Starting phenix.real_space_refine on Mon Jun 16 13:04:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8va1_43083/06_2025/8va1_43083.cif Found real_map, /net/cci-nas-00/data/ceres_data/8va1_43083/06_2025/8va1_43083.map 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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8va1_43083/06_2025/8va1_43083.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8va1_43083/06_2025/8va1_43083.map" model { file = "/net/cci-nas-00/data/ceres_data/8va1_43083/06_2025/8va1_43083.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8va1_43083/06_2025/8va1_43083.cif" } 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. Time to flip 46 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 11.49, per 1000 atoms: 0.61 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 - 3.00 Amino acid : True - 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: 4.86 Conformation dependent library (CDL) restraints added in 2.3 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... Secondary structure from input PDB file: 103 helices and 18 sheets defined 42.7% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.53 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 removed outlier: 4.498A pdb=" N ASP A 31 " --> pdb=" O ASP A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 102 Processing helix chain 'A' and resid 104 through 106 No H-bonds generated for 'chain 'A' and resid 104 through 106' Processing helix chain 'A' and resid 107 through 113 Processing helix chain 'A' and resid 116 through 125 Processing helix chain 'A' and resid 126 through 129 Processing helix chain 'A' and resid 135 through 137 No H-bonds generated for 'chain 'A' and resid 135 through 137' Processing helix chain 'A' and resid 170 through 207 Processing helix chain 'A' and resid 225 through 237 Processing helix chain 'A' and resid 260 through 272 Proline residue: A 266 - end of helix Processing helix chain 'A' and resid 283 through 287 removed outlier: 3.765A pdb=" N VAL A 287 " --> pdb=" O ILE A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 313 Processing helix chain 'A' and resid 338 through 348 removed outlier: 4.462A pdb=" N PHE A 342 " --> pdb=" O THR A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 352 No H-bonds generated for 'chain 'A' and resid 350 through 352' Processing helix chain 'A' and resid 359 through 367 removed outlier: 3.942A pdb=" N VAL A 364 " --> pdb=" O ARG A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 382 Processing helix chain 'A' and resid 413 through 425 Processing helix chain 'A' and resid 461 through 465 removed outlier: 3.528A pdb=" N PHE A 464 " --> pdb=" O ASP A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 481 removed outlier: 4.300A pdb=" N GLU A 479 " --> pdb=" O SER A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 484 No H-bonds generated for 'chain 'A' and resid 482 through 484' Processing helix chain 'A' and resid 493 through 501 Processing helix chain 'A' and resid 506 through 511 removed outlier: 3.613A pdb=" N VAL A 511 " --> pdb=" O TYR A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 528 removed outlier: 3.627A pdb=" N ASN A 528 " --> pdb=" O ASP A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 534 No H-bonds generated for 'chain 'A' and resid 532 through 534' Processing helix chain 'A' and resid 535 through 544 Processing helix chain 'A' and resid 550 through 561 Processing helix chain 'B' and resid 93 through 101 Processing helix chain 'B' and resid 104 through 112 removed outlier: 3.828A pdb=" N GLU B 108 " --> pdb=" O LYS B 104 " (cutoff:3.500A) 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) Processing helix chain 'B' and resid 116 through 125 Processing helix chain 'B' and resid 126 through 129 Processing helix chain 'B' and resid 135 through 137 No H-bonds generated for 'chain 'B' and resid 135 through 137' Processing helix chain 'B' and resid 170 through 207 removed outlier: 3.651A pdb=" N LEU B 207 " --> pdb=" O LYS B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 237 removed outlier: 3.832A pdb=" N TYR B 229 " --> pdb=" O GLY B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 243 removed outlier: 3.926A pdb=" N LYS B 242 " --> pdb=" O ASN B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 272 Proline residue: B 266 - end of helix Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'B' and resid 338 through 348 removed outlier: 4.570A pdb=" N PHE B 342 " --> pdb=" O THR B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 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 367 through 382 Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.932A pdb=" N GLY B 387 " --> pdb=" O ILE B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 412 Processing helix chain 'B' and resid 413 through 423 Processing helix chain 'B' and resid 443 through 447 Processing helix chain 'B' and resid 475 through 481 removed outlier: 3.756A pdb=" N GLU B 479 " --> pdb=" O SER B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 484 No H-bonds generated for 'chain 'B' and resid 482 through 484' Processing helix chain 'B' and resid 493 through 501 Processing helix chain 'B' and resid 506 through 511 removed outlier: 3.641A pdb=" N VAL B 511 " --> pdb=" O TYR B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 527 Processing helix chain 'B' and resid 532 through 534 No H-bonds generated for 'chain 'B' and resid 532 through 534' Processing helix chain 'B' and resid 535 through 544 removed outlier: 3.539A pdb=" N PHE B 539 " --> pdb=" O LYS B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 560 Processing helix chain 'C' and resid 92 through 101 removed outlier: 3.877A pdb=" N ILE C 96 " --> pdb=" O ASN C 92 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR C 100 " --> pdb=" O ILE C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 112 Processing helix chain 'C' and resid 116 through 126 Processing helix chain 'C' and resid 127 through 129 No H-bonds generated for 'chain 'C' and resid 127 through 129' Processing helix chain 'C' and resid 135 through 137 No H-bonds generated for 'chain 'C' and resid 135 through 137' Processing helix chain 'C' and resid 170 through 205 Processing helix chain 'C' and resid 225 through 237 removed outlier: 3.805A pdb=" N TYR C 229 " --> pdb=" O GLY C 225 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN C 237 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 272 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 308 through 313 Processing helix chain 'C' and resid 338 through 348 removed outlier: 4.586A pdb=" N PHE C 342 " --> pdb=" O THR C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 352 No H-bonds generated for 'chain 'C' and resid 350 through 352' Processing helix chain 'C' and resid 359 through 367 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 368 through 382 Processing helix chain 'C' and resid 383 through 387 removed outlier: 4.006A pdb=" N GLY C 387 " --> pdb=" O ILE C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 412 Processing helix chain 'C' and resid 413 through 425 removed outlier: 3.815A pdb=" N LEU C 417 " --> pdb=" O ASP C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 450 removed outlier: 3.806A pdb=" N GLN C 448 " --> pdb=" O ASP C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 465 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) Processing helix chain 'C' and resid 475 through 481 removed outlier: 4.015A pdb=" N GLU C 479 " --> pdb=" O SER C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 484 No H-bonds generated for 'chain 'C' and resid 482 through 484' Processing helix chain 'C' and resid 493 through 501 Processing helix chain 'C' and resid 506 through 511 Processing helix chain 'C' and resid 518 through 529 removed outlier: 3.513A pdb=" N LEU C 522 " --> pdb=" O SER C 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 534 No H-bonds generated for 'chain 'C' and resid 532 through 534' Processing helix chain 'C' and resid 535 through 544 Processing helix chain 'C' and resid 550 through 561 Processing helix chain 'D' and resid 92 through 102 removed outlier: 3.791A pdb=" N ILE D 96 " --> pdb=" O ASN D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 113 Processing helix chain 'D' and resid 116 through 125 Processing helix chain 'D' and resid 126 through 129 Processing helix chain 'D' and resid 170 through 207 Processing helix chain 'D' and resid 227 through 237 removed outlier: 3.564A pdb=" N TYR D 231 " --> pdb=" O PHE D 227 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N GLU D 233 " --> pdb=" O TYR D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 243 removed outlier: 3.857A pdb=" N LYS D 242 " --> pdb=" O ASN D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 272 Proline residue: D 266 - end of helix Processing helix chain 'D' and resid 281 through 287 removed outlier: 4.047A pdb=" N VAL D 287 " --> pdb=" O ILE D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 313 removed outlier: 3.510A pdb=" N SER D 311 " --> pdb=" O VAL D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 338 No H-bonds generated for 'chain 'D' and resid 336 through 338' Processing helix chain 'D' and resid 339 through 348 Processing helix chain 'D' and resid 359 through 365 removed outlier: 3.610A pdb=" N VAL D 364 " --> pdb=" O ARG D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 382 Processing helix chain 'D' and resid 383 through 387 removed outlier: 3.628A pdb=" N GLY D 387 " --> pdb=" O ILE D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 412 Processing helix chain 'D' and resid 413 through 425 Processing helix chain 'D' and resid 443 through 447 Processing helix chain 'D' and resid 458 through 463 removed outlier: 4.116A pdb=" N ILE D 462 " --> pdb=" O GLU