Starting phenix.real_space_refine on Sun Jun 15 19:22:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zr5_14883/06_2025/7zr5_14883.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zr5_14883/06_2025/7zr5_14883.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zr5_14883/06_2025/7zr5_14883.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zr5_14883/06_2025/7zr5_14883.map" model { file = "/net/cci-nas-00/data/ceres_data/7zr5_14883/06_2025/7zr5_14883.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zr5_14883/06_2025/7zr5_14883.cif" } resolution = 3.9 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= 0.002 sd= 0.027 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 7 5.49 5 S 91 5.16 5 C 11078 2.51 5 N 2981 2.21 5 O 3361 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 17518 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 5132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 633, 5132 Classifications: {'peptide': 633} Link IDs: {'PTRANS': 17, 'TRANS': 615} Chain breaks: 1 Chain: "B" Number of atoms: 5112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 631, 5112 Classifications: {'peptide': 631} Link IDs: {'PTRANS': 17, 'TRANS': 613} Chain breaks: 1 Chain: "C" Number of atoms: 2243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2243 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 4, 'TRANS': 261} Chain: "K" Number of atoms: 1503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1503 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 9, 'TRANS': 176} Chain breaks: 1 Chain: "P" Number of atoms: 3466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3466 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 15, 'TRANS': 413} Chain breaks: 1 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.93, per 1000 atoms: 0.62 Number of scatterers: 17518 At special positions: 0 Unit cell: (120.4, 128.14, 191.78, 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 91 16.00 P 7 15.00 O 3361 8.00 N 2981 7.00 C 11078 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: 4.33 Conformation dependent library (CDL) restraints added in 2.2 seconds 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4084 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 17 sheets defined 48.8% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.09 Creating SS restraints... Processing helix chain 'A' and resid 20 through 31 removed outlier: 3.541A pdb=" N ASN A 30 " --> pdb=" O SER A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 61 removed outlier: 3.904A pdb=" N ARG A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER A 58 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR A 60 " --> pdb=" O TYR A 56 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 101 removed outlier: 3.989A pdb=" N ILE A 99 " --> pdb=" O LYS A 95 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASN A 100 " --> pdb=" O ALA A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 115 removed outlier: 3.541A pdb=" N GLU A 115 " --> pdb=" O LYS A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 138 Processing helix chain 'A' and resid 194 through 205 removed outlier: 4.271A pdb=" N VAL A 198 " --> pdb=" O GLU A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 291 removed outlier: 4.137A pdb=" N THR A 290 " --> pdb=" O PRO A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 296 removed outlier: 4.051A pdb=" N ILE A 296 " --> pdb=" O PRO A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 307 Processing helix chain 'A' and resid 399 through 420 removed outlier: 4.253A pdb=" N VAL A 403 " --> pdb=" O LYS A 399 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA A 420 " --> pdb=" O PHE A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 433 removed outlier: 3.767A pdb=" N LYS A 428 " --> pdb=" O GLU A 424 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA A 432 " --> pdb=" O LYS A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 444 removed outlier: 4.343A pdb=" N LEU A 437 " --> pdb=" O PHE A 433 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS A 438 " --> pdb=" O SER A 434 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 439 " --> pdb=" O LYS A 435 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY A 440 " --> pdb=" O ASN A 436 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N HIS A 442 " --> pdb=" O LYS A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 452 Processing helix chain 'A' and resid 469 through 474 removed outlier: 3.656A pdb=" N SER A 474 " --> pdb=" O SER A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 496 removed outlier: 3.871A pdb=" N ASN A 496 " --> pdb=" O GLU A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 523 removed outlier: 3.673A pdb=" N GLU A 519 " --> pdb=" O GLU A 515 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN A 523 " --> pdb=" O GLU A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 560 removed outlier: 3.791A pdb=" N LYS A 550 " --> pdb=" O ASP A 546 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA A 558 " --> pdb=" O GLU A 554 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS A 559 " --> pdb=" O GLU A 555 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE A 560 " --> pdb=" O SER A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 572 removed outlier: 3.682A pdb=" N LYS A 565 " --> pdb=" O GLU A 561 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASP A 572 " --> pdb=" O LYS A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 609 Processing helix chain 'A' and resid 613 through 618 removed outlier: 4.628A pdb=" N MET A 617 " --> pdb=" O ASP A 613 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY A 618 " --> pdb=" O ASN A 614 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 613 through 618' Processing helix chain 'A' and resid 632 through 645 removed outlier: 3.577A pdb=" N GLU A 636 " --> pdb=" O HIS A 632 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ALA A 644 " --> pdb=" O GLN A 640 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP A 645 " --> pdb=" O LYS A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 665 removed outlier: 4.288A pdb=" N LYS A 652 " --> pdb=" O ASP A 648 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP A 653 " --> pdb=" O LYS A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 688 removed outlier: 4.205A pdb=" N HIS A 676 " --> pdb=" O ASP A 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 31 Processing helix chain 'B' and resid 38 through 59 removed outlier: 3.767A pdb=" N LEU B 59 " --> pdb=" O ARG B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 66 Processing helix chain 'B' and resid 94 through 103 Processing helix chain 'B' and resid 108 through 117 removed outlier: 4.186A pdb=" N ALA B 112 " --> pdb=" O SER B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 140 removed outlier: 3.602A pdb=" N VAL B 139 " --> pdb=" O ALA B 136 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA B 140 " --> pdb=" O TYR B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 205 removed outlier: 3.566A pdb=" N VAL B 198 " --> pdb=" O GLU B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 307 Processing helix chain 'B' and resid 398 through 420 removed outlier: 3.738A pdb=" N LYS B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 431 Processing helix chain 'B' and resid 433 through 443 removed outlier: 4.193A pdb=" N LEU B 437 " --> pdb=" O PHE B 433 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS B 438 " --> pdb=" O SER B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 453 Processing helix chain 'B' and resid 468 through 475 Processing helix chain 'B' and resid 490 through 496 removed outlier: 3.572A pdb=" N VAL B 494 " --> pdb=" O SER B 490 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASN B 496 " --> pdb=" O GLU B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 504 removed outlier: 4.513A pdb=" N VAL B 503 " --> pdb=" O PHE B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 507 No H-bonds generated for 'chain 'B' and resid 505 through 507' Processing helix chain 'B' and resid 516 through 525 removed outlier: 4.359A pdb=" N TYR B 520 " --> pdb=" O PRO B 516 