Starting phenix.real_space_refine on Sun Mar 17 14:19:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h69_34497/03_2024/8h69_34497.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h69_34497/03_2024/8h69_34497.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h69_34497/03_2024/8h69_34497.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h69_34497/03_2024/8h69_34497.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h69_34497/03_2024/8h69_34497.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h69_34497/03_2024/8h69_34497.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 36 5.49 5 S 128 5.16 5 C 11214 2.51 5 N 3150 2.21 5 O 3500 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 57": "NH1" <-> "NH2" Residue "A ARG 82": "NH1" <-> "NH2" Residue "A ARG 116": "NH1" <-> "NH2" Residue "A ARG 185": "NH1" <-> "NH2" Residue "A ARG 196": "NH1" <-> "NH2" Residue "A ARG 204": "NH1" <-> "NH2" Residue "A ARG 230": "NH1" <-> "NH2" Residue "A ARG 256": "NH1" <-> "NH2" Residue "A ARG 266": "NH1" <-> "NH2" Residue "A ARG 269": "NH1" <-> "NH2" Residue "A ARG 279": "NH1" <-> "NH2" Residue "A ARG 361": "NH1" <-> "NH2" Residue "A ARG 391": "NH1" <-> "NH2" Residue "A ARG 401": "NH1" <-> "NH2" Residue "A ARG 495": "NH1" <-> "NH2" Residue "A ARG 559": "NH1" <-> "NH2" Residue "B ARG 187": "NH1" <-> "NH2" Residue "B ARG 189": "NH1" <-> "NH2" Residue "B ARG 211": "NH1" <-> "NH2" Residue "B ARG 215": "NH1" <-> "NH2" Residue "B ARG 287": "NH1" <-> "NH2" Residue "B ARG 327": "NH1" <-> "NH2" Residue "B ARG 386": "NH1" <-> "NH2" Residue "B ARG 430": "NH1" <-> "NH2" Residue "B TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 465": "NH1" <-> "NH2" Residue "B ARG 486": "NH1" <-> "NH2" Residue "B ARG 584": "NH1" <-> "NH2" Residue "B ARG 706": "NH1" <-> "NH2" Residue "B ARG 723": "NH1" <-> "NH2" Residue "B ARG 734": "NH1" <-> "NH2" Residue "B ARG 754": "NH1" <-> "NH2" Residue "C ARG 3": "NH1" <-> "NH2" Residue "C ARG 8": "NH1" <-> "NH2" Residue "C ARG 15": "NH1" <-> "NH2" Residue "C ARG 62": "NH1" <-> "NH2" Residue "C ARG 70": "NH1" <-> "NH2" Residue "C ARG 136": "NH1" <-> "NH2" Residue "C ARG 143": "NH1" <-> "NH2" Residue "C ARG 251": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 18028 Number of models: 1 Model: "" Number of chains: 5 Chain: "3" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 369 Classifications: {'RNA': 18} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 4, 'rna3p_pur': 4, 'rna3p_pyr': 9} Link IDs: {'rna2p': 5, 'rna3p': 12} Chain: "5" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 411 Classifications: {'RNA': 19} Modifications used: {'rna2p_pur': 3, 'rna3p_pur': 10, 'rna3p_pyr': 6} Link IDs: {'rna2p': 3, 'rna3p': 15} Chain: "A" Number of atoms: 5790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 716, 5790 Classifications: {'peptide': 716} Link IDs: {'PTRANS': 33, 'TRANS': 682} Chain: "B" Number of atoms: 6022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 754, 6022 Classifications: {'peptide': 754} Link IDs: {'PTRANS': 32, 'TRANS': 721} Chain: "C" Number of atoms: 5436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5436 Classifications: {'peptide': 683} Link IDs: {'PTRANS': 27, 'TRANS': 655} Time building chain proxies: 9.59, per 1000 atoms: 0.53 Number of scatterers: 18028 At special positions: 0 Unit cell: (136.24, 123.76, 116.48, 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 128 16.00 P 36 15.00 O 3500 8.00 N 3150 7.00 C 11214 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.48 Conformation dependent library (CDL) restraints added in 3.0 seconds 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4058 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 22 sheets defined 42.3% alpha, 11.5% beta 8 base pairs and 18 stacking pairs defined. Time for finding SS restraints: 6.39 Creating SS restraints... Processing helix chain 'A' and resid 1 through 8 Processing helix chain 'A' and resid 10 through 22 removed outlier: 3.653A pdb=" N LEU A 16 " --> pdb=" O MET A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 48 removed outlier: 3.817A pdb=" N CYS A 39 " --> pdb=" O PHE A 35 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR A 40 " --> pdb=" O ALA A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 98 removed outlier: 3.600A pdb=" N TRP A 88 " --> pdb=" O ARG A 84 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 134 removed outlier: 3.998A pdb=" N TYR A 130 " --> pdb=" O GLU A 126 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LEU A 132 " --> pdb=" O HIS A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 160 removed outlier: 4.014A pdb=" N ALA A 159 " --> pdb=" O ALA A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 186 removed outlier: 3.864A pdb=" N GLY A 186 " --> pdb=" O MET A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 234 removed outlier: 4.059A pdb=" N ASP A 234 " --> pdb=" O ARG A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 249 removed outlier: 3.570A pdb=" N GLN A 248 " --> pdb=" O GLY A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 313 removed outlier: 3.643A pdb=" N ILE A 308 " --> pdb=" O LEU A 304 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS A 309 " --> pdb=" O TYR A 305 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N CYS A 310 " --> pdb=" O ASP A 306 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N MET A 311 " --> pdb=" O ALA A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 345 removed outlier: 4.083A pdb=" N TYR A 334 " --> pdb=" O ILE A 330 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 348 No H-bonds generated for 'chain 'A' and resid 346 through 348' Processing helix chain 'A' and resid 364 through 369 removed outlier: 3.762A pdb=" N TRP A 368 " --> pdb=" O SER A 364 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA A 369 " --> pdb=" O GLN A 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 364 through 369' Processing helix chain 'A' and resid 405 through 416 removed outlier: 3.629A pdb=" N SER A 409 " --> pdb=" O SER A 405 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS A 413 " --> pdb=" O SER A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 445 Processing helix chain 'A' and resid 446 through 449 Processing helix chain 'A' and resid 454 through 476 removed outlier: 3.553A pdb=" N TYR A 458 " --> pdb=" O ARG A 454 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR A 464 " --> pdb=" O MET A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 533 removed outlier: 3.549A pdb=" N GLU A 533 " --> pdb=" O PRO A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 582 No H-bonds generated for 'chain 'A' and resid 580 through 582' Processing helix chain 'A' and resid 583 through 598 removed outlier: 4.040A pdb=" N GLN A 591 " --> pdb=" O GLN A 587 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ILE A 592 " --> pdb=" O SER A 588 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE A 596 " --> pdb=" O ILE A 592 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU A 597 " --> pdb=" O GLU A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 604 removed outlier: 3.730A pdb=" N LYS A 603 " --> pdb=" O GLU A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 612 removed outlier: 3.722A pdb=" N PHE A 611 " --> pdb=" O MET A 607 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N PHE A 612 " --> pdb=" O THR A 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 607 through 612' Processing helix chain 'A' and resid 632 through 650 removed outlier: 3.774A pdb=" N ARG A 638 " --> pdb=" O GLY A 634 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 641 " --> pdb=" O CYS A 637 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N SER A 648 " --> pdb=" O SER A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 660 removed outlier: 3.882A pdb=" N GLU A 656 " --> pdb=" O SER A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 674 removed outlier: 4.347A pdb=" N ILE A 668 " --> pdb=" O LYS A 664 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL A 669 " --> pdb=" O LEU A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 691 Processing helix chain 'A' and resid 699 through 712 removed outlier: 3.624A pdb=" N SER A 705 " --> pdb=" O LEU A 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 11 removed outlier: 3.882A pdb=" N PHE B 9 " --> pdb=" O THR B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 22 removed outlier: 3.516A pdb=" N THR B 20 " --> pdb=" O ALA B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 50 removed outlier: 3.568A pdb=" N THR B 42 " --> pdb=" O TYR B 38 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ARG B 45 " --> pdb=" O ASP B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 94 removed outlier: 4.209A pdb=" N GLU B 90 " --> pdb=" O ASP B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 99 removed outlier: 3.506A pdb=" N SER B 98 " --> pdb=" O PHE B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 114 removed outlier: 3.678A pdb=" N ASN B 105 " --> pdb=" O GLY B 101 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU B 108 " --> pdb=" O GLU B 104 