-30) REVERT: E 265 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7340 (mt-10) REVERT: E 364 ASN cc_start: 0.8209 (t0) cc_final: 0.7762 (t160) REVERT: E 380 ASP cc_start: 0.7541 (m-30) cc_final: 0.7329 (m-30) REVERT: E 410 ARG cc_start: 0.6885 (mtm180) cc_final: 0.6500 (ttt180) REVERT: E 445 MET cc_start: 0.7311 (mtp) cc_final: 0.7017 (mtt) REVERT: E 448 GLN cc_start: 0.7491 (tt0) cc_final: 0.7259 (tt0) REVERT: F 5 LYS cc_start: 0.6807 (tttt) cc_final: 0.6294 (ttmt) REVERT: F 7 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6929 (tp30) REVERT: F 67 ASP cc_start: 0.7779 (p0) cc_final: 0.7439 (p0) REVERT: F 126 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8089 (tttp) REVERT: F 200 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7902 (mt-10) REVERT: F 376 LYS cc_start: 0.8096 (tttp) cc_final: 0.7685 (tppt) REVERT: F 453 ARG cc_start: 0.7169 (OUTLIER) cc_final: 0.5656 (mmt180) REVERT: G 5 SER cc_start: 0.7348 (p) cc_final: 0.6670 (t) REVERT: G 44 ARG cc_start: 0.5754 (mtm180) cc_final: 0.5174 (mmp80) REVERT: G 47 MET cc_start: 0.5057 (ptp) cc_final: 0.4068 (ptm) REVERT: G 48 GLU cc_start: 0.5442 (OUTLIER) cc_final: 0.5120 (mp0) REVERT: G 205 GLU cc_start: 0.4559 (mm-30) cc_final: 0.4259 (mt-10) REVERT: H 63 MET cc_start: 0.1842 (mpt) cc_final: 0.1619 (mpt) REVERT: H 87 GLU cc_start: 0.5350 (tm-30) cc_final: 0.5131 (mm-30) REVERT: J 160 LYS cc_start: 0.5521 (mmtm) cc_final: 0.5282 (mmpt) REVERT: L 78 GLU cc_start: 0.5127 (mt-10) cc_final: 0.4681 (mp0) REVERT: L 132 GLU cc_start: 0.2784 (mm-30) cc_final: 0.2218 (tt0) outliers start: 120 outliers final: 49 residues processed: 487 average time/residue: 1.7235 time to fit residues: 956.3962 Evaluate side-chains 444 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 373 time to evaluate : 3.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 454 ILE Chi-restraints excluded: chain C residue 459 GLN Chi-restraints excluded: chain C residue 547 ARG Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain D residue 364 ASN Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain F residue 7 GLU Chi-restraints excluded: chain F residue 41 ARG Chi-restraints excluded: chain F residue 126 LYS Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 453 ARG Chi-restraints excluded: chain F residue 455 SER Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 48 GLU Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 181 GLN Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain L residue 92 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 335 optimal weight: 10.0000 chunk 255 optimal weight: 4.9990 chunk 176 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 161 optimal weight: 6.9990 chunk 227 optimal weight: 1.9990 chunk 340 optimal weight: 5.9990 chunk 360 optimal weight: 0.5980 chunk 177 optimal weight: 4.9990 chunk 322 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN A 293 ASN B 397 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 GLN E 427 GLN E 437 GLN E 465 GLN ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 364 ASN F 413 GLN F 465 GLN G 10 ASN H 30 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 30085 Z= 0.249 Angle : 0.558 12.484 40768 Z= 0.286 Chirality : 0.044 0.175 4568 Planarity : 0.005 0.052 5332 Dihedral : 6.005 83.314 4248 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.86 % Favored : 98.11 % Rotamer: Outliers : 3.63 % Allowed : 16.12 % Favored : 80.25 % 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: 0.89 (0.14), residues: 3764 helix: 1.31 (0.13), residues: 1563 sheet: 0.01 (0.22), residues: 557 loop : 0.25 (0.16), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 119 HIS 0.006 0.001 HIS B 283 PHE 0.016 0.002 PHE A 559 TYR 0.017 0.002 TYR E 463 ARG 0.004 0.001 ARG E 280 *********************** 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 511 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 399 time to evaluate : 3.668 Fit side-chains REVERT: A 2 ILE cc_start: 0.8229 (OUTLIER) cc_final: 0.7729 (mm) REVERT: A 93 ARG cc_start: 0.7616 (mmp80) cc_final: 0.7269 (mmp80) REVERT: A 133 MET cc_start: 0.7556 (mtp) cc_final: 0.7179 (mtt) REVERT: A 156 ARG cc_start: 0.6923 (ttp80) cc_final: 0.6054 (ttm-80) REVERT: A 257 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7827 (mm-30) REVERT: A 323 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.7887 (mpt) REVERT: A 374 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7585 (mm-30) REVERT: A 393 GLU cc_start: 0.6622 (tt0) cc_final: 0.6092 (tp30) REVERT: A 397 GLN cc_start: 0.8486 (mm110) cc_final: 0.8260 (mm110) REVERT: A 433 SER cc_start: 0.8247 (m) cc_final: 0.7937 (t) REVERT: A 491 ARG cc_start: 0.7470 (mmt180) cc_final: 0.6574 (mtm110) REVERT: A 502 GLU cc_start: 0.6717 (mp0) cc_final: 0.6477 (tp30) REVERT: A 520 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.7750 (mt) REVERT: A 524 LYS cc_start: 0.7609 (mmmt) cc_final: 0.7294 (mttm) REVERT: B 92 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7296 (mp0) REVERT: B 282 MET cc_start: 0.8675 (mmm) cc_final: 0.8110 (tpt) REVERT: B 391 MET cc_start: 0.6977 (mmt) cc_final: 0.6051 (mmp) REVERT: B 449 GLU cc_start: 0.5258 (mp0) cc_final: 0.4355 (mt-10) REVERT: B 452 ASP cc_start: 0.6765 (m-30) cc_final: 0.5793 (t70) REVERT: B 460 ARG cc_start: 0.6800 (mtp180) cc_final: 0.6546 (mtp85) REVERT: B 471 VAL cc_start: 0.6694 (OUTLIER) cc_final: 0.6478 (m) REVERT: B 477 GLN cc_start: 0.4685 (mt0) cc_final: 0.4163 (mt0) REVERT: B 493 ASP cc_start: 0.6061 (m-30) cc_final: 0.5553 (m-30) REVERT: B 548 ILE cc_start: 0.5968 (OUTLIER) cc_final: 0.5738 (tp) REVERT: B 554 VAL cc_start: 0.5927 (p) cc_final: 0.5347 (m) REVERT: C 53 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7788 (mt-10) REVERT: C 133 MET cc_start: 0.8152 (mtp) cc_final: 0.7820 (mtp) REVERT: C 152 ASP cc_start: 0.7669 (m-30) cc_final: 0.7373 (p0) REVERT: C 260 ASN cc_start: 0.8365 (m-40) cc_final: 0.8128 (m-40) REVERT: C 425 ASN cc_start: 0.8139 (m-40) cc_final: 0.7576 (t0) REVERT: C 488 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7351 (ttt-90) REVERT: C 493 ASP cc_start: 0.7634 (m-30) cc_final: 0.7379 (m-30) REVERT: C 557 GLU cc_start: 0.7035 (mp0) cc_final: 0.6598 (tp30) REVERT: C 567 MET cc_start: 0.6898 (mmm) cc_final: 0.6471 (mmm) REVERT: C 568 LYS cc_start: 0.6994 (mttt) cc_final: 0.6649 (mppt) REVERT: D 26 ASP cc_start: 0.7962 (OUTLIER) cc_final: 0.7496 (m-30) REVERT: D 87 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7533 (mt-10) REVERT: D 109 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6374 (mp0) REVERT: D 275 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.6816 (mp0) REVERT: D 316 MET cc_start: 0.7765 (OUTLIER) cc_final: 0.7181 (mpp) REVERT: D 362 MET cc_start: 0.8694 (ttt) cc_final: 0.8450 (ttp) REVERT: D 376 LYS cc_start: 0.7535 (ttmm) cc_final: 0.6964 (tppp) REVERT: D 402 ASP cc_start: 0.6656 (m-30) cc_final: 0.6365 (m-30) REVERT: D 420 ARG cc_start: 0.7096 (mtm-85) cc_final: 0.6862 (mmm160) REVERT: E 5 LYS cc_start: 0.4902 (mttt) cc_final: 0.4445 (ptmt) REVERT: E 81 ARG cc_start: 0.7164 (mtm-85) cc_final: 0.6798 (mtt180) REVERT: E 103 LEU cc_start: 0.7684 (mp) cc_final: 0.7454 (mt) REVERT: E 206 GLN cc_start: 0.7323 (tp40) cc_final: 0.7105 (tp40) REVERT: E 209 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.6960 (mt-10) REVERT: E 248 