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN B 524 " --> pdb=" O TYR B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 560 removed outlier: 3.656A pdb=" N ALA B 558 " --> pdb=" O GLU B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 571 removed outlier: 3.685A pdb=" N CYS B 564 " --> pdb=" O PHE B 560 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS B 565 " --> pdb=" O GLU B 561 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS B 568 " --> pdb=" O CYS B 564 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLU B 569 " --> pdb=" O LYS B 565 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ILE B 570 " --> pdb=" O LEU B 566 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU B 571 " --> pdb=" O MET B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 608 removed outlier: 3.560A pdb=" N ALA B 608 " --> pdb=" O ARG B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 621 removed outlier: 3.990A pdb=" N MET B 620 " --> pdb=" O THR B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 645 removed outlier: 3.620A pdb=" N GLU B 636 " --> pdb=" O HIS B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 666 Processing helix chain 'B' and resid 672 through 688 removed outlier: 4.011A pdb=" N HIS B 676 " --> pdb=" O ASP B 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 8 removed outlier: 3.842A pdb=" N ASP C 8 " --> pdb=" O SER C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 72 Processing helix chain 'C' and resid 78 through 112 removed outlier: 3.738A pdb=" N LYS C 107 " --> pdb=" O GLU C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 119 removed outlier: 3.770A pdb=" N LEU C 119 " --> pdb=" O ASN C 115 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 115 through 119' Processing helix chain 'C' and resid 139 through 164 removed outlier: 4.267A pdb=" N MET C 164 " --> pdb=" O LYS C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 182 Processing helix chain 'C' and resid 183 through 201 removed outlier: 3.596A pdb=" N ALA C 187 " --> pdb=" O CYS C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 227 Processing helix chain 'C' and resid 234 through 243 removed outlier: 3.697A pdb=" N THR C 243 " --> pdb=" O THR C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 265 Processing helix chain 'K' and resid 537 through 543 Processing helix chain 'K' and resid 549 through 568 Processing helix chain 'K' and resid 569 through 571 No H-bonds generated for 'chain 'K' and resid 569 through 571' Processing helix chain 'K' and resid 578 through 581 Processing helix chain 'K' and resid 634 through 652 removed outlier: 4.010A pdb=" N ASP K 638 " --> pdb=" O SER K 634 " (cutoff:3.500A) Processing helix chain 'K' and resid 661 through 671 removed outlier: 3.556A pdb=" N ARG K 671 " --> pdb=" O PHE K 667 " (cutoff:3.500A) Processing helix chain 'K' and resid 686 through 697 removed outlier: 3.953A pdb=" N LYS K 690 " --> pdb=" O PRO K 686 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEU K 697 " --> pdb=" O MET K 693 " (cutoff:3.500A) Processing helix chain 'K' and resid 706 through 719 Processing helix chain 'P' and resid 28 through 30 No H-bonds generated for 'chain 'P' and resid 28 through 30' Processing helix chain 'P' and resid 31 through 36 Processing helix chain 'P' and resid 36 through 41 removed outlier: 4.022A pdb=" N LYS P 40 " --> pdb=" O ASN P 36 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA P 41 " --> pdb=" O ASP P 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 36 through 41' Processing helix chain 'P' and resid 43 through 58 removed outlier: 3.793A pdb=" N GLN P 53 " --> pdb=" O LYS P 49 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLU P 56 " --> pdb=" O SER P 52 " (cutoff:3.500A) Processing helix chain 'P' and resid 61 through 74 removed outlier: 4.012A pdb=" N SER P 69 " --> pdb=" O TYR P 65 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU P 70 " --> pdb=" O GLY P 66 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA P 71 " --> pdb=" O ASN P 67 " (cutoff:3.500A) Processing helix chain 'P' and resid 78 through 91 removed outlier: 3.851A pdb=" N GLY P 83 " --> pdb=" O GLY P 79 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N THR P 86 " --> pdb=" O LEU P 82 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG P 87 " --> pdb=" O GLY P 83 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA P 88 " --> pdb=" O ASP P 84 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE P 89 " --> pdb=" O ALA P 85 " (cutoff:3.500A) Processing helix chain 'P' and resid 95 through 110 removed outlier: 4.065A pdb=" N ARG P 101 " --> pdb=" O LYS P 97 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ARG P 102 " --> pdb=" O GLY P 98 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA P 103 " --> pdb=" O TYR P 99 " (cutoff:3.500A) Processing helix chain 'P' and resid 113 through 121 Processing helix chain 'P' and resid 133 through 151 removed outlier: 4.001A pdb=" N ILE P 142 " --> pdb=" O GLU P 138 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL P 143 " --> pdb=" O CYS P 139 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS P 144 " --> pdb=" O ASN P 140 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N GLN P 145 " --> pdb=" O LYS P 141 " (cutoff:3.500A) Processing helix chain 'P' and resid 187 through 200 Processing helix chain 'P' and resid 205 through 221 Processing helix chain 'P' and resid 246 through 258 Processing helix chain 'P' and resid 278 through 293 Processing helix chain 'P' and resid 302 through 305 Processing helix chain 'P' and resid 306 through 311 Processing helix chain 'P' and resid 314 through 323 Processing helix chain 'P' and resid 324 through 336 removed outlier: 3.830A pdb=" N TYR P 328 " --> pdb=" O THR P 324 " (cutoff:3.500A) Processing helix chain 'P' and resid 362 through 368 Processing helix chain 'P' and resid 379 through 387 Processing helix chain 'P' and resid 407 through 419 Processing helix chain 'P' and resid 438 through 440 No H-bonds generated for 'chain 'P' and resid 438 through 440' Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 14 removed outlier: 3.859A pdb=" N GLU A 13 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL B 167 " --> pdb=" O GLU A 13 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS B 142 " --> pdb=" O HIS B 184 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 19 removed outlier: 6.591A pdb=" N GLN A 18 " --> pdb=" O ILE B 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 78 removed outlier: 3.665A pdb=" N LYS A 142 " --> pdb=" O HIS A 184 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 104 through 105 removed outlier: 3.506A pdb=" N ILE A 105 " --> pdb=" O GLN B 18 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 318 through 324 removed outlier: 3.850A pdb=" N PHE A 321 " --> pdb=" O ALA A 331 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE A 329 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LYS A 354 " --> pdb=" O VAL A 381 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N SER A 383 " --> pdb=" O LYS A 354 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N TYR A 356 " --> pdb=" O SER A 383 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 456 through 457 Processing sheet with id=AA7, first strand: chain 'A' and resid 511 through 513 removed outlier: 5.684A pdb=" N ILE A 483 " --> pdb=" O VAL A 534 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 578 through 580 removed outlier: 3.884A pdb=" N THR A 579 " --> pdb=" O LEU A 626 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE A 628 " --> pdb=" O THR A 579 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N CYS A 590 " --> pdb=" O GLU A 627 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.964A pdb=" N ILE B 73 " --> pdb=" O THR B 214 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 333 through 335 removed outlier: 3.532A pdb=" N ILE B 335 " --> pdb=" O ALA B 317 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA B 317 " --> pdb=" O ILE B 335 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N VAL B 318 " --> pdb=" O MET C 128 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 322 through 325 removed outlier: 6.812A pdb=" N SER B 322 " --> pdb=" O