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU B 109 " --> pdb=" O ASN B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 153 removed outlier: 3.718A pdb=" N LEU B 143 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N GLU B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE B 150 " --> pdb=" O THR B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 173 removed outlier: 3.705A pdb=" N VAL B 170 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N MET B 171 " --> pdb=" O LEU B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 222 removed outlier: 3.671A pdb=" N ARG B 220 " --> pdb=" O SER B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 266 removed outlier: 4.075A pdb=" N ARG B 249 " --> pdb=" O GLY B 245 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLY B 250 " --> pdb=" O MET B 246 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N PHE B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N PHE B 254 " --> pdb=" O GLY B 250 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N CYS B 263 " --> pdb=" O ALA B 259 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS B 265 " --> pdb=" O SER B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 285 removed outlier: 3.666A pdb=" N LYS B 278 " --> pdb=" O GLY B 274 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL B 285 " --> pdb=" O LYS B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 291 removed outlier: 3.503A pdb=" N THR B 291 " --> pdb=" O LYS B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 325 Processing helix chain 'B' and resid 330 through 337 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 371 through 375 removed outlier: 3.650A pdb=" N ALA B 374 " --> pdb=" O GLU B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 381 Processing helix chain 'B' and resid 382 through 391 removed outlier: 3.760A pdb=" N LYS B 387 " --> pdb=" O GLU B 383 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU B 390 " --> pdb=" O ARG B 386 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS B 391 " --> pdb=" O LYS B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 394 No H-bonds generated for 'chain 'B' and resid 392 through 394' Processing helix chain 'B' and resid 415 through 427 removed outlier: 3.780A pdb=" N LEU B 424 " --> pdb=" O GLY B 420 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY B 427 " --> pdb=" O ILE B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 433 Processing helix chain 'B' and resid 455 through 471 removed outlier: 3.613A pdb=" N ASP B 464 " --> pdb=" O GLN B 460 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ARG B 465 " --> pdb=" O ALA B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 474 No H-bonds generated for 'chain 'B' and resid 472 through 474' Processing helix chain 'B' and resid 525 through 534 removed outlier: 3.546A pdb=" N ILE B 530 " --> pdb=" O GLY B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 559 removed outlier: 3.647A pdb=" N LYS B 553 " --> pdb=" O GLN B 549 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR B 557 " --> pdb=" O LYS B 553 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR B 558 " --> pdb=" O ASP B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 583 removed outlier: 3.766A pdb=" N LYS B 577 " --> pdb=" O SER B 573 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS B 578 " --> pdb=" O PHE B 574 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU B 579 " --> pdb=" O GLU B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 589 removed outlier: 3.919A pdb=" N GLY B 588 " --> pdb=" O SER B 585 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU B 589 " --> pdb=" O LYS B 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 585 through 589' Processing helix chain 'B' and resid 590 through 594 removed outlier: 3.658A pdb=" N ASP B 593 " --> pdb=" O LEU B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 612 Processing helix chain 'B' and resid 617 through 625 removed outlier: 4.307A pdb=" N GLN B 621 " --> pdb=" O ASP B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 676 removed outlier: 3.502A pdb=" N ASN B 676 " --> pdb=" O SER B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 683 removed outlier: 3.652A pdb=" N ILE B 682 " --> pdb=" O GLN B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 697 Processing helix chain 'B' and resid 701 through 705 removed outlier: 4.059A pdb=" N SER B 704 " --> pdb=" O PRO B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 731 removed outlier: 3.848A pdb=" N VAL B 719 " --> pdb=" O VAL B 715 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG B 721 " --> pdb=" O ALA B 717 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE B 724 " --> pdb=" O SER B 720 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG B 727 " --> pdb=" O ARG B 723 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE B 728 " --> pdb=" O ILE B 724 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP B 729 " --> pdb=" O ASP B 725 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 752 removed outlier: 3.541A pdb=" N GLU B 742 " --> pdb=" O GLU B 738 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE B 746 " --> pdb=" O GLU B 742 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N CYS B 747 " --> pdb=" O ILE B 743 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER B 748 " --> pdb=" O MET B 744 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR B 749 " --> pdb=" O LYS B 745 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 10 removed outlier: 4.407A pdb=" N GLU C 6 " --> pdb=" O GLU C 2 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 32 Processing helix chain 'C' and resid 42 through 51 removed outlier: 3.594A pdb=" N ARG C 46 " --> pdb=" O ASN C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 67 Processing helix chain 'C' and resid 92 through 103 removed outlier: 4.179A pdb=" N VAL C 96 " --> pdb=" O SER C 92 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG C 101 " --> pdb=" O THR C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 115 removed outlier: 3.525A pdb=" N TYR C 115 " --> pdb=" O TYR C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 127 removed outlier: 3.635A pdb=" N PHE C 119 " --> pdb=" O TYR C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 168 removed outlier: 3.756A pdb=" N PHE C 168 " --> pdb=" O MET C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 172 removed outlier: 3.673A pdb=" N VAL C 172 " --> pdb=" O PRO C 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 169 through 172' Processing helix chain 'C' and resid 181 through 197 removed outlier: 3.870A pdb=" N ILE C 185 " --> pdb=" O SER C 181 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LYS C 187 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU C 191 " --> pdb=" O LYS C 187 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU C 192 " --> pdb=" O GLU C 188 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU C 193 " --> pdb=" O LYS C 189 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N GLN C 194 " --> pdb=" O LYS C 190 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS C 197 " --> pdb=" O LEU C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 208 removed outlier: 3.569A pdb=" N LEU C 207 " --> pdb=" O VAL C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 273 removed outlier: 4.049A pdb=" N ILE C 261 " --> pdb=" O GLN C 257 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA C 262 " --> pdb=" O SER C 258 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE C 266 " --> pdb=" O ALA C 262 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG C 269 " --> pdb=" O ASN C 265 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL C 272 " --> pdb=" O ARG C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 283 removed outlier: 3.691A pdb=" N LEU C 280 " --> pdb=" O PRO C 276 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N LEU C 281 " --> pdb=" O LEU C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 286 No H-bonds generated for 'chain 'C' and resid 284 through 286' Processing helix chain 'C' and resid 294 through 298 Processing helix chain 'C' and resid 305 through 315 removed outlier: 3.894A pdb=" N MET C 315 " --> pdb=" O CYS C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 405 Processing helix chain 'C' and resid 407 through 412 Processing helix chain 'C' and resid 429 through 441 removed outlier: 3.662A pdb=" N ARG C 436 " --> pdb=" O HIS C 432 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE C 438 " --> pdb=" O LEU C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 449 Processing helix chain 'C' and resid 536 through 541 Processing helix chain 'C' and resid 541 through 556 removed outlier: 3.551A pdb=" N LEU C 546 " --> pdb=" O PRO C 542 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR C 550 " --> pdb=" O LEU C 546 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE C 554 " --> pdb=" O TYR C 550 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG C 555 " --> pdb=" O GLN C 551 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN C 556 " --> pdb=" O TRP