Starting phenix.real_space_refine on Thu Mar 5 00:38:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zr5_14883/03_2026/7zr5_14883.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zr5_14883/03_2026/7zr5_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_14883/03_2026/7zr5_14883.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zr5_14883/03_2026/7zr5_14883.map" model { file = "/net/cci-nas-00/data/ceres_data/7zr5_14883/03_2026/7zr5_14883.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zr5_14883/03_2026/7zr5_14883.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 4.17, per 1000 atoms: 0.24 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: 1.54 Conformation dependent library (CDL) restraints added in 741.2 milliseconds 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: 0.58 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: 2.88 Time building geometry restraints manager: 2.04 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 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: 3.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.760 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.040 ------------------------------------------------------------------------------- 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 : 9.66 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.006 0.000 ARG C 231 TYR 0.024 0.001 TYR A 681 PHE 0.036 0.002 PHE P 331 TRP 0.042 0.002 TRP C 7 HIS 0.016 0.001 HIS K 568 Details of bonding type rmsd covalent geometry : bond 0.00912 (17837) covalent geometry : angle 1.01771 (23992) hydrogen bonds : bond 0.16501 ( 721) hydrogen bonds : angle 6.39074 ( 2061) *********************** 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 : 0.583 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: 0.7756 (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: 0.1535 time to fit residues: 72.8987 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 : 0.553 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.6980 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 9.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.4361 r_free = 0.4361 target = 0.196547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.151473 restraints weight = 26685.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.150839 restraints weight = 20961.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.151711 restraints weight = 16836.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.152892 restraints weight = 14352.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.153506 restraints weight = 11863.069| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6709 moved from start: 0.0880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 17837 Z= 0.148 Angle : 0.615 14.709 23992 Z= 0.323 Chirality : 0.042 0.199 2610 Planarity : 0.005 0.101 3076 Dihedral : 6.970 73.996 2413 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.09 % Favored : 90.49 % Rotamer: Outliers : 2.34 % Allowed : 15.70 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.18), residues: 2124 helix: 0.69 (0.17), residues: 951 sheet: -0.71 (0.36), residues: 231 loop : -2.69 (0.18), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 231 TYR 0.022 0.001 TYR C 155 PHE 0.020 0.002 PHE A 32 TRP 0.029 0.002 TRP C 7 HIS 0.007 0.001 HIS P 352 Details of bonding type rmsd covalent geometry : bond 0.00333 (17837) covalent geometry : angle 0.61455 (23992) hydrogen bonds : bond 0.05157 ( 721) hydrogen bonds : angle 4.94218 ( 2061) *********************** 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 395 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 350 time to evaluate : 0.692 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: 0.7886 (p0) cc_final: 0.7582 (p0) REVERT: A 303 GLU cc_start: 0.7235 (mm-30) cc_final: 0.7024 (mm-30) REVERT: A 639 ARG cc_start: 0.7200 (ttt-90) cc_final: 0.6915 (ttt90) REVERT: B 95 LYS cc_start: 0.7778 (mttm) cc_final: 0.7433 (mmtm) REVERT: B 364 ASP cc_start: 0.7320 (p0) cc_final: 0.7033 (p0) REVERT: C 105 MET cc_start: 0.6985 (tpt) cc_final: 0.6680 (tpt) REVERT: P 351 MET cc_start: 0.1655 (ptp) cc_final: 0.1351 (ptp) outliers start: 45 outliers final: 27 residues processed: 371 average time/residue: 0.1553 time to fit residues: 83.2314 Evaluate side-chains 368 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 341 time to evaluate : 0.707 ------------------------------------------------------------------------------- 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 117 LEU 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 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 B residue 658 LEU Chi-restraints excluded: chain C residue 41 GLU 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 111 optimal weight: 2.9990 chunk 139 optimal weight: 6.9990 chunk 126 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 176 optimal weight: 9.9990 chunk 182 optimal weight: 0.9980 chunk 146 optimal weight: 40.0000 chunk 2 optimal weight: 0.3980 chunk 170 optimal weight: 30.0000 chunk 164 optimal weight: 6.9990 chunk 160 optimal weight: 0.6980 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 C 22 ASN C 146 GLN ** P 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 342 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.193026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.150069 restraints weight = 26959.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.147466 restraints weight = 19623.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.148623 restraints weight = 18382.