GLY C 123 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 458 through 459 removed outlier: 4.466A pdb=" N HIS B 458 " --> pdb=" O TYR B 512 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N TYR B 484 " --> pdb=" O VAL B 511 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N MET B 513 " --> pdb=" O TYR B 484 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE B 486 " --> pdb=" O MET B 513 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 575 through 580 removed outlier: 7.790A pdb=" N LEU B 626 " --> pdb=" O GLU B 576 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N VAL B 578 " --> pdb=" O LEU B 626 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N ILE B 628 " --> pdb=" O VAL B 578 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ILE B 580 " --> pdb=" O ILE B 628 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 535 through 536 removed outlier: 3.601A pdb=" N SER K 535 " --> pdb=" O LEU K 584 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'P' and resid 226 through 229 removed outlier: 6.318A pdb=" N VAL P 227 " --> pdb=" O CYS P 343 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU P 349 " --> pdb=" O TYR P 422 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE P 423 " --> pdb=" O VAL P 443 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N VAL P 445 " --> pdb=" O ILE P 423 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'P' and resid 297 through 299 Processing sheet with id=AB8, first strand: chain 'P' and resid 388 through 389 removed outlier: 6.464A pdb=" N ASP P 388 " --> pdb=" O PHE P 406 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER P 396 " --> pdb=" O GLN P 405 " (cutoff:3.500A) 721 hydrogen bonds defined for protein. 2061 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.54 Time building geometry restraints manager: 5.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.00 - 1.29: 3013 1.29 - 1.59: 14665 1.59 - 1.89: 158 1.89 - 2.18: 0 2.18 - 2.48: 1 Bond restraints: 17837 Sorted by residual: bond pdb=" CB PRO C 230 " pdb=" CG PRO C 230 " ideal model delta sigma weight residual 1.492 2.480 -0.988 5.00e-02 4.00e+02 3.90e+02 bond pdb=" CG PRO C 230 " pdb=" CD PRO C 230 " ideal model delta sigma weight residual 1.503 0.998 0.505 3.40e-02 8.65e+02 2.21e+02 bond pdb=" N PRO C 230 " pdb=" CA PRO C 230 " ideal model delta sigma weight residual 1.470 1.363 0.107 1.22e-02 6.72e+03 7.70e+01 bond pdb=" N PRO C 230 " pdb=" CD PRO C 230 " ideal model delta sigma weight residual 1.473 1.561 -0.088 1.40e-02 5.10e+03 3.96e+01 bond pdb=" CA PRO C 230 " pdb=" CB PRO C 230 " ideal model delta sigma weight residual 1.535 1.483 0.051 1.72e-02 3.38e+03 8.87e+00 ... (remaining 17832 not shown) Histogram of bond angle deviations from ideal: 0.00 - 21.21: 23989 21.21 - 42.42: 2 42.42 - 63.63: 0 63.63 - 84.84: 0 84.84 - 106.05: 1 Bond angle restraints: 23992 Sorted by residual: angle pdb=" CB PRO C 230 " pdb=" CG PRO C 230 " pdb=" CD PRO C 230 " ideal model delta sigma weight residual 106.10 0.05 106.05 3.20e+00 9.77e-02 1.10e+03 angle pdb=" CA PRO C 230 " pdb=" N PRO C 230 " pdb=" CD PRO C 230 " ideal model delta sigma weight residual 112.00 89.93 22.07 1.40e+00 5.10e-01 2.48e+02 angle pdb=" N PRO C 230 " pdb=" CA PRO C 230 " pdb=" CB PRO C 230 " ideal model delta sigma weight residual 103.19 89.02 14.17 1.00e+00 1.00e+00 2.01e+02 angle pdb=" CA PRO C 230 " pdb=" CB PRO C 230 " pdb=" CG PRO C 230 " ideal model delta sigma weight residual 104.50 88.59 15.91 1.90e+00 2.77e-01 7.01e+01 angle pdb=" CA PRO B 79 " pdb=" N PRO B 79 " pdb=" CD PRO B 79 " ideal model delta sigma weight residual 112.00 101.69 10.31 1.40e+00 5.10e-01 5.42e+01 ... (remaining 23987 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 9419 17.86 - 35.72: 1216 35.72 - 53.58: 286 53.58 - 71.44: 61 71.44 - 89.30: 25 Dihedral angle restraints: 11007 sinusoidal: 4702 harmonic: 6305 Sorted by residual: dihedral pdb=" CA MET C 112 " pdb=" C MET C 112 " pdb=" N PRO C 113 " pdb=" CA PRO C 113 " ideal model delta harmonic sigma weight residual -180.00 -143.82 -36.18 0 5.00e+00 4.00e-02 5.24e+01 dihedral pdb=" CA THR B 309 " pdb=" C THR B 309 " pdb=" N ASN B 310 " pdb=" CA ASN B 310 " ideal model delta harmonic sigma weight residual 180.00 155.54 24.46 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" N PRO C 230 " pdb=" C PRO C 230 " pdb=" CA PRO C 230 " pdb=" CB PRO C 230 " ideal model delta harmonic sigma weight residual 115.10 103.48 11.62 0 2.50e+00 1.60e-01 2.16e+01 ... (remaining 11004 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 2366 0.072 - 0.144: 231 0.144 - 0.216: 11 0.216 - 0.289: 1 0.289 - 0.361: 1 Chirality restraints: 2610 Sorted by residual: chirality pdb=" CA PRO C 230 " pdb=" N PRO C 230 " pdb=" C PRO C 230 " pdb=" CB PRO C 230 " both_signs ideal model delta sigma weight residual False 2.72 2.36 0.36 2.00e-01 2.50e+01 3.25e+00 chirality pdb=" CB THR B 190 " pdb=" CA THR B 190 " pdb=" OG1 THR B 190 " pdb=" CG2 THR B 190 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA PRO K 523 " pdb=" N PRO K 523 " pdb=" C PRO K 523 " pdb=" CB PRO K 523 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 9.95e-01 ... (remaining 2607 not shown) Planarity restraints: 3076 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 61 " 0.103 5.00e-02 4.00e+02 1.54e-01 3.77e+01 pdb=" N PRO A 62 " -0.266 5.00e-02 4.00e+02 pdb=" CA PRO A 62 " 0.086 5.00e-02 4.00e+02 pdb=" CD PRO A 62 " 0.077 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 61 " 0.064 5.00e-02 4.00e+02 9.60e-02 1.48e+01 pdb=" N PRO B 62 " -0.166 5.00e-02 4.00e+02 pdb=" CA PRO B 62 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO B 62 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 78 " -0.064 5.00e-02 4.00e+02 9.04e-02 1.31e+01 pdb=" N PRO B 79 " 0.156 5.00e-02 4.00e+02 pdb=" CA PRO B 79 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 79 " -0.048 5.00e-02 4.00e+02 ... (remaining 3073 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 335 2.67 - 3.23: 16490 3.23 - 3.79: 25380 3.79 - 4.34: 32535 4.34 - 4.90: 53677 Nonbonded interactions: 128417 Sorted by model distance: nonbonded pdb=" O LEU A 27 " pdb=" OG1 THR A 31 " model vdw 2.119 3.040 nonbonded pdb=" O GLY P 66 " pdb=" OG SER P 69 " model vdw 2.177 3.040 nonbonded pdb=" OE2 GLU C 18 " pdb=" NZ LYS K 570 " model vdw 2.204 3.120 nonbonded pdb=" O GLU A 643 " pdb=" NZ LYS A 646 " model vdw 2.204 3.120 nonbonded pdb=" O SER A 307 " pdb=" OG SER A 307 " model vdw 2.206 3.040 ... (remaining 128412 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 10 through 220 or resid 273 through 692 or resid 801)) selection = chain 'B' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.160 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: 0.040 Extract box with map and model: 0.830 Check model and map are aligned: 0.130 Set scattering table: 0.190 Process input model: 40.940 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6702 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 : 0.009 0.988 17837 Z= 0.258 Angle : 1.018 106.053 23992 Z= 0.467 Chirality : 0.043 0.361 2610 Planarity : 0.006 0.154 3076 Dihedral : 16.990 89.296 6923 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.52 % Allowed : 9.13 % Favored : 90.35 % Rotamer: Outliers : 0.26 % Allowed : 17.00 % Favored : 82.74 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.18), residues: 2124 helix: 0.38 (0.17), residues: 942 sheet: -0.54 (0.37), residues: 227 loop : -2.75 (0.18), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP C 7 HIS 0.016 0.001 HIS K 568 PHE 0.036 0.002 PHE P 331 TYR 0.024 0.001 TYR A 681 ARG 0.006 0.000 ARG C 231 Details of bonding type rmsd hydrogen bonds : bond 0.16501 ( 721) hydrogen bonds : angle 6.39074 ( 2061) covalent geometry : bond 0.00912 (17837) covalent geometry : angle 1.01771 (23992) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 327 time to evaluate : 1.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 80 GLN cc_start: 0.7757 (tt0) cc_final: 0.7459 (mt0) REVERT: B 114 MET cc_start: 0.7055 (tmm) cc_final: 0.6795 (mmm) outliers start: 5 outliers final: 4 residues processed: 328 average time/residue: 0.3517 time to fit residues: 166.0044 Evaluate side-chains 332 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 328 time to evaluate : 2.