Starting phenix.real_space_refine on Sat Jun 29 16:13:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8va1_43083/06_2024/8va1_43083_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8va1_43083/06_2024/8va1_43083.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8va1_43083/06_2024/8va1_43083_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8va1_43083/06_2024/8va1_43083_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8va1_43083/06_2024/8va1_43083_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8va1_43083/06_2024/8va1_43083.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8va1_43083/06_2024/8va1_43083.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8va1_43083/06_2024/8va1_43083_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8va1_43083/06_2024/8va1_43083_updated.pdb" } resolution = 3.4 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= 0.001 sd= 0.025 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: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 36 5.16 5 C 12113 2.51 5 N 3066 2.21 5 O 3503 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 41": "OE1" <-> "OE2" Residue "A PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 75": "OD1" <-> "OD2" Residue "A GLU 155": "OE1" <-> "OE2" Residue "A ASP 339": "OD1" <-> "OD2" Residue "A TYR 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 502": "OD1" <-> "OD2" Residue "A PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 49": "OD1" <-> "OD2" Residue "B ASP 75": "OD1" <-> "OD2" Residue "B TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 218": "OD1" <-> "OD2" Residue "B GLU 345": "OE1" <-> "OE2" Residue "B PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 379": "OE1" <-> "OE2" Residue "B PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 422": "OE1" <-> "OE2" Residue "B PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 541": "OD1" <-> "OD2" Residue "C GLU 155": "OE1" <-> "OE2" Residue "C PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 339": "OD1" <-> "OD2" Residue "C PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 496": "OD1" <-> "OD2" Residue "C TYR 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 21": "OE1" <-> "OE2" Residue "D GLU 41": "OE1" <-> "OE2" Residue "D ASP 49": "OD1" <-> "OD2" Residue "D GLU 82": "OE1" <-> "OE2" Residue "D TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 178": "OE1" <-> "OE2" Residue "D ASP 273": "OD1" <-> "OD2" Residue "D ASP 339": "OD1" <-> "OD2" Residue "D PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 18726 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 559, 4657 Classifications: {'peptide': 559} Link IDs: {'PTRANS': 20, 'TRANS': 538} Chain: "B" Number of atoms: 4664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 560, 4664 Classifications: {'peptide': 560} Link IDs: {'PTRANS': 20, 'TRANS': 539} Chain: "C" Number of atoms: 4664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 560, 4664 Classifications: {'peptide': 560} Link IDs: {'PTRANS': 20, 'TRANS': 539} Chain: "D" Number of atoms: 4605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4605 Classifications: {'peptide': 551} Link IDs: {'PTRANS': 20, 'TRANS': 530} Chain breaks: 2 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'V2V': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'V2V': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'V2V': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'V2V': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.36, per 1000 atoms: 0.50 Number of scatterers: 18726 At special positions: 0 Unit cell: (157.526, 157.526, 79.425, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 36 16.00 P 8 15.00 O 3503 8.00 N 3066 7.00 C 12113 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: 6.73 Conformation dependent library (CDL) restraints added in 2.9 seconds 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4266 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 89 helices and 21 sheets defined 36.0% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.67 Creating SS restraints... Processing helix chain 'A' and resid 29 through 31 No H-bonds generated for 'chain 'A' and resid 29 through 31' Processing helix chain 'A' and resid 93 through 101 removed outlier: 3.850A pdb=" N ASP A 98 " --> pdb=" O VAL A 95 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN A 101 " --> pdb=" O ASP A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 112 removed outlier: 4.520A pdb=" N GLU A 109 " --> pdb=" O GLU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 128 removed outlier: 4.888A pdb=" N THR A 127 " --> pdb=" O PHE A 123 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N TYR A 128 " --> pdb=" O LEU A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 136 No H-bonds generated for 'chain 'A' and resid 134 through 136' Processing helix chain 'A' and resid 171 through 206 Processing helix chain 'A' and resid 226 through 236 Processing helix chain 'A' and resid 261 through 271 Proline residue: A 266 - end of helix Processing helix chain 'A' and resid 284 through 286 No H-bonds generated for 'chain 'A' and resid 284 through 286' Processing helix chain 'A' and resid 309 through 312 Processing helix chain 'A' and resid 337 through 347 Proline residue: A 341 - end of helix removed outlier: 3.686A pdb=" N PHE A 347 " --> pdb=" O ALA A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 360 through 366 removed outlier: 3.942A pdb=" N VAL A 364 " --> pdb=" O ARG A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 381 Processing helix chain 'A' and resid 414 through 424 Processing helix chain 'A' and resid 462 through 464 No H-bonds generated for 'chain 'A' and resid 462 through 464' Processing helix chain 'A' and resid 475 through 483 removed outlier: 3.530A pdb=" N VAL A 482 " --> pdb=" O GLU A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 500 Processing helix chain 'A' and resid 507 through 510 No H-bonds generated for 'chain 'A' and resid 507 through 510' Processing helix chain 'A' and resid 519 through 527 Processing helix chain 'A' and resid 533 through 543 removed outlier: 4.317A pdb=" N ILE A 537 " --> pdb=" O GLU A 534 " (cutoff:3.500A) Proline residue: A 538 - end of helix removed outlier: 3.510A pdb=" N LYS A 542 " --> pdb=" O PHE A 539 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N HIS A 543 " --> pdb=" O LEU A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 560 Processing helix chain 'B' and resid 94 through 100 Processing helix chain 'B' and resid 105 through 113 removed outlier: 3.740A pdb=" N GLU B 109 " --> pdb=" O PRO B 105 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLU B 110 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLU B 113 " --> pdb=" O GLU B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 128 removed outlier: 3.597A pdb=" N GLN B 126 " --> pdb=" O ASN B 122 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N THR B 127 " --> pdb=" O PHE B 123 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N TYR B 128 " --> pdb=" O LEU B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 136 No H-bonds generated for 'chain 'B' and resid 134 through 136' Processing helix chain 'B' and resid 171 through 206 Processing helix chain 'B' and resid 226 through 236 Processing helix chain 'B' and resid 239 through 242 No H-bonds generated for 'chain 'B' and resid 239 through 242' Processing helix chain 'B' and resid 259 through 271 Proline residue: B 266 - end of helix Processing helix chain 'B' and resid 309 through 312 Processing helix chain 'B' and resid 337 through 347 Proline residue: B 341 - end of helix Processing helix chain 'B' and resid 360 through 366 removed outlier: 3.953A pdb=" N VAL B 364 " --> pdb=" O ARG B 361 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU B 365 " --> pdb=" O THR B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 381 Processing helix chain 'B' and resid 383 through 386 Processing helix chain 'B' and resid 409 through 411 No H-bonds generated for 'chain 'B' and resid 409 through 411' Processing helix chain 'B' and resid 414 through 422 Processing helix chain 'B' and resid 444 through 446 No H-bonds generated for 'chain 'B' and resid 444 through 446' Processing helix chain 'B' and resid 475 through 483 removed outlier: 4.276A pdb=" N TYR B 480 " --> pdb=" O ILE B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 500 Processing helix chain 'B' and resid 507 through 510 No H-bonds generated for 'chain 'B' and resid 507 through 510' Processing helix chain 'B' and resid 519 through 526 Processing helix chain 'B' and resid 533 through 543 removed outlier: 4.925A pdb=" N ILE B 537 " --> pdb=" O GLU B 534 " (cutoff:3.500A) Proline residue: B 538 - end of helix removed outlier: 3.826A pdb=" N HIS B 543 " --> pdb=" O LEU B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 559 Processing helix chain 'C' and resid 93 through 100 removed outlier: 3.524A pdb=" N TYR C 100 " --> pdb=" O ILE C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 112 Processing helix chain 'C' and resid 117 through 128 removed outlier: 4.762A