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.149509 restraints weight = 14896.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.149755 restraints weight = 12468.642| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6751 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 17837 Z= 0.207 Angle : 0.644 13.656 23992 Z= 0.340 Chirality : 0.044 0.205 2610 Planarity : 0.005 0.083 3076 Dihedral : 7.054 75.621 2409 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.99 % Favored : 90.63 % Rotamer: Outliers : 3.59 % Allowed : 16.32 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.18), residues: 2124 helix: 0.60 (0.17), residues: 960 sheet: -0.72 (0.36), residues: 231 loop : -2.79 (0.18), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 291 TYR 0.019 0.001 TYR B 356 PHE 0.029 0.002 PHE A 32 TRP 0.031 0.002 TRP C 7 HIS 0.009 0.001 HIS B 320 Details of bonding type rmsd covalent geometry : bond 0.00476 (17837) covalent geometry : angle 0.64364 (23992) hydrogen bonds : bond 0.05870 ( 721) hydrogen bonds : angle 4.92995 ( 2061) *********************** 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 428 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 359 time to evaluate : 0.457 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: 0.8482 (p) cc_final: 0.8111 (p) REVERT: A 80 GLN cc_start: 0.7419 (OUTLIER) cc_final: 0.6901 (mp10) REVERT: A 95 LYS cc_start: 0.8094 (tttt) cc_final: 0.7849 (tttt) REVERT: A 114 MET cc_start: 0.7930 (mmm) cc_final: 0.7604 (mpp) REVERT: A 125 MET cc_start: 0.7506 (OUTLIER) cc_final: 0.7280 (mtm) REVERT: A 283 ASN cc_start: 0.7872 (p0) cc_final: 0.7551 (p0) REVERT: A 385 ASP cc_start: 0.6861 (p0) cc_final: 0.6637 (p0) REVERT: B 80 GLN cc_start: 0.7700 (OUTLIER) cc_final: 0.7397 (mt0) REVERT: B 95 LYS cc_start: 0.7847 (mttm) cc_final: 0.7544 (ttmm) REVERT: B 101 ASN cc_start: 0.7560 (m110) cc_final: 0.7297 (m-40) REVERT: B 364 ASP cc_start: 0.7328 (p0) cc_final: 0.7005 (p0) REVERT: B 569 GLU cc_start: 0.7094 (pm20) cc_final: 0.6789 (pm20) REVERT: B 639 ARG cc_start: 0.7457 (ttm170) cc_final: 0.7257 (ttm170) REVERT: C 7 TRP cc_start: 0.7829 (m-90) cc_final: 0.7108 (m100) REVERT: C 38 GLU cc_start: 0.7893 (tm-30) cc_final: 0.7483 (tm-30) REVERT: C 103 GLU cc_start: 0.5075 (pm20) cc_final: 0.4806 (pm20) REVERT: C 105 MET cc_start: 0.6953 (tpt) cc_final: 0.6483 (tpt) REVERT: C 151 PHE cc_start: 0.3831 (OUTLIER) cc_final: 0.3230 (t80) REVERT: C 182 VAL cc_start: -0.4930 (OUTLIER) cc_final: -0.5333 (p) REVERT: C 249 MET cc_start: 0.5995 (mmm) cc_final: 0.5520 (mmm) REVERT: K 535 SER cc_start: 0.8668 (p) cc_final: 0.8399 (p) REVERT: K 689 MET cc_start: 0.5586 (mtp) cc_final: 0.5341 (mtp) REVERT: P 31 LEU cc_start: -0.1395 (OUTLIER) cc_final: -0.2012 (mp) REVERT: P 351 MET cc_start: 0.1708 (ptp) cc_final: 0.1470 (ptp) REVERT: P 425 ARG cc_start: -0.0699 (OUTLIER) cc_final: -0.1546 (tmm160) outliers start: 69 outliers final: 47 residues processed: 394 average time/residue: 0.1429 time to fit residues: 82.2029 Evaluate side-chains 402 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 348 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU 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 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 296 ILE Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 369 LEU 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 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 91 ILE Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 288 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 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 632 HIS Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain C residue 41 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 527 ILE Chi-restraints excluded: chain K residue 546 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 34 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 165 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 167 optimal weight: 3.9990 chunk 156 optimal weight: 1.9990 chunk 65 optimal weight: 0.4980 chunk 180 optimal weight: 5.9990 chunk 160 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 146 GLN ** C 217 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 = 0.4323 r_free = 0.4323 target = 0.194044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.150767 restraints weight = 26914.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.147676 restraints weight = 20175.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.149153 restraints weight = 16674.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.150362 restraints weight = 14477.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.150534 restraints weight = 11838.793| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 17837 Z= 0.208 Angle : 0.646 12.241 23992 Z= 0.340 Chirality : 0.044 0.202 2610 Planarity : 0.005 0.079 3076 Dihedral : 6.866 59.526 2409 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.38 % Allowed : 9.56 % Favored : 90.07 % Rotamer: Outliers : 4.42 % Allowed : 17.36 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.18), residues: 2124 helix: 0.56 (0.17), residues: 970 sheet: -0.84 (0.36), residues: 235 loop : -2.85 (0.18), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 291 TYR 0.019 0.001 TYR C 155 PHE 0.034 0.002 PHE A 113 TRP 0.025 0.002 TRP C 7 HIS 0.010 0.001 HIS B 320 Details of bonding type rmsd covalent geometry : bond 0.00478 (17837) covalent geometry : angle 0.64635 (23992) hydrogen bonds : bond 0.05575 ( 721) hydrogen bonds : angle 4.82397 ( 