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 378 ARG Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 632 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 9.9990 chunk 160 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 54 optimal weight: 0.0670 chunk 108 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 166 optimal weight: 0.1980 chunk 64 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 192 optimal weight: 30.0000 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 GLN ** P 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 311 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.197320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.152234 restraints weight = 26745.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.151757 restraints weight = 20942.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.152863 restraints weight = 15835.317| |-----------------------------------------------------------------------------| r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6714 moved from start: 0.0788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.120 17837 Z= 0.134 Angle : 0.604 14.422 23992 Z= 0.318 Chirality : 0.041 0.199 2610 Planarity : 0.005 0.102 3076 Dihedral : 6.945 77.384 2413 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.42 % Allowed : 8.76 % Favored : 90.82 % Rotamer: Outliers : 2.03 % Allowed : 15.70 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.18), residues: 2124 helix: 0.67 (0.17), residues: 963 sheet: -0.68 (0.37), residues: 229 loop : -2.72 (0.18), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 7 HIS 0.007 0.001 HIS P 352 PHE 0.015 0.001 PHE A 32 TYR 0.021 0.001 TYR C 155 ARG 0.008 0.000 ARG C 231 Details of bonding type rmsd hydrogen bonds : bond 0.05101 ( 721) hydrogen bonds : angle 4.96046 ( 2061) covalent geometry : bond 0.00300 (17837) covalent geometry : angle 0.60422 (23992) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 342 time to evaluate : 1.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 ASN cc_start: 0.7877 (p0) cc_final: 0.7546 (p0) REVERT: A 330 ARG cc_start: 0.7205 (ptp-170) cc_final: 0.6908 (ptm160) REVERT: B 95 LYS cc_start: 0.7776 (mttm) cc_final: 0.7443 (mmtm) REVERT: B 364 ASP cc_start: 0.7338 (p0) cc_final: 0.7047 (p0) REVERT: C 105 MET cc_start: 0.6969 (tpt) cc_final: 0.6701 (tpt) REVERT: C 249 MET cc_start: 0.5998 (mmm) cc_final: 0.5530 (mmm) REVERT: P 351 MET cc_start: 0.1691 (ptp) cc_final: 0.1384 (ptp) outliers start: 39 outliers final: 26 residues processed: 359 average time/residue: 0.3591 time to fit residues: 185.8256 Evaluate side-chains 357 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 331 time to evaluate : 1.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 423 LYS Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 632 HIS Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain K residue 592 ILE Chi-restraints excluded: chain P residue 33 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 36 optimal weight: 2.9990 chunk 145 optimal weight: 20.0000 chunk 201 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 26 optimal weight: 0.0770 chunk 117 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 140 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 146 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 ASN P 145 GLN ** P 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 342 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.194513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.148752 restraints weight = 26737.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.148621 restraints weight = 20291.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.150348 restraints weight = 14834.383| |-----------------------------------------------------------------------------| r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6750 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17837 Z= 0.154 Angle : 0.597 12.999 23992 Z= 0.314 Chirality : 0.042 0.200 2610 Planarity : 0.004 0.081 3076 Dihedral : 6.943 89.606 2409 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.66 % Favored : 90.96 % Rotamer: Outliers : 3.64 % Allowed : 15.70 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.18), residues: 2124 helix: 0.78 (0.17), residues: 953 sheet: -0.71 (0.36), residues: 233 loop : -2.68 (0.18), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 7 HIS 0.009 0.001 HIS K 574 PHE 0.022 0.002 PHE A 32 TYR 0.020 0.001 TYR C 155 ARG 0.004 0.000 ARG K 575 Details of bonding type rmsd hydrogen bonds : bond 0.05137 ( 721) hydrogen bonds : angle 4.78017 ( 2061) covalent geometry : bond 0.00344 (17837) covalent geometry : angle 0.59692 (23992) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 359 time to evaluate : 2.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 SER cc_start: 0.8488 (p) cc_final: 0.8106 (p) REVERT: A 93 MET cc_start: 0.6965 (mmm) cc_final: 0.6749 (mtp) REVERT: A 114 MET cc_start: 0.7797 (mmm) cc_final: 0.7550 (mpp) REVERT: A 125 MET cc_start: 0.7584 (OUTLIER) cc_final: 0.7309 (mtm) REVERT: A 215 LEU cc_start: 0.7044 (OUTLIER) cc_final: 0.6817 (tt) REVERT: A 283 ASN cc_start: 0.7908 (p0) cc_final: 0.7481 (p0) REVERT: B 80 GLN cc_start: 0.7611 (OUTLIER) cc_final: 0.7330 (mt0) REVERT: B 95 LYS cc_start: 0.7840 (mttm) cc_final: 0.7640 (ttmm) REVERT: B 101 ASN cc_start: 0.7598 (m110) cc_final: 0.7337 (m-40) REVERT: B 364 ASP cc_start: 0.7388 (p0) cc_final: 0.7073 (p0) REVERT: B 641 LYS cc_start: 0.7667 (mmmm) cc_final: 0.7459 (mptt) REVERT: C 38 GLU cc_start: 0.7853 (tm-30) cc_final: 0.7426 (tm-30) REVERT: C 103 GLU cc_start: 0.5024 (OUTLIER) cc_final: 0.4789 (pm20) REVERT: C 105 MET cc_start: 0.7019 (tpt) cc_final: 0.6613 (tpt) REVERT: C 151 PHE cc_start: 0.3832 (OUTLIER) cc_final: 0.3209 (t80) REVERT: C 182 VAL cc_start: -0.4700 (OUTLIER) cc_final: -0.5112 (p) REVERT: C 249 MET cc_start: 0.6010 (mmm) cc_final: 0.5527 (mmm) REVERT: K 535 SER cc_start: 0.8700 (p) cc_final: 0.8427 (p) REVERT: K 575 ARG cc_start: 0.8052 (mmm160) cc_final: 0.7719 (mmm160) REVERT: P 351 MET cc_start: 0.1636 (ptp) cc_final: 0.1428 (ptp) REVERT: P 425 ARG cc_start: -0.0694 (OUTLIER) cc_final: -0.1610 (tmm160) outliers start: 70 outliers final: 44 residues processed: 395 average time/residue: 0.3480 time to fit residues: 201.5497 Evaluate side-chains 401 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 350 time to evaluate : 2.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 378 ARG Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 628 ILE Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 80 GLN Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 632 HIS Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 151 PHE Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain K residue 536 SER Chi-restraints excluded: chain K residue 546 THR Chi-restraints excluded: chain K residue 571 SER Chi-restraints excluded: chain K residue 588 LEU Chi-restraints excluded: chain K residue 592 ILE Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 425 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 101 optimal weight: 0.3980 chunk 47 optimal weight: 0.7980 chunk 181 optimal weight: 9.9990 chunk 133 optimal weight: 50.0000 chunk 82 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 89 optimal weight: 0.7980 chunk 129 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 640 GLN C 146 GLN C 211 HIS ** P 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.197466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.152047 restraints weight = 26651.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.150849 restraints weight = 22522.