C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 566 removed outlier: 3.877A pdb=" N ILE C 562 " --> pdb=" O GLU C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 573 Processing helix chain 'C' and resid 579 through 583 removed outlier: 3.593A pdb=" N SER C 582 " --> pdb=" O SER C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 607 removed outlier: 3.598A pdb=" N THR C 598 " --> pdb=" O GLY C 594 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU C 607 " --> pdb=" O MET C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 619 removed outlier: 3.762A pdb=" N ILE C 616 " --> pdb=" O THR C 612 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU C 619 " --> pdb=" O ILE C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 624 removed outlier: 3.883A pdb=" N ALA C 623 " --> pdb=" O PRO C 620 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA C 624 " --> pdb=" O PHE C 621 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 620 through 624' Processing helix chain 'C' and resid 677 through 682 Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.209A pdb=" N PHE A 117 " --> pdb=" O HIS A 144 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N HIS A 146 " --> pdb=" O PHE A 117 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N GLU A 119 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N PHE A 148 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N GLY A 121 " --> pdb=" O PHE A 148 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 290 through 293 removed outlier: 5.007A pdb=" N LEU A 500 " --> pdb=" O SER A 487 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N SER A 487 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLY A 502 " --> pdb=" O MET A 485 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN A 481 " --> pdb=" O LYS A 506 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N PHE A 480 " --> pdb=" O MET A 360 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N LYS A 358 " --> pdb=" O LEU A 482 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 290 through 293 removed outlier: 3.560A pdb=" N VAL A 557 " --> pdb=" O LEU A 550 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG A 559 " --> pdb=" O MET A 548 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N MET A 548 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU A 563 " --> pdb=" O GLU A 544 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N GLU A 544 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL A 565 " --> pdb=" O VAL A 542 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N VAL A 542 " --> pdb=" O VAL A 565 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 377 through 378 removed outlier: 3.588A pdb=" N ARG B 365 " --> pdb=" O GLU A 377 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU B 364 " --> pdb=" O SER B 359 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N TYR B 355 " --> pdb=" O ILE B 368 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 420 through 421 Processing sheet with id=AA6, first strand: chain 'A' and resid 627 through 631 removed outlier: 6.691A pdb=" N GLY A 627 " --> pdb=" O GLU A 623 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLU A 623 " --> pdb=" O GLY A 627 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N GLU A 629 " --> pdb=" O ILE A 621 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AA8, first strand: chain 'B' and resid 181 through 183 removed outlier: 3.637A pdb=" N GLN B 210 " --> pdb=" O ILE B 181 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 186 through 192 removed outlier: 3.619A pdb=" N THR B 204 " --> pdb=" O ARG B 187 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN B 202 " --> pdb=" O ARG B 189 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 242 through 243 removed outlier: 6.930A pdb=" N LEU B 224 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 437 through 442 Processing sheet with id=AB3, first strand: chain 'B' and resid 489 through 490 removed outlier: 3.621A pdb=" N PHE B 490 " --> pdb=" O TYR B 497 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 643 through 644 removed outlier: 3.683A pdb=" N ALA B 643 " --> pdb=" O MET B 655 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 667 through 668 removed outlier: 4.339A pdb=" N ILE B 667 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N MET C 90 " --> pdb=" O SER C 79 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 129 through 134 removed outlier: 4.448A pdb=" N MET C 243 " --> pdb=" O GLY C 131 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N VAL C 133 " --> pdb=" O GLU C 241 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLU C 241 " --> pdb=" O VAL C 133 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 141 through 147 removed outlier: 3.679A pdb=" N ILE C 141 " --> pdb=" O VAL C 220 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 292 through 293 removed outlier: 3.593A pdb=" N ILE C 292 " --> pdb=" O ILE C 289 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 329 through 335 removed outlier: 6.965A pdb=" N GLU C 362 " --> pdb=" O THR C 333 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N THR C 371 " --> pdb=" O VAL C 386 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N VAL C 386 " --> pdb=" O THR C 371 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE C 373 " --> pdb=" O LEU C 384 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU C 384 " --> pdb=" O ILE C 373 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ARG C 375 " --> pdb=" O ILE C 382 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N ARG C 479 " --> pdb=" O ILE C 382 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N LEU C 384 " --> pdb=" O ARG C 479 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N SER C 481 " --> pdb=" O LEU C 384 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL C 386 " --> pdb=" O SER C 481 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N VAL C 478 " --> pdb=" O ILE C 463 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ILE C 463 " --> pdb=" O VAL C 478 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER C 470 " --> pdb=" O GLY C 462 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 341 through 345 Processing sheet with id=AC2, first strand: chain 'C' and resid 451 through 453 Processing sheet with id=AC3, first strand: chain 'C' and resid 636 through 639 removed outlier: 3.530A pdb=" N LEU C 636 " --> pdb=" O ILE C 647 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 656 through 659 removed outlier: 3.565A pdb=" N ASN C 659 " --> pdb=" O ARG C 664 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG C 664 " --> pdb=" O ASN C 659 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU C 665 " --> pdb=" O ALA C 672 " (cutoff:3.500A) 561 hydrogen bonds defined for protein. 1560 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 18 hydrogen bonds 36 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 18 stacking parallelities Total time for adding SS restraints: 6.14 Time building geometry restraints manager: 8.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4003 1.33 - 1.45: 4105 1.45 - 1.57: 10050 1.57 - 1.69: 71 1.69 - 1.81: 224 Bond restraints: 18453 Sorted by residual: bond pdb=" CA PHE A 205 " pdb=" CB PHE A 205 " ideal model delta sigma weight residual 1.525 1.472 0.053 1.47e-02 4.63e+03 1.29e+01 bond pdb=" N ASN B 314 " pdb=" CA ASN B 314 " ideal model delta sigma weight residual 1.457 1.407 0.050 1.41e-02 5.03e+03 1.26e+01 bond pdb=" N ASN C 429 " pdb=" CA ASN C 429 " ideal model delta sigma weight residual 1.453 1.493 -0.040 1.18e-02 7.18e+03 1.15e+01 bond pdb=" N ARG C 427 " pdb=" CA ARG C 427 " ideal model delta sigma weight residual 1.457 1.495 -0.037 1.29e-02 6.01e+03 8.45e+00 bond pdb=" N ARG C 423 " pdb=" CA ARG C 423 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.82e+00 ... (remaining 18448 not shown) Histogram of bond angle deviations from ideal: 98.14 - 105.34: 577 105.34 - 112.54: 9239 112.54 - 119.74: 6773 119.74 - 126.94: 8167 126.94 - 134.14: 302 Bond angle restraints: 25058 Sorted by residual: angle pdb=" N VAL B 286 " pdb=" CA VAL B 286 " pdb=" C VAL B 286 " ideal model delta sigma weight residual 113.16 103.05 10.11 1.49e+00 4.50e-01 4.60e+01 angle pdb=" N ALA C 587 " pdb=" CA ALA C 587 " pdb=" C ALA C 587 " ideal model delta sigma weight residual 112.23 104.58 7.65 1.26e+00 6.30e-01 3.69e+01 angle pdb=" C HIS A 297 " pdb=" N GLU A 298 " pdb=" CA GLU A 298 " ideal model delta sigma weight residual 121.54 132.09 -10.55 1.91e+00 2.74e-01 3.05e+01 angle pdb=" N LEU B 271 " pdb=" CA LEU B 271 " pdb=" C LEU B 271 " ideal model delta sigma weight residual 113.16 120.52 -7.36 1.42e+00 4.96e-01 2.68e+01 angle pdb=" N VAL C 421 " pdb=" CA VAL C 421 " pdb=" C VAL C 421 " ideal model delta sigma weight residual 109.34 98.77 10.57 2.08e+00 2.31e-01 2.58e+01 ... (remaining 25053 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 10548 17.69 - 35.37: 609 35.37 - 53.06: 134 53.06 - 70.75: 53 70.75 - 88.43: 13 Dihedral angle restraints: 11357 sinusoidal: 5090 harmonic: 6267 Sorted by residual: dihedral pdb=" CA CYS