D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 481 removed outlier: 4.026A pdb=" N GLU D 479 " --> pdb=" O SER D 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 484 No H-bonds generated for 'chain 'D' and resid 482 through 484' Processing helix chain 'D' and resid 493 through 501 Processing helix chain 'D' and resid 518 through 528 removed outlier: 4.033A pdb=" N ASN D 528 " --> pdb=" O ASP D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 534 No H-bonds generated for 'chain 'D' and resid 532 through 534' Processing helix chain 'D' and resid 535 through 544 Processing helix chain 'D' and resid 550 through 561 Processing sheet with id=AA1, 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) removed outlier: 6.253A pdb=" N ILE A 6 " --> pdb=" O GLN A 90 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 44 through 46 Processing sheet with id=AA3, 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) Processing sheet with id=AA4, first strand: chain 'A' and resid 244 through 249 removed outlier: 6.088A pdb=" N VAL A 213 " --> pdb=" O HIS A 246 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N VAL A 248 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N PHE A 215 " --> pdb=" O VAL A 248 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYS A 331 " --> pdb=" O VAL A 295 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ALA A 332 " --> pdb=" O VAL A 355 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 450 through 452 removed outlier: 6.694A pdb=" N ILE A 391 " --> pdb=" O LEU A 429 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LEU A 392 " --> pdb=" O ILE A 470 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N LEU A 469 " --> pdb=" O ILE A 488 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N TYR A 490 " --> pdb=" O LEU A 469 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N MET A 487 " --> pdb=" O LYS A 514 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N VAL A 516 " --> pdb=" O MET A 487 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N PHE A 489 " --> pdb=" O VAL A 516 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 13 removed outlier: 3.506A pdb=" N LYS B 10 " --> pdb=" O GLU B 21 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE B 19 " --> pdb=" O TYR B 12 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS B 23 " --> pdb=" O TYR B 7 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ILE B 6 " --> pdb=" O GLN B 90 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR B 87 " --> pdb=" O ASN B 81 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N LEU B 79 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 10.938A pdb=" N LEU B 91 " --> pdb=" O TYR B 77 " (cutoff:3.500A) removed outlier: 16.246A pdb=" N TYR B 77 " --> pdb=" O LEU B 91 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 75 through 81 current: chain 'B' and resid 49 through 53 Processing sheet with id=AA7, 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: 16.246A pdb=" N TYR B 77 " --> pdb=" O LEU B 91 " (cutoff:3.500A) removed outlier: 10.938A pdb=" N LEU B 91 " --> pdb=" O TYR B 77 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N LEU B 79 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR B 87 " --> pdb=" O ASN B 81 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ILE B 6 " --> pdb=" O GLN B 90 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS B 23 " --> pdb=" O TYR B 7 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 17 through 25 current: chain 'B' and resid 142 through 149 Processing sheet with id=AA8, first strand: chain 'B' and resid 244 through 249 removed outlier: 6.148A pdb=" N VAL B 213 " --> pdb=" O HIS B 246 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N VAL B 248 " --> pdb=" O VAL B 213 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N PHE B 215 " --> pdb=" O VAL B 248 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR B 274 " --> pdb=" O THR B 212 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ILE B 275 " --> pdb=" O ILE B 296 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL B 298 " --> pdb=" O ILE B 275 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N VAL B 277 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ALA B 332 " --> pdb=" O VAL B 355 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 450 through 452 removed outlier: 6.690A pdb=" N VAL B 428 " --> pdb=" O VAL B 451 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ILE B 391 " --> pdb=" O LEU B 429 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL B 390 " --> pdb=" O LEU B 468 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N ILE B 470 " --> pdb=" O VAL B 390 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU B 392 " --> pdb=" O ILE B 470 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N LEU B 469 " --> pdb=" O ILE B 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 49 through 53 removed outlier: 6.403A pdb=" N GLN C 17 " --> pdb=" O TRP C 13 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N TRP C 13 " --> pdb=" O GLN C 17 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N PHE C 19 " --> pdb=" O ILE C 11 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ILE C 11 " --> pdb=" O PHE C 19 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N GLU C 21 " --> pdb=" O ASP C 9 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE C 6 " --> pdb=" O GLN C 90 " (cutoff:3.500A) Processing sheet with id=AB2, 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=AB3, first strand: chain 'C' and resid 244 through 249 removed outlier: 6.063A pdb=" N VAL C 213 " --> pdb=" O HIS C 246 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N VAL C 248 " --> pdb=" O VAL C 213 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N PHE C 215 " --> pdb=" O VAL C 248 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N THR C 212 " --> pdb=" O TYR C 274 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N PHE C 276 " --> pdb=" O THR C 212 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU C 214 " --> pdb=" O PHE C 276 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL C 295 " --> pdb=" O LYS C 331 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N TYR C 333 " --> pdb=" O VAL C 295 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLN C 297 " --> pdb=" O TYR C 333 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 389 through 393 removed outlier: 3.727A pdb=" N VAL C 451 " --> pdb=" O VAL C 428 " (cutoff:3.500A) Processing sheet with id=AB5, 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=AB6, 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: 15.904A pdb=" N TYR D 77 " --> pdb=" O LEU D 91 " (cutoff:3.500A) removed outlier: 10.629A pdb=" N LEU D 91 " --> pdb=" O TYR D 77 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N LEU D 79 " --> pdb=" O ALA D 89 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ILE D 6 " --> pdb=" O GLN D 90 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ILE D 6 " --> pdb=" O GLU D 25 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N GLU D 25 " --> pdb=" O ILE D 6 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ILE D 8 " --> pdb=" O HIS D 23 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N HIS D 23 " --> pdb=" O ILE D 8 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP D 49 " --> pdb=" O ARG D 60 " (cutoff:3.500A) Processing sheet with id=AB7, 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=AB8, first strand: chain 'D' and resid 244 through 249 removed outlier: 6.216A pdb=" N VAL D 213 " --> pdb=" O HIS D 246 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N VAL D 248 " --> pdb=" O VAL D 213 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N PHE D 215 " --> pdb=" O VAL D 248 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ILE D 275 " --> pdb=" O ILE D 296 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR D 333 " --> pdb=" O GLN D 297 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ALA D 332 " --> pdb=" O VAL D 355 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 450 through 452 removed outlier: 8.754A pdb=" N VAL D 451 " --> pdb=" O ALA D 426 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL D 428 " --> pdb=" O VAL D 451 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N LYS D 389 " --> pdb=" O VAL D 427 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N LEU D 429 " --> pdb=" O LYS D 389 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ILE D 391 " --> pdb=" O LEU D 429 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N ILE D 470 " --> pdb=" O VAL D 390 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LEU D 392 " --> pdb=" O ILE D 470 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N LEU D 469 " --> pdb=" O ILE D 488 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N TYR D 490 " --> pdb=" O LEU D 469 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N MET D 487 " --> pdb=" O LYS D 514 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N VAL D 516 " --> pdb=" O MET D 487 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N PHE D 489 " --> pdb=" O VAL D 516 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 708 hydrogen bonds defined for protein. 