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.150930 restraints weight = 16934.831| |-----------------------------------------------------------------------------| r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6775 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17837 Z= 0.135 Angle : 0.584 11.171 23992 Z= 0.306 Chirality : 0.041 0.200 2610 Planarity : 0.004 0.076 3076 Dihedral : 6.576 69.967 2409 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.71 % Favored : 90.91 % Rotamer: Outliers : 3.33 % Allowed : 17.83 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.18), residues: 2124 helix: 0.88 (0.17), residues: 955 sheet: -0.71 (0.36), residues: 233 loop : -2.69 (0.18), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 114 HIS 0.007 0.001 HIS B 320 PHE 0.016 0.001 PHE A 32 TYR 0.019 0.001 TYR C 155 ARG 0.003 0.000 ARG A 330 Details of bonding type rmsd hydrogen bonds : bond 0.04569 ( 721) hydrogen bonds : angle 4.61823 ( 2061) covalent geometry : bond 0.00296 (17837) covalent geometry : angle 0.58449 (23992) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 346 time to evaluate : 3.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 SER cc_start: 0.8525 (p) cc_final: 0.8172 (p) REVERT: A 125 MET cc_start: 0.7568 (OUTLIER) cc_final: 0.7288 (mtm) REVERT: A 215 LEU cc_start: 0.7056 (OUTLIER) cc_final: 0.6808 (tt) REVERT: A 283 ASN cc_start: 0.7864 (p0) cc_final: 0.7611 (p0) REVERT: A 330 ARG cc_start: 0.7197 (ptp-170) cc_final: 0.6983 (ptm160) REVERT: A 519 GLU cc_start: 0.7301 (tp30) cc_final: 0.7100 (tp30) REVERT: B 80 GLN cc_start: 0.7820 (OUTLIER) cc_final: 0.7555 (mt0) REVERT: B 95 LYS cc_start: 0.7835 (mttm) cc_final: 0.7505 (ttmm) REVERT: B 101 ASN cc_start: 0.7510 (m110) cc_final: 0.7129 (m-40) REVERT: B 364 ASP cc_start: 0.7225 (p0) cc_final: 0.6856 (p0) REVERT: B 539 GLU cc_start: 0.6061 (pm20) cc_final: 0.5704 (pm20) REVERT: B 641 LYS cc_start: 0.7660 (mmmm) cc_final: 0.7409 (mptt) REVERT: C 38 GLU cc_start: 0.7868 (tm-30) cc_final: 0.7440 (tm-30) REVERT: C 103 GLU cc_start: 0.4962 (OUTLIER) cc_final: 0.4737 (pm20) REVERT: C 105 MET cc_start: 0.6976 (tpt) cc_final: 0.6549 (tpt) REVERT: C 151 PHE cc_start: 0.3678 (OUTLIER) cc_final: 0.3050 (t80) REVERT: C 182 VAL cc_start: -0.4730 (OUTLIER) cc_final: -0.5117 (p) REVERT: C 249 MET cc_start: 0.6059 (mmm) cc_final: 0.5580 (mmm) REVERT: P 31 LEU cc_start: -0.1299 (OUTLIER) cc_final: -0.1847 (mp) REVERT: P 425 ARG cc_start: -0.0542 (OUTLIER) cc_final: -0.1441 (tmm160) outliers start: 64 outliers final: 48 residues processed: 379 average time/residue: 0.3884 time to fit residues: 213.7165 Evaluate side-chains 395 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 339 time to evaluate : 2.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 378 ARG Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 628 ILE Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 640 GLN Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 80 GLN Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 423 LYS Chi-restraints excluded: chain B residue 434 SER Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 632 HIS Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 151 PHE Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain K residue 536 SER Chi-restraints excluded: chain K residue 546 THR Chi-restraints excluded: chain K residue 571 SER Chi-restraints excluded: chain K residue 588 LEU Chi-restraints excluded: chain K residue 592 ILE Chi-restraints excluded: chain K residue 689 MET Chi-restraints excluded: chain K residue 706 LEU Chi-restraints excluded: chain P residue 31 LEU Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 425 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 129 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 115 optimal weight: 0.0170 chunk 192 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 210 optimal weight: 2.9990 chunk 163 optimal weight: 7.9990 chunk 24 optimal weight: 0.9980 chunk 85 optimal weight: 0.7980 overall best weight: 1.1020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 20 HIS ** P 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.195472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.151337 restraints weight = 26965.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.148419 restraints weight = 21569.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.149774 restraints weight = 17396.661| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17837 Z= 0.168 Angle : 0.614 12.519 23992 Z= 0.321 Chirality : 0.042 0.184 2610 Planarity : 0.004 0.067 3076 Dihedral : 6.473 59.139 2409 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.99 % Favored : 90.63 % Rotamer: Outliers : 4.42 % Allowed : 17.05 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.18), residues: 2124 helix: 0.79 (0.17), residues: 964 sheet: -0.69 (0.36), residues: 231 loop : -2.73 (0.18), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 7 HIS 0.008 0.001 HIS B 320 PHE 0.020 0.002 PHE A 32 TYR 0.019 0.001 TYR C 155 ARG 0.003 0.000 ARG A 639 Details of bonding type rmsd hydrogen bonds : bond 0.05053 ( 721) hydrogen bonds : angle 4.63856 ( 2061) covalent geometry : bond 0.00382 (17837) covalent geometry : angle 0.61417 (23992) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 353 time to evaluate : 3.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 SER cc_start: 0.8484 (p) cc_final: 0.8149 (p) REVERT: A 215 LEU cc_start: 0.7127 (OUTLIER) cc_final: 0.6906 (tt) REVERT: A 275 LYS cc_start: 0.7128 (pptt) cc_final: 0.6646 (pttt) REVERT: A 283 ASN cc_start: 0.7784 (p0) cc_final: 0.7572 (p0) REVERT: A 330 ARG cc_start: 0.7239 (ptp-170) cc_final: 0.6916 (ptm160) REVERT: A 401 LEU cc_start: 0.6108 (OUTLIER) cc_final: 0.5755 (mp) REVERT: B 80 GLN cc_start: 0.7678 (OUTLIER) cc_final: 0.7375 (mt0) REVERT: B 95 LYS cc_start: 0.7902 (mttm) cc_final: 0.7584 (ttmm) REVERT: B 101 ASN cc_start: 0.7507 (m110) cc_final: 0.7047 (m-40) REVERT: B 364 ASP cc_start: 0.7328 (p0) cc_final: 0.6956 (p0) REVERT: B 641 LYS cc_start: 0.7638 (mmmm) cc_final: 0.7411 (mptt) REVERT: C 38 GLU cc_start: 0.7849 (tm-30) cc_final: 0.7455 (tm-30) REVERT: C 103 GLU cc_start: 0.4944 (OUTLIER) cc_final: 0.4719 (pm20) REVERT: C 105 MET cc_start: 0.6947 (tpt) cc_final: 0.6290 (tpt) REVERT: C 108 LYS cc_start: 0.5103 (OUTLIER) cc_final: 0.4736 (tmtt) REVERT: C 151 PHE cc_start: 0.3593 (OUTLIER) cc_final: 0.2983 (t80) REVERT: C 182 VAL cc_start: -0.4681 (OUTLIER) cc_final: -0.5085 (p) REVERT: C 249 MET cc_start: 0.6066 (mmm) cc_final: 0.5621 (mmm) REVERT: K 573 ILE cc_start: 0.7763 (mm) cc_final: 0.7555 (mm) REVERT: P 31 LEU cc_start: -0.1422 (OUTLIER) cc_final: -0.1963 (mp) REVERT: P 107 MET cc_start: 0.7444 (mmp) cc_final: 0.6622 (mmp) REVERT: P 425 ARG cc_start: -0.0503 (OUTLIER) cc_final: -0.1270 (tmm160) outliers start: 85 outliers final: 57 residues processed: 401 average time/residue: 0.4650 time to fit residues: 277.4215 Evaluate side-chains 413 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 347 time to evaluate : 4.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 378 ARG Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 628 ILE Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 80 GLN Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 423 LYS Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 632 HIS Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 151 PHE Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain K residue 527 ILE Chi-restraints excluded: chain K residue 536 SER Chi-restraints excluded: chain K residue 537 LEU Chi-restraints excluded: chain K residue 546 THR Chi-restraints excluded: chain K residue 567 LEU Chi-restraints excluded: chain K residue 571 SER Chi-restraints excluded: chain K residue 588 LEU Chi-restraints excluded: chain K residue 592 ILE Chi-restraints excluded: chain K residue 706 LEU Chi-restraints excluded: chain P residue 31 LEU Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 425 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 57 optimal weight: 2.9990 chunk 119 optimal weight: 0.0870 chunk 138 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 145 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 207 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 ASN ** B 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.197314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.153167 restraints weight = 26919.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.151331 restraints weight = 20214.