pdb=" N THR C 127 " --> pdb=" O PHE C 123 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N TYR C 128 " --> pdb=" O LEU C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 136 No H-bonds generated for 'chain 'C' and resid 134 through 136' Processing helix chain 'C' and resid 171 through 204 Processing helix chain 'C' and resid 226 through 236 Processing helix chain 'C' and resid 259 through 271 removed outlier: 4.086A pdb=" N PHE C 263 " --> pdb=" O ILE C 259 " (cutoff:3.500A) Proline residue: C 266 - end of helix Processing helix chain 'C' and resid 309 through 312 Processing helix chain 'C' and resid 337 through 347 Proline residue: C 341 - end of helix removed outlier: 3.619A pdb=" N PHE C 347 " --> pdb=" O ALA C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 360 through 366 removed outlier: 3.939A pdb=" N VAL C 364 " --> pdb=" O ARG C 361 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE C 366 " --> pdb=" O ASP C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 381 Processing helix chain 'C' and resid 383 through 386 Processing helix chain 'C' and resid 409 through 411 No H-bonds generated for 'chain 'C' and resid 409 through 411' Processing helix chain 'C' and resid 414 through 424 Processing helix chain 'C' and resid 444 through 449 removed outlier: 3.806A pdb=" N GLN C 448 " --> pdb=" O ASP C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 464 removed outlier: 4.331A pdb=" N ILE C 462 " --> pdb=" O VAL C 459 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU C 463 " --> pdb=" O ASN C 460 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE C 464 " --> pdb=" O ASP C 461 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 459 through 464' Processing helix chain 'C' and resid 475 through 483 removed outlier: 3.620A pdb=" N TYR C 480 " --> pdb=" O ILE C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 500 Processing helix chain 'C' and resid 507 through 510 No H-bonds generated for 'chain 'C' and resid 507 through 510' Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 533 through 543 removed outlier: 4.546A pdb=" N ILE C 537 " --> pdb=" O GLU C 534 " (cutoff:3.500A) Proline residue: C 538 - end of helix removed outlier: 3.949A pdb=" N HIS C 543 " --> pdb=" O LEU C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 560 Processing helix chain 'D' and resid 93 through 101 Processing helix chain 'D' and resid 108 through 112 Processing helix chain 'D' and resid 117 through 128 removed outlier: 3.523A pdb=" N GLN D 126 " --> pdb=" O ASN D 122 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N THR D 127 " --> pdb=" O PHE D 123 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N TYR D 128 " --> pdb=" O LEU D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 206 Processing helix chain 'D' and resid 228 through 236 removed outlier: 5.838A pdb=" N GLU D 233 " --> pdb=" O TYR D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 242 No H-bonds generated for 'chain 'D' and resid 239 through 242' Processing helix chain 'D' and resid 259 through 271 Proline residue: D 266 - end of helix Processing helix chain 'D' and resid 282 through 285 Processing helix chain 'D' and resid 309 through 312 Processing helix chain 'D' and resid 337 through 346 Proline residue: D 341 - end of helix Processing helix chain 'D' and resid 360 through 364 removed outlier: 3.610A pdb=" N VAL D 364 " --> pdb=" O ARG D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 381 Processing helix chain 'D' and resid 383 through 386 Processing helix chain 'D' and resid 409 through 411 No H-bonds generated for 'chain 'D' and resid 409 through 411' Processing helix chain 'D' and resid 414 through 424 Processing helix chain 'D' and resid 444 through 446 No H-bonds generated for 'chain 'D' and resid 444 through 446' Processing helix chain 'D' and resid 459 through 464 removed outlier: 4.089A pdb=" N PHE D 464 " --> pdb=" O ASN D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 483 removed outlier: 3.523A pdb=" N TYR D 480 " --> pdb=" O ILE D 477 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA D 481 " --> pdb=" O TYR D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 500 Processing helix chain 'D' and resid 519 through 527 Processing helix chain 'D' and resid 533 through 543 removed outlier: 4.748A pdb=" N ILE D 537 " --> pdb=" O GLU D 534 " (cutoff:3.500A) Proline residue: D 538 - end of helix removed outlier: 3.589A pdb=" N HIS D 543 " --> pdb=" O LEU D 540 " (cutoff:3.500A) Processing helix chain 'D' and resid 551 through 560 Processing sheet with id= A, first strand: chain 'A' and resid 49 through 53 removed outlier: 3.722A pdb=" N ASP A 49 " --> pdb=" O ARG A 60 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS A 10 " --> pdb=" O GLU A 21 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N HIS A 23 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N ILE A 8 " --> pdb=" O HIS A 23 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 44 through 46 removed outlier: 3.753A pdb=" N TYR A 77 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N LEU A 79 " --> pdb=" O PHE A 156 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N PHE A 156 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU A 155 " --> pdb=" O SER A 150 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 244 through 249 removed outlier: 3.572A pdb=" N SER A 217 " --> pdb=" O VAL A 248 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TYR A 274 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N THR A 216 " --> pdb=" O TYR A 274 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N PHE A 276 " --> pdb=" O THR A 216 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N GLU A 294 " --> pdb=" O ILE A 275 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N VAL A 277 " --> pdb=" O GLU A 294 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE A 296 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LYS A 331 " --> pdb=" O GLN A 297 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 468 through 470 Processing sheet with id= E, first strand: chain 'A' and resid 488 through 490 removed outlier: 7.146A pdb=" N LYS A 514 " --> pdb=" O PHE A 489 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 6 through 8 Processing sheet with id= G, first strand: chain 'B' and resid 17 through 23 removed outlier: 3.841A pdb=" N ASP B 49 " --> pdb=" O ARG B 60 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 44 through 46 removed outlier: 3.515A pdb=" N MET B 45 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP B 75 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL B 160 " --> pdb=" O ASP B 75 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LEU B 79 " --> pdb=" O PHE B 156 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N PHE B 156 " --> pdb=" O LEU B 79 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 244 through 249 removed outlier: 6.469A pdb=" N TYR B 274 " --> pdb=" O LEU B 214 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N THR B 216 " --> pdb=" O TYR B 274 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N PHE B 276 " --> pdb=" O THR B 216 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLU B 294 " --> pdb=" O ILE B 275 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N VAL B 277 " --> pdb=" O GLU B 294 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE B 296 " --> pdb=" O VAL B 277 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LYS B 331 " --> pdb=" O GLN B 297 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 487 through 489 removed outlier: 5.791A pdb=" N LEU B 469 " --> pdb=" O ILE B 488 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 49 through 53 removed outlier: 3.558A pdb=" N PHE C 19 " --> pdb=" O TYR C 12 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N HIS C 23 " --> pdb=" O ILE C 8 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N ILE C 8 " --> pdb=" O HIS C 23 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N GLU C 25 " --> pdb=" O ILE C 6 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N ILE C 6 " --> pdb=" O GLU C 25 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 33 through 38 removed outlier: 3.568A pdb=" N ASN C 33 " --> pdb=" O GLU C 82 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR C 77 " --> pdb=" O LEU C 158 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N LEU C 79 " --> pdb=" O PHE C 156 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N PHE C 156 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU C 155 " --> pdb=" O SER C 150 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 244 through 249 removed outlier: 3.576A pdb=" N SER C 217 " --> pdb=" O VAL C 248 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N TYR C 274 " --> pdb=" O LEU C 214 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N THR C 216 " --> pdb=" O TYR C 274 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N PHE C 276 " --> pdb=" O THR C 216 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N GLU C 294 " --> pdb=" O ILE C 275 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N VAL C 277 " --> pdb=" O GLU C 294 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ILE C 296 " --> pdb=" O VAL C 277 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 332 through 334 Processing sheet with id= O, first strand: chain 'C' and resid 389 through 393 Processing sheet with id= P, first strand: chain 'C' and resid 487 through 490 removed outlier: 3.750A pdb=" N LYS C 514 " --> pdb=" O MET C 487 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 89 through 91 removed outlier: 6.149A pdb=" N ILE D 6 " --> pdb=" O GLN D 90 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS D 5 " --> pdb=" O GLU D 25 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU D 25 " --> pdb=" O LYS D 5 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLU D 21 " --> pdb=" O ASP D 9 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ILE D 11 " --> pdb=" O PHE D 19 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N PHE D 19 " --> pdb=" O ILE D 11 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N TRP D 13 " --> pdb=" O GLN D 17 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLN D 17 " --> pdb=" O TRP D 13 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP D 49 " --> pdb=" O ARG D 60 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 44 through 46 removed outlier: 3.618A pdb=" N MET D 45 " --> pdb=" O LEU D 36 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN D 33 " --> pdb=" O GLU D 82 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LEU D 79 " --> pdb=" O PHE D 156 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N PHE D 156 " --> pdb=" O LEU D 79 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 244 through 249 removed outlier: 6.412A pdb=" N TYR D 274 " --> pdb=" O LEU D 214 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N THR D 216 " --> pdb=" O TYR D 274 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N PHE D 276 " --> pdb=" O THR D 216 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLU D 294 " --> pdb=" O ILE D 275 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N VAL D 277 " --> pdb=" O GLU D 294 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ILE D 296 " --> pdb=" O VAL D 277 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 389 through 393 Processing sheet with id= U, first strand: chain 'D' and resid 488 through 490 removed outlier: 6.413A pdb=" N LYS D 514 " --> pdb=" O PHE D 489 " (cutoff:3.500A) No H-bonds generated for sheet with id= U 595 hydrogen bonds defined for protein. 1518 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: 5.90 Time building geometry restraints manager: 7.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3086 1.31 - 1.44: 5389 1.44 - 1.57: 10618 1.57 - 1.69: 26 1.69 - 1.82: 64 Bond restraints: 19183 Sorted by residual: bond pdb=" C12 V2V B 601 " pdb=" O13 V2V B 601 " ideal model delta sigma weight residual 1.303 1.606 -0.303 2.00e-02 2.50e+03 2.29e+02 bond pdb=" C12 V2V C 601 " pdb=" O13 V2V C 601 " ideal model delta sigma weight residual 1.303 1.606 -0.303 2.00e-02 2.50e+03 2.29e+02 bond pdb=" C12 V2V D 601 " pdb=" O13 V2V D 601 " ideal model delta sigma weight residual 1.303 1.606 -0.303 2.00e-02 2.50e+03 2.29e+02 bond pdb=" C12 V2V A 601 " pdb=" O13 V2V A 601 " ideal model delta sigma weight residual 1.303 1.606 -0.303 2.00e-02 2.50e+03 2.29e+02 bond pdb=" C09 V2V C 601 " pdb=" O13 V2V C 601 " ideal model delta sigma weight residual 1.582 1.280 0.302 2.00e-02 2.50e+03 2.29e+02 ... (remaining 19178 not shown) Histogram of bond angle deviations from ideal: 95.41 - 103.25: 135 103.25 - 111.09: 6963 111.09 - 118.93: 8085 118.93 - 126.78: 10613 126.78 - 134.62: 132 Bond angle restraints: 25928 Sorted by residual: angle pdb=" C ASN B 300 " pdb=" CA ASN B 300 " pdb=" CB ASN B 300 " ideal model delta sigma weight residual 110.95 102.32 8.63 1.55e+00 4.16e-01 3.10e+01 angle pdb=" N VAL C 16 " pdb=" CA VAL C 16 " pdb=" C VAL C 16 " ideal model delta sigma weight residual 113.20 108.00 5.20 9.60e-01 1.09e+00 2.93e+01 angle pdb=" CA PRO B 408 " pdb=" N PRO B 408 " pdb=" CD PRO B 408 " ideal model delta sigma weight residual 112.00 105.72 6.28 1.40e+00 5.10e-01 2.01e+01 angle pdb=" CB MET B 378 " pdb=" CG MET B 378 " pdb=" SD MET B 378 " ideal model delta sigma weight residual 112.70 125.23 -12.53 3.00e+00 1.11e-01 1.75e+01 angle pdb=" C LEU C 522 " pdb=" N MET C 523 " pdb=" CA MET C 523 " ideal model delta sigma weight residual 120.28 114.58 5.70 1.44e+00 4.82e-01 1.57e+01 ... (remaining 25923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 9862 17.86 - 35.71: 1208 35.71 - 53.57: 285 53.57 - 71.42: 44 71.42 - 89.28: 27 Dihedral angle restraints: 11426 sinusoidal: 4796 harmonic: 6630 Sorted by residual: dihedral pdb=" C ASN B 300 " pdb=" N ASN B 300 " pdb=" CA ASN B 300 " pdb=" CB ASN B 300 " ideal model delta harmonic sigma weight residual -122.60 -112.27 -10.33 0 2.50e+00 1.60e-01 1.71e+01 dihedral pdb=" CA LYS C 514 " pdb=" C LYS C 514 " pdb=" N ILE C 515 " pdb=" CA ILE C 515 " ideal model delta harmonic sigma weight residual 180.00 159.94 20.06 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA GLU D 228 " pdb=" C GLU D 228 " pdb=" N TYR D 229 " pdb=" CA TYR D 229 " ideal model delta harmonic sigma weight residual 180.00 160.16 19.84 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 11423 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2071 0.050 - 0.100: 567 0.100 - 0.149: 136 0.149 - 0.199: 6 0.199 - 0.249: 2 Chirality restraints: 2782 Sorted by residual: chirality pdb=" CA ASN B 300 " pdb=" N ASN B 300 " pdb=" C ASN B 300 " pdb=" CB ASN B 300 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CG LEU C 522 " pdb=" CB LEU C 522 " pdb=" CD1 LEU C 522 " pdb=" CD2 LEU C 522 " both_signs ideal model delta sigma weight residual False -2.59 -2.82 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" C09 V2V D 601 " pdb=" C10 V2V D 601 " pdb=" N03 V2V D 601 " pdb=" O13 V2V D 601 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.19 2.00e-01 2.50e+01 8.69e-01 ... (remaining 2779 not shown) Planarity restraints: 3318 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 407 " -0.054 5.00e-02 4.00e+02 7.84e-02 9.83e+00 pdb=" N PRO B 408 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO B 408 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 408 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 92 " 0.043 5.00e-02 4.00e+02 6.52e-02 6.79e+00 pdb=" N PRO C 93 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO C 93 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 93 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 433 " -0.042 5.00e-02 4.00e+02 6.34e-02 6.44e+00 pdb=" N PRO A 434 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 434 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 434 " -0.035 5.00e-02 4.00e+02 ... (remaining 3315 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 455 2.67 - 3.23: 18426 3.23 - 3.78: 29479 3.78 - 4.34: 40643 4.34 - 4.90: 66224 Nonbonded interactions: 155227 Sorted by model distance: nonbonded pdb=" OD1 ASP B 472 " pdb=" N TYR B 473 " model vdw 2.111 2.520 nonbonded pdb=" OD1 ASP A 444 " pdb=" N LYS A 445 " model vdw 2.166 2.520 nonbonded pdb=" O ASP D 472 " pdb=" OH TYR D 507 " model vdw 2.200 2.440 nonbonded pdb=" OD1 ASP D 502 " pdb=" N PHE D 503 " model vdw 2.204 2.520 nonbonded pdb=" NZ LYS C 196 " pdb=" O THR C 286 " model vdw 2.206 2.520 ... (remaining 155222 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 3 through 398 or resid 405 through 435 or resid 439 throug \ h 561 or resid 601)) selection = (chain 'B' and (resid 3 through 398 or resid 405 through 435 or resid 439 throug \ h 561 or resid 601)) selection = (chain 'C' and (resid 3 through 398 or resid 405 through 435 or resid 439 throug \ h 561 or resid 601)) selection = (chain 'D' and (resid 3 through 561 or resid 601)) } 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: 0.010 Normalize map: mean=0, sd=1: 1.150 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: 0.010 Extract box with map and model: 3.990 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 46.860 Find NCS groups from input model: 1.470 Set up NCS constraints: 0.090 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: 0.000 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 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 : 0.010 0.303 19183 Z= 0.648 Angle : 0.672 12.534 25928 Z= 0.364 Chirality : 0.047 0.249 2782 Planarity : 0.005 0.078 3318 Dihedral : 16.587 89.275 7160 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 0.49 % Allowed : 23.66 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.47 (0.18), residues: 2218 helix: 0.69 (0.20), residues: 701 sheet: -0.69 (0.26), residues: 419 loop : -0.74 (0.19), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 299 HIS 0.006 0.001 HIS C 281 PHE 0.022 0.002 PHE B 519 TYR 0.033 0.002 TYR C 473 ARG 0.016 0.001 ARG A 220 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 2041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 508 time to evaluate : 2.