2061) *********************** 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 434 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 349 time to evaluate : 0.688 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: 0.8532 (p) cc_final: 0.8181 (p) REVERT: A 80 GLN cc_start: 0.7391 (OUTLIER) cc_final: 0.6910 (mp10) REVERT: A 125 MET cc_start: 0.7453 (OUTLIER) cc_final: 0.7232 (mtm) REVERT: A 275 LYS cc_start: 0.7249 (pptt) cc_final: 0.6907 (ptpt) REVERT: A 283 ASN cc_start: 0.7827 (p0) cc_final: 0.7541 (p0) REVERT: A 286 LYS cc_start: 0.8274 (mptt) cc_final: 0.8068 (mmtm) REVERT: A 328 GLU cc_start: 0.7504 (tp30) cc_final: 0.7281 (tm-30) REVERT: A 330 ARG cc_start: 0.7309 (ptp-170) cc_final: 0.6925 (ptm160) REVERT: A 401 LEU cc_start: 0.6097 (OUTLIER) cc_final: 0.5778 (mp) REVERT: B 80 GLN cc_start: 0.7700 (OUTLIER) cc_final: 0.7402 (mt0) REVERT: B 95 LYS cc_start: 0.7892 (mttm) cc_final: 0.7558 (ttmm) REVERT: B 101 ASN cc_start: 0.7444 (m110) cc_final: 0.7057 (m-40) REVERT: B 364 ASP cc_start: 0.7313 (p0) cc_final: 0.6977 (p0) REVERT: B 569 GLU cc_start: 0.7026 (pm20) cc_final: 0.6708 (pm20) REVERT: C 7 TRP cc_start: 0.7852 (m-90) cc_final: 0.7470 (m-90) REVERT: C 38 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7447 (tm-30) REVERT: C 105 MET cc_start: 0.6914 (tpt) cc_final: 0.6448 (tpt) REVERT: C 151 PHE cc_start: 0.3706 (OUTLIER) cc_final: 0.3095 (t80) REVERT: C 182 VAL cc_start: -0.4938 (OUTLIER) cc_final: -0.5339 (p) REVERT: C 249 MET cc_start: 0.6048 (mmm) cc_final: 0.5603 (mmm) REVERT: P 31 LEU cc_start: -0.1555 (OUTLIER) cc_final: -0.2059 (mp) REVERT: P 351 MET cc_start: 0.1666 (ptp) cc_final: 0.1447 (ptp) REVERT: P 425 ARG cc_start: -0.0663 (OUTLIER) cc_final: -0.1519 (tmm160) outliers start: 85 outliers final: 58 residues processed: 392 average time/residue: 0.1440 time to fit residues: 82.3667 Evaluate side-chains 411 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 345 time to evaluate : 0.640 ------------------------------------------------------------------------------- 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 99 ILE Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 125 MET 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 369 LEU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain A residue 486 ILE 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 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 97 ASP Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 288 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 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 543 LEU 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 628 ILE 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 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 527 ILE Chi-restraints excluded: chain K residue 537 LEU Chi-restraints excluded: chain K residue 546 THR Chi-restraints excluded: chain K residue 560 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 175 optimal weight: 0.0670 chunk 129 optimal weight: 1.9990 chunk 12 optimal weight: 0.0870 chunk 169 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 143 optimal weight: 2.9990 chunk 204 optimal weight: 20.0000 chunk 183 optimal weight: 6.9990 chunk 87 optimal weight: 0.0970 chunk 39 optimal weight: 1.9990 chunk 157 optimal weight: 0.9980 overall best weight: 0.4294 ------------------------------------------------------------------------------- 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 C 146 GLN C 211 HIS K 524 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.197414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.153686 restraints weight = 26863.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.151710 restraints weight = 19690.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.153840 restraints weight = 16260.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.154565 restraints weight = 13408.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.154825 restraints weight = 11072.177| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6690 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 17837 Z= 0.113 Angle : 0.573 10.153 23992 Z= 0.300 Chirality : 0.040 0.182 2610 Planarity : 0.004 0.071 3076 Dihedral : 6.191 59.333 2409 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.43 % Favored : 91.20 % Rotamer: Outliers : 3.43 % Allowed : 18.76 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.18), residues: 2124 helix: 0.86 (0.17), residues: 956 sheet: -0.65 (0.37), residues: 221 loop : -2.73 (0.18), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 639 TYR 0.019 0.001 TYR C 155 PHE 0.013 0.001 PHE C 151 TRP 0.025 0.002 TRP C 114 HIS 0.005 0.001 HIS B 320 Details of bonding type rmsd covalent geometry : bond 0.00243 (17837) covalent geometry : angle 0.57331 (23992) hydrogen bonds : bond 0.04087 ( 721) hydrogen bonds : angle 4.52491 ( 2061) *********************** 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 413 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 347 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 SER cc_start: 0.8548 (p) cc_final: 0.8261 (p) REVERT: A 125 MET cc_start: 0.7467 (OUTLIER) cc_final: 0.7189 (mtm) REVERT: A 275 LYS cc_start: 0.7275 (pptt) cc_final: 0.6936 (ptpt) REVERT: A 328 GLU cc_start: 0.7478 (tp30) cc_final: 0.7259 (tm-30) REVERT: A 330 ARG cc_start: 0.7266 (ptp-170) cc_final: 0.6869 (ptm-80) REVERT: A 401 LEU cc_start: 0.5778 (OUTLIER) cc_final: 0.5549 (mp) REVERT: B 80 GLN cc_start: 0.7510 (OUTLIER) cc_final: 0.7133 (mt0) REVERT: B 95 LYS cc_start: 0.7871 (mttm) cc_final: 0.7507 (ttmm) REVERT: B 101 ASN cc_start: 0.7734 (m-40) cc_final: 0.7217 (m-40) REVERT: B 364 ASP cc_start: 0.7307 (p0) cc_final: 0.6968 (p0) REVERT: B 414 GLU cc_start: 0.6574 (tt0) cc_final: 0.6356 (tt0) REVERT: C 105 MET cc_start: 0.6897 (tpt) cc_final: 0.6312 (tpt) REVERT: C 108 LYS cc_start: 0.5190 (OUTLIER) cc_final: 0.4818 (tmtt) REVERT: C 151 PHE cc_start: 0.3745 (OUTLIER) cc_final: 0.3127 (t80) REVERT: C 182 VAL cc_start: -0.4699 (OUTLIER) cc_final: -0.5107 (p) REVERT: C 249 MET cc_start: 0.5963 (mmm) cc_final: 0.5510 (mmm) REVERT: K 575 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7793 (mtp-110) REVERT: K 623 GLU cc_start: 0.7305 (mp0) cc_final: 0.6840 (pm20) REVERT: K 693 MET cc_start: 0.6922 (mtm) cc_final: 0.6673 (mtm) REVERT: P 107 MET cc_start: 0.7308 (mmp) cc_final: 0.6491 (mmp) REVERT: P 425 ARG cc_start: -0.1153 (OUTLIER) cc_final: -0.1838 (tmm160) outliers start: 66 outliers final: 42 residues processed: 383 average time/residue: 0.1461 time to fit residues: 81.7073 Evaluate side-chains 390 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 340 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER 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 115 GLU 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 296 ILE Chi-restraints excluded: chain A residue 355 LEU 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 479 THR 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 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 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 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 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 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 546 THR 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 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 123 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 83 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 85 optimal weight: 0.5980 chunk 93 optimal weight: 0.9980 chunk 126 optimal weight: 1.9990 chunk 44 optimal weight: 0.0770 chunk 70 optimal weight: 1.9990 chunk 82 optimal weight: 0.0010 overall best weight: 0.4144 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** K 524 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.197789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.151909 restraints weight = 26688.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.151946 restraints weight = 21207.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.152070 restraints weight = 16003.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.152549 restraints weight = 17528.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.153968 restraints weight = 14242.027| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6730 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 17837 Z= 0.113 Angle : 0.587 9.852 23992 Z= 0.303 Chirality : 0.041 0.175 2610 Planarity : 0.004 0.063 3076 Dihedral : 5.974 66.323 2409 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.33 % Allowed : 8.62 % Favored : 91.05 % Rotamer: Outliers : 3.59 % Allowed : 19.28 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.18), residues: 2124 helix: 0.91 (0.17), residues: 961 sheet: -0.61 (0.37), residues: 220 loop : -2.73 (0.18), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 475 TYR 0.018 0.001 TYR C 155 PHE 0.013 0.001 PHE C 151 TRP 0.018 0.001 TRP C 114 HIS 0.005 0.001 HIS K 574 Details of bonding type rmsd covalent geometry : bond 0.00244 (17837) covalent geometry : angle 0.58676 (23992) hydrogen bonds : bond 0.03985 ( 721) hydrogen bonds : angle 4.43691 ( 2061) *********************** 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 406 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 337 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 SER cc_start: 0.8534 (p) cc_final: 0.8175 (p) REVERT: A 125 MET cc_start: 0.7470 (OUTLIER) cc_final: 0.7208 (mtm) REVERT: A 275 LYS cc_start: 0.7268 (pptt) cc_final: 0.6912 (ptpt) REVERT: A 328 GLU cc_start: 0.7468 (tp30) cc_final: 0.7224 (tm-30) REVERT: A 330 ARG cc_start: 0.7304 (ptp-170) cc_final: 0.6959 (ptm-80) REVERT: A 401 LEU cc_start: 0.5799 (OUTLIER) cc_final: 0.5548 (mp) REVERT: A 519 GLU cc_start: 0.7161 (tp30) cc_final: 0.6943 (tp30) REVERT: A 648 ASP cc_start: 0.7361 (t0) cc_final: 0.6977 (t0) REVERT: B 80 GLN cc_start: 0.7510 (OUTLIER) cc_final: 0.7177 (mt0) REVERT: B 95 LYS cc_start: 0.7890 (mttm) cc_final: 0.7565 (ttmm) REVERT: B 101 ASN cc_start: 0.7779 (m-40) cc_final: 0.7406 (m110) REVERT: B 177 ARG cc_start: 0.7827 (ptt-90) cc_final: 0.7045 (ptt-90) REVERT: B 191 GLU cc_start: 0.7665 (tp30) cc_final: 0.7432 (tp30) REVERT: B 364 ASP cc_start: 0.7353 (p0) cc_final: 0.6958 (p0) REVERT: C 103 GLU cc_start: 0.5170 (pm20) cc_final: 0.4907 (pm20) REVERT: C 105 MET cc_start: 0.6927 (tpt) cc_final: 0.6213 (tpt) REVERT: C 108 LYS cc_start: 0.5281 (OUTLIER) cc_final: 0.4926 (tmmt) REVERT: C 151 PHE cc_start: 0.3647 (OUTLIER) cc_final: 0.3004 (t80) REVERT: C 182 VAL cc_start: -0.4890 (OUTLIER) cc_final: -0.5230 (p) REVERT: C 249 MET cc_start: 0.6054 (mmm) cc_final: 0.5600 (mmm) REVERT: K 575 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7798 (mtp-110) REVERT: K 623 GLU cc_start: 0.7339 (mp0) cc_final: 0.6903 (pm20) REVERT: K 693 MET cc_start: 0.7007 (mtm) cc_final: 0.6789 (mtm) REVERT: P 107 MET cc_start: 0.7379 (mmp) cc_final: 0.6548 (mmp) REVERT: P 425 ARG cc_start: -0.1174 (OUTLIER) cc_final: -0.1654 (tmm160) outliers start: 69 outliers final: 46 residues processed: 375 average