1896 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: 6.45 Time building geometry restraints manager: 5.66 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=" C11 V2V B 601 " pdb=" C12 V2V B 601 " ideal model delta sigma weight residual 1.537 1.334 0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" C11 V2V A 601 " pdb=" C12 V2V A 601 " ideal model delta sigma weight residual 1.537 1.336 0.201 2.00e-02 2.50e+03 1.01e+02 bond pdb=" C11 V2V C 601 " pdb=" C12 V2V C 601 " ideal model delta sigma weight residual 1.537 1.337 0.200 2.00e-02 2.50e+03 9.99e+01 bond pdb=" C11 V2V D 601 " pdb=" C12 V2V D 601 " ideal model delta sigma weight residual 1.537 1.338 0.199 2.00e-02 2.50e+03 9.90e+01 bond pdb=" C12 V2V B 601 " pdb=" O13 V2V B 601 " ideal model delta sigma weight residual 1.430 1.606 -0.176 2.00e-02 2.50e+03 7.74e+01 ... (remaining 19178 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 25589 2.72 - 5.43: 277 5.43 - 8.15: 41 8.15 - 10.87: 8 10.87 - 13.58: 13 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=" O17 V2V B 601 " pdb=" P16 V2V B 601 " pdb=" O18 V2V B 601 " ideal model delta sigma weight residual 122.16 108.58 13.58 3.00e+00 1.11e-01 2.05e+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=" O17 V2V A 601 " pdb=" P16 V2V A 601 " pdb=" O18 V2V A 601 " ideal model delta sigma weight residual 122.16 109.11 13.05 3.00e+00 1.11e-01 1.89e+01 ... (remaining 25923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.56: 11122 35.56 - 71.12: 387 71.12 - 106.68: 25 106.68 - 142.24: 3 142.24 - 177.80: 9 Dihedral angle restraints: 11546 sinusoidal: 4916 harmonic: 6630 Sorted by residual: dihedral pdb=" O23 V2V A 601 " pdb=" O19 V2V A 601 " pdb=" P20 V2V A 601 " pdb=" P16 V2V A 601 " ideal model delta sinusoidal sigma weight residual 215.23 37.43 177.80 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O21 V2V C 601 " pdb=" O19 V2V C 601 " pdb=" P20 V2V C 601 " pdb=" P16 V2V C 601 " ideal model delta sinusoidal sigma weight residual 105.56 -72.23 177.79 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O22 V2V A 601 " pdb=" O19 V2V A 601 " pdb=" P20 V2V A 601 " pdb=" P16 V2V A 601 " ideal model delta sinusoidal sigma weight residual 330.16 157.34 172.82 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 11543 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 2399 0.069 - 0.138: 366 0.138 - 0.206: 11 0.206 - 0.275: 2 0.275 - 0.344: 4 Chirality restraints: 2782 Sorted by residual: chirality pdb=" C11 V2V D 601 " pdb=" C10 V2V D 601 " pdb=" C12 V2V D 601 " pdb=" O33 V2V D 601 " both_signs ideal model delta sigma weight residual False -2.71 -2.37 -0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" C11 V2V C 601 " pdb=" C10 V2V C 601 " pdb=" C12 V2V C 601 " pdb=" O33 V2V C 601 " both_signs ideal model delta sigma weight residual False -2.71 -2.39 -0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" C11 V2V B 601 " pdb=" C10 V2V B 601 " pdb=" C12 V2V B 601 " pdb=" O33 V2V B 601 " both_signs ideal model delta sigma weight residual False -2.71 -2.40 -0.32 2.00e-01 2.50e+01 2.53e+00 ... (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: 449 2.67 - 3.23: 18345 3.23 - 3.78: 29391 3.78 - 4.34: 40487 4.34 - 4.90: 66179 Nonbonded interactions: 154851 Sorted by model distance: nonbonded pdb=" OD1 ASP B 472 " pdb=" N TYR B 473 " model vdw 2.111 3.120 nonbonded pdb=" OD1 ASP A 444 " pdb=" N LYS A 445 " model vdw 2.166 3.120 nonbonded pdb=" O ASP D 472 " pdb=" OH TYR D 507 " model vdw 2.200 3.040 nonbonded pdb=" OD1 ASP D 502 " pdb=" N PHE D 503 " model vdw 2.204 3.120 nonbonded pdb=" NZ LYS C 196 " pdb=" O THR C 286 " model vdw 2.206 3.120 ... (remaining 154846 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 0.000 Normalize map: mean=0, sd=1: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.720 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 44.400 Find NCS groups from input model: 1.100 Set up NCS constraints: 0.070 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.540 ------------------------------------------------------------------------------- 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 : 0.008 0.203 19183 Z= 0.386 Angle : 0.766 13.582 25928 Z= 0.384 Chirality : 0.048 0.344 2782 Planarity : 0.005 0.078 3318 Dihedral : 18.181 177.798 7280 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 Details of bonding type rmsd hydrogen bonds : bond 0.20452 ( 689) hydrogen bonds : angle 7.34897 ( 1896) covalent geometry : bond 0.00796 (19183) covalent geometry : angle 0.76618 (25928) *********************** 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 to be fit. rotamer outliers: 10 poor density : 508 time to evaluate : 2.033 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: 0.3858 time to fit residues: 274.3989 Evaluate side-chains 482 residues out of total 2041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 475 time to evaluate : 2.160 ------------------------------------------------------------------------------- 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: 0.6980 chunk 93 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 chunk 89 optimal weight: 0.9990 chunk 174 optimal weight: 0.4980 chunk 67 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 201 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 237 GLN A 543 HIS ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 GLN C 186 GLN C 297 GLN ** D 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.138783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.120441 restraints weight = 28963.017| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.27 r_work: 0.3395 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.0927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 19183 Z= 0.178 Angle : 0.599 7.010 25928 Z= 0.318 Chirality : 0.046 0.161 2782 Planarity : 0.004 0.057 3318 Dihedral : 13.182 171.752 2666 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 3.67 % Allowed : 19.94 % Favored : 76.38 % 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: -0.24 (0.18), residues: 2218 helix: 0.90 (0.20), residues: 697 sheet: -0.69 (0.27), residues: 407 loop : -0.56 (0.19), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 299 HIS 0.004 0.001 HIS D 206 PHE 0.022 0.001 PHE C 414 TYR 0.034 0.002 TYR B 12 ARG 0.006 0.001 ARG D 554 Details of bonding type rmsd hydrogen bonds : bond 0.04604 ( 689) hydrogen bonds : angle 5.46289 ( 1896) covalent geometry : bond 0.00402 (19183) covalent geometry : angle 0.59937 (25928) *********************** 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 586 residues out of total 2041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 511 time to evaluate : 2.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 VAL cc_start: 0.8662 (p) cc_final: 0.8429 (m) REVERT: A 51 LYS cc_start: 0.7763 (mmmt) cc_final: 0.7087 (mmmt) REVERT: A 92 ASN cc_start: 0.7940 (t0) cc_final: 0.6953 (t0) REVERT: A 192 GLN cc_start: 0.7062 (mm-40) cc_final: 0.6648 (mm-40) REVERT: A 237 GLN cc_start: 0.7399 (mt0) cc_final: 0.7048 (mt0) REVERT: A 463 LEU cc_start: 0.7979 (mt) cc_final: 0.7743 (mp) REVERT: B 21 GLU cc_start: 0.7658 (pt0) cc_final: 0.7409 (pt0) REVERT: B 55 ASN cc_start: 0.7370 (p0) cc_final: 0.6887 (t0) REVERT: B 101 GLN cc_start: 0.7468 (mm-40) cc_final: 0.7224 (mm-40) REVERT: B 152 ASP cc_start: 0.7606 (p0) cc_final: 0.7185 (p0) REVERT: B 153 VAL cc_start: 0.7726 (t) cc_final: 0.7498 (t) REVERT: B 223 MET cc_start: 0.7978 (mmm) cc_final: 0.7673 (tpp) REVERT: B 236 ARG cc_start: 0.7898 (tmm-80) cc_final: 0.7625 (tmm-80) REVERT: B 240 ASP cc_start: 0.7078 (t70) cc_final: 0.6763 (t0) REVERT: B 345 GLU cc_start: 0.7806 (tt0) cc_final: 0.7500 (tm-30) REVERT: B 368 GLU cc_start: 0.7764 (tm-30) cc_final: 0.7463 (pm20) REVERT: B 373 GLN cc_start: 0.7414 (tp40) cc_final: 0.7140 (tp40) REVERT: B 439 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7226 (mpp80) REVERT: B 461 ASP cc_start: 0.6802 (p0) cc_final: 0.6555 (p0) REVERT: B 519 PHE cc_start: 0.8032 (t80) cc_final: 0.7470 (t80) REVERT: B 523 MET cc_start: 0.8126 (mmm) cc_final: 0.7911 (mmm) REVERT: C 9 ASP cc_start: 0.7036 (t70) cc_final: 0.6688 (t0) REVERT: C 289 PHE cc_start: 0.8320 (m-80) cc_final: 0.8101 (m-80) REVERT: C 298 VAL cc_start: 0.7152 (OUTLIER) cc_final: 0.6945 (m) REVERT: C 310 PHE cc_start: 0.8562 (m-80) cc_final: 0.8183 (m-80) REVERT: C 375 LYS cc_start: 0.7376 (tppt) cc_final: 0.7110 (tppp) REVERT: C 378 MET cc_start: 0.6118 (mmm) cc_final: 0.5915 (mmm) REVERT: C 409 PHE cc_start: 0.6821 (t80) cc_final: 0.6587 (t80) REVERT: C 473 TYR cc_start: 0.7812 (m-10) cc_final: 0.7080 (m-10) REVERT: C 507 TYR cc_start: 0.8268 (t80) cc_final: 0.7809 (t80) REVERT: C 510 PHE cc_start: 0.8153 (t80) cc_final: 0.7733 (t80) REVERT: D 5 LYS cc_start: 0.7934 (mtmm) cc_final: 0.7728 (mtmm) REVERT: D 102 ASN cc_start: 0.7583 (m-40) cc_final: 0.7364 (m110) REVERT: D 141 THR cc_start: 0.8375 (m) cc_final: 0.8094 (p) REVERT: D 174 ARG cc_start: 0.7976 (mtp180) cc_final: 0.7450 (ttp-110) REVERT: D 184 ARG cc_start: 0.7932 (ttt90) cc_final: 0.7664 (mtt90) REVERT: D 236 ARG cc_start: 0.7450 (ttp80) cc_final: 0.7144 (ttp80) REVERT: D 246 HIS cc_start: 0.7389 (m170) cc_final: 0.7106 (m170) REVERT: D 463 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8204 (mm) REVERT: D 502 ASP cc_start: 0.6967 (t0) cc_final: 0.6764 (t0) outliers start: 75 outliers final: 46 residues processed: 548 average time/residue: 0.3937 time to fit residues: 309.7145 Evaluate side-chains 536 residues out of total 2041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 487 time to evaluate : 2.