C 239 " pdb=" C CYS C 239 " pdb=" N TRP C 240 " pdb=" CA TRP C 240 " ideal model delta harmonic sigma weight residual -180.00 -150.90 -29.10 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CA GLN B 545 " pdb=" C GLN B 545 " pdb=" N MET B 546 " pdb=" CA MET B 546 " ideal model delta harmonic sigma weight residual 180.00 151.22 28.78 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA LYS C 197 " pdb=" C LYS C 197 " pdb=" N ILE C 198 " pdb=" CA ILE C 198 " ideal model delta harmonic sigma weight residual 180.00 151.29 28.71 0 5.00e+00 4.00e-02 3.30e+01 ... (remaining 11354 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1906 0.057 - 0.113: 698 0.113 - 0.170: 154 0.170 - 0.226: 24 0.226 - 0.283: 8 Chirality restraints: 2790 Sorted by residual: chirality pdb=" CA LEU B 224 " pdb=" N LEU B 224 " pdb=" C LEU B 224 " pdb=" CB LEU B 224 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CB ILE B 450 " pdb=" CA ILE B 450 " pdb=" CG1 ILE B 450 " pdb=" CG2 ILE B 450 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CG LEU B 604 " pdb=" CB LEU B 604 " pdb=" CD1 LEU B 604 " pdb=" CD2 LEU B 604 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 2787 not shown) Planarity restraints: 3100 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 633 " 0.035 2.00e-02 2.50e+03 2.86e-02 1.44e+01 pdb=" CG PHE C 633 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE C 633 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE C 633 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE C 633 " 0.024 2.00e-02 2.50e+03 pdb=" CE2 PHE C 633 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE C 633 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 537 " 0.013 2.00e-02 2.50e+03 1.88e-02 8.87e+00 pdb=" CG TRP A 537 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP A 537 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP A 537 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 537 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP A 537 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 537 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 537 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 537 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP A 537 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 344 " 0.020 2.00e-02 2.50e+03 2.18e-02 8.35e+00 pdb=" CG PHE B 344 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE B 344 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE B 344 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE B 344 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE B 344 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 344 " 0.010 2.00e-02 2.50e+03 ... (remaining 3097 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 126 2.51 - 3.11: 12856 3.11 - 3.71: 28482 3.71 - 4.30: 41001 4.30 - 4.90: 64994 Nonbonded interactions: 147459 Sorted by model distance: nonbonded pdb=" O ASN C 425 " pdb=" O GLN C 426 " model vdw 1.917 3.040 nonbonded pdb=" OG SER C 273 " pdb=" OE1 GLU C 578 " model vdw 2.196 2.440 nonbonded pdb=" N GLN C 426 " pdb=" OE1 GLN C 426 " model vdw 2.197 2.520 nonbonded pdb=" O SER B 293 " pdb=" OG SER C 643 " model vdw 2.208 2.440 nonbonded pdb=" OG1 THR C 129 " pdb=" OG1 THR C 245 " model vdw 2.259 2.440 ... (remaining 147454 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.530 Check model and map are aligned: 0.260 Set scattering table: 0.180 Process input model: 53.600 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 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 0.082 18453 Z= 0.585 Angle : 1.121 10.572 25058 Z= 0.630 Chirality : 0.061 0.283 2790 Planarity : 0.007 0.060 3100 Dihedral : 12.846 88.432 7299 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.45 % Favored : 92.36 % Rotamer: Outliers : 1.52 % Allowed : 3.98 % Favored : 94.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.98 (0.14), residues: 2147 helix: -4.07 (0.09), residues: 819 sheet: -2.19 (0.33), residues: 214 loop : -2.92 (0.16), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.004 TRP A 537 HIS 0.008 0.002 HIS A 326 PHE 0.060 0.004 PHE C 633 TYR 0.044 0.004 TYR B 30 ARG 0.017 0.001 ARG B 249 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 1909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 533 time to evaluate : 2.182 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.4501 (ptp) cc_final: 0.4051 (mtm) REVERT: A 79 ILE cc_start: 0.8001 (mt) cc_final: 0.7784 (mp) REVERT: A 86 MET cc_start: 0.8795 (tpt) cc_final: 0.8517 (tpt) REVERT: A 342 LEU cc_start: 0.8745 (tp) cc_final: 0.8477 (tp) REVERT: A 540 TYR cc_start: 0.9020 (m-80) cc_final: 0.8700 (m-10) REVERT: A 674 ASP cc_start: 0.6162 (t0) cc_final: 0.5854 (t0) REVERT: B 49 TYR cc_start: 0.8897 (m-80) cc_final: 0.8662 (m-10) REVERT: B 87 CYS cc_start: 0.7974 (m) cc_final: 0.7773 (m) REVERT: B 281 LYS cc_start: 0.8027 (mttt) cc_final: 0.7423 (mtpp) REVERT: B 303 THR cc_start: 0.9213 (m) cc_final: 0.8978 (p) REVERT: B 322 ILE cc_start: 0.9280 (pp) cc_final: 0.9065 (pt) REVERT: B 518 ASN cc_start: 0.7223 (m110) cc_final: 0.7007 (m-40) REVERT: B 537 ASN cc_start: 0.8220 (m-40) cc_final: 0.7339 (t0) REVERT: B 663 THR cc_start: 0.8209 (p) cc_final: 0.7995 (m) REVERT: B 665 SER cc_start: 0.8471 (m) cc_final: 0.8150 (t) REVERT: B 720 SER cc_start: 0.8976 (m) cc_final: 0.8543 (t) REVERT: C 46 ARG cc_start: 0.7515 (mmt-90) cc_final: 0.6895 (mmt180) REVERT: C 47 MET cc_start: 0.7108 (tpp) cc_final: 0.6699 (tpp) REVERT: C 160 GLN cc_start: 0.8137 (mt0) cc_final: 0.7708 (pt0) REVERT: C 217 PHE cc_start: 0.6133 (p90) cc_final: 0.5735 (p90) REVERT: C 285 HIS cc_start: 0.6643 (m-70) cc_final: 0.6064 (m-70) REVERT: C 402 MET cc_start: -0.0513 (mtt) cc_final: -0.1115 (mtp) REVERT: C 428 LEU cc_start: 0.4241 (OUTLIER) cc_final: 0.3960 (mp) REVERT: C 526 LYS cc_start: 0.7672 (OUTLIER) cc_final: 0.7409 (tptt) REVERT: C 535 MET cc_start: 0.6616 (mpm) cc_final: 0.5787 (mmm) REVERT: C 536 MET cc_start: 0.3010 (pmm) cc_final: 0.2239 (pmm) REVERT: C 543 GLU cc_start: 0.6362 (OUTLIER) cc_final: 0.5742 (mm-30) REVERT: C 589 ARG cc_start: 0.4514 (OUTLIER) cc_final: 0.3984 (mtp180) outliers start: 29 outliers final: 4 residues processed: 550 average time/residue: 0.3620 time to fit residues: 284.0420 Evaluate side-chains 339 residues out of total 1909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 331 time to evaluate : 2.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 526 LYS Chi-restraints excluded: chain C residue 532 SER Chi-restraints excluded: chain C residue 543 GLU Chi-restraints excluded: chain C residue 589 ARG Chi-restraints excluded: chain C residue 633 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 10.0000 chunk 163 optimal weight: 8.9990 chunk 90 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 169 optimal weight: 1.9990 chunk 65 optimal weight: 0.0770 chunk 102 optimal weight: 7.9990 chunk 126 optimal weight: 2.9990 chunk 196 optimal weight: 50.0000 overall best weight: 0.9142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 ASN A 670 GLN B 58 ASN B 153 ASN B 186 GLN B 284 ASN B 306 ASN B 329 GLN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 649 HIS C 110 HIS C 134 HIS C 182 GLN ** C 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 510 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 18453 Z= 0.217 Angle : 0.695 11.711 25058 Z= 0.362 Chirality : 0.044 0.294 2790 Planarity : 0.005 0.055 3100 Dihedral : 12.397 83.749 2927 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 2.67 % Allowed : 12.41 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.81 (0.15), residues: 2147 helix: -2.64 (0.14), residues: 845 sheet: -2.07 (0.31), residues: 242 loop : -2.50 (0.17), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 537 HIS 0.012 0.001 HIS C 110 PHE 0.038 0.002 PHE C 595 TYR 0.018 0.002 TYR C 205 ARG 0.009 0.001 ARG B 563 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 1909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 396 time to evaluate : 2.108 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.4734 (ptp) cc_final: 0.4299 (mtm) REVERT: A 524 GLU cc_start: 0.7953 (mp0) cc_final: 0.7431 (mp0) REVERT: A 540 TYR cc_start: 0.9040 (m-80) cc_final: 0.8760 (m-10) REVERT: A 674 ASP cc_start: 0.6251 (t0) cc_final: 0.5796 (t0) REVERT: A 691 GLU cc_start: 0.8357 (mt-10) cc_final: 0.8137 (mt-10) REVERT: B 41 ASP cc_start: 0.7844 (t0) cc_final: 0.7497 (t0) REVERT: B 49 TYR cc_start: 0.8880 (m-80) cc_final: 0.8655 (m-10) REVERT: B 87 CYS cc_start: 0.7800 (m) cc_final: 0.7454 (m) REVERT: B 284 ASN cc_start: 0.7911 (m-40) cc_final: 0.7622 (m110) REVERT: B 443 SER cc_start: 0.8774 (t) cc_final: 0.8526 (p) REVERT: B 537 ASN cc_start: 0.8138 (m-40) cc_final: 0.7913 (t0) REVERT: B 601 ILE cc_start: 0.9046 (OUTLIER) cc_final: 0.8763 (tt) REVERT: B 604 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8417 (mp) REVERT: B 608 GLU cc_start: 0.6735 (tt0) cc_final: 0.5765 (tt0) REVERT: B 663 THR cc_start: 0.8259 (p) cc_final: 0.7640 (m) REVERT: B 665 SER cc_start: 0.8514 (m) cc_final: 0.8293 (t) REVERT: C 28 MET cc_start: 0.7428 (tmm) cc_final: 