time/residue: 0.1444 time to fit residues: 79.2095 Evaluate side-chains 391 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 337 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER 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 117 LEU Chi-restraints excluded: chain A residue 125 MET 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 394 MET Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 521 CYS 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 628 ILE Chi-restraints excluded: chain A residue 640 GLN 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 84 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 123 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 439 LEU 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 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 575 ARG Chi-restraints excluded: chain K residue 588 LEU Chi-restraints excluded: chain K residue 592 ILE Chi-restraints excluded: chain K residue 644 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 425 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 102 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 33 optimal weight: 0.3980 chunk 204 optimal weight: 20.0000 chunk 137 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.4349 r_free = 0.4349 target = 0.196075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.151268 restraints weight = 26945.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.150909 restraints weight = 20570.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.151052 restraints weight = 15923.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.152014 restraints weight = 13753.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.152601 restraints weight = 12254.414| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6701 moved from start: 0.2083 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= 0.138 Angle : 0.605 10.210 23992 Z= 0.314 Chirality : 0.042 0.193 2610 Planarity : 0.004 0.060 3076 Dihedral : 6.020 65.622 2409 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.33 % Allowed : 8.90 % Favored : 90.77 % Rotamer: Outliers : 3.95 % Allowed : 19.23 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.18), residues: 2124 helix: 0.91 (0.17), residues: 960 sheet: -0.50 (0.36), residues: 223 loop : -2.76 (0.18), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 502 TYR 0.017 0.001 TYR C 155 PHE 0.015 0.001 PHE A 32 TRP 0.017 0.002 TRP B 157 HIS 0.007 0.001 HIS B 320 Details of bonding type rmsd covalent geometry : bond 0.00308 (17837) covalent geometry : angle 0.60457 (23992) hydrogen bonds : bond 0.04497 ( 721) hydrogen bonds : angle 4.47122 ( 2061) *********************** 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 414 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 338 time to evaluate : 0.787 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: 0.8509 (p) cc_final: 0.8112 (p) REVERT: A 275 LYS cc_start: 0.7327 (pptt) cc_final: 0.6983 (ptpt) REVERT: A 303 GLU cc_start: 0.7173 (mm-30) cc_final: 0.6927 (mm-30) REVERT: A 328 GLU cc_start: 0.7509 (tp30) cc_final: 0.7292 (tm-30) REVERT: A 330 ARG cc_start: 0.7302 (ptp-170) cc_final: 0.7071 (ptp-170) REVERT: A 401 LEU cc_start: 0.5933 (OUTLIER) cc_final: 0.5618 (mp) REVERT: A 465 GLU cc_start: 0.6837 (mt-10) cc_final: 0.6616 (mt-10) REVERT: A 648 ASP cc_start: 0.7362 (t0) cc_final: 0.6976 (t0) REVERT: B 80 GLN cc_start: 0.7572 (OUTLIER) cc_final: 0.7235 (mt0) REVERT: B 95 LYS cc_start: 0.7918 (mttm) cc_final: 0.7590 (ttmm) REVERT: B 101 ASN cc_start: 0.7819 (m-40) cc_final: 0.7425 (m110) REVERT: B 191 GLU cc_start: 0.7701 (tp30) cc_final: 0.7443 (tp30) REVERT: B 364 ASP cc_start: 0.7355 (p0) cc_final: 0.6948 (p0) REVERT: B 406 LYS cc_start: 0.6681 (OUTLIER) cc_final: 0.6257 (mttm) REVERT: B 565 LYS cc_start: 0.8125 (pttm) cc_final: 0.7563 (pttt) REVERT: B 672 ASP cc_start: 0.6657 (p0) cc_final: 0.6448 (p0) REVERT: C 103 GLU cc_start: 0.5251 (OUTLIER) cc_final: 0.5002 (pm20) REVERT: C 105 MET cc_start: 0.6953 (tpt) cc_final: 0.6149 (tpt) REVERT: C 108 LYS cc_start: 0.5210 (OUTLIER) cc_final: 0.4862 (tmmt) REVERT: C 151 PHE cc_start: 0.3859 (OUTLIER) cc_final: 0.3177 (t80) REVERT: C 182 VAL cc_start: -0.4750 (OUTLIER) cc_final: -0.5089 (p) REVERT: C 249 MET cc_start: 0.5959 (mmm) cc_final: 0.5476 (mmm) REVERT: K 575 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7824 (mtp-110) REVERT: K 577 LEU cc_start: 0.6654 (OUTLIER) cc_final: 0.6442 (pp) REVERT: K 623 GLU cc_start: 0.7434 (mp0) cc_final: 0.7127 (pm20) REVERT: K 693 MET cc_start: 0.7006 (mtm) cc_final: 0.6763 (mtm) REVERT: K 706 LEU cc_start: 0.7111 (OUTLIER) cc_final: 0.6866 (mm) REVERT: P 107 MET cc_start: 0.7247 (mmp) cc_final: 0.6493 (mmp) REVERT: P 141 LYS cc_start: 0.7429 (mttm) cc_final: 0.7163 (mttm) REVERT: P 425 ARG cc_start: -0.1409 (OUTLIER) cc_final: -0.1832 (tmm160) outliers start: 76 outliers final: 55 residues processed: 380 average time/residue: 0.1474 time to fit residues: 81.7953 Evaluate side-chains 399 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 333 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 58 SER 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 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 479 THR 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 628 ILE Chi-restraints excluded: chain A residue 640 GLN 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 81 GLU 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 279 GLN 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 