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE 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 453 VAL 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 96 ILE Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 141 THR 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 416 ARG 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 460 ASN Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain C residue 16 VAL 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 96 ILE Chi-restraints excluded: chain C residue 101 GLN Chi-restraints excluded: chain C residue 113 GLU 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 482 VAL 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 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 46 optimal weight: 2.9990 chunk 195 optimal weight: 0.7980 chunk 174 optimal weight: 0.9980 chunk 205 optimal weight: 0.0470 chunk 197 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 209 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 176 optimal weight: 0.9980 chunk 160 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 overall best weight: 0.7278 ------------------------------------------------------------------------------- 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 ** A 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 543 HIS ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 ASN ** C 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 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 = 0.3778 r_free = 0.3778 target = 0.139030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.120557 restraints weight = 28807.801| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.27 r_work: 0.3397 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 19183 Z= 0.158 Angle : 0.572 7.102 25928 Z= 0.301 Chirality : 0.045 0.170 2782 Planarity : 0.004 0.054 3318 Dihedral : 12.449 165.848 2651 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 4.41 % Allowed : 20.58 % Favored : 75.01 % 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: 0.98 (0.20), residues: 699 sheet: -0.76 (0.26), residues: 443 loop : -0.49 (0.20), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 299 HIS 0.004 0.001 HIS D 543 PHE 0.029 0.001 PHE A 519 TYR 0.036 0.002 TYR B 12 ARG 0.006 0.001 ARG A 220 Details of bonding type rmsd hydrogen bonds : bond 0.03954 ( 689) hydrogen bonds : angle 5.14932 ( 1896) covalent geometry : bond 0.00362 (19183) covalent geometry : angle 0.57180 (25928) *********************** 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 601 residues out of total 2041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 511 time to evaluate : 2.566 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 ARG cc_start: 0.8105 (ttm170) cc_final: 0.7557 (ttp80) REVERT: A 50 VAL cc_start: 0.8641 (p) cc_final: 0.8403 (m) REVERT: A 51 LYS cc_start: 0.7786 (mmmt) cc_final: 0.7071 (mmmt) REVERT: A 76 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.8181 (mmtp) REVERT: A 191 ARG cc_start: 0.8094 (mtm-85) cc_final: 0.5572 (ttt90) REVERT: A 192 GLN cc_start: 0.7090 (mm-40) cc_final: 0.6689 (mm-40) REVERT: A 463 LEU cc_start: 0.7940 (mt) cc_final: 0.7682 (mp) REVERT: A 548 ASP cc_start: 0.7013 (p0) cc_final: 0.6788 (p0) REVERT: B 7 TYR cc_start: 0.8134 (m-80) cc_final: 0.7722 (m-80) REVERT: B 21 GLU cc_start: 0.7615 (pt0) cc_final: 0.7344 (pt0) REVERT: B 25 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7661 (mt-10) REVERT: B 49 ASP cc_start: 0.7019 (p0) cc_final: 0.6376 (p0) REVERT: B 101 GLN cc_start: 0.7684 (mm-40) cc_final: 0.7441 (mm-40) REVERT: B 152 ASP cc_start: 0.7669 (p0) cc_final: 0.7326 (p0) REVERT: B 153 VAL cc_start: 0.7737 (t) cc_final: 0.7489 (t) REVERT: B 223 MET cc_start: 0.8016 (mmm) cc_final: 0.7725 (tpp) REVERT: B 240 ASP cc_start: 0.7046 (t70) cc_final: 0.6756 (t0) REVERT: B 306 LYS cc_start: 0.8285 (mtpt) cc_final: 0.7995 (tttp) REVERT: B 373 GLN cc_start: 0.7421 (tp40) cc_final: 0.7122 (tp40) REVERT: B 439 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7217 (mpp80) REVERT: B 461 ASP cc_start: 0.6943 (p0) cc_final: 0.6661 (p0) REVERT: B 501 ARG cc_start: 0.6977 (ttm170) cc_final: 0.6755 (ttm170) REVERT: B 548 ASP cc_start: 0.7721 (p0) cc_final: 0.7516 (p0) REVERT: B 550 ARG cc_start: 0.7257 (mtm110) cc_final: 0.6856 (mtm110) REVERT: C 9 ASP cc_start: 0.7047 (t70) cc_final: 0.6693 (t0) REVERT: C 60 ARG cc_start: 0.7976 (ttp80) cc_final: 0.7089 (ttt-90) REVERT: C 104 LYS cc_start: 0.8435 (ttpt) cc_final: 0.7992 (ttpt) REVERT: C 107 GLN cc_start: 0.7791 (mt0) cc_final: 0.7499 (mt0) REVERT: C 109 GLU cc_start: 0.7699 (tm-30) cc_final: 0.7491 (tm-30) REVERT: C 186 GLN cc_start: 0.8212 (mm-40) cc_final: 0.7971 (mm110) REVERT: C 298 VAL cc_start: 0.7108 (OUTLIER) cc_final: 0.6900 (m) REVERT: C 375 LYS cc_start: 0.7344 (tppt) cc_final: 0.7075 (tppp) REVERT: C 378 MET cc_start: 0.6240 (mmm) cc_final: 0.6039 (mmm) REVERT: D 5 LYS cc_start: 0.7980 (mtmm) cc_final: 0.7764 (mtmm) REVERT: D 141 THR cc_start: 0.8347 (m) cc_final: 0.8084 (p) REVERT: D 159 ASP cc_start: 0.7133 (t70) cc_final: 0.6931 (t0) REVERT: D 174 ARG cc_start: 0.7986 (mtp180) cc_final: 0.7487 (ttp-110) REVERT: D 184 ARG cc_start: 0.7939 (ttt90) cc_final: 0.7655 (mtt90) REVERT: D 236 ARG cc_start: 0.7401 (ttp80) cc_final: 0.7196 (ttp80) REVERT: D 283 LEU cc_start: 0.8146 (mt) cc_final: 0.7932 (mm) REVERT: D 463 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8160 (mm) REVERT: D 502 ASP cc_start: 0.6992 (t0) cc_final: 0.6743 (t0) REVERT: D 519 PHE cc_start: 0.7961 (t80) cc_final: 0.7704 (t80) REVERT: D 523 MET cc_start: 0.8151 (mmm) cc_final: 0.7846 (mmm) REVERT: D 556 VAL cc_start: 0.5972 (OUTLIER) cc_final: 0.5768 (p) outliers start: 90 outliers final: 64 residues processed: 561 average time/residue: 0.4551 time to fit residues: 361.3518 Evaluate side-chains 561 residues out of total 2041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 491 time to evaluate : 2.263 ------------------------------------------------------------------------------- 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 76 LYS 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 160 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 374 ILE 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 12 TYR 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 129 LEU 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 321 ILE Chi-restraints excluded: chain B residue 336 SER 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 460 ASN Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain C residue 16 VAL 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 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 308 VAL Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 462 ILE Chi-restraints excluded: chain C residue 482 VAL 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 12 TYR 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 161 VAL Chi-restraints excluded: chain D residue 164 THR 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 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 104 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 147 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 179 optimal weight: 1.9990 chunk 86 optimal weight: 0.4980 chunk 4 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 126 GLN ** A 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 543 HIS ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 HIS ** D 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.138536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.119836 restraints weight = 28886.375| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.28 r_work: 0.3380 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 19183 Z= 0.198 Angle : 0.584 7.972 25928 Z= 0.308 Chirality : 0.046 0.202 2782 Planarity : 0.004 0.055 3318 Dihedral : 11.968 159.133 2651 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 4.61 % Allowed : 20.92 % Favored : 74.47 % 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: -0.30 (0.18), residues: 2218 helix: 0.89 (0.20), residues: 703 sheet: -0.91 (0.26), residues: 407 loop : -0.54 (0.19), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 299 HIS 0.004 0.001 HIS B 206 PHE 0.021 0.002 PHE B 19 TYR 0.032 0.002 TYR B 449 ARG 0.010 0.001 ARG D 554 Details of bonding type rmsd hydrogen bonds : bond 0.03928 ( 689) hydrogen bonds : angle 5.07587 ( 1896) covalent geometry : bond 0.00456 (19183) covalent geometry : angle 0.58427 (25928) *********************** 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 609 residues out of total 2041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 515 time to evaluate : 2.018 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 ARG cc_start: 0.8143 (ttm170) cc_final: 0.7544 (ttp-170) REVERT: A 49 ASP cc_start: 0.7703 (t0) cc_final: 0.6725 (t0) REVERT: A 50 VAL cc_start: 0.8673 (OUTLIER) cc_final: 0.8323 (m) REVERT: A 51 LYS cc_start: 0.7796 (mmmt) cc_final: 0.7000 (mmmt) REVERT: A 92 ASN cc_start: 0.7917 (t0) cc_final: 0.7412 (t0) REVERT: A 191 ARG cc_start: 0.8109 (mtm-85) cc_final: 0.5581 (ttt90) REVERT: A 192 GLN cc_start: 0.7131 (mm-40) cc_final: 0.6689 (mm-40) REVERT: A 240 ASP cc_start: 0.7404 (t0) cc_final: 0.7152 (t70) REVERT: A 532 GLU cc_start: 0.7524 (tt0) cc_final: 0.7197 (tt0) REVERT: A 548 ASP cc_start: 0.7208 (p0) cc_final: 0.7000 (p0) REVERT: B 31 ASP cc_start: 0.7633 (t0) cc_final: 0.7404 (t0) REVERT: B 236 ARG cc_start: 0.7842 (tmm-80) cc_final: 0.7573 (ttp80) REVERT: B 240 ASP cc_start: 0.7050 (t70) cc_final: 0.6770 (t0) REVERT: B 262 LYS cc_start: 0.7008 (mttt) cc_final: 0.6484 (tptt) REVERT: B 373 GLN cc_start: 0.7434 (tp40) cc_final: 0.7088 (tp40) REVERT: B 422 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7909 (mm-30) REVERT: B 439 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7170 (mpp80) REVERT: B 461 ASP cc_start: 0.7010 (p0) cc_final: 0.6769 (p0) REVERT: B 548 ASP cc_start: 0.7683 (p0) cc_final: 0.7465 (p0) REVERT: C 9 ASP cc_start: 0.7047 (t70) cc_final: 0.6709 (t0) REVERT: C 49 ASP cc_start: 0.7773 (m-30) cc_final: 0.7545 (m-30) REVERT: C 60 ARG cc_start: 0.7987 (ttp80) cc_final: 0.7616 (ttp80) REVERT: C 187 SER cc_start: 0.7696 (t) cc_final: 0.7493 (p) REVERT: C 298 VAL cc_start: 0.7167 (OUTLIER) cc_final: 0.6939 (m) REVERT: C 375 LYS cc_start: 0.7365 (tppt) cc_final: 0.7092 (tppp) REVERT: C 378 MET cc_start: 0.6278 (mmm) cc_final: 0.6070 (mmm) REVERT: C 514 LYS cc_start: 0.7748 (mptt) cc_final: 0.7369 (mptt) REVERT: D 5 LYS cc_start: 0.8026 (mtmm) cc_final: 0.7756 (mtmm) REVERT: D 141 THR cc_start: 0.8344 (m) cc_final: 0.8067 (p) REVERT: D 159 ASP cc_start: 0.7099 (t70) cc_final: 0.6883 (t0) REVERT: D 174 ARG cc_start: 0.7985 (mtp180) cc_final: 0.7455 (ttp-110) REVERT: D 184 ARG cc_start: 0.7896 (ttt90) cc_final: 0.7623 (mtt90) REVERT: D 236 ARG cc_start: 0.7426 (ttp80) cc_final: 0.7207 (ttp80) REVERT: D 463 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8164 (mm) REVERT: D 502 ASP cc_start: 0.7097 (t0) cc_final: 0.6790 (t0) REVERT: D 519 PHE cc_start: 0.7991 (t80) cc_final: 0.7743 (t80) REVERT: D 523 MET cc_start: 0.8146 (mmm) cc_final: 0.7848 (mmm) outliers start: 94 outliers final: 71 residues processed: 565 average time/residue: 0.3852 time to fit residues: 309.1124 Evaluate side-chains 574 residues out of total 2041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 499 time to evaluate : 2.414 ------------------------------------------------------------------------------- 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 50 VAL 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 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 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 12 TYR 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 212 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 321 ILE Chi-restraints excluded: chain B residue 336 SER 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 460 ASN Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain C residue 16 VAL 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 223 MET Chi-restraints excluded: chain C residue 237 GLN Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 462 ILE Chi-restraints excluded: chain C residue 482 VAL 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 12 TYR Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 127 THR 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 216 THR 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 468 LEU Chi-restraints excluded: chain D residue 515 ILE Chi-restraints excluded: chain D residue 545 LYS 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 40 optimal weight: 7.9990 chunk 188 optimal weight: 0.9980 chunk 170 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 147 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 171 optimal weight: 0.6980 chunk 148 optimal weight: 0.6980 chunk 161 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 chunk 180 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 126 GLN ** A 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 543 HIS ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 528 ASN ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 GLN D 62 ASN D 102 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.139360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.120697 restraints weight = 28922.136| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.28 r_work: 0.3392 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19183 Z= 0.164 Angle : 0.575 9.199 25928 Z= 0.301 Chirality : 0.045 0.217 2782 Planarity : 0.004 0.054 3318 Dihedral : 11.403 154.404 2651 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 4.70 % Allowed : 21.41 % Favored : 73.89 % 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: -0.26 (0.18), residues: 2218 helix: 0.93 (0.20), residues: 702 sheet: -0.96 (0.26), residues: 414 loop : -0.49 (0.20), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 299 HIS 0.004 0.001 HIS C 446 PHE 0.017 0.001 PHE B 19 TYR 0.033 0.002 TYR B 449 ARG 0.007 0.000 ARG D 554 Details of bonding type rmsd hydrogen bonds : bond 0.03636 ( 689) hydrogen bonds : angle 4.98618 ( 1896) covalent geometry : bond 0.00379 (19183) covalent geometry : angle 0.57498 (25928) *********************** 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 601 residues out of total 2041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 505 time to evaluate : 2.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ARG cc_start: 0.8280 (ttm170) cc_final: 0.7743 (ttp-170) REVERT: A 49 ASP cc_start: 0.7765 (t0) cc_final: 0.6673 (t0) REVERT: A 50 VAL cc_start: 0.8618 (OUTLIER) cc_final: 0.8262 (m) REVERT: A 51 LYS cc_start: 0.7770 (mmmt) cc_final: 0.6935 (mmmt) REVERT: A 92 ASN cc_start: 0.7915 (t0) cc_final: 0.7417 (t0) REVERT: A 191 ARG cc_start: 0.8075 (mtm-85) cc_final: 0.5220 (ttt90) REVERT: A 192 GLN cc_start: 0.7336 (mm-40) cc_final: 0.6838 (mm-40) REVERT: A 430 PHE cc_start: 0.7310 (m-10) cc_final: 0.7041 (m-80) REVERT: A 532 GLU cc_start: 0.7596 (tt0) cc_final: 0.7263 (tt0) REVERT: A 557 ARG cc_start: 0.6945 (ttm-80) cc_final: 0.6448 (ttm-80) REVERT: B 31 ASP cc_start: 0.7687 (t0) cc_final: 0.7421 (t0) REVERT: B 49 ASP cc_start: 0.6960 (p0) cc_final: 0.6315 (p0) REVERT: B 236 ARG cc_start: 0.7905 (tmm-80) cc_final: 0.7541 (ttp80) REVERT: B 240 ASP cc_start: 0.7005 (t70) cc_final: 0.6735 (t0) REVERT: B 262 LYS cc_start: 0.7006 (mttt) cc_final: 0.6506 (tptt) REVERT: B 373 GLN cc_start: 0.7420 (tp40) cc_final: 0.7074 (tp40) REVERT: B 410 PHE cc_start: 0.7701 (p90) cc_final: 0.7430 (p90) REVERT: B 439 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7121 (mpp80) REVERT: B 461 ASP cc_start: 0.7029 (p0) cc_final: 0.6816 (p0) REVERT: B 548 ASP cc_start: 0.7663 (p0) cc_final: 0.7440 (p0) REVERT: C 9 ASP cc_start: 0.7035 (t70) cc_final: 0.6684 (t0) REVERT: C 98 ASP cc_start: 0.8114 (t0) cc_final: 0.7761 (t0) REVERT: C 107 GLN cc_start: 0.7852 (mt0) cc_final: 0.7454 (mt0) REVERT: C 187 SER cc_start: 0.7843 (t) cc_final: 0.7502 (p) REVERT: C 298 VAL cc_start: 0.7165 (OUTLIER) cc_final: 0.6936 (m) REVERT: C 375 LYS cc_start: 0.7331 (tppt) cc_final: 0.7057 (tppp) REVERT: C 542 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7720 (tmmt) REVERT: D 5 LYS cc_start: 0.7998 (mtmm) cc_final: 0.7664 (mtmm) REVERT: D 159 ASP cc_start: 0.7098 (t70) cc_final: 0.6866 (t0) REVERT: D 174 ARG cc_start: 0.7976 (mtp180) cc_final: 0.7445 (ttp-110) REVERT: D 184 ARG cc_start: 0.7897 (ttt90) cc_final: 0.7634 (mtt90) REVERT: D 218 ASP cc_start: 0.7515 (p0) cc_final: 0.7258 (p0) REVERT: D 236 ARG cc_start: 0.7392 (ttp80) cc_final: 0.7091 (tmm-80) REVERT: D 246 HIS cc_start: 0.7374 (m170) cc_final: 0.7140 (m170) REVERT: D 288 ARG cc_start: 0.7037 (mtm-85) cc_final: 0.6780 (mtm-85) REVERT: D 463 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8157 (mm) REVERT: D 519 PHE cc_start: 0.8005 (t80) cc_final: 0.7747 (t80) REVERT: D 523 MET cc_start: 0.8192 (mmm) cc_final: 0.7844 (mmm) REVERT: D 534 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7440 (mp0) outliers start: 96 outliers final: 67 residues processed: 558 average time/residue: 0.3774 time to fit residues: 296.8485 Evaluate side-chains 562 residues out of total 2041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 489 time to evaluate : 2.260 ------------------------------------------------------------------------------- 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 50 VAL 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 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 374 ILE Chi-restraints excluded: chain A residue 409 PHE 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 12 TYR 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 212 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 439 ARG Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain B residue 460 ASN 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 45 MET Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 96 ILE 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 223 MET Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 308 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 C residue 542 LYS Chi-restraints excluded: chain D residue 12 TYR Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 127 THR 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 298 VAL Chi-restraints excluded: chain D residue 316 LYS 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 534 GLU 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 29 optimal weight: 1.9990 chunk 178 optimal weight: 0.3980 chunk 37 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 202 optimal weight: 0.0870 chunk 104 optimal weight: 2.9990 chunk 148 optimal weight: 7.9990 chunk 127 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 210 optimal weight: 4.9990 overall best weight: 1.0762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN A 543 HIS ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 GLN C 448 GLN D 102 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.141772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.122815 restraints weight = 28567.342| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.21 r_work: 0.3452 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 19183 Z= 0.206 Angle : 0.605 9.785 25928 Z= 0.318 Chirality : 0.046 0.174 2782 Planarity : 0.004 0.054 3318 Dihedral : 11.160 158.972 2648 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 4.46 % Allowed : 22.20 % Favored : 73.35 % 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: -0.37 (0.18), residues: 2218 helix: 0.87 (0.20), residues: 703 sheet: -1.03 (0.26), residues: 412 loop : -0.58 (0.19), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 299 HIS 0.004 0.001 HIS B 206 PHE 0.021 0.002 PHE A 276 TYR 0.031 0.002 TYR B 12 ARG 0.008 0.000 ARG B 180 Details of bonding type rmsd hydrogen bonds : bond 0.03787 ( 689) hydrogen bonds : angle 4.99277 ( 1896) covalent geometry : bond 0.00474 (19183) covalent geometry : angle 0.60504 (25928) *********************** 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 598 residues out of total 2041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 507 time to evaluate : 2.