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LYS cc_start: 0.7808 (mmmt) cc_final: 0.7281 (mmmt) REVERT: A 240 ASP cc_start: 0.7563 (t0) cc_final: 0.7270 (t70) REVERT: B 21 GLU cc_start: 0.7188 (pt0) cc_final: 0.6564 (pt0) REVERT: B 152 ASP cc_start: 0.7536 (p0) cc_final: 0.7056 (p0) REVERT: B 153 VAL cc_start: 0.7916 (t) cc_final: 0.7672 (t) REVERT: B 223 MET cc_start: 0.7806 (mmm) cc_final: 0.7584 (tpp) REVERT: B 337 GLU cc_start: 0.7571 (mp0) cc_final: 0.7315 (mp0) REVERT: B 345 GLU cc_start: 0.7910 (tt0) cc_final: 0.7631 (tm-30) REVERT: B 431 LYS cc_start: 0.8309 (tptp) cc_final: 0.7923 (tptp) REVERT: B 447 LYS cc_start: 0.7631 (mmpt) cc_final: 0.7418 (mmmt) REVERT: B 519 PHE cc_start: 0.7984 (t80) cc_final: 0.7524 (t80) REVERT: C 9 ASP cc_start: 0.7226 (t70) cc_final: 0.6892 (t0) REVERT: C 37 ARG cc_start: 0.7534 (ttp-170) cc_final: 0.7186 (ttm-80) REVERT: C 107 GLN cc_start: 0.7825 (mt0) cc_final: 0.7430 (mt0) REVERT: C 256 ARG cc_start: 0.7857 (mmm-85) cc_final: 0.6299 (tpm170) REVERT: D 174 ARG cc_start: 0.7980 (mtp180) cc_final: 0.7503 (ttp-110) REVERT: D 185 LYS cc_start: 0.8288 (mttt) cc_final: 0.8073 (mtmt) outliers start: 10 outliers final: 7 residues processed: 508 average time/residue: 0.3799 time to fit residues: 271.1044 Evaluate side-chains 482 residues out of total 2041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 475 time to evaluate : 1.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 447 LYS Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 522 LEU Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 237 GLN Chi-restraints excluded: chain D residue 515 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 187 optimal weight: 4.9990 chunk 168 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 113 optimal weight: 6.9990 chunk 89 optimal weight: 0.9990 chunk 174 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 105 optimal weight: 0.5980 chunk 129 optimal weight: 4.9990 chunk 201 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 62 ASN ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 ASN ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 GLN C 186 GLN C 297 GLN C 547 GLN ** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.0769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 19183 Z= 0.253 Angle : 0.557 7.145 25928 Z= 0.293 Chirality : 0.044 0.159 2782 Planarity : 0.004 0.056 3318 Dihedral : 6.779 87.357 2546 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 3.92 % Allowed : 19.75 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.40 (0.18), residues: 2218 helix: 0.70 (0.20), residues: 688 sheet: -0.70 (0.25), residues: 440 loop : -0.62 (0.20), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 299 HIS 0.005 0.001 HIS C 281 PHE 0.018 0.001 PHE B 276 TYR 0.033 0.001 TYR B 12 ARG 0.005 0.000 ARG D 557 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 2041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 500 time to evaluate : 1.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LYS cc_start: 0.7727 (mmmt) cc_final: 0.7078 (mmmt) REVERT: A 126 GLN cc_start: 0.8486 (mm110) cc_final: 0.8280 (mm110) REVERT: A 192 GLN cc_start: 0.6902 (mm-40) cc_final: 0.6476 (mm-40) REVERT: A 447 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7652 (mtmm) REVERT: B 21 GLU cc_start: 0.7181 (pt0) cc_final: 0.6862 (pt0) REVERT: B 220 ARG cc_start: 0.7092 (ptp-170) cc_final: 0.6814 (ptm160) REVERT: B 223 MET cc_start: 0.8143 (mmm) cc_final: 0.7762 (tpp) REVERT: B 236 ARG cc_start: 0.7749 (tmm-80) cc_final: 0.7495 (ttp80) REVERT: B 240 ASP cc_start: 0.6950 (t70) cc_final: 0.6658 (t0) REVERT: B 337 GLU cc_start: 0.7602 (mp0) cc_final: 0.7347 (mp0) REVERT: B 422 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7909 (mm-30) REVERT: B 431 LYS cc_start: 0.8374 (tptp) cc_final: 0.7923 (tptp) REVERT: B 461 ASP cc_start: 0.6818 (p0) cc_final: 0.6604 (p0) REVERT: C 9 ASP cc_start: 0.7264 (t70) cc_final: 0.6905 (t0) REVERT: C 289 PHE cc_start: 0.8322 (m-80) cc_final: 0.8111 (m-80) REVERT: C 298 VAL cc_start: 0.7224 (OUTLIER) cc_final: 0.6964 (m) REVERT: C 378 MET cc_start: 0.6431 (mmm) cc_final: 0.6126 (mmm) REVERT: C 386 LYS cc_start: 0.8040 (mmmm) cc_final: 0.7740 (mmtm) REVERT: C 409 PHE cc_start: 0.6957 (t80) cc_final: 0.6750 (t80) REVERT: C 514 LYS cc_start: 0.7803 (mmtt) cc_final: 0.7548 (mptt) REVERT: D 141 THR cc_start: 0.8358 (m) cc_final: 0.8065 (p) REVERT: D 174 ARG cc_start: 0.7955 (mtp180) cc_final: 0.7474 (ttp-110) REVERT: D 220 ARG cc_start: 0.7549 (ttp80) cc_final: 0.7167 (ttp80) REVERT: D 367 ASP cc_start: 0.7373 (t0) cc_final: 0.6897 (t0) REVERT: D 463 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8241 (mm) REVERT: D 502 ASP cc_start: 0.7111 (t0) cc_final: 0.6812 (t0) outliers start: 80 outliers final: 51 residues processed: 539 average time/residue: 0.3485 time to fit residues: 267.9839 Evaluate side-chains 534 residues out of total 2041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 480 time to evaluate : 1.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 447 LYS Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 192 GLN Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 414 PHE Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 74 GLU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 101 GLN Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 117 GLN Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 223 MET Chi-restraints excluded: chain C residue 237 GLN Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 380 ASP Chi-restraints excluded: chain D residue 435 PHE Chi-restraints excluded: chain D residue 463 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 112 optimal weight: 0.0570 chunk 62 optimal weight: 0.9980 chunk 167 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 201 optimal weight: 0.9990 chunk 218 optimal weight: 2.9990 chunk 179 optimal weight: 0.9990 chunk 200 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 162 optimal weight: 0.7980 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN B 297 GLN B 460 ASN ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 ASN C 186 GLN ** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.1018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 19183 Z= 0.233 Angle : 0.540 7.499 25928 Z= 0.282 Chirality : 0.044 0.158 2782 Planarity : 0.004 0.086 3318 Dihedral : 6.540 86.896 2535 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 3.82 % Allowed : 21.66 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.35 (0.18), residues: 2218 helix: 0.71 (0.20), residues: 685 sheet: -0.66 (0.26), residues: 432 loop : -0.56 (0.20), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 299 HIS 0.004 0.001 HIS C 281 PHE 0.024 0.001 PHE A 519 TYR 0.029 0.001 TYR B 12 ARG 0.009 0.000 ARG D 180 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 2041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 492 time to evaluate : 1.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LYS cc_start: 0.7730 (mmmt) cc_final: 0.7053 (mmmt) REVERT: A 76 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8205 (mmtp) REVERT: A 82 GLU cc_start: 0.7195 (mt-10) cc_final: 0.6779 (mm-30) REVERT: A 126 GLN cc_start: 0.8421 (mm110) cc_final: 0.8193 (mm110) REVERT: A 192 GLN cc_start: 0.6910 (mm-40) cc_final: 0.6471 (mm-40) REVERT: A 379 GLU cc_start: 0.6432 (tm-30) cc_final: 0.6094 (tm-30) REVERT: A 532 GLU cc_start: 0.7485 (tt0) cc_final: 0.7123 (tt0) REVERT: B 7 TYR cc_start: 0.8187 (m-80) cc_final: 0.7971 (m-80) REVERT: B 21 GLU cc_start: 0.7249 (pt0) cc_final: 0.7040 (pt0) REVERT: B 25 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7877 (mp0) REVERT: B 223 MET cc_start: 0.8142 (mmm) cc_final: 0.7819 (tpp) REVERT: B 236 ARG cc_start: 0.7758 (tmm-80) cc_final: 0.7510 (ttp80) REVERT: B 240 ASP cc_start: 0.6935 (t70) cc_final: 0.6652 (t0) REVERT: B 306 LYS cc_start: 0.8028 (mtpt) cc_final: 0.7671 (tttt) REVERT: B 337 GLU cc_start: 0.7588 (mp0) cc_final: 0.7321 (mp0) REVERT: B 431 LYS cc_start: 0.8327 (tptp) cc_final: 0.7960 (tptp) REVERT: B 447 LYS cc_start: 0.8035 (mmmt) cc_final: 0.7468 (mmtt) REVERT: B 461 ASP cc_start: 0.6889 (p0) cc_final: 0.6661 (p0) REVERT: C 9 ASP cc_start: 0.7257 (t70) cc_final: 0.6892 (t0) REVERT: C 298 VAL cc_start: 0.7254 (OUTLIER) cc_final: 0.6989 (m) REVERT: C 378 MET cc_start: 0.6475 (mmm) cc_final: 0.6203 (mmm) REVERT: C 386 LYS cc_start: 0.8027 (mmmm) cc_final: 0.7744 (mmtm) REVERT: C 409 PHE cc_start: 0.6957 (t80) cc_final: 0.6693 (t80) REVERT: D 41 GLU cc_start: 0.7371 (mm-30) cc_final: 0.7044 (tp30) REVERT: D 141 THR cc_start: 0.8324 (m) cc_final: 0.8031 (p) REVERT: D 220 ARG cc_start: 0.7579 (ttp80) cc_final: 0.7125 (ttp80) REVERT: D 288 ARG cc_start: 0.6917 (mtm-85) cc_final: 0.6668 (mtm-85) REVERT: D 364 VAL cc_start: 0.8434 (OUTLIER) cc_final: 0.8202 (p) REVERT: D 367 ASP cc_start: 0.7433 (t0) cc_final: 0.6820 (t0) REVERT: D 463 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8214 (mm) REVERT: D 502 ASP cc_start: 0.7121 (t0) cc_final: 0.6797 (t0) REVERT: D 519 PHE cc_start: 0.7984 (t80) cc_final: 0.7682 (t80) REVERT: D 556 VAL cc_start: 0.6512 (OUTLIER) cc_final: 0.6216 (p) REVERT: D 557 ARG cc_start: 0.7263 (ttm-80) cc_final: 0.6990 (tpp80) outliers start: 78 outliers final: 62 residues processed: 537 average time/residue: 0.3494 time to fit residues: 267.2998 Evaluate side-chains 549 residues out of total 2041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 481 time to evaluate : 2.