0.7171 (tmm) REVERT: C 47 MET cc_start: 0.7245 (tpp) cc_final: 0.6735 (tpp) REVERT: C 90 MET cc_start: 0.8187 (mpp) cc_final: 0.7683 (mmm) REVERT: C 136 ARG cc_start: 0.5334 (ppt170) cc_final: 0.4662 (mmt90) REVERT: C 146 ASP cc_start: 0.6311 (OUTLIER) cc_final: 0.4823 (t70) REVERT: C 160 GLN cc_start: 0.7921 (mt0) cc_final: 0.7501 (tt0) REVERT: C 171 GLU cc_start: 0.7868 (mp0) cc_final: 0.7481 (pm20) REVERT: C 217 PHE cc_start: 0.5678 (p90) cc_final: 0.5377 (p90) REVERT: C 230 GLU cc_start: 0.7530 (mm-30) cc_final: 0.7303 (mm-30) REVERT: C 254 ASP cc_start: 0.5946 (m-30) cc_final: 0.5567 (m-30) REVERT: C 257 GLN cc_start: 0.7934 (tm-30) cc_final: 0.7602 (tm-30) REVERT: C 428 LEU cc_start: 0.4237 (OUTLIER) cc_final: 0.3910 (mt) REVERT: C 432 HIS cc_start: 0.4545 (m90) cc_final: 0.4312 (m90) REVERT: C 536 MET cc_start: 0.2931 (pmm) cc_final: 0.2726 (pmm) REVERT: C 564 TRP cc_start: 0.5700 (t60) cc_final: 0.4288 (t60) REVERT: C 604 ARG cc_start: 0.4160 (mpt-90) cc_final: 0.3463 (mmp80) outliers start: 51 outliers final: 24 residues processed: 423 average time/residue: 0.3236 time to fit residues: 200.6061 Evaluate side-chains 349 residues out of total 1909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 321 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain B residue 153 ASN Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 476 ASN Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 532 SER Chi-restraints excluded: chain C residue 668 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 109 optimal weight: 5.9990 chunk 60 optimal weight: 0.5980 chunk 163 optimal weight: 10.0000 chunk 133 optimal weight: 0.8980 chunk 54 optimal weight: 0.5980 chunk 196 optimal weight: 8.9990 chunk 212 optimal weight: 0.0040 chunk 175 optimal weight: 9.9990 chunk 194 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 157 optimal weight: 6.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 ASN B 184 HIS B 186 GLN B 292 ASN B 310 ASN ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 676 ASN ** C 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.3888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18453 Z= 0.184 Angle : 0.644 11.257 25058 Z= 0.329 Chirality : 0.043 0.224 2790 Planarity : 0.004 0.043 3100 Dihedral : 11.880 81.689 2912 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.93 % Allowed : 14.88 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.16), residues: 2147 helix: -1.77 (0.16), residues: 849 sheet: -2.16 (0.32), residues: 225 loop : -2.13 (0.17), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 537 HIS 0.004 0.001 HIS A 510 PHE 0.042 0.002 PHE C 595 TYR 0.022 0.001 TYR B 689 ARG 0.006 0.001 ARG C 213 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 366 time to evaluate : 2.151 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.4553 (ptp) cc_final: 0.3944 (mtm) REVERT: A 84 ARG cc_start: 0.7619 (mmm160) cc_final: 0.7415 (mmm160) REVERT: A 234 ASP cc_start: 0.7478 (p0) cc_final: 0.7158 (p0) REVERT: A 595 MET cc_start: 0.7474 (mtp) cc_final: 0.7190 (mtm) REVERT: A 609 LYS cc_start: 0.7274 (OUTLIER) cc_final: 0.7000 (tptt) REVERT: B 41 ASP cc_start: 0.7880 (t0) cc_final: 0.7615 (t0) REVERT: B 45 ARG cc_start: 0.7612 (mtp85) cc_final: 0.7287 (mtm180) REVERT: B 103 PHE cc_start: 0.6912 (m-80) cc_final: 0.6702 (m-80) REVERT: B 126 ARG cc_start: 0.7521 (mtm110) cc_final: 0.7279 (ptm160) REVERT: B 127 GLN cc_start: 0.8220 (pm20) cc_final: 0.8003 (pm20) REVERT: B 176 LYS cc_start: 0.7982 (mppt) cc_final: 0.7702 (mtmt) REVERT: B 303 THR cc_start: 0.9095 (m) cc_final: 0.8858 (p) REVERT: B 321 MET cc_start: 0.8539 (mtt) cc_final: 0.8338 (mtt) REVERT: B 419 LEU cc_start: 0.8991 (tp) cc_final: 0.8731 (tp) REVERT: B 537 ASN cc_start: 0.8316 (m-40) cc_final: 0.7836 (t0) REVERT: B 665 SER cc_start: 0.8648 (m) cc_final: 0.8245 (t) REVERT: B 689 TYR cc_start: 0.3523 (m-80) cc_final: 0.3215 (m-80) REVERT: B 694 ASN cc_start: 0.7957 (m110) cc_final: 0.7658 (t0) REVERT: C 28 MET cc_start: 0.7350 (tmm) cc_final: 0.7101 (tmm) REVERT: C 47 MET cc_start: 0.7378 (tpp) cc_final: 0.6848 (tpp) REVERT: C 146 ASP cc_start: 0.6203 (OUTLIER) cc_final: 0.4960 (t0) REVERT: C 171 GLU cc_start: 0.7784 (mp0) cc_final: 0.7477 (pm20) REVERT: C 217 PHE cc_start: 0.5914 (p90) cc_final: 0.5177 (p90) REVERT: C 230 GLU cc_start: 0.7626 (mm-30) cc_final: 0.7408 (mm-30) REVERT: C 251 ARG cc_start: 0.5086 (mpp80) cc_final: 0.4665 (mmm-85) REVERT: C 312 LYS cc_start: 0.7218 (mttt) cc_final: 0.6839 (mmtt) REVERT: C 331 LYS cc_start: 0.5412 (mttt) cc_final: 0.5117 (mtpt) REVERT: C 428 LEU cc_start: 0.4273 (OUTLIER) cc_final: 0.3779 (mp) REVERT: C 467 MET cc_start: 0.3326 (mpp) cc_final: 0.3044 (mpp) REVERT: C 536 MET cc_start: 0.2845 (pmm) cc_final: 0.2592 (pmm) outliers start: 56 outliers final: 27 residues processed: 391 average time/residue: 0.3335 time to fit residues: 190.2542 Evaluate side-chains 352 residues out of total 1909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 322 time to evaluate : 2.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 609 LYS Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain B residue 30 TYR Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 153 ASN Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 523 MET Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 720 SER Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 668 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 194 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 21 optimal weight: 8.9990 chunk 93 optimal weight: 9.9990 chunk 131 optimal weight: 4.9990 chunk 197 optimal weight: 20.0000 chunk 208 optimal weight: 0.0070 chunk 103 optimal weight: 2.9990 chunk 186 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 overall best weight: 2.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 670 GLN B 153 ASN B 292 ASN ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 ASN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 ASN ** C 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 432 HIS ** C 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.4453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 18453 Z= 0.413 Angle : 0.750 12.848 25058 Z= 0.384 Chirality : 0.047 0.254 2790 Planarity : 0.005 0.048 3100 Dihedral : 12.025 80.811 2911 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 19.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 4.50 % Allowed : 15.24 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.95 (0.17), residues: 2147 helix: -1.67 (0.16), residues: 842 sheet: -2.21 (0.30), residues: 243 loop : -2.09 (0.18), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 537 HIS 0.006 0.001 HIS B 47 PHE 0.028 0.002 PHE C 595 TYR 0.017 0.002 TYR B 467 ARG 0.006 0.001 ARG C 8 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 324 time to evaluate : 1.909 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: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.4243 (ptp) cc_final: 0.3710 (mtm) REVERT: A 155 MET cc_start: -0.0171 (OUTLIER) cc_final: -0.0414 (ptp) REVERT: A 257 ILE cc_start: 0.9366 (OUTLIER) cc_final: 0.9041 (mp) REVERT: A 524 GLU cc_start: 0.8515 (mp0) cc_final: 0.7972 (mp0) REVERT: A 537 TRP cc_start: 0.8242 (m-90) cc_final: 0.7481 (m-10) REVERT: A 566 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7706 (ttt-90) REVERT: A 609 LYS cc_start: 0.7698 (OUTLIER) cc_final: 0.7320 (tptt) REVERT: A 661 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7881 (pm20) REVERT: A 670 GLN cc_start: 0.7511 (tp-100) cc_final: 0.5883 (tp40) REVERT: B 41 ASP cc_start: 0.7973 (t0) cc_final: 0.7705 (t0) REVERT: B 176 LYS cc_start: 0.8292 (mppt) cc_final: 0.7893 (mtmt) REVERT: B 303 THR cc_start: 0.9242 (m) cc_final: 0.8984 (p) REVERT: B 537 ASN cc_start: 0.8500 (m-40) cc_final: 0.7728 (t0) REVERT: B 578 LYS cc_start: 0.7322 (OUTLIER) cc_final: 0.7020 (tmtt) REVERT: B 604 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8386 (mp) REVERT: B 656 GLU cc_start: 0.8019 (pm20) cc_final: 0.7786 (pm20) REVERT: B 665 SER cc_start: 0.8641 (m) cc_final: 0.8344 (t) REVERT: C 46 ARG cc_start: 0.8190 (tpp-160) cc_final: 0.7890 (mmt90) REVERT: C 47 MET cc_start: 0.7308 (tpp) cc_final: 0.6945 (tpp) REVERT: C 171 GLU cc_start: 0.7965 (mp0) cc_final: 0.7755 (pm20) REVERT: C 216 ARG cc_start: 0.6941 (ptp-110) cc_final: 0.6723 (ptp-110) REVERT: C 229 ILE cc_start: 0.9240 (tp) cc_final: 0.8802 (tt) REVERT: C 251 ARG cc_start: 0.5586 (mpp80) cc_final: 0.5148 (mmm-85) REVERT: C 294 MET cc_start: 0.6958 (ppp) cc_final: 0.6739 (ppp) REVERT: C 312 LYS cc_start: 0.7255 (mttt) cc_final: 0.6970 (mmtt) REVERT: C 402 MET cc_start: 0.0267 (mtp) cc_final: -0.0709 (tpp) REVERT: C 428 LEU cc_start: 0.4418 (OUTLIER) cc_final: 0.4145 (mt) REVERT: C 536 MET cc_start: 0.2696 (pmm) cc_final: 0.2467 (pmm) REVERT: C 604 ARG cc_start: 0.4432 (mpt-90) cc_final: 0.3610 (mmp80) outliers start: 86 outliers final: 54 residues processed: 379 average time/residue: 0.3225 time to fit residues: 180.9382 Evaluate side-chains 358 residues out of total 1909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 296 time to evaluate : 2.