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ARG cc_start: 0.8410 (ttm170) cc_final: 0.7912 (ttp-170) REVERT: A 49 ASP cc_start: 0.7939 (t0) cc_final: 0.7382 (t0) REVERT: A 50 VAL cc_start: 0.8693 (OUTLIER) cc_final: 0.8129 (m) REVERT: A 51 LYS cc_start: 0.7979 (mmmt) cc_final: 0.7461 (mmmt) REVERT: A 92 ASN cc_start: 0.8019 (t0) cc_final: 0.7533 (t0) REVERT: A 191 ARG cc_start: 0.8256 (mtm-85) cc_final: 0.5288 (ttt90) REVERT: A 192 GLN cc_start: 0.7578 (mm-40) cc_final: 0.7082 (mm-40) REVERT: A 379 GLU cc_start: 0.6698 (tp30) cc_final: 0.6394 (tp30) REVERT: A 435 PHE cc_start: 0.7376 (m-10) cc_final: 0.6473 (m-10) REVERT: A 532 GLU cc_start: 0.7825 (tt0) cc_final: 0.7551 (tt0) REVERT: B 31 ASP cc_start: 0.7813 (t0) cc_final: 0.7561 (t0) REVERT: B 236 ARG cc_start: 0.8068 (tmm-80) cc_final: 0.7668 (ttp80) REVERT: B 240 ASP cc_start: 0.7352 (t70) cc_final: 0.7075 (t0) REVERT: B 262 LYS cc_start: 0.7116 (mttt) cc_final: 0.6648 (tptt) REVERT: B 373 GLN cc_start: 0.7637 (tp40) cc_final: 0.7310 (tp40) REVERT: B 439 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7107 (mpp80) REVERT: B 461 ASP cc_start: 0.7295 (p0) cc_final: 0.7018 (p0) REVERT: B 548 ASP cc_start: 0.7885 (p0) cc_final: 0.7648 (p0) REVERT: C 9 ASP cc_start: 0.7283 (t70) cc_final: 0.6954 (t0) REVERT: C 98 ASP cc_start: 0.8244 (t0) cc_final: 0.7929 (t0) REVERT: C 107 GLN cc_start: 0.7651 (mt0) cc_final: 0.7340 (mt0) REVERT: C 187 SER cc_start: 0.7952 (t) cc_final: 0.7632 (p) REVERT: C 298 VAL cc_start: 0.7493 (OUTLIER) cc_final: 0.7226 (m) REVERT: C 375 LYS cc_start: 0.7394 (tppt) cc_final: 0.7131 (tppp) REVERT: C 542 LYS cc_start: 0.8352 (ptmt) cc_final: 0.7929 (tmmt) REVERT: D 5 LYS cc_start: 0.8211 (mtmm) cc_final: 0.7941 (mtmm) REVERT: D 159 ASP cc_start: 0.7349 (t70) cc_final: 0.7114 (t0) REVERT: D 174 ARG cc_start: 0.8174 (mtp180) cc_final: 0.7632 (ttp-110) REVERT: D 184 ARG cc_start: 0.7970 (ttt90) cc_final: 0.7670 (mtt90) REVERT: D 218 ASP cc_start: 0.7851 (p0) cc_final: 0.7597 (p0) REVERT: D 220 ARG cc_start: 0.7768 (ttp80) cc_final: 0.7348 (ttp80) REVERT: D 236 ARG cc_start: 0.7526 (ttp80) cc_final: 0.7246 (tmm-80) REVERT: D 288 ARG cc_start: 0.7351 (mtm-85) cc_final: 0.7094 (mtm-85) REVERT: D 331 LYS cc_start: 0.8089 (mmmm) cc_final: 0.7844 (mmmt) REVERT: D 463 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8368 (mm) REVERT: D 519 PHE cc_start: 0.8119 (t80) cc_final: 0.7881 (t80) REVERT: D 523 MET cc_start: 0.8364 (mmm) cc_final: 0.8068 (mmm) REVERT: D 534 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7708 (mp0) REVERT: D 545 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7967 (tmtt) outliers start: 91 outliers final: 75 residues processed: 560 average time/residue: 0.3743 time to fit residues: 296.0536 Evaluate side-chains 578 residues out of total 2041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 497 time to evaluate : 2.152 ------------------------------------------------------------------------------- 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 50 VAL Chi-restraints excluded: chain A residue 70 TYR 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 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 364 VAL Chi-restraints excluded: chain A residue 372 THR 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 12 TYR 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 212 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 429 LEU Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain C residue 16 VAL 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 212 THR Chi-restraints excluded: chain C residue 223 MET Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 462 ILE Chi-restraints excluded: chain C residue 482 VAL 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 27 LEU Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 127 THR 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 298 VAL Chi-restraints excluded: chain D residue 432 MET 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 534 GLU Chi-restraints excluded: chain D residue 545 LYS 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 126 optimal weight: 0.8980 chunk 191 optimal weight: 0.7980 chunk 173 optimal weight: 0.9980 chunk 147 optimal weight: 0.9980 chunk 199 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 152 optimal weight: 7.9990 chunk 167 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 126 GLN ** A 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 543 HIS ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 ASN ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 GLN C 448 GLN C 547 GLN D 102 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.142671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.123883 restraints weight = 28329.898| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.19 r_work: 0.3463 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.1879 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= 0.177 Angle : 0.595 10.185 25928 Z= 0.312 Chirality : 0.046 0.251 2782 Planarity : 0.004 0.054 3318 Dihedral : 10.947 161.917 2648 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 4.51 % Allowed : 22.59 % Favored : 72.91 % 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: -0.38 (0.18), residues: 2218 helix: 0.88 (0.20), residues: 701 sheet: -1.04 (0.26), residues: 412 loop : -0.59 (0.19), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 299 HIS 0.004 0.001 HIS B 206 PHE 0.019 0.001 PHE D 123 TYR 0.028 0.002 TYR B 12 ARG 0.007 0.000 ARG D 554 Details of bonding type rmsd hydrogen bonds : bond 0.03594 ( 689) hydrogen bonds : angle 4.92965 ( 1896) covalent geometry : bond 0.00409 (19183) covalent geometry : angle 0.59541 (25928) *********************** 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 588 residues out of total 2041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 496 time to evaluate : 2.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 VAL cc_start: 0.8689 (OUTLIER) cc_final: 0.8290 (m) REVERT: A 51 LYS cc_start: 0.7978 (mmmt) cc_final: 0.7642 (mmmt) REVERT: A 82 GLU cc_start: 0.7695 (mt-10) cc_final: 0.7458 (mt-10) REVERT: A 92 ASN cc_start: 0.8018 (t0) cc_final: 0.7582 (t0) REVERT: A 192 GLN cc_start: 0.7595 (mm-40) cc_final: 0.7138 (mm-40) REVERT: A 379 GLU cc_start: 0.6722 (tp30) cc_final: 0.6320 (tp30) REVERT: A 430 PHE cc_start: 0.7377 (m-10) cc_final: 0.7046 (m-80) REVERT: A 435 PHE cc_start: 0.7393 (m-10) cc_final: 0.6484 (m-10) REVERT: A 532 GLU cc_start: 0.7846 (tt0) cc_final: 0.7583 (tt0) REVERT: A 557 ARG cc_start: 0.7391 (ttm-80) cc_final: 0.7185 (ttm-80) REVERT: B 31 ASP cc_start: 0.7832 (t0) cc_final: 0.7344 (t0) REVERT: B 49 ASP cc_start: 0.7031 (p0) cc_final: 0.6403 (p0) REVERT: B 236 ARG cc_start: 0.8059 (tmm-80) cc_final: 0.7646 (ttp80) REVERT: B 240 ASP cc_start: 0.7331 (t70) cc_final: 0.7055 (t0) REVERT: B 262 LYS cc_start: 0.7104 (mttt) cc_final: 0.6648 (tptt) REVERT: B 373 GLN cc_start: 0.7611 (tp40) cc_final: 0.7332 (tp40) REVERT: B 374 ILE cc_start: 0.8091 (tp) cc_final: 0.7732 (tt) REVERT: B 410 PHE cc_start: 0.7824 (p90) cc_final: 0.7438 (p90) REVERT: B 439 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7126 (mpp80) REVERT: B 461 ASP cc_start: 0.7344 (p0) cc_final: 0.7069 (p0) REVERT: B 504 TYR cc_start: 0.8237 (m-80) cc_final: 0.7740 (m-80) REVERT: B 545 LYS cc_start: 0.8467 (tttt) cc_final: 0.8143 (ttpp) REVERT: B 548 ASP cc_start: 0.7830 (p0) cc_final: 0.7620 (p0) REVERT: C 9 ASP cc_start: 0.7295 (t70) cc_final: 0.6972 (t0) REVERT: C 98 ASP cc_start: 0.8229 (t0) cc_final: 0.7926 (t0) REVERT: C 107 GLN cc_start: 0.7692 (mt0) cc_final: 0.7339 (mt0) REVERT: C 187 SER cc_start: 0.7898 (t) cc_final: 0.7583 (p) REVERT: C 289 PHE cc_start: 0.8370 (m-80) cc_final: 0.7994 (m-10) REVERT: C 298 VAL cc_start: 0.7473 (OUTLIER) cc_final: 0.7207 (m) REVERT: C 375 LYS cc_start: 0.7394 (tppt) cc_final: 0.7131 (tppp) REVERT: C 473 TYR cc_start: 0.7968 (m-10) cc_final: 0.7199 (m-10) REVERT: C 542 LYS cc_start: 0.8306 (ptmt) cc_final: 0.8064 (ttpt) REVERT: D 5 LYS cc_start: 0.8217 (mtmm) cc_final: 0.7934 (mtmm) REVERT: D 159 ASP cc_start: 0.7298 (t70) cc_final: 0.7066 (t0) REVERT: D 174 ARG cc_start: 0.8181 (mtp180) cc_final: 0.7626 (ttp-110) REVERT: D 184 ARG cc_start: 0.8010 (ttt90) cc_final: 0.7675 (mtt90) REVERT: D 218 ASP cc_start: 0.7836 (p0) cc_final: 0.7582 (p0) REVERT: D 220 ARG cc_start: 0.7789 (ttp80) cc_final: 0.7497 (ttp80) REVERT: D 288 ARG cc_start: 0.7340 (mtm-85) cc_final: 0.7080 (mtm-85) REVERT: D 331 LYS cc_start: 0.8081 (mmmm) cc_final: 0.7841 (mmmt) REVERT: D 463 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8354 (mm) REVERT: D 519 PHE cc_start: 0.8165 (t80) cc_final: 0.7924 (t80) REVERT: D 523 MET cc_start: 0.8279 (mmm) cc_final: 0.7965 (mmm) REVERT: D 534 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7706 (mp0) REVERT: D 545 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7917 (tmtt) outliers start: 92 outliers final: 71 residues processed: 552 average time/residue: 0.3778 time to fit residues: 295.3991 Evaluate side-chains 568 residues out of total 2041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 491 time to evaluate : 2.334 ------------------------------------------------------------------------------- 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 50 VAL Chi-restraints excluded: chain A residue 70 TYR 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 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 364 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 409 PHE Chi-restraints excluded: chain A residue 410 PHE 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 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 212 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 337 GLU Chi-restraints excluded: chain B residue 416 ARG 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 488 ILE Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 104 LYS 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 223 MET Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 462 ILE Chi-restraints excluded: chain C residue 482 VAL 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 127 THR 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 298 VAL Chi-restraints excluded: chain D residue 432 MET Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 534 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 78 optimal weight: 2.9990 chunk 208 optimal weight: 5.9990 chunk 220 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 59 optimal weight: 0.0470 chunk 87 optimal weight: 1.9990 chunk 209 optimal weight: 0.9980 chunk 186 optimal weight: 0.5980 chunk 148 optimal weight: 8.9990 chunk 75 optimal weight: 0.4980 chunk 91 optimal weight: 0.9980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN ** A 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 543 HIS ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 GLN D 102 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.139674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.121047 restraints weight = 28772.661| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.27 r_work: 0.3397 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 19183 Z= 0.148 Angle : 0.598 12.836 25928 Z= 0.310 Chirality : 0.045 0.210 2782 Planarity : 0.004 0.054 3318 Dihedral : 10.796 164.691 2648 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 4.07 % Allowed : 23.22 % 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: -0.31 (0.18), residues: 2218 helix: 0.94 (0.20), residues: 701 sheet: -1.00 (0.26), residues: 412 loop : -0.55 (0.20), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 299 HIS 0.005 0.001 HIS D 246 PHE 0.015 0.001 PHE A 414 TYR 0.022 0.001 TYR B 12 ARG 0.006 0.000 ARG D 554 Details of bonding type rmsd hydrogen bonds : bond 0.03450 ( 689) hydrogen bonds : angle 4.84645 ( 1896) covalent geometry : bond 0.00343 (19183) covalent geometry : angle 0.59759 (25928) *********************** 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 580 residues out of total 2041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 497 time to evaluate : 2.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ARG cc_start: 0.8236 (ttm170) cc_final: 0.7504 (ttp-170) REVERT: A 50 VAL cc_start: 0.8654 (OUTLIER) cc_final: 0.8238 (m) REVERT: A 51 LYS cc_start: 0.7771 (mmmt) cc_final: 0.7423 (mmmt) REVERT: A 92 ASN cc_start: 0.7889 (t0) cc_final: 0.7386 (t0) REVERT: A 101 GLN cc_start: 0.7568 (tp40) cc_final: 0.7119 (tp40) REVERT: A 191 ARG cc_start: 0.8081 (mtm-85) cc_final: 0.5185 (ttt90) REVERT: A 192 GLN cc_start: 0.7639 (mm-40) cc_final: 0.7067 (mm-40) REVERT: A 379 GLU cc_start: 0.6650 (tp30) cc_final: 0.6274 (tp30) REVERT: A 435 PHE cc_start: 0.7268 (m-10) cc_final: 0.6363 (m-10) REVERT: A 514 LYS cc_start: 0.8119 (tptp) cc_final: 0.7899 (tppp) REVERT: A 532 GLU cc_start: 0.7659 (tt0) cc_final: 0.7404 (tt0) REVERT: B 31 ASP cc_start: 0.7655 (t0) cc_final: 0.7160 (t0) REVERT: B 38 ASN cc_start: 0.7533 (p0) cc_final: 0.7263 (p0) REVERT: B 49 ASP cc_start: 0.6959 (p0) cc_final: 0.6308 (p0) REVERT: B 153 VAL cc_start: 0.7830 (t) cc_final: 0.6610 (t) REVERT: B 155 GLU cc_start: 0.7423 (mt-10) cc_final: 0.6877 (mp0) REVERT: B 236 ARG cc_start: 0.7904 (tmm-80) cc_final: 0.7510 (ttp80) REVERT: B 240 ASP cc_start: 0.6862 (t70) cc_final: 0.6639 (t0) REVERT: B 243 TYR cc_start: 0.8192 (m-80) cc_final: 0.7945 (m-80) REVERT: B 262 LYS cc_start: 0.6961 (mttt) cc_final: 0.6497 (tptt) REVERT: B 306 LYS cc_start: 0.8244 (mtpt) cc_final: 0.7886 (tttt) REVERT: B 373 GLN cc_start: 0.7393 (tp40) cc_final: 0.7114 (tp40) REVERT: B 374 ILE cc_start: 0.7982 (tp) cc_final: 0.7613 (tt) REVERT: B 439 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7025 (mpp80) REVERT: B 461 ASP cc_start: 0.7094 (p0) cc_final: 0.6893 (p0) REVERT: B 548 ASP cc_start: 0.7675 (p0) cc_final: 0.7452 (p0) REVERT: C 98 ASP cc_start: 0.8046 (t0) cc_final: 0.7728 (t0) REVERT: C 185 LYS cc_start: 0.8220 (mttt) cc_final: 0.8008 (mttt) REVERT: C 187 SER cc_start: 0.7796 (t) cc_final: 0.7480 (p) REVERT: C 298 VAL cc_start: 0.7151 (OUTLIER) cc_final: 0.6919 (m) REVERT: C 375 LYS cc_start: 0.7334 (tppt) cc_final: 0.7039 (tppp) REVERT: C 473 TYR cc_start: 0.7918 (m-10) cc_final: 0.7127 (m-10) REVERT: D 5 LYS cc_start: 0.8156 (mtmm) cc_final: 0.7844 (mtmm) REVERT: D 159 ASP cc_start: 0.7047 (t70) cc_final: 0.6800 (t0) REVERT: D 184 ARG cc_start: 0.7920 (ttt90) cc_final: 0.7590 (mtt90) REVERT: D 218 ASP cc_start: 0.7572 (p0) cc_final: 0.7327 (p0) REVERT: D 220 ARG cc_start: 0.7667 (ttp80) cc_final: 0.7388 (ttp80) REVERT: D 288 ARG cc_start: 0.6998 (mtm-85) cc_final: 0.6770 (mtm-85) REVERT: D 331 LYS cc_start: 0.7881 (mmmm) cc_final: 0.7364 (mmmm) REVERT: D 463 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8150 (mm) REVERT: D 519 PHE cc_start: 0.8021 (t80) cc_final: 0.7752 (t80) REVERT: D 523 MET cc_start: 0.8042 (mmm) cc_final: 0.7707 (mmm) REVERT: D 534 GLU cc_start: 0.7734 (pm20) cc_final: 0.7453 (mp0) REVERT: D 545 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7790 (tmtt) outliers start: 83 outliers final: 64 residues processed: 549 average time/residue: 0.4052 time to fit residues: 315.8350 Evaluate side-chains 555 residues out of total 2041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 486 time to evaluate : 2.227 ------------------------------------------------------------------------------- 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 50 VAL Chi-restraints excluded: chain A residue 70 TYR Chi-restraints excluded: chain A residue 98 ASP 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 364 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 410 PHE 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 141 THR Chi-restraints excluded: chain B residue 192 GLN Chi-restraints excluded: chain B residue 212 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 337 GLU 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 488 ILE Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 104 LYS 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 223 MET Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 462 ILE Chi-restraints excluded: chain C residue 482 VAL 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 127 THR 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 298 VAL Chi-restraints excluded: chain D residue 463 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 26 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 217 optimal weight: 0.3980 chunk 101 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 198 optimal weight: 0.3980 chunk 152 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 126 GLN ** A 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 543 HIS ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 ASN C 56 GLN ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 GLN C 448 GLN ** C 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.140146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.121583 restraints weight = 28885.985| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.28 r_work: 0.3402 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.2109 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= 0.143 Angle : 0.605 12.907 25928 Z= 0.315 Chirality : 0.045 0.223 2782 Planarity : 0.004 0.054 3318 Dihedral : 10.770 169.111 2648 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.77 % Allowed : 24.25 % Favored : 71.97 % 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: -0.28 (0.18), residues: 2218 helix: 0.99 (0.20), residues: 698 sheet: -0.97 (0.26), residues: 409 loop : -0.55 (0.19), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 299 HIS 0.006 0.001 HIS D 246 PHE 0.028 0.001 PHE A 409 TYR 0.019 0.001 TYR B 12 ARG 0.009 0.000 ARG A 220 Details of bonding type rmsd hydrogen bonds : bond 0.03371 ( 689) hydrogen bonds : angle 4.78295 ( 1896) covalent geometry : bond 0.00333 (19183) covalent geometry : angle 0.60466 (25928) *********************** 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 561 residues out of total 2041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 484 time to evaluate : 3.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 VAL cc_start: 0.8646 (OUTLIER) cc_final: 0.8234 (m) REVERT: A 51 LYS cc_start: 0.7776 (mmmt) cc_final: 0.7428 (mmmt) REVERT: A 92 ASN cc_start: 0.7862 (t0) cc_final: 0.7417 (t0) REVERT: A 101 GLN cc_start: 0.7548 (tp40) cc_final: 0.7143 (tp40) REVERT: A 192 GLN cc_start: 0.7629 (mm-40) cc_final: 0.7053 (mm-40) REVERT: A 220 ARG cc_start: 0.7958 (ptm-80) cc_final: 0.7698 (ttm-80) REVERT: A 435 PHE cc_start: 0.7277 (m-10) cc_final: 0.6287 (m-10) REVERT: A 514 LYS cc_start: 0.8092 (tptp) cc_final: 0.7879 (tppp) REVERT: A 532 GLU cc_start: 0.7688 (tt0) cc_final: 0.7418 (tt0) REVERT: A 557 ARG cc_start: 0.6840 (ttm-80) cc_final: 0.6638 (ttm-80) REVERT: B 7 TYR cc_start: 0.8122 (m-80) cc_final: 0.7619 (m-80) REVERT: B 31 ASP cc_start: 0.7658 (t0) cc_final: 0.7169 (t0) REVERT: B 49 ASP cc_start: 0.6964 (p0) cc_final: 0.6299 (p0) REVERT: B 155 GLU cc_start: 0.7262 (mt-10) cc_final: 0.7034 (mt-10) REVERT: B 243 TYR cc_start: 0.8155 (m-80) cc_final: 0.7897 (m-80) REVERT: B 262 LYS cc_start: 0.6971 (mttt) cc_final: 0.6485 (tptt) REVERT: B 306 LYS cc_start: 0.8112 (mtpt) cc_final: 0.7840 (tttp) REVERT: B 373 GLN cc_start: 0.7384 (tp40) cc_final: 0.7101 (tp40) REVERT: B 374 ILE cc_start: 0.7967 (tp) cc_final: 0.7587 (tt) REVERT: B 439 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7039 (mpp80) REVERT: C 49 ASP cc_start: 0.7859 (m-30) cc_final: 0.7508 (m-30) REVERT: C 98 ASP cc_start: 0.8033 (t0) cc_final: 0.7718 (t0) REVERT: C 107 GLN cc_start: 0.7769 (mt0) cc_final: 0.7366 (mt0) REVERT: C 185 LYS cc_start: 0.8221 (mttt) cc_final: 0.8015 (mttt) REVERT: C 187 SER cc_start: 0.7792 (t) cc_final: 0.7472 (p) REVERT: C 298 VAL cc_start: 0.7137 (OUTLIER) cc_final: 0.6905 (m) REVERT: C 375 LYS