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 70 TYR Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain B residue 12 TYR Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 192 GLN Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 223 MET Chi-restraints excluded: chain C residue 237 GLN Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 462 ILE Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 519 PHE Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 273 ASP Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 380 ASP Chi-restraints excluded: chain D residue 435 PHE Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 468 LEU Chi-restraints excluded: chain D residue 515 ILE Chi-restraints excluded: chain D residue 545 LYS Chi-restraints excluded: chain D residue 556 VAL Chi-restraints excluded: chain D residue 558 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 199 optimal weight: 1.9990 chunk 151 optimal weight: 7.9990 chunk 104 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 chunk 202 optimal weight: 3.9990 chunk 214 optimal weight: 0.6980 chunk 105 optimal weight: 0.6980 chunk 192 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 102 ASN B 297 GLN B 460 ASN ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 GLN C 448 GLN ** D 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 19183 Z= 0.342 Angle : 0.584 6.597 25928 Z= 0.306 Chirality : 0.045 0.205 2782 Planarity : 0.004 0.067 3318 Dihedral : 6.526 87.039 2531 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 4.85 % Allowed : 22.10 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.44 (0.18), residues: 2218 helix: 0.63 (0.20), residues: 683 sheet: -0.71 (0.26), residues: 422 loop : -0.62 (0.19), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 299 HIS 0.005 0.001 HIS C 326 PHE 0.023 0.002 PHE B 276 TYR 0.030 0.002 TYR B 12 ARG 0.009 0.001 ARG A 220 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 2041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 503 time to evaluate : 2.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.7704 (t0) cc_final: 0.7073 (t0) REVERT: A 51 LYS cc_start: 0.7704 (mmmt) cc_final: 0.7013 (mmmt) REVERT: A 76 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8296 (mmtp) REVERT: A 82 GLU cc_start: 0.7298 (mt-10) cc_final: 0.6768 (mm-30) REVERT: A 126 GLN cc_start: 0.8411 (mm110) cc_final: 0.8140 (mm110) REVERT: A 144 THR cc_start: 0.8652 (OUTLIER) cc_final: 0.8396 (p) REVERT: A 192 GLN cc_start: 0.6940 (mm-40) cc_final: 0.6492 (mm-40) REVERT: A 379 GLU cc_start: 0.6649 (OUTLIER) cc_final: 0.6392 (tp30) REVERT: A 532 GLU cc_start: 0.7538 (tt0) cc_final: 0.7183 (tt0) REVERT: B 7 TYR cc_start: 0.8162 (m-80) cc_final: 0.7561 (m-80) REVERT: B 25 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7787 (mt-10) REVERT: B 223 MET cc_start: 0.8020 (mmm) cc_final: 0.7737 (tpp) REVERT: B 236 ARG cc_start: 0.7808 (tmm-80) cc_final: 0.7560 (ttp80) REVERT: B 240 ASP cc_start: 0.6924 (t70) cc_final: 0.6653 (t0) REVERT: B 337 GLU cc_start: 0.7592 (mp0) cc_final: 0.7310 (mp0) REVERT: B 374 ILE cc_start: 0.8036 (tp) cc_final: 0.7693 (tt) REVERT: B 381 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7620 (tm-30) REVERT: B 431 LYS cc_start: 0.8404 (tptp) cc_final: 0.8026 (tptp) REVERT: B 439 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7144 (mpp80) REVERT: B 447 LYS cc_start: 0.8162 (mmmt) cc_final: 0.7641 (mmtt) REVERT: B 461 ASP cc_start: 0.6975 (p0) cc_final: 0.6753 (p0) REVERT: B 523 MET cc_start: 0.8178 (mmm) cc_final: 0.7964 (mmm) REVERT: B 543 HIS cc_start: 0.8021 (m90) cc_final: 0.7761 (m-70) REVERT: C 9 ASP cc_start: 0.7275 (t70) cc_final: 0.6954 (t0) REVERT: C 298 VAL cc_start: 0.7278 (OUTLIER) cc_final: 0.7006 (m) REVERT: C 377 GLU cc_start: 0.6960 (mt-10) cc_final: 0.6435 (mt-10) REVERT: C 378 MET cc_start: 0.6513 (mmm) cc_final: 0.6238 (mmm) REVERT: C 386 LYS cc_start: 0.8045 (mmmm) cc_final: 0.7806 (mmtm) REVERT: C 409 PHE cc_start: 0.6932 (t80) cc_final: 0.6648 (t80) REVERT: C 468 LEU cc_start: 0.8147 (tp) cc_final: 0.7947 (tt) REVERT: D 141 THR cc_start: 0.8221 (m) cc_final: 0.7910 (p) REVERT: D 174 ARG cc_start: 0.7950 (mtp180) cc_final: 0.7444 (ttp-110) REVERT: D 220 ARG cc_start: 0.7605 (ttp80) cc_final: 0.7198 (ttp80) REVERT: D 236 ARG cc_start: 0.7414 (ttp80) cc_final: 0.7127 (ttp80) REVERT: D 367 ASP cc_start: 0.7456 (t0) cc_final: 0.6897 (t0) REVERT: D 463 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8225 (mm) REVERT: D 502 ASP cc_start: 0.7254 (t0) cc_final: 0.6949 (t0) REVERT: D 519 PHE cc_start: 0.7993 (t80) cc_final: 0.7721 (t80) REVERT: D 556 VAL cc_start: 0.6556 (OUTLIER) cc_final: 0.6286 (p) outliers start: 99 outliers final: 69 residues processed: 556 average time/residue: 0.3565 time to fit residues: 282.8716 Evaluate side-chains 566 residues out of total 2041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 489 time to evaluate : 1.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 38 ASN Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 192 GLN Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 462 ILE Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 515 ILE Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 519 PHE Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 184 ARG Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 273 ASP Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 435 PHE Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 468 LEU Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 515 ILE Chi-restraints excluded: chain D residue 545 LYS Chi-restraints excluded: chain D residue 556 VAL Chi-restraints excluded: chain D residue 558 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 178 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 183 optimal weight: 5.9990 chunk 148 optimal weight: 7.9990 chunk 0 optimal weight: 3.9990 chunk 109 optimal weight: 0.0770 chunk 192 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 297 GLN B 460 ASN ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 GLN ** D 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 19183 Z= 0.374 Angle : 0.604 7.551 25928 Z= 0.315 Chirality : 0.046 0.157 2782 Planarity : 0.004 0.057 3318 Dihedral : 6.449 87.591 2528 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 4.80 % Allowed : 22.44 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.61 (0.18), residues: 2218 helix: 0.52 (0.20), residues: 685 sheet: -0.89 (0.25), residues: 425 loop : -0.70 (0.19), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 299 HIS 0.005 0.001 HIS C 326 PHE 0.024 0.002 PHE C 215 TYR 0.033 0.002 TYR B 449 ARG 0.013 0.001 ARG A 220 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 2041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 510 time to evaluate : 1.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.7656 (t0) cc_final: 0.6971 (t0) REVERT: A 51 LYS cc_start: 0.7520 (mmmt) cc_final: 0.6806 (mmmt) REVERT: A 76 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8187 (mmtp) REVERT: A 82 GLU cc_start: 0.7303 (mt-10) cc_final: 0.6766 (mm-30) REVERT: A 192 GLN cc_start: 0.7153 (mm-40) cc_final: 0.6662 (mm-40) REVERT: A 379 GLU cc_start: 0.6697 (tm-30) cc_final: 0.6433 (tp30) REVERT: A 532 GLU cc_start: 0.7584 (tt0) cc_final: 0.7244 (tt0) REVERT: B 7 TYR cc_start: 0.8113 (m-80) cc_final: 0.7642 (m-80) REVERT: B 31 ASP cc_start: 0.7681 (t0) cc_final: 0.7377 (t0) REVERT: B 188 PHE cc_start: 0.8459 (t80) cc_final: 0.8143 (t80) REVERT: B 236 ARG cc_start: 0.7825 (tmm-80) cc_final: 0.7579 (ttp80) REVERT: B 240 ASP cc_start: 0.6919 (t70) cc_final: 0.6642 (t0) REVERT: B 337 GLU cc_start: 0.7600 (mp0) cc_final: 0.7296 (mp0) REVERT: B 381 GLU cc_start: 0.7848 (tm-30) cc_final: 0.7641 (tm-30) REVERT: B 431 LYS cc_start: 0.8373 (tptp) cc_final: 0.7800 (tptp) REVERT: B 439 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7195 (mpp80) REVERT: B 447 LYS cc_start: 0.8181 (mmmt) cc_final: 0.7962 (tppt) REVERT: B 461 ASP cc_start: 0.7001 (p0) cc_final: 0.6751 (p0) REVERT: B 523 MET cc_start: 0.8105 (mmm) cc_final: 0.7832 (mmm) REVERT: B 543 HIS cc_start: 0.8046 (m90) cc_final: 0.7796 (m-70) REVERT: C 9 ASP cc_start: 0.7312 (t70) cc_final: 0.6965 (t0) REVERT: C 60 ARG cc_start: 0.8287 (ttp80) cc_final: 0.7752 (ttp-110) REVERT: C 140 LYS cc_start: 0.8375 (ptmm) cc_final: 0.8053 (ptmm) REVERT: C 298 VAL cc_start: 0.7280 (OUTLIER) cc_final: 0.7003 (m) REVERT: C 378 MET cc_start: 0.6523 (mmm) cc_final: 0.6265 (mmm) REVERT: C 409 PHE cc_start: 0.6928 (t80) cc_final: 0.6727 (t80) REVERT: C 468 LEU cc_start: 0.8160 (tp) cc_final: 0.7952 (tt) REVERT: D 141 THR cc_start: 0.8202 (m) cc_final: 0.7881 (p) REVERT: D 174 ARG cc_start: 0.7949 (mtp180) cc_final: 0.7364 (ttp-110) REVERT: D 220 ARG cc_start: 0.7599 (ttp80) cc_final: 0.7188 (ttp80) REVERT: D 236 ARG cc_start: 0.7441 (ttp80) cc_final: 0.7155 (ttp80) REVERT: D 288 ARG cc_start: 0.6943 (mtm-85) cc_final: 0.6648 (mtm-85) REVERT: D 367 ASP cc_start: 0.7572 (t0) cc_final: 0.7023 (t0) REVERT: D 424 ASN cc_start: 0.7103 (m-40) cc_final: 0.6867 (m110) REVERT: D 463 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8230 (mm) REVERT: D 502 ASP cc_start: 0.7284 (t0) cc_final: 0.6986 (t0) REVERT: D 519 PHE cc_start: 0.8013 (t80) cc_final: 0.7747 (t80) REVERT: D 556 VAL cc_start: 0.6611 (OUTLIER) cc_final: 0.6381 (p) outliers start: 98 outliers final: 79 residues processed: 565 average time/residue: 0.3390 time to fit residues: 275.5193 Evaluate side-chains 576 residues out of total 2041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 492 time to evaluate : 2.