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 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 116 VAL 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 575 ARG Chi-restraints excluded: chain K residue 577 LEU 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 425 ARG Chi-restraints excluded: chain P residue 445 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 57 optimal weight: 0.5980 chunk 111 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 210 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 118 optimal weight: 0.3980 chunk 155 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 chunk 119 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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** B 279 GLN K 540 HIS P 145 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.194948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.149703 restraints weight = 26732.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.148702 restraints weight = 20268.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.150022 restraints weight = 17035.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.151803 restraints weight = 13963.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.152138 restraints weight = 10776.557| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6748 moved from start: 0.2222 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= 0.152 Angle : 0.620 9.922 23992 Z= 0.320 Chirality : 0.042 0.180 2610 Planarity : 0.004 0.057 3076 Dihedral : 6.076 65.700 2409 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.33 % Allowed : 9.18 % Favored : 90.49 % Rotamer: Outliers : 4.37 % Allowed : 19.02 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.18), residues: 2124 helix: 0.91 (0.17), residues: 961 sheet: -0.49 (0.37), residues: 218 loop : -2.75 (0.18), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 502 TYR 0.017 0.001 TYR C 155 PHE 0.016 0.001 PHE A 32 TRP 0.018 0.002 TRP C 114 HIS 0.007 0.001 HIS B 320 Details of bonding type rmsd covalent geometry : bond 0.00347 (17837) covalent geometry : angle 0.61955 (23992) hydrogen bonds : bond 0.04610 ( 721) hydrogen bonds : angle 4.46759 ( 2061) *********************** 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 421 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 337 time to evaluate : 0.702 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: 0.8577 (p) cc_final: 0.8193 (p) REVERT: A 125 MET cc_start: 0.7412 (OUTLIER) cc_final: 0.7184 (mtm) REVERT: A 275 LYS cc_start: 0.7362 (pptt) cc_final: 0.6957 (ptpt) REVERT: A 330 ARG cc_start: 0.7260 (ptp-170) cc_final: 0.7054 (ptp-170) REVERT: A 338 ARG cc_start: 0.7770 (ttm110) cc_final: 0.7459 (mtm110) REVERT: A 401 LEU cc_start: 0.5939 (OUTLIER) cc_final: 0.5628 (mp) REVERT: A 648 ASP cc_start: 0.7383 (t0) cc_final: 0.6992 (t0) REVERT: B 80 GLN cc_start: 0.7468 (OUTLIER) cc_final: 0.7134 (mt0) REVERT: B 95 LYS cc_start: 0.7925 (mttm) cc_final: 0.7592 (ttmm) REVERT: B 101 ASN cc_start: 0.7824 (m-40) cc_final: 0.7384 (m110) REVERT: B 191 GLU cc_start: 0.7696 (tp30) cc_final: 0.7451 (tp30) REVERT: B 364 ASP cc_start: 0.7319 (p0) cc_final: 0.6950 (p0) REVERT: B 406 LYS cc_start: 0.6779 (OUTLIER) cc_final: 0.6427 (mttm) REVERT: B 565 LYS cc_start: 0.8091 (pttm) cc_final: 0.7780 (pttp) REVERT: C 105 MET cc_start: 0.6914 (tpt) cc_final: 0.6169 (tpt) REVERT: C 108 LYS cc_start: 0.5164 (OUTLIER) cc_final: 0.4820 (tmmt) REVERT: C 151 PHE cc_start: 0.3785 (OUTLIER) cc_final: 0.3109 (t80) REVERT: C 182 VAL cc_start: -0.4737 (OUTLIER) cc_final: -0.5043 (p) REVERT: C 249 MET cc_start: 0.5946 (mmm) cc_final: 0.5479 (mmm) REVERT: K 575 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7803 (mtp-110) REVERT: K 693 MET cc_start: 0.7011 (mtm) cc_final: 0.6778 (mtm) REVERT: K 706 LEU cc_start: 0.7202 (OUTLIER) cc_final: 0.6960 (mm) REVERT: P 107 MET cc_start: 0.7339 (mmp) cc_final: 0.6573 (mmp) REVERT: P 141 LYS cc_start: 0.7468 (mttm) cc_final: 0.7177 (mttm) REVERT: P 425 ARG cc_start: -0.1412 (OUTLIER) cc_final: -0.1866 (tmm160) outliers start: 84 outliers final: 56 residues processed: 383 average time/residue: 0.1438 time to fit residues: 80.5087 Evaluate side-chains 398 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 332 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 81 GLU 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 370 ILE Chi-restraints excluded: chain A residue 378 ARG Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 486 ILE 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 553 MET Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 611 LEU 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 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 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 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 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 525 LEU Chi-restraints excluded: chain K residue 537 LEU Chi-restraints excluded: chain K residue 540 HIS Chi-restraints excluded: chain K residue 546 THR Chi-restraints excluded: chain K residue 560 THR 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 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 95 optimal weight: 0.7980 chunk 211 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 166 optimal weight: 0.0570 chunk 152 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 129 optimal weight: 0.7980 chunk 205 optimal weight: 10.0000 chunk 191 optimal weight: 0.8980 overall best weight: 0.6698 ------------------------------------------------------------------------------- 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** B 625 HIS K 540 HIS P 36 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.196884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.151773 restraints weight = 26774.