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain A residue 479 ASP Chi-restraints excluded: chain A residue 509 SER Chi-restraints excluded: chain A residue 566 ARG Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 609 LYS Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 688 GLU Chi-restraints excluded: chain B residue 2 ASP Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 30 TYR Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 476 ASN Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 523 MET Chi-restraints excluded: chain B residue 578 LYS Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain B residue 635 LYS Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain B residue 677 THR Chi-restraints excluded: chain B residue 720 SER Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 110 HIS Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 633 PHE Chi-restraints excluded: chain C residue 668 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 173 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 155 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 178 optimal weight: 6.9990 chunk 144 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 106 optimal weight: 0.8980 chunk 187 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 ASN ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 ASN ** C 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.4867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18453 Z= 0.215 Angle : 0.646 11.550 25058 Z= 0.327 Chirality : 0.044 0.280 2790 Planarity : 0.004 0.039 3100 Dihedral : 11.750 79.486 2911 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 3.88 % Allowed : 16.76 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.17), residues: 2147 helix: -1.28 (0.17), residues: 838 sheet: -2.05 (0.31), residues: 251 loop : -1.93 (0.18), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 78 HIS 0.002 0.001 HIS A 146 PHE 0.030 0.001 PHE C 595 TYR 0.021 0.001 TYR B 689 ARG 0.006 0.000 ARG B 572 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 317 time to evaluate : 2.058 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: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.4428 (ptp) cc_final: 0.3905 (mtm) REVERT: A 257 ILE cc_start: 0.9315 (OUTLIER) cc_final: 0.8906 (mp) REVERT: A 524 GLU cc_start: 0.8380 (mp0) cc_final: 0.7843 (mp0) REVERT: A 609 LYS cc_start: 0.7664 (OUTLIER) cc_final: 0.7345 (tptt) REVERT: A 661 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7836 (pm20) REVERT: A 670 GLN cc_start: 0.7193 (tp-100) cc_final: 0.6980 (tp-100) REVERT: B 20 THR cc_start: 0.8963 (OUTLIER) cc_final: 0.8508 (m) REVERT: B 126 ARG cc_start: 0.7535 (mtm110) cc_final: 0.7221 (ptm160) REVERT: B 133 LEU cc_start: 0.8866 (mm) cc_final: 0.8538 (mp) REVERT: B 176 LYS cc_start: 0.8250 (mppt) cc_final: 0.7936 (mtmt) REVERT: B 303 THR cc_start: 0.9173 (m) cc_final: 0.8872 (p) REVERT: B 358 GLU cc_start: 0.7473 (tm-30) cc_final: 0.7200 (tm-30) REVERT: B 537 ASN cc_start: 0.8364 (m-40) cc_final: 0.7898 (t0) REVERT: B 578 LYS cc_start: 0.7254 (OUTLIER) cc_final: 0.6851 (pttp) REVERT: B 665 SER cc_start: 0.8608 (m) cc_final: 0.8385 (t) REVERT: B 694 ASN cc_start: 0.8071 (m110) cc_final: 0.7566 (t0) REVERT: C 46 ARG cc_start: 0.7994 (tpp-160) cc_final: 0.7596 (mmt90) REVERT: C 187 LYS cc_start: 0.8307 (pptt) cc_final: 0.7821 (mtmt) REVERT: C 209 ARG cc_start: 0.7274 (tpm170) cc_final: 0.6890 (tpm170) REVERT: C 229 ILE cc_start: 0.9204 (OUTLIER) cc_final: 0.8870 (tt) REVERT: C 251 ARG cc_start: 0.5603 (mpp80) cc_final: 0.5228 (mmm-85) REVERT: C 266 ILE cc_start: 0.7781 (mm) cc_final: 0.7539 (mm) REVERT: C 294 MET cc_start: 0.6965 (ppp) cc_final: 0.6661 (ppp) REVERT: C 331 LYS cc_start: 0.5512 (mttt) cc_final: 0.5208 (mtpt) REVERT: C 428 LEU cc_start: 0.4471 (OUTLIER) cc_final: 0.4099 (mt) REVERT: C 536 MET cc_start: 0.2499 (pmm) cc_final: 0.2118 (pmm) REVERT: C 604 ARG cc_start: 0.4310 (mpt-90) cc_final: 0.3839 (mmp80) outliers start: 74 outliers final: 39 residues processed: 363 average time/residue: 0.3093 time to fit residues: 166.1108 Evaluate side-chains 341 residues out of total 1909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 295 time to evaluate : 2.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain A residue 479 ASP Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 609 LYS Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 688 GLU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 30 TYR Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 476 ASN Chi-restraints excluded: chain B residue 477 MET Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 523 MET Chi-restraints excluded: chain B residue 578 LYS Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 635 LYS Chi-restraints excluded: chain B residue 677 THR Chi-restraints excluded: chain B residue 720 SER Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 609 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 70 optimal weight: 0.5980 chunk 188 optimal weight: 6.9990 chunk 41 optimal weight: 0.8980 chunk 122 optimal weight: 0.8980 chunk 51 optimal weight: 8.9990 chunk 208 optimal weight: 3.9990 chunk 173 optimal weight: 0.0980 chunk 96 optimal weight: 0.1980 chunk 17 optimal weight: 0.4980 chunk 69 optimal weight: 0.9990 chunk 109 optimal weight: 7.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 ASN B 16 ASN ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.5181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18453 Z= 0.168 Angle : 0.629 10.686 25058 Z= 0.317 Chirality : 0.043 0.268 2790 Planarity : 0.004 0.045 3100 Dihedral : 11.574 79.468 2911 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.99 % Allowed : 18.18 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.17), residues: 2147 helix: -1.03 (0.17), residues: 832 sheet: -1.99 (0.32), residues: 222 loop : -1.79 (0.18), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 537 HIS 0.004 0.001 HIS A 146 PHE 0.032 0.001 PHE C 595 TYR 0.025 0.001 TYR B 689 ARG 0.007 0.000 ARG C 216 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 330 time to evaluate : 1.810 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 12 MET cc_start: 0.4405 (ptp) cc_final: 0.3939 (mtm) REVERT: A 358 LYS cc_start: 0.8518 (tptm) cc_final: 0.8205 (tptt) REVERT: A 410 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7575 (mt-10) REVERT: A 524 GLU cc_start: 0.8419 (mp0) cc_final: 0.7896 (mp0) REVERT: A 583 ARG cc_start: 0.8413 (mtm110) cc_final: 0.8196 (mtm180) REVERT: A 609 LYS cc_start: 0.7609 (OUTLIER) cc_final: 0.7305 (tptt) REVERT: A 661 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7586 (pm20) REVERT: A 670 GLN cc_start: 0.6628 (tp-100) cc_final: 0.6229 (tp-100) REVERT: B 20 THR cc_start: 0.8883 (OUTLIER) cc_final: 0.8563 (m) REVERT: B 116 GLN cc_start: 0.8046 (pp30) cc_final: 0.7822 (mm-40) REVERT: B 284 ASN cc_start: 0.7514 (m-40) cc_final: 0.7200 (m110) REVERT: B 303 THR cc_start: 0.9136 (m) cc_final: 0.8834 (p) REVERT: B 358 GLU cc_start: 0.7467 (tm-30) cc_final: 0.7184 (tm-30) REVERT: B 497 TYR cc_start: 0.8057 (t80) cc_final: 0.7844 (t80) REVERT: B 537 ASN cc_start: 0.8344 (m-40) cc_final: 0.7864 (t0) REVERT: B 578 LYS cc_start: 0.7346 (OUTLIER) cc_final: 0.6965 (pttp) REVERT: B 694 ASN cc_start: 0.8088 (m110) cc_final: 0.7697 (t0) REVERT: C 187 LYS cc_start: 0.8302 (pptt) cc_final: 0.7765 (mtmt) REVERT: C 209 ARG cc_start: 0.7254 (tpm170) cc_final: 0.7041 (tpm170) REVERT: C 229 ILE cc_start: 0.9161 (tp) cc_final: 0.8793 (tt) REVERT: C 251 ARG cc_start: 0.5413 (mpp80) cc_final: 0.5110 (mmm-85) REVERT: C 285 HIS cc_start: 0.7562 (m-70) cc_final: 0.7353 (m-70) REVERT: C 294 MET cc_start: 0.6926 (ppp) cc_final: 0.6612 (ppp) REVERT: C 331 LYS cc_start: 0.5318 (mttt) cc_final: 0.5099 (mttt) REVERT: C 428 LEU cc_start: 0.4447 (OUTLIER) cc_final: 0.4244 (mt) REVERT: C 604 ARG cc_start: 0.4123 (mpt-90) cc_final: 0.3897 (mmp80) outliers start: 57 outliers final: 36 residues processed: 369 average time/residue: 0.3203 time to fit residues: 175.1901 Evaluate side-chains 351 residues out of total 1909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 309 time to evaluate : 2.