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 192 GLN Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 389 LYS Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 237 GLN Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 462 ILE Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 519 PHE Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 316 LYS Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 468 LEU Chi-restraints excluded: chain D residue 488 ILE Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 515 ILE Chi-restraints excluded: chain D residue 545 LYS Chi-restraints excluded: chain D residue 556 VAL Chi-restraints excluded: chain D residue 558 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 72 optimal weight: 2.9990 chunk 193 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 52 optimal weight: 0.4980 chunk 214 optimal weight: 0.9990 chunk 178 optimal weight: 5.9990 chunk 99 optimal weight: 0.0010 chunk 17 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 112 optimal weight: 0.6980 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 38 ASN A 297 GLN B 297 GLN B 460 ASN ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 GLN ** C 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 GLN ** D 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19183 Z= 0.198 Angle : 0.547 8.224 25928 Z= 0.283 Chirality : 0.044 0.167 2782 Planarity : 0.004 0.056 3318 Dihedral : 6.184 86.862 2528 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.86 % Favored : 94.09 % Rotamer: Outliers : 3.97 % Allowed : 23.32 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.39 (0.18), residues: 2218 helix: 0.68 (0.20), residues: 685 sheet: -0.77 (0.25), residues: 430 loop : -0.55 (0.20), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 299 HIS 0.004 0.001 HIS D 543 PHE 0.017 0.001 PHE B 156 TYR 0.022 0.001 TYR B 449 ARG 0.010 0.000 ARG A 220 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 2041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 488 time to evaluate : 2.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.7628 (t0) cc_final: 0.7210 (t0) REVERT: A 51 LYS cc_start: 0.7656 (mmmt) cc_final: 0.7174 (mmmt) REVERT: A 82 GLU cc_start: 0.7246 (mt-10) cc_final: 0.6692 (mm-30) REVERT: A 144 THR cc_start: 0.8644 (OUTLIER) cc_final: 0.8409 (p) REVERT: A 192 GLN cc_start: 0.7140 (mm-40) cc_final: 0.6639 (mm-40) REVERT: A 435 PHE cc_start: 0.7140 (m-10) cc_final: 0.6204 (m-10) REVERT: A 471 SER cc_start: 0.8244 (t) cc_final: 0.8017 (p) REVERT: A 532 GLU cc_start: 0.7515 (tt0) cc_final: 0.7213 (tt0) REVERT: B 7 TYR cc_start: 0.8153 (m-80) cc_final: 0.7300 (m-80) REVERT: B 25 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7766 (mt-10) REVERT: B 108 GLU cc_start: 0.7479 (mt-10) cc_final: 0.7269 (mt-10) REVERT: B 236 ARG cc_start: 0.7771 (tmm-80) cc_final: 0.7524 (ttp80) REVERT: B 240 ASP cc_start: 0.6882 (t70) cc_final: 0.6616 (t0) REVERT: B 306 LYS cc_start: 0.8074 (mtpt) cc_final: 0.7701 (tttt) REVERT: B 337 GLU cc_start: 0.7537 (mp0) cc_final: 0.7237 (mp0) REVERT: B 431 LYS cc_start: 0.8360 (tptp) cc_final: 0.7922 (tptp) REVERT: B 439 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7158 (mpp80) REVERT: B 461 ASP cc_start: 0.6975 (p0) cc_final: 0.6664 (p0) REVERT: B 523 MET cc_start: 0.8024 (mmm) cc_final: 0.7702 (mmm) REVERT: B 543 HIS cc_start: 0.8072 (m90) cc_final: 0.7846 (m-70) REVERT: C 9 ASP cc_start: 0.7253 (t70) cc_final: 0.6921 (t0) REVERT: C 298 VAL cc_start: 0.7261 (OUTLIER) cc_final: 0.6983 (m) REVERT: C 378 MET cc_start: 0.6542 (mmm) cc_final: 0.6286 (mmm) REVERT: C 514 LYS cc_start: 0.7523 (mptt) cc_final: 0.7280 (mptt) REVERT: D 141 THR cc_start: 0.8174 (m) cc_final: 0.7888 (p) REVERT: D 174 ARG cc_start: 0.7959 (mtp180) cc_final: 0.7357 (ttp-110) REVERT: D 220 ARG cc_start: 0.7616 (ttp80) cc_final: 0.7217 (ttp80) REVERT: D 288 ARG cc_start: 0.6889 (mtm-85) cc_final: 0.6650 (mtm-85) REVERT: D 367 ASP cc_start: 0.7553 (t0) cc_final: 0.6922 (t0) REVERT: D 424 ASN cc_start: 0.7032 (m-40) cc_final: 0.6824 (m110) REVERT: D 463 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8218 (mm) REVERT: D 502 ASP cc_start: 0.7242 (t0) cc_final: 0.6939 (t0) REVERT: D 519 PHE cc_start: 0.7980 (t80) cc_final: 0.7758 (t80) outliers start: 81 outliers final: 62 residues processed: 535 average time/residue: 0.3474 time to fit residues: 265.7398 Evaluate side-chains 537 residues out of total 2041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 471 time to evaluate : 1.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 410 PHE Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 192 GLN Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 389 LYS Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 205 PHE Chi-restraints excluded: chain C residue 237 GLN Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 462 ILE Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 519 PHE Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 273 ASP Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 435 PHE Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 488 ILE Chi-restraints excluded: chain D residue 515 ILE Chi-restraints excluded: chain D residue 558 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 207 optimal weight: 0.8980 chunk 24 optimal weight: 0.3980 chunk 122 optimal weight: 1.9990 chunk 156 optimal weight: 0.0270 chunk 121 optimal weight: 0.9980 chunk 180 optimal weight: 0.7980 chunk 119 optimal weight: 0.0970 chunk 213 optimal weight: 3.9990 chunk 133 optimal weight: 0.8980 chunk 130 optimal weight: 0.8980 chunk 98 optimal weight: 0.6980 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 GLN B 297 GLN B 460 ASN B 528 ASN ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 GLN C 448 GLN D 62 ASN ** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19183 Z= 0.176 Angle : 0.549 8.662 25928 Z= 0.282 Chirality : 0.044 0.252 2782 Planarity : 0.004 0.054 3318 Dihedral : 6.070 86.358 2528 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.82 % Favored : 94.14 % Rotamer: Outliers : 3.87 % Allowed : 23.71 % Favored : 72.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.31 (0.18), residues: 2218 helix: 0.70 (0.20), residues: 689 sheet: -0.71 (0.26), residues: 425 loop : -0.48 (0.20), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 299 HIS 0.005 0.001 HIS C 446 PHE 0.027 0.001 PHE A 519 TYR 0.020 0.001 TYR B 449 ARG 0.006 0.000 ARG A 220 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 2041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 484 time to evaluate : 1.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.7620 (t0) cc_final: 0.7215 (t0) REVERT: A 51 LYS cc_start: 0.7642 (mmmt) cc_final: 0.7178 (mmmt) REVERT: A 78 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7929 (tp) REVERT: A 92 ASN cc_start: 0.7657 (t0) cc_final: 0.7376 (t0) REVERT: A 144 THR cc_start: 0.8632 (m) cc_final: 0.8408 (p) REVERT: A 192 GLN cc_start: 0.7424 (mm-40) cc_final: 0.6835 (mm-40) REVERT: A 435 PHE cc_start: 0.7107 (m-10) cc_final: 0.6217 (m-10) REVERT: A 514 LYS cc_start: 0.8057 (tptp) cc_final: 0.7841 (tppp) REVERT: A 532 GLU cc_start: 0.7483 (tt0) cc_final: 0.7164 (tt0) REVERT: B 7 TYR cc_start: 0.8094 (m-80) cc_final: 0.7665 (m-80) REVERT: B 25 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7865 (mt-10) REVERT: B 31 ASP cc_start: 0.7623 (t0) cc_final: 0.7377 (t0) REVERT: B 152 ASP cc_start: 0.7581 (p0) cc_final: 0.7119 (p0) REVERT: B 153 VAL cc_start: 0.7731 (t) cc_final: 0.7494 (t) REVERT: B 220 ARG cc_start: 0.6986 (ptp-110) cc_final: 0.6747 (ptm160) REVERT: B 236 ARG cc_start: 0.7756 (tmm-80) cc_final: 0.7508 (ttp80) REVERT: B 240 ASP cc_start: 0.6875 (t70) cc_final: 0.6599 (t0) REVERT: B 306 LYS cc_start: 0.8079 (mtpt) cc_final: 0.7544 (tttt) REVERT: B 316 LYS cc_start: 0.8284 (tttt) cc_final: 0.8031 (tttt) REVERT: B 337 GLU cc_start: 0.7524 (mp0) cc_final: 0.7224 (mp0) REVERT: B 374 ILE cc_start: 0.7897 (tp) cc_final: 0.7554 (tt) REVERT: B 439 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7142 (mpp80) REVERT: B 461 ASP cc_start: 0.6966 (p0) cc_final: 0.6679 (p0) REVERT: B 523 MET cc_start: 0.8027 (mmm) cc_final: 0.7688 (mmm) REVERT: B 543 HIS cc_start: 0.8091 (m90) cc_final: 0.7858 (m-70) REVERT: C 9 ASP cc_start: 0.7220 (t70) cc_final: 0.6886 (t0) REVERT: C 298 VAL cc_start: 0.7248 (OUTLIER) cc_final: 0.6965 (m) REVERT: C 378 MET cc_start: 0.6405 (mmm) cc_final: 0.6180 (mmm) REVERT: C 523 MET cc_start: 0.7925 (mmp) cc_final: 0.7490 (mmp) REVERT: D 141 THR cc_start: 0.8153 (m) cc_final: 0.7881 (p) REVERT: D 174 ARG cc_start: 0.7942 (mtp180) cc_final: 0.7450 (ttp-110) REVERT: D 220 ARG cc_start: 0.7608 (ttp80) cc_final: 0.7214 (ttp80) REVERT: D 288 ARG cc_start: 0.6877 (mtm-85) cc_final: 0.6640 (mtm-85) REVERT: D 424 ASN cc_start: 0.7017 (m-40) cc_final: 0.6802 (m110) REVERT: D 463 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8206 (mm) REVERT: D 502 ASP cc_start: 0.7210 (t0) cc_final: 0.6958 (t0) REVERT: D 519 PHE cc_start: 0.7970 (t80) cc_final: 0.7764 (t80) outliers start: 79 outliers final: 63 residues processed: 532 average time/residue: 0.3911 time to fit residues: 300.0636 Evaluate side-chains 540 residues out of total 2041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 473 time to evaluate : 2.