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7574 (mm-30) REVERT: E 265 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7341 (mt-10) REVERT: E 364 ASN cc_start: 0.8164 (t0) cc_final: 0.7880 (t0) REVERT: E 380 ASP cc_start: 0.7533 (m-30) cc_final: 0.7324 (m-30) REVERT: E 382 LEU cc_start: 0.8486 (mt) cc_final: 0.8134 (mt) REVERT: E 410 ARG cc_start: 0.6830 (mtm180) cc_final: 0.6501 (ttt180) REVERT: E 428 GLN cc_start: 0.8071 (mt0) cc_final: 0.7816 (mt0) REVERT: E 445 MET cc_start: 0.7325 (mtp) cc_final: 0.7036 (mtt) REVERT: E 448 GLN cc_start: 0.7497 (tt0) cc_final: 0.7283 (tt0) REVERT: F 5 LYS cc_start: 0.6828 (tttt) cc_final: 0.6287 (ttmt) REVERT: F 7 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6935 (tp30) REVERT: F 36 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8386 (ttpp) REVERT: F 41 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.6807 (tmm-80) REVERT: F 50 VAL cc_start: 0.9002 (t) cc_final: 0.8752 (m) REVERT: F 67 ASP cc_start: 0.7768 (p0) cc_final: 0.7443 (p0) REVERT: F 126 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8078 (tttp) REVERT: F 206 GLN cc_start: 0.7793 (mm-40) cc_final: 0.7401 (mt0) REVERT: G 5 SER cc_start: 0.7265 (p) cc_final: 0.6575 (t) REVERT: G 23 LYS cc_start: 0.7181 (mtpm) cc_final: 0.6942 (mtpt) REVERT: G 44 ARG cc_start: 0.5825 (mtm180) cc_final: 0.5218 (mmp80) REVERT: G 47 MET cc_start: 0.4968 (ptp) cc_final: 0.4396 (ptp) REVERT: G 48 GLU cc_start: 0.5721 (OUTLIER) cc_final: 0.5311 (mp0) REVERT: H 63 MET cc_start: 0.1819 (mpt) cc_final: 0.1525 (mpt) REVERT: H 87 GLU cc_start: 0.5522 (tm-30) cc_final: 0.5262 (mm-30) REVERT: H 90 MET cc_start: 0.4436 (ptt) cc_final: 0.4224 (ptp) REVERT: J 145 GLU cc_start: 0.2334 (pm20) cc_final: 0.1396 (tm-30) REVERT: J 160 LYS cc_start: 0.5641 (mmtm) cc_final: 0.5366 (mmpt) REVERT: J 164 GLU cc_start: 0.4978 (tp30) cc_final: 0.4722 (tp30) REVERT: K 104 MET cc_start: 0.4965 (mmt) cc_final: 0.4628 (pp-130) REVERT: L 78 GLU cc_start: 0.5200 (mt-10) cc_final: 0.4677 (mp0) REVERT: L 132 GLU cc_start: 0.2567 (mm-30) cc_final: 0.1928 (tt0) outliers start: 112 outliers final: 50 residues processed: 474 average time/residue: 1.7357 time to fit residues: 940.1100 Evaluate side-chains 451 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 381 time to evaluate : 3.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 459 GLN Chi-restraints excluded: chain C residue 488 ARG Chi-restraints excluded: chain C residue 547 ARG Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain D residue 364 ASN Chi-restraints excluded: chain D residue 388 ASN Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 209 GLU Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain E residue 374 ASP Chi-restraints excluded: chain F residue 7 GLU Chi-restraints excluded: chain F residue 36 LYS Chi-restraints excluded: chain F residue 41 ARG Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 126 LYS Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 48 GLU Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 181 GLN Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain L residue 92 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 300 optimal weight: 5.9990 chunk 204 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 268 optimal weight: 5.9990 chunk 148 optimal weight: 4.9990 chunk 307 optimal weight: 3.9990 chunk 249 optimal weight: 0.0980 chunk 0 optimal weight: 2.9990 chunk 184 optimal weight: 2.9990 chunk 323 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN B 283 HIS B 316 GLN C 283 HIS ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 363 ASN D 413 GLN E 377 GLN E 427 GLN E 437 GLN E 458 HIS E 465 GLN ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 364 ASN F 413 GLN F 427 GLN F 465 GLN G 10 ASN H 84 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 30085 Z= 0.400 Angle : 0.676 13.077 40768 Z= 0.346 Chirality : 0.048 0.200 4568 Planarity : 0.006 0.053 5332 Dihedral : 6.428 88.983 4248 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 4.61 % Allowed : 15.86 % Favored : 79.53 % 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: 0.52 (0.14), residues: 3764 helix: 0.93 (0.13), residues: 1549 sheet: -0.15 (0.21), residues: 570 loop : 0.13 (0.16), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 187 HIS 0.009 0.002 HIS B 283 PHE 0.021 0.002 PHE A 559 TYR 0.021 0.002 TYR E 463 ARG 0.007 0.001 ARG E 280 *********************** 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 521 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 379 time to evaluate : 3.187 Fit side-chains revert: symmetry clash REVERT: A 2 ILE cc_start: 0.8293 (OUTLIER) cc_final: 0.7844 (mm) REVERT: A 93 ARG cc_start: 0.7536 (mmp80) cc_final: 0.7170 (mmp80) REVERT: A 124 LYS cc_start: 0.7481 (OUTLIER) cc_final: 0.7124 (mtpt) REVERT: A 133 MET cc_start: 0.7593 (mtp) cc_final: 0.7268 (mtt) REVERT: A 156 ARG cc_start: 0.6839 (ttp80) cc_final: 0.6345 (ttm-80) REVERT: A 257 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7748 (mm-30) REVERT: A 323 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.8089 (mpt) REVERT: A 374 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7590 (mm-30) REVERT: A 433 SER cc_start: 0.8233 (m) cc_final: 0.7922 (t) REVERT: A 491 ARG cc_start: 0.7513 (mmt180) cc_final: 0.6668 (mtm110) REVERT: A 520 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.7996 (mt) REVERT: A 524 LYS cc_start: 0.7562 (mmmt) cc_final: 0.7250 (ttmm) REVERT: B 29 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8266 (mmtp) REVERT: B 114 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7651 (mp0) REVERT: B 282 MET cc_start: 0.8752 (mmm) cc_final: 0.8193 (tpt) REVERT: B 329 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.6428 (mmt-90) REVERT: B 449 GLU cc_start: 0.5241 (mp0) cc_final: 0.4455 (mt-10) REVERT: B 452 ASP cc_start: 0.6739 (m-30) cc_final: 0.5711 (t70) REVERT: B 477 GLN cc_start: 0.4770 (mt0) cc_final: 0.4178 (mt0) REVERT: B 493 ASP cc_start: 0.5925 (m-30) cc_final: 0.5387 (m-30) REVERT: B 548 ILE cc_start: 0.6109 (tt) cc_final: 0.5826 (tp) REVERT: C 53 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.7812 (mt-10) REVERT: C 133 MET cc_start: 0.8151 (mtp) cc_final: 0.7892 (mtp) REVERT: C 152 ASP cc_start: 0.7764 (m-30) cc_final: 0.7376 (p0) REVERT: C 260 ASN cc_start: 0.8393 (m-40) cc_final: 0.8140 (m-40) REVERT: C 367 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8321 (ttmt) REVERT: C 425 ASN cc_start: 0.8130 (m-40) cc_final: 0.7566 (t0) REVERT: C 488 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7303 (ttt-90) REVERT: C 493 ASP cc_start: 0.7719 (m-30) cc_final: 0.7448 (m-30) REVERT: C 510 LYS cc_start: 0.8753 (OUTLIER) cc_final: 0.8425 (mmtm) REVERT: C 557 GLU cc_start: 0.7171 (mp0) cc_final: 0.6568 (tp30) REVERT: C 567 MET cc_start: 0.6950 (mmm) cc_final: 0.6566 (mmm) REVERT: D 6 LYS cc_start: 0.7064 (OUTLIER) cc_final: 0.6564 (ttpt) REVERT: D 26 ASP cc_start: 0.8014 (OUTLIER) cc_final: 0.7534 (m-30) REVERT: D 87 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7597 (mt-10) REVERT: D 109 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6559 (mp0) REVERT: D 275 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.7065 (mp0) REVERT: D 316 MET cc_start: 0.7863 (OUTLIER) cc_final: 0.7344 (mpp) REVERT: D 362 MET cc_start: 0.8723 (ttt) cc_final: 0.8474 (ttp) REVERT: D 376 LYS cc_start: 0.7529 (ttmm) cc_final: 0.7019 (tppp) REVERT: D 402 ASP cc_start: 0.6790 (OUTLIER) cc_final: 0.6494 (m-30) REVERT: E 25 LYS cc_start: 0.7891 (OUTLIER) cc_final: 0.7527 (mtmt) REVERT: E 81 ARG cc_start: 0.7258 (mtt-85) cc_final: 0.6809 (mtt180) REVERT: E 128 GLU cc_start: 0.7422 (pt0) cc_final: 0.7133 (pt0) REVERT: E 206 GLN cc_start: 0.7310 (tp40) cc_final: 0.7097 (tp40) REVERT: E 209 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6945 (mt-10) REVERT: E 248 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7554 (mm-30) REVERT: E 265 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7369 (mt-10) REVERT: E 364 ASN cc_start: 0.8171 (t0) cc_final: 0.7913 (t0) REVERT: E 382 LEU cc_start: 0.8490 (mt) cc_final: 0.8154 (mt) REVERT: E 410 ARG cc_start: 0.6871 (mtm180) cc_final: 0.6527 (ttt180) REVERT: E 428 GLN cc_start: 0.8077 (mt0) cc_final: 0.7841 (mt0) REVERT: E 457 ASP cc_start: 0.5789 (t70) cc_final: 0.5424 (t0) REVERT: F 5 LYS cc_start: 0.7107 (tttt) cc_final: 0.6420 (ttmt) REVERT: F 7 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.6959 (tp30) REVERT: F 50 VAL cc_start: 0.9072 (OUTLIER) cc_final: 0.8827 (m) REVERT: F 67 ASP cc_start: 0.8030 (p0) cc_final: 0.7747 (p0) REVERT: F 200 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7905 (mt-10) REVERT: F 376 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.8052 (tttp) REVERT: F 452 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7844 (mttp) REVERT: F 453 ARG cc_start: 0.7134 (OUTLIER) cc_final: 0.5667 (mmt180) REVERT: F 461 LYS cc_start: 0.7243 (OUTLIER) cc_final: 0.6847 (ttmp) REVERT: G 5 SER cc_start: 0.7266 (p) cc_final: 0.6554 (t) REVERT: G 48 GLU cc_start: 0.5480 (OUTLIER) cc_final: 0.5076 (mp0) REVERT: H 15 LEU cc_start: 0.3466 (tt) cc_final: 0.2876 (mm) REVERT: H 63 MET cc_start: 0.1864 (mpt) cc_final: 0.1548 (mpt) REVERT: H 104 LEU cc_start: 0.4434 (pp) cc_final: 0.4080 (mt) REVERT: J 160 LYS cc_start: 0.5911 (mmtm) cc_final: 0.5502 (mmpt) REVERT: K 104 MET cc_start: 0.5072 (mmt) cc_final: 0.4825 (pp-130) REVERT: L 78 GLU cc_start: 0.5137 (mt-10) cc_final: 0.4680 (mp0) outliers start: 142 outliers final: 65 residues processed: 479 average time/residue: 1.7243 time to fit residues: 939.0988 Evaluate side-chains 447 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 353 time to evaluate : 3.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 481 ARG Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 329 ARG Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 485 GLU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 550 ARG Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 367 LYS Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 459 GLN Chi-restraints excluded: chain C residue 488 ARG Chi-restraints excluded: chain C residue 510 LYS Chi-restraints excluded: chain C residue 547 ARG Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain D residue 345 ARG Chi-restraints excluded: chain D residue 364 ASN Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain E residue 25 LYS Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 209 GLU Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain E residue 374 ASP Chi-restraints excluded: chain F residue 7 GLU Chi-restraints excluded: chain F residue 41 ARG Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 126 LYS Chi-restraints excluded: chain F residue 156 SER Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 376 LYS Chi-restraints excluded: chain F residue 452 LYS Chi-restraints excluded: chain F residue 453 ARG Chi-restraints excluded: chain F residue 455 SER Chi-restraints excluded: chain F residue 461 LYS Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 48 GLU Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 181 GLN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain L residue 92 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 121 optimal weight: 1.9990 chunk 324 optimal weight: 6.9990 chunk 71 optimal weight: 0.1980 chunk 211 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 360 optimal weight: 1.9990 chunk 299 optimal weight: 0.0050 chunk 167 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 119 optimal weight: 2.9990 chunk 189 optimal weight: 4.9990 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 GLN ** E 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 413 GLN F 465 GLN G 10 ASN L 130 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30085 Z= 0.181 Angle : 0.522 12.504 40768 Z= 0.267 Chirality : 0.043 0.164 4568 Planarity : 0.004 0.054 5332 Dihedral : 5.934 87.747 4248 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.86 % Favored : 98.11 % Rotamer: Outliers : 3.15 % Allowed : 17.74 % Favored : 79.11 % 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: 0.85 (0.14), residues: 3764 helix: 1.27 (0.13), residues: 1566 sheet: -0.06 (0.21), residues: 565 loop : 0.25 (0.16), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 119 HIS 0.003 0.001 HIS D 249 PHE 0.013 0.001 PHE A 559 TYR 0.014 0.001 TYR E 463 ARG 0.006 0.000 ARG B 93 *********************** 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 486 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 389 time to evaluate : 3.501 Fit side-chains revert: symmetry clash REVERT: A 93 ARG cc_start: 0.7615 (mmp80) cc_final: 0.7258 (mmp80) REVERT: A 133 MET cc_start: 0.7562 (mtp) cc_final: 0.7274 (mtt) REVERT: A 156 ARG cc_start: 0.6882 (ttp80) cc_final: 0.6095 (ttm-80) REVERT: A 176 GLU cc_start: 0.7281 (mm-30) cc_final: 0.7059 (mp0) REVERT: A 257 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7764 (mm-30) REVERT: A 323 MET cc_start: 0.8701 (OUTLIER) cc_final: 0.7817 (mpt) REVERT: A 374 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7515 (mm-30) REVERT: A 393 GLU cc_start: 0.6922 (tt0) cc_final: 0.6091 (tp30) REVERT: A 397 GLN cc_start: 0.8294 (mm110) cc_final: 0.8007 (mp10) REVERT: A 433 SER cc_start: 0.8248 (m) cc_final: 0.7937 (t) REVERT: A 491 ARG cc_start: 0.7472 (mmt180) cc_final: 0.6609 (mtm110) REVERT: A 520 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8046 (mt) REVERT: A 524 LYS cc_start: 0.7605 (mmmt) cc_final: 0.7342 (ttmm) REVERT: B 29 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.8233 (mmtp) REVERT: B 180 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.6333 (mp0) REVERT: B 282 MET cc_start: 0.8672 (mmm) cc_final: 0.8063 (tpt) REVERT: B 449 GLU cc_start: 0.5279 (mp0) cc_final: 0.4381 (mt-10) REVERT: B 452 ASP cc_start: 0.6724 (m-30) cc_final: 0.5773 (t70) REVERT: B 460 ARG cc_start: 0.6762 (mtp180) cc_final: 0.6526 (mtp85) REVERT: B 477 GLN cc_start: 0.4837 (mt0) cc_final: 0.4222 (mt0) REVERT: B 493 ASP cc_start: 0.6093 (m-30) cc_final: 0.5561 (m-30) REVERT: B 548 ILE cc_start: 0.6177 (OUTLIER) cc_final: 0.5956 (tp) REVERT: B 567 MET cc_start: 0.5231 (tpt) cc_final: 0.4953 (tpt) REVERT: C 53 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7753 (mt-10) REVERT: C 133 MET cc_start: 0.8158 (mtp) cc_final: 0.7759 (mtp) REVERT: C 152 ASP cc_start: 0.7730 (m-30) cc_final: 0.7328 (p0) REVERT: C 260 ASN cc_start: 0.8378 (m-40) cc_final: 0.8161 (m-40) REVERT: C 483 VAL cc_start: 0.7582 (t) cc_final: 0.7283 (p) REVERT: C 488 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7305 (ttt-90) REVERT: C 510 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8311 (mmtm) REVERT: C 557 GLU cc_start: 0.7081 (mp0) cc_final: 0.6825 (mp0) REVERT: C 567 MET cc_start: 0.6959 (mmm) cc_final: 0.6601 (mmm) REVERT: D 26 ASP cc_start: 0.7950 (OUTLIER) cc_final: 0.7487 (m-30) REVERT: D 87 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7583 (mt-10) REVERT: D 109 GLU cc_start: 0.7036 (OUTLIER) cc_final: 0.6435 (mp0) REVERT: D 275 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.7050 (mp0) REVERT: D 316 MET cc_start: 0.7713 (OUTLIER) cc_final: 0.7158 (mpp) REVERT: D 362 MET cc_start: 0.8696 (ttt) cc_final: 0.8451 (ttp) REVERT: D 364 ASN cc_start: 0.7992 (OUTLIER) cc_final: 0.6985 (t0) REVERT: D 376 LYS cc_start: 0.7584 (ttmm) cc_final: 0.7079 (tppp) REVERT: D 402 ASP cc_start: 0.6892 (m-30) cc_final: 0.6603 (m-30) REVERT: E 5 LYS cc_start: 0.5182 (mttt) cc_final: 0.4635 (ptmt) REVERT: E 49 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.8109 (tm-30) REVERT: E 81 ARG cc_start: 0.7250 (mtt-85) cc_final: 0.6862 (mtt180) REVERT: E 103 LEU cc_start: 0.7667 (mp) cc_final: 0.7442 (mt) REVERT: E 128 GLU cc_start: 0.7449 (pt0) cc_final: 0.7136 (pt0) REVERT: E 206 GLN cc_start: 0.7273 (tp40) cc_final: 0.7069 (tp40) REVERT: E 209 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.6915 (mt-10) REVERT: E 248 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7548 (mm-30) REVERT: E 265 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7342 (mt-10) REVERT: E 364 ASN cc_start: 0.8064 (t0) cc_final: 0.7851 (t0) REVERT: E 410 ARG cc_start: 0.6879 (mtm180) cc_final: 0.6570 (ttt180) REVERT: E 428 GLN cc_start: 0.8084 (mt0) cc_final: 0.7879 (mt0) REVERT: E 448 GLN cc_start: 0.7277 (tt0) cc_final: 0.6635 (tm-30) REVERT: E 456 LYS cc_start: 0.5939 (mmmm) cc_final: 0.5612 (mmtm) REVERT: E 457 ASP cc_start: 0.5773 (t70) cc_final: 0.5425 (t0) REVERT: F 5 LYS cc_start: 0.7154 (tttt) cc_final: 0.6488 (ttmt) REVERT: F 7 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6891 (tp30) REVERT: F 50 VAL cc_start: 0.8974 (t) cc_final: 0.8729 (m) REVERT: F 67 ASP cc_start: 0.7830 (p0) cc_final: 0.7536 (p0) REVERT: F 126 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.8089 (tttp) REVERT: F 149 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8409 (mtmm) REVERT: F 200 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7896 (mt-10) REVERT: F 206 GLN cc_start: 0.7743 (mm-40) cc_final: 0.7367 (mt0) REVERT: G 5 SER cc_start: 0.7162 (p) cc_final: 0.6454 (t) REVERT: G 23 LYS cc_start: 0.7208 (mtpm) cc_final: 0.6638 (mtpp) REVERT: G 48 GLU cc_start: 0.5684 (OUTLIER) cc_final: 0.5371 (mp0) REVERT: H 15 LEU cc_start: 0.3436 (tt) cc_final: 0.2866 (mm) REVERT: H 63 MET cc_start: 0.2177 (mpt) cc_final: 0.1889 (mpt) REVERT: J 121 LEU cc_start: 0.4786 (OUTLIER) cc_final: 0.4533 (mm) REVERT: J 160 LYS cc_start: 0.5973 (mmtm) cc_final: 0.5459 (mmpt) REVERT: K 104 MET cc_start: 0.5093 (mmt) cc_final: 0.4866 (pp-130) REVERT: L 78 GLU cc_start: 0.5277 (mt-10) cc_final: 0.4697 (mp0) outliers start: 97 outliers final: 37 residues processed: 457 average time/residue: 1.7400 time to fit residues: 907.8983 Evaluate side-chains 426 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 366 time to evaluate : 3.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 481 ARG Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 459 GLN Chi-restraints excluded: chain C residue 488 ARG Chi-restraints excluded: chain C residue 510 LYS Chi-restraints excluded: chain C residue 547 ARG Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 364 ASN Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 209 GLU Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 374 ASP Chi-restraints excluded: chain F residue 7 GLU Chi-restraints excluded: chain F residue 126 LYS Chi-restraints excluded: chain F residue 149 LYS Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 48 GLU Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain G residue 181 GLN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain L residue 92 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 347 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 205 optimal weight: 2.9990 chunk 263 optimal weight: 0.9990 chunk 204 optimal weight: 2.9990 chunk 303 optimal weight: 0.2980 chunk 201 optimal weight: 4.9990 chunk 359 optimal weight: 4.9990 chunk 224 optimal weight: 1.9990 chunk 219 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 overall best weight: 1.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN C 425 ASN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 GLN E 427 GLN E 458 HIS ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 413 GLN G 10 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 30085 Z= 0.255 Angle : 0.574 11.649 40768 Z= 0.291 Chirality : 0.044 0.174 4568 Planarity : 0.005 0.053 5332 Dihedral : 6.057 89.960 4248 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.28 % Favored : 97.69 % Rotamer: Outliers : 3.63 % Allowed : 17.77 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.14), residues: 3764 helix: 1.24 (0.13), residues: 1563 sheet: -0.09 (0.21), residues: 569 loop : 0.22 (0.16), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP J 100 HIS 0.004 0.001 HIS D 249 PHE 0.019 0.002 PHE A 559 TYR 0.016 0.002 TYR E 463 ARG 0.012 0.001 ARG D 410 *********************** 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 483 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 371 time to evaluate : 3.485 Fit side-chains REVERT: A 93 ARG cc_start: 0.7577 (mmp80) cc_final: 0.7197 (mmp80) REVERT: A 124 LYS cc_start: 0.7470 (OUTLIER) cc_final: 0.7103 (mtpt) REVERT: A 133 MET cc_start: 0.7579 (mtp) cc_final: 0.7286 (mtt) REVERT: A 156 ARG cc_start: 0.6928 (ttp80) cc_final: 0.6108 (ttm-80) REVERT: A 176 GLU cc_start: 0.7259 (mm-30) cc_final: 0.7040 (mp0) REVERT: A 257 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7727 (mm-30) REVERT: A 323 MET cc_start: 0.8714 (OUTLIER) cc_final: 0.7888 (mpt) REVERT: A 374 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7497 (mm-30) REVERT: A 433 SER cc_start: 0.8254 (m) cc_final: 0.7947 (t) REVERT: A 491 ARG cc_start: 0.7466 (mmt180) cc_final: 0.6539 (ttp-110) REVERT: A 520 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.8003 (mt) REVERT: A 524 LYS cc_start: 0.7596 (mmmt) cc_final: 0.7336 (ttmm) REVERT: B 29 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.8238 (mmtp) REVERT: B 180 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.6386 (mp0) REVERT: B 282 MET cc_start: 0.8679 (mmm) cc_final: 0.8078 (tpt) REVERT: B 449 GLU cc_start: 0.5266 (mp0) cc_final: 0.4497 (mt-10) REVERT: B 452 ASP cc_start: 0.6749 (m-30) cc_final: 0.5783 (t70) REVERT: B 460 ARG cc_start: 0.6740 (mtp180) cc_final: 0.6498 (mtp85) REVERT: B 477 GLN cc_start: 0.4725 (mt0) cc_final: 0.4114 (mt0) REVERT: B 493 ASP cc_start: 0.6111 (m-30) cc_final: 0.5578 (m-30) REVERT: B 548 ILE cc_start: 0.6155 (OUTLIER) cc_final: 0.5901 (tp) REVERT: B 567 MET cc_start: 0.5207 (tpt) cc_final: 0.4910 (tpt) REVERT: C 53 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7766 (mt-10) REVERT: C 133 MET cc_start: 0.8200 (mtp) cc_final: 0.7930 (mtp) REVERT: C 152 ASP cc_start: 0.7721 (m-30) cc_final: 0.7341 (p0) REVERT: C 260 ASN cc_start: 0.8390 (m-40) cc_final: 0.8173 (m-40) REVERT: C 480 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.6125 (mp0) REVERT: C 483 VAL cc_start: 0.7566 (t) cc_final: 