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 479 ASP Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 609 LYS Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 688 GLU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 30 TYR Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 476 ASN Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 523 MET Chi-restraints excluded: chain B residue 578 LYS Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 635 LYS Chi-restraints excluded: chain B residue 677 THR Chi-restraints excluded: chain B residue 720 SER Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 564 TRP Chi-restraints excluded: chain C residue 609 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 201 optimal weight: 6.9990 chunk 23 optimal weight: 0.5980 chunk 119 optimal weight: 0.6980 chunk 152 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 175 optimal weight: 9.9990 chunk 116 optimal weight: 1.9990 chunk 208 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 chunk 126 optimal weight: 0.6980 chunk 96 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 ASN ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 634 HIS ** C 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.5401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18453 Z= 0.190 Angle : 0.650 11.943 25058 Z= 0.323 Chirality : 0.043 0.300 2790 Planarity : 0.004 0.044 3100 Dihedral : 11.525 79.396 2911 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 3.09 % Allowed : 18.81 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.17), residues: 2147 helix: -0.93 (0.17), residues: 841 sheet: -1.86 (0.32), residues: 238 loop : -1.71 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 309 HIS 0.004 0.001 HIS A 437 PHE 0.032 0.001 PHE C 595 TYR 0.021 0.001 TYR B 689 ARG 0.011 0.000 ARG B 563 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 321 time to evaluate : 2.089 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 12 MET cc_start: 0.4393 (ptp) cc_final: 0.3937 (mtm) REVERT: A 358 LYS cc_start: 0.8429 (tptm) cc_final: 0.8171 (tptt) REVERT: A 410 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7600 (mt-10) REVERT: A 461 LYS cc_start: 0.8593 (ttpt) cc_final: 0.8346 (ttpp) REVERT: A 524 GLU cc_start: 0.8490 (mp0) cc_final: 0.7993 (mp0) REVERT: A 595 MET cc_start: 0.7934 (mtm) cc_final: 0.7365 (mtm) REVERT: A 609 LYS cc_start: 0.7693 (OUTLIER) cc_final: 0.7367 (tptt) REVERT: A 661 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7701 (pm20) REVERT: A 670 GLN cc_start: 0.6914 (tp-100) cc_final: 0.6540 (tp-100) REVERT: A 688 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7310 (mp0) REVERT: B 20 THR cc_start: 0.8862 (OUTLIER) cc_final: 0.8542 (m) REVERT: B 116 GLN cc_start: 0.8095 (pp30) cc_final: 0.7889 (mm-40) REVERT: B 277 GLU cc_start: 0.8011 (tm-30) cc_final: 0.7688 (tp30) REVERT: B 303 THR cc_start: 0.9171 (m) cc_final: 0.8837 (p) REVERT: B 358 GLU cc_start: 0.7472 (tm-30) cc_final: 0.7193 (tm-30) REVERT: B 497 TYR cc_start: 0.8188 (t80) cc_final: 0.7858 (t80) REVERT: B 537 ASN cc_start: 0.8490 (m-40) cc_final: 0.7927 (t0) REVERT: B 694 ASN cc_start: 0.8011 (m110) cc_final: 0.7642 (t0) REVERT: C 89 VAL cc_start: 0.8320 (m) cc_final: 0.8084 (p) REVERT: C 187 LYS cc_start: 0.8323 (pptt) cc_final: 0.7791 (mtmt) REVERT: C 209 ARG cc_start: 0.7309 (tpm170) cc_final: 0.7070 (tpm170) REVERT: C 229 ILE cc_start: 0.9198 (tp) cc_final: 0.8851 (tt) REVERT: C 251 ARG cc_start: 0.5494 (mpp80) cc_final: 0.5196 (mmm-85) REVERT: C 266 ILE cc_start: 0.7716 (mm) cc_final: 0.7378 (mm) REVERT: C 294 MET cc_start: 0.6879 (ppp) cc_final: 0.6634 (ppp) REVERT: C 331 LYS cc_start: 0.5326 (mttt) cc_final: 0.5085 (mttt) REVERT: C 428 LEU cc_start: 0.4441 (OUTLIER) cc_final: 0.4132 (mt) REVERT: C 536 MET cc_start: 0.2698 (pmm) cc_final: 0.2312 (pmm) outliers start: 59 outliers final: 43 residues processed: 355 average time/residue: 0.3085 time to fit residues: 163.1883 Evaluate side-chains 352 residues out of total 1909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 303 time to evaluate : 2.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain A residue 479 ASP Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 609 LYS Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 688 GLU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 30 TYR Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 476 ASN Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 523 MET Chi-restraints excluded: chain B residue 538 ASP Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain B residue 677 THR Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 668 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 128 optimal weight: 0.7980 chunk 83 optimal weight: 4.9990 chunk 124 optimal weight: 0.6980 chunk 62 optimal weight: 0.0370 chunk 40 optimal weight: 2.9990 chunk 132 optimal weight: 0.6980 chunk 141 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 163 optimal weight: 10.0000 chunk 189 optimal weight: 5.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 ASN ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.5583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 18453 Z= 0.182 Angle : 0.666 11.927 25058 Z= 0.333 Chirality : 0.043 0.275 2790 Planarity : 0.004 0.059 3100 Dihedral : 11.460 79.638 2911 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 3.30 % Allowed : 19.02 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.18), residues: 2147 helix: -0.76 (0.18), residues: 831 sheet: -1.67 (0.33), residues: 235 loop : -1.68 (0.18), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 309 HIS 0.005 0.001 HIS A 437 PHE 0.032 0.001 PHE C 595 TYR 0.030 0.001 TYR A 130 ARG 0.012 0.000 ARG A 204 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 317 time to evaluate : 1.987 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: symmetry clash REVERT: A 12 MET cc_start: 0.4372 (ptp) cc_final: 0.3931 (mtm) REVERT: A 311 MET cc_start: 0.7880 (pmm) cc_final: 0.7549 (mtm) REVERT: A 358 LYS cc_start: 0.8412 (tptm) cc_final: 0.8165 (tptt) REVERT: A 410 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7598 (mt-10) REVERT: A 461 LYS cc_start: 0.8573 (ttpt) cc_final: 0.8342 (ttpp) REVERT: A 524 GLU cc_start: 0.8473 (mp0) cc_final: 0.7991 (mp0) REVERT: A 595 MET cc_start: 0.7960 (mtm) cc_final: 0.7561 (mtm) REVERT: A 609 LYS cc_start: 0.7591 (OUTLIER) cc_final: 0.7286 (tptt) REVERT: A 661 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7860 (pm20) REVERT: A 670 GLN cc_start: 0.6912 (tp-100) cc_final: 0.6506 (tp-100) REVERT: B 20 THR cc_start: 0.8805 (OUTLIER) cc_final: 0.8579 (m) REVERT: B 116 GLN cc_start: 0.8099 (pp30) cc_final: 0.7859 (mm-40) REVERT: B 223 THR cc_start: 0.8752 (m) cc_final: 0.8521 (m) REVERT: B 303 THR cc_start: 0.9184 (m) cc_final: 0.8833 (p) REVERT: B 358 GLU cc_start: 0.7469 (tm-30) cc_final: 0.7181 (tm-30) REVERT: B 414 MET cc_start: 0.6694 (OUTLIER) cc_final: 0.5516 (tpt) REVERT: B 470 CYS cc_start: 0.8077 (m) cc_final: 0.7830 (m) REVERT: B 497 TYR cc_start: 0.8173 (t80) cc_final: 0.7789 (t80) REVERT: B 537 ASN cc_start: 0.8473 (m-40) cc_final: 0.7896 (t0) REVERT: B 578 LYS cc_start: 0.7189 (OUTLIER) cc_final: 0.6908 (tmtt) REVERT: B 694 ASN cc_start: 0.7998 (m110) cc_final: 0.7694 (t0) REVERT: C 89 VAL cc_start: 0.8324 (m) cc_final: 0.8114 (p) REVERT: C 187 LYS cc_start: 0.8293 (pptt) cc_final: 0.7741 (mtmt) REVERT: C 209 ARG cc_start: 0.7321 (tpm170) cc_final: 0.7048 (tpm170) REVERT: C 229 ILE cc_start: 0.9054 (tp) cc_final: 0.8717 (tt) REVERT: C 251 ARG cc_start: 0.5394 (mpp80) cc_final: 0.5137 (mmm-85) REVERT: C 266 ILE cc_start: 0.7645 (mm) cc_final: 0.7318 (mm) REVERT: C 294 MET cc_start: 0.6857 (ppp) cc_final: 0.6649 (ppp) REVERT: C 331 LYS cc_start: 0.5292 (mttt) cc_final: 0.5038 (mtpt) REVERT: C 428 LEU cc_start: 0.4377 (OUTLIER) cc_final: 0.3952 (mp) REVERT: C 536 MET cc_start: 0.2596 (pmm) cc_final: 0.2226 (pmm) REVERT: C 551 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.8089 (pp30) outliers start: 63 outliers final: 43 residues processed: 354 average time/residue: 0.3079 time to fit residues: 162.2995 Evaluate side-chains 342 residues out of total 1909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 291 time to evaluate : 2.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 479 ASP Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 609 LYS Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 688 GLU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 30 TYR Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 476 ASN Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 578 LYS Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 635 LYS Chi-restraints excluded: chain B residue 677 THR Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 420 PHE Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 551 GLN Chi-restraints excluded: chain C residue 564 TRP Chi-restraints excluded: chain C residue 609 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 199 optimal weight: 1.9990 chunk 181 optimal weight: 30.0000 chunk 194 optimal weight: 0.6980 chunk 116 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 152 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 175 optimal weight: 10.0000 chunk 183 optimal weight: 5.9990 chunk 193 optimal weight: 0.9980 chunk 127 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.5714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18453 Z= 0.196 Angle : 0.680 12.172 25058 Z= 0.337 Chirality : 0.043 0.284 2790 Planarity : 0.004 0.065 3100 Dihedral : 11.430 79.387 2911 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 3.51 % Allowed : 18.96 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.18), residues: 2147 helix: -0.76 (0.18), residues: 843 sheet: -1.64 (0.33), residues: 235 loop : -1.67 (0.19), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 309 HIS 0.005 0.001 HIS A 437 PHE 0.032 0.001 PHE C 595 TYR 0.019 0.001 TYR B 689 ARG 0.016 0.001 ARG A 583 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 