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 70 TYR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 410 PHE Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 414 PHE Chi-restraints excluded: chain B residue 420 TYR Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 205 PHE Chi-restraints excluded: chain C residue 237 GLN Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 462 ILE Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 519 PHE Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 273 ASP Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 398 ARG Chi-restraints excluded: chain D residue 435 PHE Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 515 ILE Chi-restraints excluded: chain D residue 558 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 132 optimal weight: 0.2980 chunk 85 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 41 optimal weight: 0.7980 chunk 136 optimal weight: 0.9980 chunk 145 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 168 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 GLN B 297 GLN ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 GLN C 448 GLN ** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19183 Z= 0.228 Angle : 0.568 9.789 25928 Z= 0.291 Chirality : 0.044 0.167 2782 Planarity : 0.004 0.054 3318 Dihedral : 6.081 85.859 2528 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 4.46 % Allowed : 23.62 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.34 (0.18), residues: 2218 helix: 0.68 (0.20), residues: 692 sheet: -0.71 (0.25), residues: 444 loop : -0.50 (0.20), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 299 HIS 0.005 0.001 HIS D 543 PHE 0.022 0.001 PHE C 409 TYR 0.018 0.001 TYR B 12 ARG 0.010 0.000 ARG A 220 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 2041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 488 time to evaluate : 2.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.7637 (t0) cc_final: 0.7221 (t0) REVERT: A 51 LYS cc_start: 0.7680 (mmmt) cc_final: 0.7198 (mmmt) REVERT: A 78 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7978 (tp) REVERT: A 92 ASN cc_start: 0.7645 (t0) cc_final: 0.7374 (t0) REVERT: A 144 THR cc_start: 0.8632 (OUTLIER) cc_final: 0.8411 (p) REVERT: A 192 GLN cc_start: 0.7446 (mm-40) cc_final: 0.6847 (mm-40) REVERT: A 378 MET cc_start: 0.7224 (mmm) cc_final: 0.6872 (mmm) REVERT: A 514 LYS cc_start: 0.8064 (tptp) cc_final: 0.7851 (tppp) REVERT: A 532 GLU cc_start: 0.7522 (tt0) cc_final: 0.7199 (tt0) REVERT: B 7 TYR cc_start: 0.8114 (m-80) cc_final: 0.7452 (m-80) REVERT: B 25 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7830 (mt-10) REVERT: B 108 GLU cc_start: 0.7673 (mt-10) cc_final: 0.7417 (mt-10) REVERT: B 152 ASP cc_start: 0.7648 (p0) cc_final: 0.7148 (p0) REVERT: B 153 VAL cc_start: 0.7712 (t) cc_final: 0.7463 (t) REVERT: B 306 LYS cc_start: 0.8121 (mtpt) cc_final: 0.7790 (tttm) REVERT: B 316 LYS cc_start: 0.8308 (tttt) cc_final: 0.8041 (tttt) REVERT: B 337 GLU cc_start: 0.7525 (mp0) cc_final: 0.7237 (mp0) REVERT: B 374 ILE cc_start: 0.7901 (tp) cc_final: 0.7541 (tt) REVERT: B 439 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7150 (mpp80) REVERT: B 461 ASP cc_start: 0.7014 (p0) cc_final: 0.6683 (p0) REVERT: B 523 MET cc_start: 0.8103 (mmm) cc_final: 0.7753 (mmm) REVERT: B 543 HIS cc_start: 0.8099 (m90) cc_final: 0.7859 (m-70) REVERT: B 550 ARG cc_start: 0.7333 (mtm110) cc_final: 0.7084 (mtm110) REVERT: C 9 ASP cc_start: 0.7279 (t70) cc_final: 0.6928 (t0) REVERT: C 98 ASP cc_start: 0.7948 (t0) cc_final: 0.7734 (t0) REVERT: C 104 LYS cc_start: 0.8614 (tmmt) cc_final: 0.8375 (tmmt) REVERT: C 298 VAL cc_start: 0.7263 (OUTLIER) cc_final: 0.6987 (m) REVERT: C 378 MET cc_start: 0.6411 (mmm) cc_final: 0.6192 (mmm) REVERT: C 473 TYR cc_start: 0.7939 (m-10) cc_final: 0.7288 (m-10) REVERT: C 514 LYS cc_start: 0.7760 (mptt) cc_final: 0.7506 (mptt) REVERT: C 542 LYS cc_start: 0.8008 (ttmt) cc_final: 0.7783 (tttm) REVERT: D 44 THR cc_start: 0.8524 (m) cc_final: 0.8305 (t) REVERT: D 174 ARG cc_start: 0.7942 (mtp180) cc_final: 0.7419 (ttp-110) REVERT: D 220 ARG cc_start: 0.7600 (ttp80) cc_final: 0.7207 (ttp80) REVERT: D 288 ARG cc_start: 0.6888 (mtm-85) cc_final: 0.6651 (mtm-85) REVERT: D 367 ASP cc_start: 0.7543 (t0) cc_final: 0.6897 (t0) REVERT: D 424 ASN cc_start: 0.7025 (m-40) cc_final: 0.6806 (m110) REVERT: D 463 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8161 (mm) REVERT: D 502 ASP cc_start: 0.7265 (t0) cc_final: 0.7004 (t0) REVERT: D 519 PHE cc_start: 0.7990 (t80) cc_final: 0.7773 (t80) outliers start: 91 outliers final: 71 residues processed: 547 average time/residue: 0.3413 time to fit residues: 267.6176 Evaluate side-chains 548 residues out of total 2041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 472 time to evaluate : 1.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 70 TYR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 410 PHE Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 420 TYR Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 205 PHE Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 237 GLN Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 462 ILE Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 519 PHE Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 273 ASP Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 316 LYS Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 488 ILE Chi-restraints excluded: chain D residue 515 ILE Chi-restraints excluded: chain D residue 558 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 194 optimal weight: 0.5980 chunk 204 optimal weight: 2.9990 chunk 187 optimal weight: 4.9990 chunk 199 optimal weight: 0.9980 chunk 120 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 156 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 180 optimal weight: 0.9990 chunk 188 optimal weight: 0.6980 chunk 198 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 528 ASN B 102 ASN B 297 GLN ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 GLN C 448 GLN ** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19183 Z= 0.240 Angle : 0.579 10.133 25928 Z= 0.298 Chirality : 0.045 0.167 2782 Planarity : 0.004 0.054 3318 Dihedral : 6.078 85.342 2528 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 4.12 % Allowed : 24.06 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.33 (0.18), residues: 2218 helix: 0.68 (0.20), residues: 688 sheet: -0.65 (0.25), residues: 434 loop : -0.52 (0.20), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 299 HIS 0.005 0.001 HIS D 543 PHE 0.021 0.001 PHE D 123 TYR 0.018 0.001 TYR B 12 ARG 0.010 0.000 ARG A 220 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 2041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 488 time to evaluate : 2.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.7632 (t0) cc_final: 0.7219 (t0) REVERT: A 51 LYS cc_start: 0.7677 (mmmt) cc_final: 0.7199 (mmmt) REVERT: A 78 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7985 (tp) REVERT: A 92 ASN cc_start: 0.7743 (t0) cc_final: 0.7438 (t0) REVERT: A 144 THR cc_start: 0.8630 (OUTLIER) cc_final: 0.8402 (p) REVERT: A 192 GLN cc_start: 0.7459 (mm-40) cc_final: 0.6847 (mm-40) REVERT: A 378 MET cc_start: 0.7233 (mmm) cc_final: 0.6874 (mmm) REVERT: A 435 PHE cc_start: 0.7196 (m-10) cc_final: 0.6212 (m-10) REVERT: A 514 LYS cc_start: 0.8063 (tptp) cc_final: 0.7845 (tppp) REVERT: A 532 GLU cc_start: 0.7537 (tt0) cc_final: 0.7214 (tt0) REVERT: B 7 TYR cc_start: 0.8129 (m-80) cc_final: 0.7473 (m-80) REVERT: B 25 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7825 (mt-10) REVERT: B 31 ASP cc_start: 0.7635 (t0) cc_final: 0.7386 (t0) REVERT: B 55 ASN cc_start: 0.7675 (p0) cc_final: 0.7279 (t0) REVERT: B 108 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7359 (mt-10) REVERT: B 152 ASP cc_start: 0.7652 (p0) cc_final: 0.7155 (p0) REVERT: B 153 VAL cc_start: 0.7716 (t) cc_final: 0.7478 (t) REVERT: B 306 LYS cc_start: 0.8155 (mtpt) cc_final: 0.7802 (tttt) REVERT: B 316 LYS cc_start: 0.8301 (tttt) cc_final: 0.8051 (tttt) REVERT: B 337 GLU cc_start: 0.7530 (mp0) cc_final: 0.7264 (mp0) REVERT: B 374 ILE cc_start: 