cc_start: 0.7282 (tppt) cc_final: 0.6985 (tppp) REVERT: C 473 TYR cc_start: 0.7917 (m-10) cc_final: 0.7186 (m-10) REVERT: C 514 LYS cc_start: 0.7770 (mptt) cc_final: 0.7449 (mptt) REVERT: D 5 LYS cc_start: 0.8178 (mtmm) cc_final: 0.7854 (mtmm) REVERT: D 44 THR cc_start: 0.8599 (m) cc_final: 0.8318 (t) REVERT: D 159 ASP cc_start: 0.7043 (t70) cc_final: 0.6790 (t0) REVERT: D 184 ARG cc_start: 0.7898 (ttt90) cc_final: 0.7571 (ttt90) REVERT: D 220 ARG cc_start: 0.7660 (ttp80) cc_final: 0.7394 (ttp80) REVERT: D 244 ASP cc_start: 0.6560 (p0) cc_final: 0.6141 (p0) REVERT: D 288 ARG cc_start: 0.6977 (mtm-85) cc_final: 0.6770 (mtm-85) REVERT: D 331 LYS cc_start: 0.7884 (mmmm) cc_final: 0.7380 (mmmm) REVERT: D 463 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8148 (mm) REVERT: D 519 PHE cc_start: 0.8011 (t80) cc_final: 0.7529 (t80) REVERT: D 523 MET cc_start: 0.8079 (mmm) cc_final: 0.7482 (mmm) REVERT: D 545 LYS cc_start: 0.7956 (OUTLIER) cc_final: 0.7669 (tmtt) REVERT: D 554 ARG cc_start: 0.7683 (mtm110) cc_final: 0.7349 (mpp80) outliers start: 77 outliers final: 63 residues processed: 535 average time/residue: 0.3921 time to fit residues: 297.6392 Evaluate side-chains 549 residues out of total 2041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 481 time to evaluate : 2.152 ------------------------------------------------------------------------------- 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 50 VAL Chi-restraints excluded: chain A residue 70 TYR Chi-restraints excluded: chain A residue 98 ASP 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 374 ILE Chi-restraints excluded: chain A residue 410 PHE 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 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 298 VAL Chi-restraints excluded: chain B residue 337 GLU 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 488 ILE Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 104 LYS 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 223 MET Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 462 ILE Chi-restraints excluded: chain C residue 482 VAL 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 127 THR 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 298 VAL Chi-restraints excluded: chain D residue 463 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 187 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 159 optimal weight: 0.4980 chunk 97 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 chunk 103 optimal weight: 0.1980 chunk 3 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 191 optimal weight: 0.6980 chunk 182 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 126 GLN ** A 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 543 HIS ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 GLN C 448 GLN ** C 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.143281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.124543 restraints weight = 28252.363| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.20 r_work: 0.3479 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.2187 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= 0.145 Angle : 0.607 10.309 25928 Z= 0.317 Chirality : 0.045 0.195 2782 Planarity : 0.004 0.053 3318 Dihedral : 10.760 172.994 2648 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.38 % Allowed : 24.74 % Favored : 71.88 % 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: -0.25 (0.18), residues: 2218 helix: 1.00 (0.20), residues: 698 sheet: -0.96 (0.26), residues: 408 loop : -0.53 (0.20), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 299 HIS 0.009 0.001 HIS D 246 PHE 0.019 0.001 PHE A 519 TYR 0.018 0.001 TYR B 12 ARG 0.009 0.001 ARG C 60 Details of bonding type rmsd hydrogen bonds : bond 0.03356 ( 689) hydrogen bonds : angle 4.74915 ( 1896) covalent geometry : bond 0.00339 (19183) covalent geometry : angle 0.60689 (25928) ********************** 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 551 residues out of total 2041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 482 time to evaluate : 2.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.7941 (t0) cc_final: 0.7481 (t0) REVERT: A 50 VAL cc_start: 0.8704 (OUTLIER) cc_final: 0.8125 (m) REVERT: A 51 LYS cc_start: 0.7958 (mmmt) cc_final: 0.7423 (mmmt) REVERT: A 92 ASN cc_start: 0.7953 (t0) cc_final: 0.7586 (t0) REVERT: A 192 GLN cc_start: 0.7877 (mm-40) cc_final: 0.7322 (mm-40) REVERT: A 240 ASP cc_start: 0.7595 (t0) cc_final: 0.7312 (t70) REVERT: A 404 THR cc_start: 0.8364 (m) cc_final: 0.8012 (p) REVERT: A 435 PHE cc_start: 0.7471 (m-10) cc_final: 0.6592 (m-10) REVERT: A 487 MET cc_start: 0.7824 (mtm) cc_final: 0.7517 (mtp) REVERT: A 532 GLU cc_start: 0.7937 (tt0) cc_final: 0.7669 (tt0) REVERT: B 7 TYR cc_start: 0.8227 (m-80) cc_final: 0.7808 (m-80) REVERT: B 29 LEU cc_start: 0.8882 (mt) cc_final: 0.8608 (mt) REVERT: B 31 ASP cc_start: 0.7804 (t0) cc_final: 0.7313 (t0) REVERT: B 38 ASN cc_start: 0.7734 (p0) cc_final: 0.7477 (p0) REVERT: B 49 ASP cc_start: 0.7041 (p0) cc_final: 0.6358 (p0) REVERT: B 88 ILE cc_start: 0.8651 (mm) cc_final: 0.8403 (mm) REVERT: B 236 ARG cc_start: 0.7957 (tmm-80) cc_final: 0.7666 (ttp80) REVERT: B 262 LYS cc_start: 0.7056 (mttt) cc_final: 0.6606 (tptt) REVERT: B 306 LYS cc_start: 0.8237 (mtpt) cc_final: 0.7844 (tttt) REVERT: B 373 GLN cc_start: 0.7610 (tp40) cc_final: 0.7348 (tp40) REVERT: B 379 GLU cc_start: 0.7882 (tp30) cc_final: 0.7441 (mt-10) REVERT: B 411 LYS cc_start: 0.8038 (mttt) cc_final: 0.7806 (mmtp) REVERT: B 439 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7108 (mpp80) REVERT: C 49 ASP cc_start: 0.8120 (m-30) cc_final: 0.7840 (m-30) REVERT: C 98 ASP cc_start: 0.8196 (t0) cc_final: 0.7891 (t0) REVERT: C 107 GLN cc_start: 0.7648 (mt0) cc_final: 0.7295 (mt0) REVERT: C 187 SER cc_start: 0.7883 (t) cc_final: 0.7585 (p) REVERT: C 289 PHE cc_start: 0.8380 (m-10) cc_final: 0.8121 (m-10) REVERT: C 298 VAL cc_start: 0.7334 (OUTLIER) cc_final: 0.7072 (m) REVERT: C 473 TYR cc_start: 0.7955 (m-10) cc_final: 0.7254 (m-10) REVERT: D 5 LYS cc_start: 0.8017 (mtmm) cc_final: 0.7744 (mtmm) REVERT: D 44 THR cc_start: 0.8690 (m) cc_final: 0.8419 (t) REVERT: D 102 ASN cc_start: 0.7798 (m-40) cc_final: 0.7540 (m110) REVERT: D 159 ASP cc_start: 0.7288 (t70) cc_final: 0.7048 (t0) REVERT: D 184 ARG cc_start: 0.7988 (ttt90) cc_final: 0.7655 (ttt90) REVERT: D 220 ARG cc_start: 0.7792 (ttp80) cc_final: 0.7537 (ttp80) REVERT: D 244 ASP cc_start: 0.6784 (p0) cc_final: 0.6357 (p0) REVERT: D 288 ARG cc_start: 0.7293 (mtm-85) cc_final: 0.7082 (mtm-85) REVERT: D 331 LYS cc_start: 0.8079 (mmmm) cc_final: 0.7629 (mmmm) REVERT: D 463 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8347 (mm) REVERT: D 519 PHE cc_start: 0.8140 (t80) cc_final: 0.7724 (t80) REVERT: D 523 MET cc_start: 0.8306 (mmm) cc_final: 0.7716 (mmm) outliers start: 69 outliers final: 61 residues processed: 526 average time/residue: 0.4038 time to fit residues: 304.6468 Evaluate side-chains 546 residues out of total 2041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 481 time to evaluate : 2.220 ------------------------------------------------------------------------------- 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 50 VAL Chi-restraints excluded: chain A residue 70 TYR Chi-restraints excluded: chain A residue 98 ASP 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 374 ILE Chi-restraints excluded: chain A residue 410 PHE 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 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 337 GLU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 104 LYS 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 223 MET Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 462 ILE Chi-restraints excluded: chain C residue 482 VAL 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 127 THR 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 298 VAL Chi-restraints excluded: chain D residue 316 LYS Chi-restraints excluded: chain D residue 463 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 131 optimal weight: 4.9990 chunk 195 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 124 optimal weight: 0.0870 chunk 129 optimal weight: 6.9990 chunk 145 optimal weight: 1.9990 chunk 61 optimal weight: 0.0980 chunk 101 optimal weight: 1.9990 chunk 148 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 overall best weight: 1.0364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN ** A 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 543 HIS ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 GLN C 448 GLN ** C 543 HIS ** 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 = 0.3773 r_free = 0.3773 target = 0.138835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.120296 restraints weight = 28893.479| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.27 r_work: 0.3386 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 19183 Z= 0.203 Angle : 0.634 10.032 25928 Z= 0.332 Chirality : 0.047 0.205 2782 Planarity : 0.004 0.052 3318 Dihedral : 10.910 178.558 2648 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 3.58 % Allowed : 24.79 % Favored : 71.63 % 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: -0.37 (0.18), residues: 2218 helix: 0.89 (0.20), residues: 701 sheet: -1.05 (0.26), residues: 412 loop : -0.58 (0.19), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 299 HIS 0.009 0.001 HIS D 246 PHE 0.021 0.002 PHE C 215 TYR 0.023 0.002 TYR B 12 ARG 0.010 0.001 ARG B 37 Details of bonding type rmsd hydrogen bonds : bond 0.03620 ( 689) hydrogen bonds : angle 4.85908 ( 1896) covalent geometry : bond 0.00468 (19183) covalent geometry : angle 0.63438 (25928) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10490.76 seconds wall clock time: 183 minutes 56.48 seconds (11036.48 seconds total)