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.152871 restraints weight = 16512.904| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6724 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17837 Z= 0.129 Angle : 0.605 11.618 23992 Z= 0.313 Chirality : 0.041 0.183 2610 Planarity : 0.004 0.064 3076 Dihedral : 6.157 59.778 2409 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.33 % Allowed : 8.43 % Favored : 91.24 % Rotamer: Outliers : 4.21 % Allowed : 18.24 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.18), residues: 2124 helix: 0.92 (0.17), residues: 956 sheet: -0.61 (0.35), residues: 235 loop : -2.71 (0.18), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 114 HIS 0.006 0.001 HIS B 320 PHE 0.016 0.001 PHE B 15 TYR 0.018 0.001 TYR C 155 ARG 0.003 0.000 ARG A 639 Details of bonding type rmsd hydrogen bonds : bond 0.04366 ( 721) hydrogen bonds : angle 4.51073 ( 2061) covalent geometry : bond 0.00286 (17837) covalent geometry : angle 0.60534 (23992) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 344 time to evaluate : 5.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 SER cc_start: 0.8536 (p) cc_final: 0.8216 (p) REVERT: A 215 LEU cc_start: 0.7190 (OUTLIER) cc_final: 0.6973 (tt) REVERT: A 275 LYS cc_start: 0.7184 (pptt) cc_final: 0.6693 (pttt) REVERT: A 330 ARG cc_start: 0.7163 (ptp-170) cc_final: 0.6878 (ptm160) REVERT: A 401 LEU cc_start: 0.5924 (OUTLIER) cc_final: 0.5647 (mp) REVERT: B 80 GLN cc_start: 0.7552 (OUTLIER) cc_final: 0.7249 (mt0) REVERT: B 95 LYS cc_start: 0.7909 (mttm) cc_final: 0.7611 (ttmm) REVERT: B 101 ASN cc_start: 0.7724 (m-40) cc_final: 0.7346 (m110) REVERT: B 364 ASP cc_start: 0.7261 (p0) cc_final: 0.6887 (p0) REVERT: B 489 GLU cc_start: 0.7528 (pm20) cc_final: 0.7312 (pm20) REVERT: C 38 GLU cc_start: 0.7899 (tm-30) cc_final: 0.7458 (tm-30) REVERT: C 103 GLU cc_start: 0.4982 (OUTLIER) cc_final: 0.4748 (pm20) REVERT: C 105 MET cc_start: 0.6969 (tpt) cc_final: 0.6340 (tpt) REVERT: C 108 LYS cc_start: 0.5246 (OUTLIER) cc_final: 0.4894 (tmtt) REVERT: C 151 PHE cc_start: 0.3789 (OUTLIER) cc_final: 0.3144 (t80) REVERT: C 182 VAL cc_start: -0.4836 (OUTLIER) cc_final: -0.5193 (p) REVERT: C 249 MET cc_start: 0.5960 (mmm) cc_final: 0.5472 (mmm) REVERT: K 575 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7777 (mtp-110) REVERT: K 693 MET cc_start: 0.6895 (mtm) cc_final: 0.6695 (mtm) REVERT: P 31 LEU cc_start: -0.1442 (OUTLIER) cc_final: -0.1881 (mp) REVERT: P 107 MET cc_start: 0.7283 (mmp) cc_final: 0.6457 (mmp) REVERT: P 425 ARG cc_start: -0.1167 (OUTLIER) cc_final: -0.1822 (tmm160) outliers start: 81 outliers final: 56 residues processed: 384 average time/residue: 0.4661 time to fit residues: 264.8801 Evaluate side-chains 406 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 340 time to evaluate : 2.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 378 ARG Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 628 ILE Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 80 GLN Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 423 LYS Chi-restraints excluded: chain B residue 434 SER Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 632 HIS Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 151 PHE Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain K residue 536 SER Chi-restraints excluded: chain K residue 537 LEU Chi-restraints excluded: chain K residue 546 THR Chi-restraints excluded: chain K residue 567 LEU Chi-restraints excluded: chain K residue 571 SER Chi-restraints excluded: chain K residue 575 ARG Chi-restraints excluded: chain K residue 588 LEU Chi-restraints excluded: chain K residue 592 ILE Chi-restraints excluded: chain K residue 706 LEU Chi-restraints excluded: chain P residue 31 LEU Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 425 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 32 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 148 optimal weight: 8.9990 chunk 50 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 123 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.196645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.150956 restraints weight = 26695.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.150730 restraints weight = 21383.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.151603 restraints weight = 16542.082| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6778 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17837 Z= 0.144 Angle : 0.617 10.974 23992 Z= 0.319 Chirality : 0.041 0.178 2610 Planarity : 0.004 0.057 3076 Dihedral : 6.108 63.101 2409 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.33 % Allowed : 8.76 % Favored : 90.91 % Rotamer: Outliers : 4.26 % Allowed : 18.35 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.18), residues: 2124 helix: 0.92 (0.17), residues: 952 sheet: -0.49 (0.36), residues: 218 loop : -2.71 (0.18), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 114 HIS 0.007 0.001 HIS B 320 PHE 0.016 0.001 PHE B 15 TYR 0.017 0.001 TYR C 155 ARG 0.003 0.000 ARG A 456 Details of bonding type rmsd hydrogen bonds : bond 0.04557 ( 721) hydrogen bonds : angle 4.50627 ( 2061) covalent geometry : bond 0.00325 (17837) covalent geometry : angle 0.61679 (23992) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 346 time to evaluate : 4.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 SER cc_start: 0.8504 (p) cc_final: 0.8131 (p) REVERT: A 275 LYS cc_start: 0.7272 (pptt) cc_final: 0.6906 (ptpt) REVERT: A 330 ARG cc_start: 0.7240 (ptp-170) cc_final: 0.6920 (ptm160) REVERT: A 338 ARG cc_start: 0.7890 (ttm110) cc_final: 0.7473 (mtm110) REVERT: A 401 LEU cc_start: 0.5980 (OUTLIER) cc_final: 0.5727 (mp) REVERT: A 639 ARG cc_start: 0.7719 (ptm-80) cc_final: 0.7251 (ptm160) REVERT: A 648 ASP cc_start: 0.7343 (t0) cc_final: 0.6962 (t0) REVERT: B 80 GLN cc_start: 0.7613 (OUTLIER) cc_final: 0.7296 (mt0) REVERT: B 95 LYS cc_start: 0.7930 (mttm) cc_final: 0.7616 (ttmm) REVERT: B 101 ASN cc_start: 0.7826 (m-40) cc_final: 0.7456 (m110) REVERT: B 364 ASP cc_start: 0.7360 (p0) cc_final: 0.6972 (p0) REVERT: B 539 GLU cc_start: 0.5932 (pm20) cc_final: 0.5718 (pm20) REVERT: C 38 GLU cc_start: 0.7881 (tm-30) cc_final: 0.7451 (tm-30) REVERT: C 103 GLU cc_start: 0.4960 (OUTLIER) cc_final: 0.4724 (pm20) REVERT: C 105 MET cc_start: 0.6975 (tpt) cc_final: 0.6176 (tpt) REVERT: C 108 LYS cc_start: 0.5245 (OUTLIER) cc_final: 0.4903 (tmmt) REVERT: C 151 PHE cc_start: 0.3638 (OUTLIER) cc_final: 0.2993 (t80) REVERT: C 182 VAL cc_start: -0.4733 (OUTLIER) cc_final: -0.5068 (p) REVERT: C 249 MET cc_start: 0.6021 (mmm) cc_final: 0.5586 (mmm) REVERT: K 573 ILE cc_start: 0.7775 (OUTLIER) cc_final: 0.7544 (mm) REVERT: K 575 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7799 (mtp-110) REVERT: K 623 GLU cc_start: 0.7441 (mp0) cc_final: 0.6974 (pm20) REVERT: K 640 TYR cc_start: 0.7351 (t80) cc_final: 0.7004 (t80) REVERT: K 693 MET cc_start: 0.7026 (mtm) cc_final: 0.6799 (mtm) REVERT: P 31 LEU cc_start: -0.1500 (OUTLIER) cc_final: -0.1974 (mp) REVERT: P 107 MET cc_start: 0.7378 (mmp) cc_final: 0.6594 (mmp) REVERT: P 141 LYS cc_start: 0.7596 (mttm) cc_final: 0.7389 (mttm) REVERT: P 425 ARG cc_start: -0.1302 (OUTLIER) cc_final: -0.1808 (tmm160) outliers start: 82 outliers final: 60 residues processed: 386 average time/residue: 0.4398 time to fit residues: 250.1347 Evaluate side-chains 408 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 338 time to evaluate : 2.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 378 ARG Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 628 ILE Chi-restraints excluded: chain A residue 640 GLN Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 80 GLN Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 434 SER Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 632 HIS Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 151 PHE Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain K residue 527 ILE Chi-restraints excluded: chain K residue 536 SER Chi-restraints excluded: chain K residue 537 LEU Chi-restraints excluded: chain K residue 546 THR Chi-restraints excluded: chain K residue 567 LEU Chi-restraints excluded: chain K residue 571 SER Chi-restraints excluded: chain K residue 573 ILE Chi-restraints excluded: chain K residue 575 ARG Chi-restraints excluded: chain K residue 588 LEU Chi-restraints excluded: chain K residue 592 ILE Chi-restraints excluded: chain K residue 706 LEU Chi-restraints excluded: chain P residue 31 LEU Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 425 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 4 optimal weight: 0.3980 chunk 115 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 168 optimal weight: 0.8980 chunk 174 optimal weight: 10.0000 chunk 107 optimal weight: 0.9990 chunk 185 optimal weight: 8.9990 chunk 33 optimal weight: 0.4980 chunk 109 optimal weight: 0.0980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 36 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.198697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.151766 restraints weight = 26662.