0.7890 (tp) cc_final: 0.7529 (tt) REVERT: B 410 PHE cc_start: 0.7676 (p90) cc_final: 0.7448 (p90) REVERT: B 439 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7171 (mpp80) REVERT: B 461 ASP cc_start: 0.7006 (p0) cc_final: 0.6687 (p0) REVERT: B 523 MET cc_start: 0.8120 (mmm) cc_final: 0.7764 (mmm) REVERT: B 543 HIS cc_start: 0.8107 (m90) cc_final: 0.7866 (m-70) REVERT: C 9 ASP cc_start: 0.7287 (t70) cc_final: 0.6937 (t0) REVERT: C 98 ASP cc_start: 0.7968 (t0) cc_final: 0.7746 (t0) REVERT: C 109 GLU cc_start: 0.7564 (tm-30) cc_final: 0.7318 (pp20) REVERT: C 298 VAL cc_start: 0.7268 (OUTLIER) cc_final: 0.6991 (m) REVERT: C 378 MET cc_start: 0.6407 (mmm) cc_final: 0.6193 (mmm) REVERT: C 473 TYR cc_start: 0.7941 (m-10) cc_final: 0.7360 (m-10) REVERT: C 514 LYS cc_start: 0.7718 (mptt) cc_final: 0.7475 (mptt) REVERT: C 542 LYS cc_start: 0.8010 (ttmt) cc_final: 0.7651 (ptmm) REVERT: C 550 ARG cc_start: 0.6536 (mmt90) cc_final: 0.5977 (mmm160) REVERT: D 44 THR cc_start: 0.8520 (m) cc_final: 0.8302 (t) REVERT: D 141 THR cc_start: 0.8109 (m) cc_final: 0.7838 (p) REVERT: D 174 ARG cc_start: 0.7943 (mtp180) cc_final: 0.7345 (ttp-110) REVERT: D 218 ASP cc_start: 0.7539 (p0) cc_final: 0.7316 (p0) REVERT: D 220 ARG cc_start: 0.7614 (ttp80) cc_final: 0.7229 (ttp80) REVERT: D 236 ARG cc_start: 0.7375 (ttp80) cc_final: 0.7071 (tmm-80) REVERT: D 288 ARG cc_start: 0.6889 (mtm-85) cc_final: 0.6629 (mtm-85) REVERT: D 367 ASP cc_start: 0.7578 (t0) cc_final: 0.6914 (t0) REVERT: D 424 ASN cc_start: 0.7024 (m-40) cc_final: 0.6786 (m110) REVERT: D 463 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8207 (mm) REVERT: D 502 ASP cc_start: 0.7268 (t0) cc_final: 0.7011 (t0) REVERT: D 519 PHE cc_start: 0.8021 (t80) cc_final: 0.7801 (t80) outliers start: 84 outliers final: 69 residues processed: 546 average time/residue: 0.3532 time to fit residues: 277.3171 Evaluate side-chains 557 residues out of total 2041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 483 time to evaluate : 1.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 70 TYR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 410 PHE Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 420 TYR Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 205 PHE Chi-restraints excluded: chain C residue 237 GLN Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 462 ILE Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 519 PHE Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 273 ASP Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 488 ILE Chi-restraints excluded: chain D residue 515 ILE Chi-restraints excluded: chain D residue 558 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 130 optimal weight: 0.4980 chunk 210 optimal weight: 8.9990 chunk 128 optimal weight: 8.9990 chunk 100 optimal weight: 3.9990 chunk 146 optimal weight: 0.2980 chunk 221 optimal weight: 1.9990 chunk 203 optimal weight: 0.8980 chunk 176 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 136 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 528 ASN B 102 ASN B 297 GLN ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 GLN C 448 GLN ** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19183 Z= 0.220 Angle : 0.586 10.862 25928 Z= 0.300 Chirality : 0.045 0.205 2782 Planarity : 0.004 0.056 3318 Dihedral : 6.024 84.587 2528 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.13 % Favored : 93.82 % Rotamer: Outliers : 3.48 % Allowed : 25.04 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.31 (0.18), residues: 2218 helix: 0.65 (0.20), residues: 692 sheet: -0.59 (0.26), residues: 422 loop : -0.50 (0.20), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 299 HIS 0.004 0.001 HIS C 543 PHE 0.017 0.001 PHE C 409 TYR 0.017 0.001 TYR B 12 ARG 0.010 0.000 ARG A 220 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 2041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 490 time to evaluate : 2.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.7628 (t0) cc_final: 0.7220 (t0) REVERT: A 51 LYS cc_start: 0.7667 (mmmt) cc_final: 0.7193 (mmmt) REVERT: A 78 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7970 (tp) REVERT: A 92 ASN cc_start: 0.7758 (t0) cc_final: 0.7405 (t0) REVERT: A 144 THR cc_start: 0.8629 (m) cc_final: 0.8417 (p) REVERT: A 192 GLN cc_start: 0.7459 (mm-40) cc_final: 0.6852 (mm-40) REVERT: A 435 PHE cc_start: 0.7214 (m-10) cc_final: 0.6223 (m-10) REVERT: A 514 LYS cc_start: 0.8041 (tptp) cc_final: 0.7822 (tppp) REVERT: A 532 GLU cc_start: 0.7537 (tt0) cc_final: 0.7226 (tt0) REVERT: B 7 TYR cc_start: 0.8127 (m-80) cc_final: 0.7562 (m-80) REVERT: B 25 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7834 (mt-10) REVERT: B 31 ASP cc_start: 0.7668 (t0) cc_final: 0.7411 (t0) REVERT: B 152 ASP cc_start: 0.7671 (p0) cc_final: 0.7184 (p0) REVERT: B 153 VAL cc_start: 0.7697 (t) cc_final: 0.7459 (t) REVERT: B 306 LYS cc_start: 0.8083 (mtpt) cc_final: 0.7818 (tttm) REVERT: B 316 LYS cc_start: 0.8292 (tttt) cc_final: 0.8069 (tttt) REVERT: B 374 ILE cc_start: 0.7868 (tp) cc_final: 0.7520 (tt) REVERT: B 439 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7183 (mpp80) REVERT: B 461 ASP cc_start: 0.7017 (p0) cc_final: 0.6699 (p0) REVERT: B 523 MET cc_start: 0.8100 (mmm) cc_final: 0.7756 (mmm) REVERT: B 543 HIS cc_start: 0.8122 (m90) cc_final: 0.7874 (m-70) REVERT: B 545 LYS cc_start: 0.8260 (tttt) cc_final: 0.8013 (tttp) REVERT: C 9 ASP cc_start: 0.7273 (t70) cc_final: 0.6918 (t0) REVERT: C 98 ASP cc_start: 0.7944 (t0) cc_final: 0.7708 (t0) REVERT: C 298 VAL cc_start: 0.7265 (OUTLIER) cc_final: 0.6987 (m) REVERT: C 320 PHE cc_start: 0.8225 (t80) cc_final: 0.7876 (t80) REVERT: C 378 MET cc_start: 0.6408 (mmm) cc_final: 0.6193 (mmm) REVERT: C 468 LEU cc_start: 0.7997 (tp) cc_final: 0.7723 (tt) REVERT: C 514 LYS cc_start: 0.7710 (mptt) cc_final: 0.7417 (mptt) REVERT: C 542 LYS cc_start: 0.8004 (ttmt) cc_final: 0.7657 (ptmm) REVERT: D 44 THR cc_start: 0.8517 (m) cc_final: 0.8300 (t) REVERT: D 141 THR cc_start: 0.8112 (m) cc_final: 0.7827 (p) REVERT: D 174 ARG cc_start: 0.7947 (mtp180) cc_final: 0.7344 (ttp-110) REVERT: D 218 ASP cc_start: 0.7511 (p0) cc_final: 0.7260 (p0) REVERT: D 220 ARG cc_start: 0.7622 (ttp80) cc_final: 0.7235 (ttp80) REVERT: D 240 ASP cc_start: 0.7112 (t0) cc_final: 0.6887 (t0) REVERT: D 288 ARG cc_start: 0.6891 (mtm-85) cc_final: 0.6657 (mtm-85) REVERT: D 424 ASN cc_start: 0.7014 (m-40) cc_final: 0.6776 (m110) REVERT: D 463 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8219 (mm) REVERT: D 502 ASP cc_start: 0.7251 (t0) cc_final: 0.7002 (t0) REVERT: D 519 PHE cc_start: 0.7994 (t80) cc_final: 0.7790 (t80) REVERT: D 545 LYS cc_start: 0.7617 (tmtt) cc_final: 0.7326 (tmtt) REVERT: D 550 ARG cc_start: 0.6865 (mtm180) cc_final: 0.6525 (ptp90) outliers start: 71 outliers final: 66 residues processed: 540 average time/residue: 0.3485 time to fit residues: 269.6109 Evaluate side-chains 550 residues out of total 2041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 480 time to evaluate : 2.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 70 TYR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 410 PHE Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 420 TYR Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 205 PHE Chi-restraints excluded: chain C residue 237 GLN Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 462 ILE Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 519 PHE Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 273 ASP Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 488 ILE Chi-restraints excluded: chain D residue 515 ILE Chi-restraints excluded: chain D residue 558 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 139 optimal weight: 0.5980 chunk 187 optimal weight: 5.9990 chunk 53 optimal weight: 0.0060 chunk 162 optimal weight: 0.0980 chunk 26 optimal weight: 0.3980 chunk 48 optimal weight: 0.6980 chunk 176 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 181 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 237 GLN A 297 GLN ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 GLN C 448 GLN ** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.145776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.127201 restraints weight = 28119.761| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.18 r_work: 0.3508 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19183 Z= 0.172 Angle : 0.577 10.817 25928 Z= 0.294 Chirality : 0.044 0.220 2782 Planarity : 0.004 0.054 3318 Dihedral : 5.885 83.255 2528 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.41 % Favored : 94.54 % Rotamer: Outliers : 3.33 % Allowed : 25.28 % Favored : 71.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.19 (0.19), residues: 2218 helix: 0.69 (0.21), residues: 694 sheet: -0.45 (0.25), residues: 438 loop : -0.42 (0.20), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 299 HIS 0.011 0.001 HIS C 433 PHE 0.022 0.001 PHE D 123 TYR 0.025 0.001 TYR C 507 ARG 0.008 0.000 ARG A 557 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5288.62 seconds wall clock time: 94 minutes 1.36 seconds (5641.36 seconds total)