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.150254 restraints weight = 21275.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.151429 restraints weight = 16427.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.152199 restraints weight = 14263.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.152199 restraints weight = 12950.673| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6778 moved from start: 0.2310 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= 0.132 Angle : 0.629 15.550 23992 Z= 0.323 Chirality : 0.041 0.181 2610 Planarity : 0.004 0.057 3076 Dihedral : 5.895 66.106 2407 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.33 % Allowed : 8.47 % Favored : 91.20 % Rotamer: Outliers : 3.38 % Allowed : 20.22 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.18), residues: 2124 helix: 0.95 (0.17), residues: 962 sheet: -0.45 (0.37), residues: 218 loop : -2.74 (0.18), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 639 TYR 0.017 0.001 TYR K 640 PHE 0.013 0.001 PHE C 151 TRP 0.021 0.002 TRP C 114 HIS 0.007 0.001 HIS K 542 Details of bonding type rmsd covalent geometry : bond 0.00298 (17837) covalent geometry : angle 0.62936 (23992) hydrogen bonds : bond 0.04288 ( 721) hydrogen bonds : angle 4.42460 ( 2061) *********************** 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 392 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 327 time to evaluate : 0.639 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: symmetry clash REVERT: A 26 SER cc_start: 0.8588 (p) cc_final: 0.8280 (p) REVERT: A 275 LYS cc_start: 0.7369 (pptt) cc_final: 0.6956 (ptpt) REVERT: A 338 ARG cc_start: 0.7752 (ttm110) cc_final: 0.7429 (mtm110) REVERT: A 401 LEU cc_start: 0.5847 (OUTLIER) cc_final: 0.5598 (mp) REVERT: A 648 ASP cc_start: 0.7388 (t0) cc_final: 0.6997 (t0) REVERT: A 684 ILE cc_start: 0.8125 (mt) cc_final: 0.7846 (mp) REVERT: B 80 GLN cc_start: 0.7573 (OUTLIER) cc_final: 0.7230 (mt0) REVERT: B 95 LYS cc_start: 0.7892 (mttm) cc_final: 0.7559 (ttmm) REVERT: B 101 ASN cc_start: 0.7813 (m-40) cc_final: 0.7366 (m110) REVERT: B 191 GLU cc_start: 0.7686 (tp30) cc_final: 0.7453 (tp30) REVERT: B 364 ASP cc_start: 0.7318 (p0) cc_final: 0.6924 (p0) REVERT: B 406 LYS cc_start: 0.6678 (OUTLIER) cc_final: 0.6346 (mttm) REVERT: B 565 LYS cc_start: 0.8114 (pttm) cc_final: 0.7590 (pttt) REVERT: C 105 MET cc_start: 0.6920 (tpt) cc_final: 0.6200 (tpt) REVERT: C 108 LYS cc_start: 0.5287 (OUTLIER) cc_final: 0.4919 (tmmt) REVERT: C 151 PHE cc_start: 0.3688 (OUTLIER) cc_final: 0.3028 (t80) REVERT: C 182 VAL cc_start: -0.4691 (OUTLIER) cc_final: -0.4985 (p) REVERT: C 249 MET cc_start: 0.6042 (mmm) cc_final: 0.5598 (mmm) REVERT: K 573 ILE cc_start: 0.7745 (mm) cc_final: 0.7507 (mm) REVERT: K 575 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.7775 (mtp-110) REVERT: K 693 MET cc_start: 0.7068 (mtm) cc_final: 0.6840 (mtm) REVERT: P 107 MET cc_start: 0.7355 (mmp) cc_final: 0.6601 (mmp) REVERT: P 141 LYS cc_start: 0.7484 (mttm) cc_final: 0.7142 (mttm) outliers start: 65 outliers final: 50 residues processed: 366 average time/residue: 0.1484 time to fit residues: 79.1383 Evaluate side-chains 382 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 325 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET 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 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 479 THR Chi-restraints excluded: chain A residue 486 ILE 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 571 LEU 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 640 GLN 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 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 318 VAL Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain B residue 439 LEU 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 C residue 6 VAL 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 525 LEU Chi-restraints excluded: chain K residue 537 LEU Chi-restraints excluded: chain K residue 546 THR 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 70 optimal weight: 2.9990 chunk 109 optimal weight: 0.4980 chunk 4 optimal weight: 0.2980 chunk 185 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 chunk 155 optimal weight: 0.7980 chunk 101 optimal weight: 0.4980 chunk 173 optimal weight: 0.7980 chunk 87 optimal weight: 0.7980 chunk 135 optimal weight: 30.0000 chunk 90 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 HIS ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 HIS ** K 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.197558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.151122 restraints weight = 26711.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.151586 restraints weight = 19543.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.152808 restraints weight = 14552.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.153377 restraints weight = 12513.