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.152204 restraints weight = 20658.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.153445 restraints weight = 15987.732| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6792 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17837 Z= 0.118 Angle : 0.601 10.708 23992 Z= 0.309 Chirality : 0.041 0.207 2610 Planarity : 0.004 0.057 3076 Dihedral : 5.942 67.693 2409 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.33 % Allowed : 8.05 % Favored : 91.62 % Rotamer: Outliers : 3.74 % Allowed : 19.07 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.18), residues: 2124 helix: 0.99 (0.18), residues: 952 sheet: -0.47 (0.37), residues: 216 loop : -2.66 (0.18), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 114 HIS 0.006 0.001 HIS P 352 PHE 0.013 0.001 PHE C 151 TYR 0.018 0.001 TYR C 155 ARG 0.003 0.000 ARG A 475 Details of bonding type rmsd hydrogen bonds : bond 0.04016 ( 721) hydrogen bonds : angle 4.36743 ( 2061) covalent geometry : bond 0.00262 (17837) covalent geometry : angle 0.60082 (23992) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 326 time to evaluate : 1.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 SER cc_start: 0.8532 (p) cc_final: 0.8164 (p) REVERT: A 125 MET cc_start: 0.7517 (OUTLIER) cc_final: 0.7300 (mtm) REVERT: A 275 LYS cc_start: 0.7286 (pptt) cc_final: 0.6939 (ptpt) REVERT: A 330 ARG cc_start: 0.7173 (ptp-170) cc_final: 0.6964 (ptm160) REVERT: A 401 LEU cc_start: 0.5774 (OUTLIER) cc_final: 0.5491 (mp) REVERT: A 466 MET cc_start: 0.6982 (OUTLIER) cc_final: 0.6566 (tpp) REVERT: A 639 ARG cc_start: 0.7583 (ptm-80) cc_final: 0.7313 (ptm160) REVERT: A 648 ASP cc_start: 0.7337 (t0) cc_final: 0.6930 (t0) REVERT: B 80 GLN cc_start: 0.7549 (OUTLIER) cc_final: 0.7236 (mt0) REVERT: B 95 LYS cc_start: 0.7890 (mttm) cc_final: 0.7577 (ttmm) REVERT: B 101 ASN cc_start: 0.7735 (m-40) cc_final: 0.7314 (m110) REVERT: B 177 ARG cc_start: 0.7786 (ptt-90) cc_final: 0.7075 (ptt-90) REVERT: B 364 ASP cc_start: 0.7324 (p0) cc_final: 0.6935 (p0) REVERT: B 406 LYS cc_start: 0.6449 (OUTLIER) cc_final: 0.6063 (mttm) REVERT: B 603 GLU cc_start: 0.6445 (mt-10) cc_final: 0.6235 (mt-10) REVERT: C 38 GLU cc_start: 0.7855 (tm-30) cc_final: 0.7415 (tm-30) REVERT: C 105 MET cc_start: 0.6955 (tpt) cc_final: 0.6215 (tpt) REVERT: C 108 LYS cc_start: 0.5251 (OUTLIER) cc_final: 0.4908 (tmmt) REVERT: C 151 PHE cc_start: 0.3508 (OUTLIER) cc_final: 0.2889 (t80) REVERT: C 182 VAL cc_start: -0.4708 (OUTLIER) cc_final: -0.5030 (p) REVERT: C 249 MET cc_start: 0.6095 (mmm) cc_final: 0.5647 (mmm) REVERT: K 573 ILE cc_start: 0.7737 (OUTLIER) cc_final: 0.7486 (mm) REVERT: K 575 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7792 (mtp-110) REVERT: K 640 TYR cc_start: 0.7321 (t80) cc_final: 0.7007 (t80) REVERT: K 693 MET cc_start: 0.7039 (mtm) cc_final: 0.6832 (mtm) REVERT: P 107 MET cc_start: 0.7410 (mmp) cc_final: 0.6635 (mmp) REVERT: P 141 LYS cc_start: 0.7609 (mttm) cc_final: 0.7385 (mttm) REVERT: P 384 LEU cc_start: -0.0766 (OUTLIER) cc_final: -0.1065 (mt) REVERT: P 425 ARG cc_start: -0.1160 (OUTLIER) cc_final: -0.1733 (tmm160) outliers start: 72 outliers final: 52 residues processed: 364 average time/residue: 0.3455 time to fit residues: 182.4564 Evaluate side-chains 386 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 322 time to evaluate : 1.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 378 ARG Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 80 GLN Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain B residue 434 SER Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 632 HIS Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 151 PHE Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain K residue 537 LEU Chi-restraints excluded: chain K residue 546 THR Chi-restraints excluded: chain K residue 567 LEU Chi-restraints excluded: chain K residue 573 ILE Chi-restraints excluded: chain K residue 575 ARG Chi-restraints excluded: chain K residue 588 LEU Chi-restraints excluded: chain K residue 592 ILE Chi-restraints excluded: chain K residue 706 LEU Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 358 GLU Chi-restraints excluded: chain P residue 384 LEU Chi-restraints excluded: chain P residue 425 ARG Chi-restraints excluded: chain P residue 445 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 194 optimal weight: 1.9990 chunk 176 optimal weight: 10.0000 chunk 92 optimal weight: 0.5980 chunk 54 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 143 optimal weight: 0.9980 chunk 140 optimal weight: 30.0000 chunk 43 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 HIS ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.195913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.149083 restraints weight = 26758.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.151512 restraints weight = 17044.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.150600 restraints weight = 13319.454| |-----------------------------------------------------------------------------| r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6831 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17837 Z= 0.166 Angle : 0.648 10.680 23992 Z= 0.334 Chirality : 0.042 0.187 2610 Planarity : 0.004 0.052 3076 Dihedral : 6.108 64.962 2409 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.33 % Allowed : 8.85 % Favored : 90.82 % Rotamer: Outliers : 3.69 % Allowed : 19.80 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.18), residues: 2124 helix: 0.86 (0.17), residues: 968 sheet: -0.47 (0.36), residues: 218 loop : -2.75 (0.18), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 7 HIS 0.008 0.001 HIS B 320 PHE 0.018 0.002 PHE A 32 TYR 0.017 0.001 TYR C 155 ARG 0.004 0.000 ARG B 639 Details of bonding type rmsd hydrogen bonds : bond 0.04840 ( 721) hydrogen bonds : angle 4.49513 ( 2061) covalent geometry : bond 0.00381 (17837) covalent geometry : angle 0.64773 (23992) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 333 time to evaluate : 2.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 SER cc_start: 0.8544 (p) cc_final: 0.8163 (p) REVERT: A 80 GLN cc_start: 0.7338 (OUTLIER) cc_final: 0.6869 (mp10) REVERT: A 99 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.8223 (pt) REVERT: A 125 MET cc_start: 0.7503 (OUTLIER) cc_final: 0.7298 (mtm) REVERT: A 275 LYS cc_start: 0.7386 (pptt) cc_final: 0.6993 (ptpt) REVERT: A 338 ARG cc_start: 0.7861 (ttm110) cc_final: 0.7556 (mtm110) REVERT: A 401 LEU cc_start: 0.5990 (OUTLIER) cc_final: 0.5668 (mp) REVERT: A 466 MET cc_start: 0.7016 (OUTLIER) cc_final: 0.6597 (tpp) REVERT: A 639 ARG cc_start: 0.7768 (ptm-80) cc_final: 0.7289 (ptm160) REVERT: A 648 ASP cc_start: 0.7387 (t0) cc_final: 0.7133 (t0) REVERT: B 80 GLN cc_start: 0.7604 (OUTLIER) cc_final: 0.7292 (mt0) REVERT: B 95 LYS cc_start: 0.7903 (mttm) cc_final: 0.7576 (ttmm) REVERT: B 101 ASN cc_start: 0.7800 (m-40) cc_final: 0.7381 (m110) REVERT: B 364 ASP cc_start: 0.7355 (p0) cc_final: 0.6956 (p0) REVERT: B 406 LYS cc_start: 0.6709 (OUTLIER) cc_final: 0.6345 (mttm) REVERT: B 606 MET cc_start: 0.7993 (tpp) cc_final: 0.7575 (mpp) REVERT: C 38 GLU cc_start: 0.7831 (tm-30) cc_final: 0.7408 (tm-30) REVERT: C 103 GLU cc_start: 0.4991 (pm20) cc_final: 0.4755 (pm20) REVERT: C 105 MET cc_start: 0.6981 (tpt) cc_final: 0.6178 (tpt) REVERT: C 108 LYS cc_start: 0.5172 (OUTLIER) cc_final: 0.4853 (tmmt) REVERT: C 151 PHE cc_start: 0.3610 (OUTLIER) cc_final: 0.2956 (t80) REVERT: C 182 VAL cc_start: -0.4682 (OUTLIER) cc_final: -0.4979 (p) REVERT: C 249 MET cc_start: 0.6096 (mmm) cc_final: 0.5658 (mmm) REVERT: K 573 ILE cc_start: 0.7781 (OUTLIER) cc_final: 0.7529 (mm) REVERT: K 575 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7836 (mtp-110) REVERT: K 623 GLU cc_start: 0.7489 (mp0) cc_final: 0.7005 (pm20) REVERT: K 693 MET cc_start: 0.7133 (mtm) cc_final: 0.6903 (mtm) REVERT: P 107 MET cc_start: 0.7382 (mmp) cc_final: 0.6620 (mmp) REVERT: P 141 LYS cc_start: 0.7633 (mttm) cc_final: 0.7417 (mttm) outliers start: 71 outliers final: 53 residues processed: 371 average time/residue: 0.4605 time to fit residues: 250.1021 Evaluate side-chains 394 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 329 time to evaluate : 3.