305 time to evaluate : 2.083 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: symmetry clash REVERT: A 12 MET cc_start: 0.4417 (ptp) cc_final: 0.3941 (mtm) REVERT: A 94 ILE cc_start: 0.8600 (mt) cc_final: 0.8386 (tp) REVERT: A 311 MET cc_start: 0.7684 (pmm) cc_final: 0.7475 (mtm) REVERT: A 358 LYS cc_start: 0.8362 (tptm) cc_final: 0.8084 (tptt) REVERT: A 410 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7625 (mt-10) REVERT: A 524 GLU cc_start: 0.8430 (mp0) cc_final: 0.7935 (mp0) REVERT: A 661 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7922 (pm20) REVERT: A 670 GLN cc_start: 0.6908 (tp-100) cc_final: 0.6466 (tp-100) REVERT: B 20 THR cc_start: 0.8838 (OUTLIER) cc_final: 0.8574 (m) REVERT: B 45 ARG cc_start: 0.8185 (mtm-85) cc_final: 0.7926 (mtp85) REVERT: B 223 THR cc_start: 0.8738 (m) cc_final: 0.8490 (m) REVERT: B 303 THR cc_start: 0.9163 (m) cc_final: 0.8839 (p) REVERT: B 358 GLU cc_start: 0.7489 (tm-30) cc_final: 0.7183 (tm-30) REVERT: B 414 MET cc_start: 0.6864 (OUTLIER) cc_final: 0.5598 (tpt) REVERT: B 470 CYS cc_start: 0.8082 (m) cc_final: 0.7839 (m) REVERT: B 497 TYR cc_start: 0.8198 (t80) cc_final: 0.7806 (t80) REVERT: B 537 ASN cc_start: 0.8513 (m-40) cc_final: 0.7994 (t0) REVERT: B 578 LYS cc_start: 0.7108 (OUTLIER) cc_final: 0.6760 (tmtt) REVERT: B 694 ASN cc_start: 0.8023 (m110) cc_final: 0.7703 (t0) REVERT: B 706 ARG cc_start: 0.7596 (mtp-110) cc_final: 0.7202 (ttm-80) REVERT: C 53 MET cc_start: 0.5789 (mmt) cc_final: 0.5226 (mmt) REVERT: C 89 VAL cc_start: 0.8360 (m) cc_final: 0.8135 (p) REVERT: C 164 MET cc_start: 0.8097 (mmm) cc_final: 0.7180 (mmp) REVERT: C 187 LYS cc_start: 0.8301 (pptt) cc_final: 0.7738 (mtmt) REVERT: C 209 ARG cc_start: 0.7152 (tpm170) cc_final: 0.6886 (tpm170) REVERT: C 229 ILE cc_start: 0.9134 (tp) cc_final: 0.8822 (tt) REVERT: C 251 ARG cc_start: 0.5395 (mpp80) cc_final: 0.5130 (mmm-85) REVERT: C 266 ILE cc_start: 0.7557 (mm) cc_final: 0.7243 (mm) REVERT: C 294 MET cc_start: 0.6955 (ppp) cc_final: 0.6663 (ppp) REVERT: C 331 LYS cc_start: 0.5402 (mttt) cc_final: 0.5168 (mtpt) REVERT: C 428 LEU cc_start: 0.4195 (OUTLIER) cc_final: 0.3877 (mp) REVERT: C 536 MET cc_start: 0.2597 (pmm) cc_final: 0.2218 (pmm) REVERT: C 570 MET cc_start: 0.7179 (ppp) cc_final: 0.6870 (ppp) outliers start: 67 outliers final: 51 residues processed: 346 average time/residue: 0.3111 time to fit residues: 162.2346 Evaluate side-chains 353 residues out of total 1909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 296 time to evaluate : 1.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 479 ASP Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 688 GLU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 30 TYR Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 476 ASN Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 538 ASP Chi-restraints excluded: chain B residue 578 LYS Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 635 LYS Chi-restraints excluded: chain B residue 677 THR Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 420 PHE Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 551 GLN Chi-restraints excluded: chain C residue 564 TRP Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 668 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 205 optimal weight: 5.9990 chunk 125 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 142 optimal weight: 0.9980 chunk 215 optimal weight: 7.9990 chunk 198 optimal weight: 6.9990 chunk 171 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 132 optimal weight: 1.9990 chunk 105 optimal weight: 0.0470 chunk 136 optimal weight: 9.9990 overall best weight: 1.5882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 GLN ** B 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 HIS ** C 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.5884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18453 Z= 0.275 Angle : 0.730 14.040 25058 Z= 0.362 Chirality : 0.045 0.310 2790 Planarity : 0.004 0.069 3100 Dihedral : 11.513 79.386 2911 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 3.46 % Allowed : 18.96 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.17), residues: 2147 helix: -0.91 (0.17), residues: 853 sheet: -1.71 (0.32), residues: 239 loop : -1.73 (0.19), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 309 HIS 0.005 0.001 HIS A 437 PHE 0.032 0.002 PHE C 595 TYR 0.022 0.002 TYR A 564 ARG 0.014 0.001 ARG A 583 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 304 time to evaluate : 2.100 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 12 MET cc_start: 0.4635 (ptp) cc_final: 0.4164 (mtm) REVERT: A 94 ILE cc_start: 0.8589 (mt) cc_final: 0.8381 (tp) REVERT: A 311 MET cc_start: 0.7784 (pmm) cc_final: 0.7577 (mtm) REVERT: A 410 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7688 (mt-10) REVERT: A 524 GLU cc_start: 0.8544 (mp0) cc_final: 0.8051 (mp0) REVERT: A 661 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7904 (pm20) REVERT: A 670 GLN cc_start: 0.6993 (tp-100) cc_final: 0.6581 (tp40) REVERT: B 20 THR cc_start: 0.8937 (OUTLIER) cc_final: 0.8439 (m) REVERT: B 45 ARG cc_start: 0.8232 (mtm-85) cc_final: 0.7971 (mtp85) REVERT: B 223 THR cc_start: 0.8816 (m) cc_final: 0.8603 (m) REVERT: B 303 THR cc_start: 0.9192 (m) cc_final: 0.8902 (p) REVERT: B 358 GLU cc_start: 0.7596 (tm-30) cc_final: 0.7342 (tm-30) REVERT: B 470 CYS cc_start: 0.8066 (m) cc_final: 0.7851 (m) REVERT: B 497 TYR cc_start: 0.8271 (t80) cc_final: 0.7852 (t80) REVERT: B 537 ASN cc_start: 0.8548 (m-40) cc_final: 0.8062 (t0) REVERT: B 578 LYS cc_start: 0.7307 (OUTLIER) cc_final: 0.6950 (tmtt) REVERT: B 604 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8231 (mp) REVERT: B 694 ASN cc_start: 0.7995 (m110) cc_final: 0.7678 (t0) REVERT: C 53 MET cc_start: 0.5908 (mmt) cc_final: 0.5671 (mmt) REVERT: C 89 VAL cc_start: 0.8373 (m) cc_final: 0.8147 (p) REVERT: C 187 LYS cc_start: 0.8368 (pptt) cc_final: 0.7767 (mtmt) REVERT: C 216 ARG cc_start: 0.6919 (ptp-110) cc_final: 0.6712 (ptp-110) REVERT: C 229 ILE cc_start: 0.9284 (OUTLIER) cc_final: 0.8973 (tt) REVERT: C 251 ARG cc_start: 0.5456 (mpp80) cc_final: 0.5248 (mmm-85) REVERT: C 266 ILE cc_start: 0.7574 (mm) cc_final: 0.7317 (mm) REVERT: C 294 MET cc_start: 0.7083 (ppp) cc_final: 0.6634 (ppp) REVERT: C 331 LYS cc_start: 0.5523 (mttt) cc_final: 0.5313 (mtpt) REVERT: C 428 LEU cc_start: 0.4161 (OUTLIER) cc_final: 0.3837 (mp) REVERT: C 467 MET cc_start: 0.4554 (mpp) cc_final: 0.4168 (mpp) REVERT: C 536 MET cc_start: 0.2564 (pmm) cc_final: 0.2019 (pmm) REVERT: C 552 TRP cc_start: 0.6284 (t60) cc_final: 0.6004 (t-100) REVERT: C 570 MET cc_start: 0.7141 (ppp) cc_final: 0.6841 (ppp) REVERT: C 575 MET cc_start: 0.5310 (tmm) cc_final: 0.4964 (tmm) outliers start: 66 outliers final: 48 residues processed: 344 average time/residue: 0.3121 time to fit residues: 161.4221 Evaluate side-chains 352 residues out of total 1909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 297 time to evaluate : 2.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 479 ASP Chi-restraints excluded: chain A residue 481 GLN Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 688 GLU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 476 ASN Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 538 ASP Chi-restraints excluded: chain B residue 578 LYS Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain B residue 635 LYS Chi-restraints excluded: chain B residue 677 THR Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 420 PHE Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 551 GLN Chi-restraints excluded: chain C residue 564 TRP Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 668 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 20.0000 chunk 52 optimal weight: 0.7980 chunk 158 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 171 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 176 optimal weight: 1.9990 chunk 21 optimal weight: 0.1980 chunk 31 optimal weight: 4.9990 chunk 150 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.180270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.138221 restraints weight = 31943.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.134397 restraints weight = 22153.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.135612 restraints weight = 20256.178| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.6035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18453 Z= 0.195 Angle : 0.703 15.554 25058 Z= 0.347 Chirality : 0.044 0.291 2790 Planarity : 0.004 0.065 3100 Dihedral : 11.378 80.386 2911 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.88 % Allowed : 19.54 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.18), residues: 2147 helix: -0.71 (0.18), residues: 835 sheet: -1.71 (0.31), residues: 248 loop : -1.62 (0.19), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 309 HIS 0.005 0.001 HIS A 437 PHE 0.033 0.001 PHE C 595 TYR 0.018 0.001 TYR B 689 ARG 0.014 0.001 ARG A 583 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4094.42 seconds wall clock time: 74 minutes 54.18 seconds (4494.18 seconds total)