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.154423 restraints weight = 11983.677| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 moved from start: 0.2401 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= 0.125 Angle : 0.626 14.865 23992 Z= 0.320 Chirality : 0.041 0.178 2610 Planarity : 0.004 0.059 3076 Dihedral : 5.807 66.265 2407 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.33 % Allowed : 8.71 % Favored : 90.96 % Rotamer: Outliers : 3.22 % Allowed : 20.63 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.18), residues: 2124 helix: 1.02 (0.18), residues: 954 sheet: -0.42 (0.37), residues: 218 loop : -2.69 (0.18), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 639 TYR 0.017 0.001 TYR C 155 PHE 0.012 0.001 PHE C 151 TRP 0.019 0.002 TRP C 114 HIS 0.006 0.001 HIS B 320 Details of bonding type rmsd covalent geometry : bond 0.00282 (17837) covalent geometry : angle 0.62593 (23992) hydrogen bonds : bond 0.04100 ( 721) hydrogen bonds : angle 4.38002 ( 2061) ********************** 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 386 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 324 time to evaluate : 0.662 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: 0.8572 (p) cc_final: 0.8241 (p) REVERT: A 32 PHE cc_start: 0.7576 (OUTLIER) cc_final: 0.7365 (p90) REVERT: A 275 LYS cc_start: 0.7377 (pptt) cc_final: 0.6965 (ptpt) REVERT: A 330 ARG cc_start: 0.7233 (ptp-170) cc_final: 0.6982 (ptm160) REVERT: A 338 ARG cc_start: 0.7747 (ttm110) cc_final: 0.7437 (mtm110) REVERT: A 401 LEU cc_start: 0.5747 (OUTLIER) cc_final: 0.5486 (mp) REVERT: A 648 ASP cc_start: 0.7391 (t0) cc_final: 0.6988 (t0) REVERT: A 683 MET cc_start: 0.6755 (tmm) cc_final: 0.6512 (tmm) REVERT: B 80 GLN cc_start: 0.7489 (OUTLIER) cc_final: 0.7135 (mt0) REVERT: B 95 LYS cc_start: 0.7866 (mttm) cc_final: 0.7540 (ttmm) REVERT: B 101 ASN cc_start: 0.7806 (m-40) cc_final: 0.7371 (m110) REVERT: B 177 ARG cc_start: 0.7783 (ptt-90) cc_final: 0.7017 (ptt-90) REVERT: B 364 ASP cc_start: 0.7315 (p0) cc_final: 0.6931 (p0) REVERT: B 406 LYS cc_start: 0.6626 (OUTLIER) cc_final: 0.6300 (mttm) REVERT: B 565 LYS cc_start: 0.8061 (pttm) cc_final: 0.7580 (pttt) REVERT: C 105 MET cc_start: 0.6938 (tpt) cc_final: 0.6235 (tpt) REVERT: C 108 LYS cc_start: 0.5255 (OUTLIER) cc_final: 0.4892 (tmmt) REVERT: C 151 PHE cc_start: 0.3607 (OUTLIER) cc_final: 0.2975 (t80) REVERT: C 182 VAL cc_start: -0.4693 (OUTLIER) cc_final: -0.5014 (p) REVERT: C 249 MET cc_start: 0.5999 (mmm) cc_final: 0.5554 (mmm) REVERT: K 573 ILE cc_start: 0.7742 (mm) cc_final: 0.7521 (mm) REVERT: K 575 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7765 (mtp-110) REVERT: K 693 MET cc_start: 0.6997 (mtm) cc_final: 0.6769 (mtm) REVERT: K 706 LEU cc_start: 0.6907 (OUTLIER) cc_final: 0.6677 (mm) REVERT: P 107 MET cc_start: 0.7352 (mmp) cc_final: 0.6594 (mmp) REVERT: P 141 LYS cc_start: 0.7431 (mttm) cc_final: 0.7098 (mttm) outliers start: 62 outliers final: 48 residues processed: 363 average time/residue: 0.1463 time to fit residues: 77.3844 Evaluate side-chains 378 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 321 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 86 LEU 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 479 THR Chi-restraints excluded: chain A residue 486 ILE 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 571 LEU 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 640 GLN 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 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 318 VAL Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain B residue 439 LEU 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 632 HIS Chi-restraints excluded: chain C residue 6 VAL 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 560 THR 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 445 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 194 optimal weight: 9.9990 chunk 117 optimal weight: 0.9990 chunk 206 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 155 optimal weight: 0.7980 chunk 200 optimal weight: 9.9990 chunk 71 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 38 optimal weight: 0.0770 chunk 198 optimal weight: 6.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- 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 625 HIS ** K 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 304 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 = 0.4357 r_free = 0.4357 target = 0.197045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.151093 restraints weight = 26844.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.151918 restraints weight = 16594.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.152507 restraints weight = 14228.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.155449 restraints weight = 11716.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.155094 restraints weight = 9087.438| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6714 moved from start: 0.2470 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= 0.137 Angle : 0.643 14.640 23992 Z= 0.328 Chirality : 0.041 0.179 2610 Planarity : 0.004 0.061 3076 Dihedral : 5.837 65.999 2407 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.33 % Allowed : 8.62 % Favored : 91.05 % Rotamer: Outliers : 3.33 % Allowed : 20.43 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.18), residues: 2124 helix: 1.01 (0.17), residues: 957 sheet: -0.43 (0.37), residues: 218 loop : -2.69 (0.18), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 639 TYR 0.016 0.001 TYR C 155 PHE 0.014 0.001 PHE A 32 TRP 0.018 0.002 TRP C 114 HIS 0.006 0.001 HIS B 320 Details of bonding type rmsd covalent geometry : bond 0.00312 (17837) covalent geometry : angle 0.64289 (23992) hydrogen bonds : bond 0.04281 ( 721) hydrogen bonds : angle 4.39819 ( 2061) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2974.64 seconds wall clock time: 52 minutes 5.51 seconds (3125.51 seconds total)