0.7260 (p) REVERT: C 510 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8371 (mmtm) REVERT: C 557 GLU cc_start: 0.7114 (mp0) cc_final: 0.6497 (tp30) REVERT: C 567 MET cc_start: 0.7004 (mmm) cc_final: 0.6658 (mmm) REVERT: D 26 ASP cc_start: 0.7972 (OUTLIER) cc_final: 0.7504 (m-30) REVERT: D 87 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7574 (mt-10) REVERT: D 109 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6541 (mp0) REVERT: D 275 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.7083 (mp0) REVERT: D 316 MET cc_start: 0.7732 (OUTLIER) cc_final: 0.7242 (mpp) REVERT: D 345 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.8057 (mtt90) REVERT: D 362 MET cc_start: 0.8706 (ttt) cc_final: 0.8456 (ttp) REVERT: D 376 LYS cc_start: 0.7548 (ttmm) cc_final: 0.7043 (tppp) REVERT: D 402 ASP cc_start: 0.6978 (OUTLIER) cc_final: 0.6673 (m-30) REVERT: D 410 ARG cc_start: 0.7035 (mtp85) cc_final: 0.6771 (mtp85) REVERT: D 433 GLU cc_start: 0.8142 (mp0) cc_final: 0.7937 (mp0) REVERT: E 49 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8091 (tm-30) REVERT: E 81 ARG cc_start: 0.7323 (mtt-85) cc_final: 0.6873 (mtt180) REVERT: E 103 LEU cc_start: 0.7709 (mp) cc_final: 0.7453 (mt) REVERT: E 128 GLU cc_start: 0.7446 (pt0) cc_final: 0.7123 (pt0) REVERT: E 209 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.6945 (mt-10) REVERT: E 248 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7523 (mm-30) REVERT: E 265 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7348 (mt-10) REVERT: E 364 ASN cc_start: 0.8045 (t0) cc_final: 0.7829 (t0) REVERT: E 393 ARG cc_start: 0.7144 (mtm180) cc_final: 0.6867 (mtm180) REVERT: E 410 ARG cc_start: 0.6889 (mtm180) cc_final: 0.6553 (ttt180) REVERT: E 428 GLN cc_start: 0.8087 (mt0) cc_final: 0.7848 (mt0) REVERT: E 445 MET cc_start: 0.7394 (mtp) cc_final: 0.7119 (mtt) REVERT: E 448 GLN cc_start: 0.7328 (tt0) cc_final: 0.6672 (tm-30) REVERT: E 456 LYS cc_start: 0.5940 (mmmm) cc_final: 0.5615 (mmtm) REVERT: E 457 ASP cc_start: 0.5774 (t70) cc_final: 0.5399 (t0) REVERT: F 5 LYS cc_start: 0.7275 (tttt) cc_final: 0.6598 (ttmt) REVERT: F 7 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6904 (tp30) REVERT: F 50 VAL cc_start: 0.9027 (OUTLIER) cc_final: 0.8777 (m) REVERT: F 67 ASP cc_start: 0.7850 (p0) cc_final: 0.7574 (p0) REVERT: F 126 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.8133 (tttp) REVERT: F 149 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8525 (mtmm) REVERT: F 200 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7887 (mt-10) REVERT: F 206 GLN cc_start: 0.7775 (mm-40) cc_final: 0.7393 (mt0) REVERT: F 453 ARG cc_start: 0.7133 (OUTLIER) cc_final: 0.5648 (mmt180) REVERT: G 5 SER cc_start: 0.7299 (p) cc_final: 0.6577 (t) REVERT: G 48 GLU cc_start: 0.5685 (OUTLIER) cc_final: 0.5396 (mp0) REVERT: G 159 ARG cc_start: 0.6133 (OUTLIER) cc_final: 0.5851 (mtt90) REVERT: J 121 LEU cc_start: 0.4772 (OUTLIER) cc_final: 0.4477 (mm) REVERT: J 160 LYS cc_start: 0.6069 (mmtm) cc_final: 0.5509 (mmpt) REVERT: K 104 MET cc_start: 0.5103 (mmt) cc_final: 0.4891 (pp-130) REVERT: L 78 GLU cc_start: 0.5268 (mt-10) cc_final: 0.4655 (mp0) outliers start: 112 outliers final: 54 residues processed: 450 average time/residue: 1.6966 time to fit residues: 875.8453 Evaluate side-chains 447 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 365 time to evaluate : 3.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 481 ARG Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 459 GLN Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain C residue 510 LYS Chi-restraints excluded: chain C residue 536 ILE Chi-restraints excluded: chain C residue 547 ARG Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain D residue 345 ARG Chi-restraints excluded: chain D residue 364 ASN Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 209 GLU Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 374 ASP Chi-restraints excluded: chain F residue 7 GLU Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 126 LYS Chi-restraints excluded: chain F residue 149 LYS Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 453 ARG Chi-restraints excluded: chain F residue 455 SER Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 48 GLU Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 159 ARG Chi-restraints excluded: chain G residue 181 GLN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain L residue 92 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 222 optimal weight: 0.9980 chunk 143 optimal weight: 0.8980 chunk 214 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 69 optimal weight: 8.9990 chunk 228 optimal weight: 0.5980 chunk 244 optimal weight: 2.9990 chunk 177 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 282 optimal weight: 0.0670 overall best weight: 1.1120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN C 425 ASN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 GLN E 427 GLN ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 413 GLN G 10 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 30085 Z= 0.214 Angle : 0.542 11.631 40768 Z= 0.275 Chirality : 0.043 0.169 4568 Planarity : 0.005 0.054 5332 Dihedral : 5.944 89.973 4248 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.78 % Favored : 98.19 % Rotamer: Outliers : 3.50 % Allowed : 18.03 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.14), residues: 3764 helix: 1.32 (0.13), residues: 1564 sheet: -0.08 (0.21), residues: 566 loop : 0.24 (0.16), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 100 HIS 0.007 0.001 HIS D 458 PHE 0.016 0.001 PHE A 559 TYR 0.015 0.001 TYR E 463 ARG 0.009 0.000 ARG D 410 *********************** 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 487 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 379 time to evaluate : 3.080 Fit side-chains REVERT: A 93 ARG cc_start: 0.7616 (mmp80) cc_final: 0.7242 (mmp80) REVERT: A 124 LYS cc_start: 0.7472 (OUTLIER) cc_final: 0.7101 (mtpt) REVERT: A 133 MET cc_start: 0.7586 (mtp) cc_final: 0.7289 (mtt) REVERT: A 156 ARG cc_start: 0.6926 (ttp80) cc_final: 0.6048 (ttm-80) REVERT: A 176 GLU cc_start: 0.7149 (mm-30) cc_final: 0.6939 (mp0) REVERT: A 323 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.7853 (mpt) REVERT: A 374 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7500 (mm-30) REVERT: A 433 SER cc_start: 0.8264 (m) cc_final: 0.7961 (t) REVERT: A 491 ARG cc_start: 0.7460 (mmt180) cc_final: 0.6540 (ttp-110) REVERT: A 520 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8026 (mt) REVERT: A 524 LYS cc_start: 0.7581 (mmmt) cc_final: 0.7329 (ttmm) REVERT: B 29 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.8232 (mmtp) REVERT: B 180 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.6372 (mp0) REVERT: B 282 MET cc_start: 0.8646 (mmm) cc_final: 0.8033 (tpt) REVERT: B 449 GLU cc_start: 0.5294 (mp0) cc_final: 0.4447 (mt-10) REVERT: B 452 ASP cc_start: 0.6753 (m-30) cc_final: 0.5805 (t70) REVERT: B 460 ARG cc_start: 0.6761 (mtp180) cc_final: 0.6519 (mtp85) REVERT: B 477 GLN cc_start: 0.4759 (mt0) cc_final: 0.4136 (mt0) REVERT: B 493 ASP cc_start: 0.6140 (m-30) cc_final: 0.5606 (m-30) REVERT: B 548 ILE cc_start: 0.6176 (OUTLIER) cc_final: 0.5931 (tp) REVERT: B 567 MET cc_start: 0.5207 (tpt) cc_final: 0.4907 (tpt) REVERT: C 53 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7764 (mt-10) REVERT: C 133 MET cc_start: 0.8182 (mtp) cc_final: 0.7909 (mtp) REVERT: C 152 ASP cc_start: 0.7715 (m-30) cc_final: 0.7337 (p0) REVERT: C 260 ASN cc_start: 0.8401 (m-40) cc_final: 0.8168 (m-40) REVERT: C 480 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6082 (mp0) REVERT: C 483 VAL cc_start: 0.7538 (t) cc_final: 0.7230 (p) REVERT: C 510 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8372 (mmtm) REVERT: C 557 GLU cc_start: 0.7113 (mp0) cc_final: 0.6420 (tp30) REVERT: C 567 MET cc_start: 0.7066 (mmm) cc_final: 0.6722 (mmm) REVERT: D 26 ASP cc_start: 0.7952 (OUTLIER) cc_final: 0.7481 (m-30) REVERT: D 87 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7526 (mt-10) REVERT: D 109 GLU cc_start: 0.7057 (OUTLIER) cc_final: 0.6467 (mp0) REVERT: D 275 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.7082 (mp0) REVERT: D 316 MET cc_start: 0.7704 (OUTLIER) cc_final: 0.7216 (mpp) REVERT: D 362 MET cc_start: 0.8693 (ttt) cc_final: 0.8449 (ttp) REVERT: D 364 ASN cc_start: 0.7990 (OUTLIER) cc_final: 0.6994 (t0) REVERT: D 376 LYS cc_start: 0.7577 (ttmm) cc_final: 0.7060 (tppp) REVERT: D 402 ASP cc_start: 0.6969 (OUTLIER) cc_final: 0.6662 (m-30) REVERT: D 410 ARG cc_start: 0.7023 (mtp85) cc_final: 0.6764 (mtp85) REVERT: E 81 ARG cc_start: 0.7309 (mtt-85) cc_final: 0.6865 (mtt180) REVERT: E 103 LEU cc_start: 0.7653 (mp) cc_final: 0.7427 (mt) REVERT: E 128 GLU cc_start: 0.7464 (pt0) cc_final: 0.7117 (pt0) REVERT: E 209 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.6976 (mt-10) REVERT: E 236 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.6240 (mtt90) REVERT: E 248 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7517 (mm-30) REVERT: E 265 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7348 (mt-10) REVERT: E 362 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.8477 (ttt) REVERT: E 364 ASN cc_start: 0.8047 (t0) cc_final: 0.7831 (t0) REVERT: E 393 ARG cc_start: 0.7126 (ttm170) cc_final: 0.6834 (mtm180) REVERT: E 410 ARG cc_start: 0.6879 (mtm180) cc_final: 0.6533 (ttt180) REVERT: E 428 GLN cc_start: 0.8077 (mt0) cc_final: 0.7782 (mt0) REVERT: E 448 GLN cc_start: 0.7320 (tt0) cc_final: 0.6745 (tm-30) REVERT: E 456 LYS cc_start: 0.5940 (mmmm) cc_final: 0.5654 (mmtm) REVERT: E 457 ASP cc_start: 0.5763 (t70) cc_final: 0.5403 (t0) REVERT: F 5 LYS cc_start: 0.7305 (tttt) cc_final: 0.6620 (ttmt) REVERT: F 7 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6899 (tp30) REVERT: F 50 VAL cc_start: 0.8981 (OUTLIER) cc_final: 0.8748 (m) REVERT: F 67 ASP cc_start: 0.7841 (p0) cc_final: 0.7567 (p0) REVERT: F 126 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.8111 (tttp) REVERT: F 149 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.8309 (mtmm) REVERT: F 200 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7891 (mt-10) REVERT: F 206 GLN cc_start: 0.7774 (mm-40) cc_final: 0.7384 (mt0) REVERT: F 452 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7828 (mttp) REVERT: F 453 ARG cc_start: 0.7115 (OUTLIER) cc_final: 0.5635 (mmt180) REVERT: G 5 SER cc_start: 0.7163 (p) cc_final: 0.6446 (t) REVERT: G 48 GLU cc_start: 0.5666 (OUTLIER) cc_final: 0.5364 (mp0) REVERT: H 62 LEU cc_start: 0.2600 (OUTLIER) cc_final: 0.2310 (tt) REVERT: H 63 MET cc_start: 0.2177 (mpt) cc_final: 0.1573 (mtp) REVERT: J 121 LEU cc_start: 0.4975 (OUTLIER) cc_final: 0.4653 (mm) REVERT: J 145 GLU cc_start: 0.2571 (pm20) cc_final: 0.1758 (OUTLIER) REVERT: J 160 LYS cc_start: 0.6093 (mmtm) cc_final: 0.5380 (mmpt) REVERT: K 104 MET cc_start: 0.5233 (OUTLIER) cc_final: 0.5002 (pp-130) REVERT: L 78 GLU cc_start: 0.5329 (mt-10) cc_final: 0.4681 (mp0) outliers start: 108 outliers final: 57 residues processed: 453 average time/residue: 1.6974 time to fit residues: 876.3914 Evaluate side-chains 457 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 370 time to evaluate : 3.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 481 ARG Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 459 GLN Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain C residue 510 LYS Chi-restraints excluded: chain C residue 536 ILE Chi-restraints excluded: chain C residue 547 ARG Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 280 ARG Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 364 ASN Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 209 GLU Chi-restraints excluded: chain E residue 236 ARG Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 362 MET Chi-restraints excluded: chain E residue 374 ASP Chi-restraints excluded: chain F residue 7 GLU Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 126 LYS Chi-restraints excluded: chain F residue 149 LYS Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 398 ILE Chi-restraints excluded: chain F residue 452 LYS Chi-restraints excluded: chain F residue 453 ARG Chi-restraints excluded: chain F residue 455 SER Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 48 GLU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 181 GLN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain K residue 104 MET Chi-restraints excluded: chain L residue 92 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 327 optimal weight: 4.9990 chunk 344 optimal weight: 0.8980 chunk 314 optimal weight: 3.9990 chunk 335 optimal weight: 8.9990 chunk 201 optimal weight: 0.9980 chunk 145 optimal weight: 2.9990 chunk 263 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 chunk 302 optimal weight: 6.9990 chunk 316 optimal weight: 7.9990 chunk 333 optimal weight: 10.0000 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN C 425 ASN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 GLN E 427 GLN ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 413 GLN G 10 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 30085 Z= 0.313 Angle : 0.616 14.960 40768 Z= 0.312 Chirality : 0.046 0.179 4568 Planarity : 0.005 0.053 5332 Dihedral : 6.175 86.414 4248 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.36 % Favored : 97.61 % Rotamer: Outliers : 3.54 % Allowed : 18.52 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.14), residues: 3764 helix: 1.11 (0.13), residues: 1566 sheet: -0.11 (0.21), residues: 567 loop : 0.16 (0.16), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP J 100 HIS 0.005 0.001 HIS B 283 PHE 0.021 0.002 PHE A 559 TYR 0.017 0.002 TYR E 463 ARG 0.009 0.001 ARG D 410 *********************** 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 477 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 368 time to evaluate : 3.333 Fit side-chains REVERT: A 93 ARG cc_start: 0.7577 (mmp80) cc_final: 0.7186 (mmp80) REVERT: A 124 LYS cc_start: 0.7432 (OUTLIER) cc_final: 0.7042 (mtpt) REVERT: A 133 MET cc_start: 0.7598 (mtp) cc_final: 0.7232 (mtt) REVERT: A 156 ARG cc_start: 0.6898 (ttp80) cc_final: 0.6041 (ttm-80) REVERT: A 323 MET cc_start: 0.8721 (OUTLIER) cc_final: 0.7962 (mpt) REVERT: A 374 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7508 (mm-30) REVERT: A 433 SER cc_start: 0.8252 (m) cc_final: 0.7945 (t) REVERT: A 491 ARG cc_start: 0.7475 (mmt180) cc_final: 0.6552 (ttp-110) REVERT: A 520 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7970 (mt) REVERT: A 524 LYS cc_start: 0.7592 (mmmt) cc_final: 0.7330 (ttmm) REVERT: B 29 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.8246 (mmtp) REVERT: B 180 