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 378 ARG Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 628 ILE Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 80 GLN Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain B residue 423 LYS Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 632 HIS Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 151 PHE Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain K residue 536 SER Chi-restraints excluded: chain K residue 560 THR Chi-restraints excluded: chain K residue 573 ILE Chi-restraints excluded: chain K residue 575 ARG Chi-restraints excluded: chain K residue 588 LEU Chi-restraints excluded: chain K residue 592 ILE Chi-restraints excluded: chain K residue 706 LEU Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 358 GLU Chi-restraints excluded: chain P residue 445 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 93 optimal weight: 1.9990 chunk 29 optimal weight: 0.3980 chunk 87 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 23 optimal weight: 0.3980 chunk 116 optimal weight: 0.9990 chunk 175 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 184 optimal weight: 0.0570 chunk 50 optimal weight: 0.9980 chunk 190 optimal weight: 4.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 HIS ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.195858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.149489 restraints weight = 26820.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.150993 restraints weight = 17669.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.151064 restraints weight = 13789.270| |-----------------------------------------------------------------------------| r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6777 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17837 Z= 0.124 Angle : 0.620 10.705 23992 Z= 0.318 Chirality : 0.041 0.183 2610 Planarity : 0.004 0.054 3076 Dihedral : 5.929 66.918 2409 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.33 % Allowed : 8.15 % Favored : 91.53 % Rotamer: Outliers : 3.22 % Allowed : 20.53 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.18), residues: 2124 helix: 1.03 (0.18), residues: 954 sheet: -0.43 (0.37), residues: 218 loop : -2.65 (0.18), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 114 HIS 0.005 0.001 HIS B 320 PHE 0.013 0.001 PHE B 15 TYR 0.017 0.001 TYR C 155 ARG 0.004 0.000 ARG B 639 Details of bonding type rmsd hydrogen bonds : bond 0.04068 ( 721) hydrogen bonds : angle 4.36611 ( 2061) covalent geometry : bond 0.00279 (17837) covalent geometry : angle 0.62043 (23992) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 320 time to evaluate : 2.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 SER cc_start: 0.8537 (p) cc_final: 0.8189 (p) REVERT: A 80 GLN cc_start: 0.7284 (OUTLIER) cc_final: 0.6802 (mp10) REVERT: A 99 ILE cc_start: 0.8377 (OUTLIER) cc_final: 0.8153 (pt) REVERT: A 275 LYS cc_start: 0.7356 (pptt) cc_final: 0.6928 (ptpt) REVERT: A 330 ARG cc_start: 0.7260 (ptp-170) cc_final: 0.6994 (ptm160) REVERT: A 338 ARG cc_start: 0.7785 (ttm110) cc_final: 0.7471 (mtm110) REVERT: A 401 LEU cc_start: 0.5757 (OUTLIER) cc_final: 0.5487 (mp) REVERT: A 466 MET cc_start: 0.7032 (OUTLIER) cc_final: 0.6685 (tpp) REVERT: A 639 ARG cc_start: 0.7734 (ptm-80) cc_final: 0.7031 (ptm160) REVERT: A 648 ASP cc_start: 0.7359 (t0) cc_final: 0.6962 (t0) REVERT: B 80 GLN cc_start: 0.7532 (OUTLIER) cc_final: 0.7215 (mt0) REVERT: B 95 LYS cc_start: 0.7847 (mttm) cc_final: 0.7547 (ttmm) REVERT: B 101 ASN cc_start: 0.7799 (m-40) cc_final: 0.7404 (m110) REVERT: B 364 ASP cc_start: 0.7325 (p0) cc_final: 0.6923 (p0) REVERT: B 406 LYS cc_start: 0.6528 (OUTLIER) cc_final: 0.6215 (mttm) REVERT: B 606 MET cc_start: 0.7828 (tpp) cc_final: 0.7450 (mpp) REVERT: C 38 GLU cc_start: 0.7851 (tm-30) cc_final: 0.7422 (tm-30) REVERT: C 103 GLU cc_start: 0.4992 (pm20) cc_final: 0.4729 (pm20) REVERT: C 105 MET cc_start: 0.6965 (tpt) cc_final: 0.6230 (tpt) REVERT: C 108 LYS cc_start: 0.5302 (OUTLIER) cc_final: 0.4941 (tmmt) REVERT: C 151 PHE cc_start: 0.3540 (OUTLIER) cc_final: 0.2906 (t80) REVERT: C 182 VAL cc_start: -0.4737 (OUTLIER) cc_final: -0.5036 (p) REVERT: C 249 MET cc_start: 0.6068 (mmm) cc_final: 0.5637 (mmm) REVERT: K 573 ILE cc_start: 0.7736 (OUTLIER) cc_final: 0.7481 (mm) REVERT: K 575 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7801 (mtp-110) REVERT: K 640 TYR cc_start: 0.7344 (t80) cc_final: 0.7002 (t80) REVERT: K 693 MET cc_start: 0.7090 (mtm) cc_final: 0.6866 (mtm) REVERT: K 706 LEU cc_start: 0.6868 (OUTLIER) cc_final: 0.6651 (mm) REVERT: P 107 MET cc_start: 0.7390 (mmp) cc_final: 0.6627 (mmp) REVERT: P 141 LYS cc_start: 0.7630 (mttm) cc_final: 0.7415 (mttm) outliers start: 62 outliers final: 44 residues processed: 356 average time/residue: 0.5115 time to fit residues: 269.3018 Evaluate side-chains 374 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 318 time to evaluate : 2.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 378 ARG Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 628 ILE Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 80 GLN Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 632 HIS Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 151 PHE Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain K residue 536 SER Chi-restraints excluded: chain K residue 573 ILE Chi-restraints excluded: chain K residue 575 ARG Chi-restraints excluded: chain K residue 588 LEU Chi-restraints excluded: chain K residue 592 ILE Chi-restraints excluded: chain K residue 648 GLU Chi-restraints excluded: chain K residue 706 LEU Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 358 GLU Chi-restraints excluded: chain P residue 445 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 199 optimal weight: 6.9990 chunk 52 optimal weight: 0.4980 chunk 44 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 211 optimal weight: 0.1980 chunk 46 optimal weight: 0.3980 chunk 176 optimal weight: 6.9990 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 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.196671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.151064 restraints weight = 26711.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.150578 restraints weight = 18252.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.151903 restraints weight = 15388.020| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17837 Z= 0.144 Angle : 0.640 10.628 23992 Z= 0.328 Chirality : 0.041 0.176 2610 Planarity : 0.004 0.058 3076 Dihedral : 5.885 65.950 2407 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.33 % Allowed : 8.85 % Favored : 90.82 % Rotamer: Outliers : 3.33 % Allowed : 20.74 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.18), residues: 2124 helix: 1.01 (0.17), residues: 957 sheet: -0.42 (0.37), residues: 218 loop : -2.66 (0.18), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 114 HIS 0.007 0.001 HIS B 320 PHE 0.015 0.001 PHE A 32 TYR 0.017 0.001 TYR C 155 ARG 0.004 0.000 ARG B 639 Details of bonding type rmsd hydrogen bonds : bond 0.04456 ( 721) hydrogen bonds : angle 4.40220 ( 2061) covalent geometry : bond 0.00328 (17837) covalent geometry : angle 0.64002 (23992) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7519.84 seconds wall clock time: 137 minutes 19.01 seconds (8239.01 seconds total)