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.6430 (mp0) REVERT: B 282 MET cc_start: 0.8689 (mmm) cc_final: 0.8093 (tpt) REVERT: B 449 GLU cc_start: 0.5312 (mp0) cc_final: 0.4561 (mt-10) REVERT: B 452 ASP cc_start: 0.6773 (m-30) cc_final: 0.5810 (t70) REVERT: B 477 GLN cc_start: 0.4868 (mt0) cc_final: 0.4272 (mt0) REVERT: B 493 ASP cc_start: 0.6091 (m-30) cc_final: 0.5546 (m-30) REVERT: B 548 ILE cc_start: 0.6269 (OUTLIER) cc_final: 0.5995 (tp) REVERT: B 567 MET cc_start: 0.5282 (tpt) cc_final: 0.5005 (tpt) REVERT: C 53 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7788 (mt-10) REVERT: C 133 MET cc_start: 0.8222 (mtp) cc_final: 0.7947 (mtp) REVERT: C 152 ASP cc_start: 0.7698 (m-30) cc_final: 0.7345 (p0) REVERT: C 260 ASN cc_start: 0.8432 (m-40) cc_final: 0.8168 (m-40) REVERT: C 480 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6165 (mp0) REVERT: C 483 VAL cc_start: 0.7572 (t) cc_final: 0.7269 (p) REVERT: C 510 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8414 (mmtm) REVERT: C 557 GLU cc_start: 0.7135 (mp0) cc_final: 0.6504 (tp30) REVERT: C 567 MET cc_start: 0.7065 (mmm) cc_final: 0.6772 (mmm) REVERT: D 26 ASP cc_start: 0.7990 (OUTLIER) cc_final: 0.7508 (m-30) REVERT: D 49 GLU cc_start: 0.8402 (tt0) cc_final: 0.8201 (tt0) REVERT: D 87 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7635 (mt-10) REVERT: D 109 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6595 (mp0) REVERT: D 275 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.7081 (mp0) REVERT: D 316 MET cc_start: 0.7815 (OUTLIER) cc_final: 0.7352 (mpp) REVERT: D 345 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.8056 (mtt90) REVERT: D 362 MET cc_start: 0.8714 (ttt) cc_final: 0.8449 (ttp) REVERT: D 376 LYS cc_start: 0.7554 (ttmm) cc_final: 0.7043 (tppp) REVERT: D 402 ASP cc_start: 0.6953 (OUTLIER) cc_final: 0.6614 (m-30) REVERT: E 49 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8069 (tm-30) REVERT: E 81 ARG cc_start: 0.7317 (mtt-85) cc_final: 0.6889 (mtp85) REVERT: E 103 LEU cc_start: 0.7672 (mp) cc_final: 0.7406 (mt) REVERT: E 128 GLU cc_start: 0.7392 (pt0) cc_final: 0.7078 (pt0) REVERT: E 209 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.7031 (mt-10) REVERT: E 236 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.6328 (mtt90) REVERT: E 248 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7536 (mm-30) REVERT: E 265 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7342 (mt-10) REVERT: E 362 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.8456 (ttt) REVERT: E 364 ASN cc_start: 0.8019 (t0) cc_final: 0.7803 (t0) REVERT: E 410 ARG cc_start: 0.6901 (mtm180) cc_final: 0.6523 (ttt180) REVERT: E 428 GLN cc_start: 0.8052 (mt0) cc_final: 0.7787 (mt0) REVERT: E 456 LYS cc_start: 0.5980 (mmmm) cc_final: 0.5743 (mmtm) REVERT: E 457 ASP cc_start: 0.5758 (t70) cc_final: 0.5403 (t0) REVERT: F 5 LYS cc_start: 0.7370 (tttt) cc_final: 0.6754 (ttmt) REVERT: F 7 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.6943 (tp30) REVERT: F 50 VAL cc_start: 0.9053 (OUTLIER) cc_final: 0.8816 (m) REVERT: F 67 ASP cc_start: 0.7963 (p0) cc_final: 0.7685 (p0) REVERT: F 126 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.8122 (tttp) REVERT: F 200 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7903 (mt-10) REVERT: F 452 LYS cc_start: 0.8062 (OUTLIER) cc_final: 0.7841 (mttp) REVERT: F 453 ARG cc_start: 0.7164 (OUTLIER) cc_final: 0.5685 (mmt180) REVERT: F 461 LYS cc_start: 0.7229 (OUTLIER) cc_final: 0.6841 (ttmp) REVERT: G 5 SER cc_start: 0.7304 (p) cc_final: 0.6590 (t) REVERT: G 48 GLU cc_start: 0.5611 (OUTLIER) cc_final: 0.5345 (mp0) REVERT: H 63 MET cc_start: 0.2327 (mpt) cc_final: 0.1712 (mtp) REVERT: J 121 LEU cc_start: 0.4809 (OUTLIER) cc_final: 0.4562 (mm) REVERT: J 160 LYS cc_start: 0.5998 (mmtm) cc_final: 0.5386 (mmpt) REVERT: K 104 MET cc_start: 0.5225 (OUTLIER) cc_final: 0.4988 (pp-130) REVERT: L 78 GLU cc_start: 0.5256 (mt-10) cc_final: 0.4602 (mp0) REVERT: L 132 GLU cc_start: 0.2710 (mm-30) cc_final: 0.2311 (tt0) outliers start: 109 outliers final: 59 residues processed: 441 average time/residue: 1.7107 time to fit residues: 862.8248 Evaluate side-chains 457 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 367 time to evaluate : 3.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 481 ARG Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 550 ARG Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 459 GLN Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain C residue 510 LYS Chi-restraints excluded: chain C residue 536 ILE Chi-restraints excluded: chain C residue 547 ARG Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 280 ARG Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain D residue 345 ARG Chi-restraints excluded: chain D residue 364 ASN Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 209 GLU Chi-restraints excluded: chain E residue 236 ARG Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain E residue 362 MET Chi-restraints excluded: chain E residue 374 ASP Chi-restraints excluded: chain F residue 7 GLU Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 126 LYS Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 452 LYS Chi-restraints excluded: chain F residue 453 ARG Chi-restraints excluded: chain F residue 455 SER Chi-restraints excluded: chain F residue 461 LYS Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 48 GLU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 181 GLN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain K residue 104 MET Chi-restraints excluded: chain L residue 92 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 219 optimal weight: 1.9990 chunk 354 optimal weight: 10.0000 chunk 216 optimal weight: 1.9990 chunk 168 optimal weight: 0.0060 chunk 246 optimal weight: 0.7980 chunk 371 optimal weight: 5.9990 chunk 342 optimal weight: 5.9990 chunk 295 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 228 optimal weight: 5.9990 chunk 181 optimal weight: 0.1980 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN C 425 ASN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 GLN E 427 GLN E 458 HIS ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 413 GLN G 10 ASN G 17 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 30085 Z= 0.201 Angle : 0.542 13.997 40768 Z= 0.275 Chirality : 0.043 0.169 4568 Planarity : 0.004 0.053 5332 Dihedral : 5.921 88.091 4248 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.81 % Favored : 98.17 % Rotamer: Outliers : 3.08 % Allowed : 19.07 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.14), residues: 3764 helix: 1.29 (0.13), residues: 1562 sheet: -0.08 (0.21), residues: 566 loop : 0.22 (0.16), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP J 100 HIS 0.003 0.001 HIS A 185 PHE 0.015 0.001 PHE A 559 TYR 0.015 0.001 TYR E 463 ARG 0.008 0.000 ARG D 410 ********************** 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 471 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 376 time to evaluate : 3.231 Fit side-chains REVERT: A 93 ARG cc_start: 0.7591 (mmp80) cc_final: 0.7209 (mmp80) REVERT: A 124 LYS cc_start: 0.7468 (OUTLIER) cc_final: 0.7088 (mtpt) REVERT: A 133 MET cc_start: 0.7579 (mtp) cc_final: 0.7279 (mtt) REVERT: A 156 ARG cc_start: 0.6688 (ttp80) cc_final: 0.6202 (ttm-80) REVERT: A 323 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.7846 (mpt) REVERT: A 374 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7440 (mm-30) REVERT: A 402 ILE cc_start: 0.8485 (mp) cc_final: 0.8284 (pt) REVERT: A 433 SER cc_start: 0.8258 (m) cc_final: 0.7949 (t) REVERT: A 491 ARG cc_start: 0.7467 (mmt180) cc_final: 0.6563 (ttp-110) REVERT: A 520 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.8022 (mt) REVERT: A 524 LYS cc_start: 0.7569 (mmmt) cc_final: 0.7343 (ttmm) REVERT: B 29 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.8250 (mmtp) REVERT: B 180 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.6365 (mp0) REVERT: B 282 MET cc_start: 0.8630 (mmm) cc_final: 0.8016 (tpt) REVERT: B 449 GLU cc_start: 0.5338 (mp0) cc_final: 0.4560 (mt-10) REVERT: B 452 ASP cc_start: 0.6712 (m-30) cc_final: 0.5789 (t70) REVERT: B 477 GLN cc_start: 0.4903 (mt0) cc_final: 0.4277 (mt0) REVERT: B 493 ASP cc_start: 0.6143 (m-30) cc_final: 0.5604 (m-30) REVERT: B 548 ILE cc_start: 0.6275 (OUTLIER) cc_final: 0.6029 (tp) REVERT: B 567 MET cc_start: 0.5228 (tpt) cc_final: 0.4942 (tpt) REVERT: C 53 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7748 (mt-10) REVERT: C 133 MET cc_start: 0.8195 (mtp) cc_final: 0.7920 (mtp) REVERT: C 152 ASP cc_start: 0.7692 (m-30) cc_final: 0.7336 (p0) REVERT: C 260 ASN cc_start: 0.8388 (m-40) cc_final: 0.8156 (m-40) REVERT: C 480 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6940 (mm-30) REVERT: C 483 VAL cc_start: 0.7501 (t) cc_final: 0.7192 (p) REVERT: C 488 ARG cc_start: 0.7885 (ttp-110) cc_final: 0.7442 (ttp80) REVERT: C 510 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8350 (mmtm) REVERT: C 536 ILE cc_start: 0.6168 (OUTLIER) cc_final: 0.5815 (mm) REVERT: C 567 MET cc_start: 0.7006 (mmm) cc_final: 0.6738 (mmm) REVERT: D 26 ASP cc_start: 0.7925 (OUTLIER) cc_final: 0.7453 (m-30) REVERT: D 87 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7556 (mt-10) REVERT: D 109 GLU cc_start: 0.7105 (OUTLIER) cc_final: 0.6567 (mp0) REVERT: D 275 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.6779 (mp0) REVERT: D 316 MET cc_start: 0.7709 (OUTLIER) cc_final: 0.7220 (mpp) REVERT: D 362 MET cc_start: 0.8690 (ttt) cc_final: 0.8444 (ttp) REVERT: D 364 ASN cc_start: 0.8026 (OUTLIER) cc_final: 0.7045 (t0) REVERT: D 376 LYS cc_start: 0.7612 (ttmm) cc_final: 0.7105 (tppp) REVERT: D 402 ASP cc_start: 0.6933 (OUTLIER) cc_final: 0.6609 (m-30) REVERT: E 49 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8061 (tm-30) REVERT: E 81 ARG cc_start: 0.7271 (mtt-85) cc_final: 0.6884 (mtp85) REVERT: E 103 LEU cc_start: 0.7642 (mp) cc_final: 0.7408 (mt) REVERT: E 128 GLU cc_start: 0.7393 (pt0) cc_final: 0.7065 (pt0) REVERT: E 174 ARG cc_start: 0.7713 (mmm-85) cc_final: 0.7505 (mmm-85) REVERT: E 209 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.7024 (mt-10) REVERT: E 236 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.6184 (mtt90) REVERT: E 248 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7520 (mm-30) REVERT: E 265 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7352 (mt-10) REVERT: E 364 ASN cc_start: 0.8029 (t0) cc_final: 0.7818 (t0) REVERT: E 410 ARG cc_start: 0.6862 (mtm180) cc_final: 0.6516 (ttt180) REVERT: E 448 GLN cc_start: 0.7296 (tt0) cc_final: 0.6742 (tm-30) REVERT: E 456 LYS cc_start: 0.5955 (mmmm) cc_final: 0.5659 (mmtm) REVERT: E 457 ASP cc_start: 0.5832 (t70) cc_final: 0.5446 (t0) REVERT: F 5 LYS cc_start: 0.7411 (tttt) cc_final: 0.6781 (ttmt) REVERT: F 7 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6908 (tp30) REVERT: F 50 VAL cc_start: 0.8979 (OUTLIER) cc_final: 0.8750 (m) REVERT: F 67 ASP cc_start: 0.7840 (p0) cc_final: 0.7548 (p0) REVERT: F 126 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.8116 (tttp) REVERT: F 200 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7892 (mt-10) REVERT: F 206 GLN cc_start: 0.7753 (mm-40) cc_final: 0.7379 (mt0) REVERT: F 453 ARG cc_start: 0.7112 (OUTLIER) cc_final: 0.5619 (mmt180) REVERT: F 461 LYS cc_start: 0.7275 (OUTLIER) cc_final: 0.6898 (ttmp) REVERT: G 5 SER cc_start: 0.7136 (p) cc_final: 0.6411 (t) REVERT: G 48 GLU cc_start: 0.5578 (OUTLIER) cc_final: 0.5306 (mp0) REVERT: H 63 MET cc_start: 0.2361 (mpt) cc_final: 0.1743 (mtp) REVERT: J 121 LEU cc_start: 0.4879 (OUTLIER) cc_final: 0.4598 (mm) REVERT: J 145 GLU cc_start: 0.2539 (pm20) cc_final: 0.1783 (OUTLIER) REVERT: J 160 LYS cc_start: 0.6038 (mmtm) cc_final: 0.5475 (mmpt) REVERT: L 78 GLU cc_start: 0.5334 (mt-10) cc_final: 0.4646 (mp0) REVERT: L 132 GLU cc_start: 0.2721 (mm-30) cc_final: 0.2228 (tt0) outliers start: 95 outliers final: 56 residues processed: 439 average time/residue: 1.7278 time to fit residues: 864.8518 Evaluate side-chains 455 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 371 time to evaluate : 3.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 550 ARG Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 459 GLN Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain C residue 510 LYS Chi-restraints excluded: chain C residue 536 ILE Chi-restraints excluded: chain C residue 547 ARG Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 280 ARG Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain D residue 364 ASN Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 209 GLU Chi-restraints excluded: chain E residue 236 ARG Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain E residue 374 ASP Chi-restraints excluded: chain F residue 7 GLU Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 126 LYS Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 453 ARG Chi-restraints excluded: chain F residue 455 SER Chi-restraints excluded: chain F residue 461 LYS Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 48 GLU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 181 GLN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain L residue 92 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 235 optimal weight: 0.3980 chunk 315 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 272 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 296 optimal weight: 0.8980 chunk 124 optimal weight: 0.0770 chunk 304 optimal weight: 0.5980 chunk 37 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN C 425 ASN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 GLN E 427 GLN ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 413 GLN G 10 ASN H 82 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.161186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.126507 restraints weight = 35354.958| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.25 r_work: 0.3227 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 30085 Z= 0.163 Angle : 0.511 13.440 40768 Z= 0.258 Chirality : 0.042 0.161 4568 Planarity : 0.004 0.054 5332 Dihedral : 5.703 89.772 4248 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.89 % Favored : 98.09 % Rotamer: Outliers : 2.85 % Allowed : 19.49 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.14), residues: 3764 helix: 1.44 (0.13), residues: 1568 sheet: -0.04 (0.21), residues: 566 loop : 0.25 (0.16), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 424 HIS 0.003 0.001 HIS D 249 PHE 0.013 0.001 PHE A 559 TYR 0.014 0.001 TYR A 166 ARG 0.007 0.000 ARG B 488 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13793.52 seconds wall clock time: 242 minutes 35.97 seconds (14555.97 seconds total)