Starting phenix.real_space_refine on Tue Aug 26 23:04:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6row_4975/08_2025/6row_4975.cif Found real_map, /net/cci-nas-00/data/ceres_data/6row_4975/08_2025/6row_4975.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6row_4975/08_2025/6row_4975.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6row_4975/08_2025/6row_4975.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6row_4975/08_2025/6row_4975.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6row_4975/08_2025/6row_4975.map" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 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 S 122 5.16 5 C 14378 2.51 5 N 4012 2.21 5 O 4381 1.98 5 H 20156 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 43049 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 9475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 9475 Classifications: {'peptide': 596} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 570} Chain breaks: 15 Chain: "B" Number of atoms: 9828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 619, 9828 Classifications: {'peptide': 619} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 590} Chain breaks: 14 Chain: "C" Number of atoms: 9290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 9290 Classifications: {'peptide': 583} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 558} Chain breaks: 15 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 8988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 8988 Classifications: {'peptide': 566} Link IDs: {'PTRANS': 27, 'TRANS': 538} Chain breaks: 14 Chain: "E" Number of atoms: 2133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2133 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 15, 'TRANS': 283} Chain breaks: 4 Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 887 Unresolved non-hydrogen angles: 1151 Unresolved non-hydrogen dihedrals: 744 Unresolved non-hydrogen chiralities: 86 Planarities with less than four sites: {'GLU:plan': 12, 'TYR:plan': 13, 'GLN:plan1': 14, 'PHE:plan': 18, 'HIS:plan': 2, 'ASP:plan': 16, 'ASN:plan1': 15, 'TRP:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 477 Chain: "F" Number of atoms: 2093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2093 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 13, 'TRANS': 279} Chain breaks: 4 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 873 Unresolved non-hydrogen angles: 1132 Unresolved non-hydrogen dihedrals: 731 Unresolved non-hydrogen chiralities: 84 Planarities with less than four sites: {'GLU:plan': 12, 'TYR:plan': 13, 'GLN:plan1': 13, 'PHE:plan': 17, 'HIS:plan': 2, 'ASP:plan': 18, 'ASN:plan1': 15, 'TRP:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 473 Chain: "G" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1242 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain breaks: 8 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 557 Unresolved non-hydrogen angles: 720 Unresolved non-hydrogen dihedrals: 493 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'ASP:plan': 10, 'ARG:plan': 12, 'TRP:plan': 5, 'ASN:plan1': 5, 'PHE:plan': 12, 'GLN:plan1': 5, 'GLU:plan': 6, 'TYR:plan': 8, 'HIS:plan': 4} Unresolved non-hydrogen planarities: 342 Time building chain proxies: 7.17, per 1000 atoms: 0.17 Number of scatterers: 43049 At special positions: 0 Unit cell: (136.32, 176.79, 183.18, 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 122 16.00 O 4381 8.00 N 4012 7.00 C 14378 6.00 H 20156 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=19, symmetry=0 Simple disulfide: pdb=" SG CYS A 106 " - pdb=" SG CYS A 818 " distance=2.02 Simple disulfide: pdb=" SG CYS A 114 " - pdb=" SG CYS A 778 " distance=2.01 Simple disulfide: pdb=" SG CYS A 173 " - pdb=" SG CYS A 466 " distance=2.03 Simple disulfide: pdb=" SG CYS A 700 " - pdb=" SG CYS A 832 " distance=2.02 Simple disulfide: pdb=" SG CYS A 709 " - pdb=" SG CYS A 719 " distance=2.57 Simple disulfide: pdb=" SG CYS B 106 " - pdb=" SG CYS B 818 " distance=2.18 Simple disulfide: pdb=" SG CYS B 114 " - pdb=" SG CYS B 778 " distance=2.06 Simple disulfide: pdb=" SG CYS B 173 " - pdb=" SG CYS B 466 " distance=2.02 Simple disulfide: pdb=" SG CYS B 700 " - pdb=" SG CYS B 832 " distance=2.02 Simple disulfide: pdb=" SG CYS B 709 " - pdb=" SG CYS B 719 " distance=2.04 Simple disulfide: pdb=" SG CYS C 106 " - pdb=" SG CYS C 818 " distance=2.05 Simple disulfide: pdb=" SG CYS C 114 " - pdb=" SG CYS C 778 " distance=2.70 Simple disulfide: pdb=" SG CYS C 173 " - pdb=" SG CYS C 466 " distance=2.03 Simple disulfide: pdb=" SG CYS C 700 " - pdb=" SG CYS C 832 " distance=2.02 Simple disulfide: pdb=" SG CYS C 709 " - pdb=" SG CYS C 719 " distance=2.02 Simple disulfide: pdb=" SG CYS D 106 " - pdb=" SG CYS D 818 " distance=2.03 Simple disulfide: pdb=" SG CYS D 114 " - pdb=" SG CYS D 778 " distance=1.87 Simple disulfide: pdb=" SG CYS D 173 " - pdb=" SG CYS D 466 " distance=2.02 Simple disulfide: pdb=" SG CYS D 700 " - pdb=" SG CYS D 832 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.97 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 476.8 nanoseconds 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5828 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 19 sheets defined 49.6% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 85 through 97 Processing helix chain 'A' and resid 109 through 121 removed outlier: 7.052A pdb=" N LYS A 116 " --> pdb=" O PHE A 112 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N PHE A 117 " --> pdb=" O THR A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 150 removed outlier: 3.565A pdb=" N GLU A 150 " --> pdb=" O VAL A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 172 Processing helix chain 'A' and resid 185 through 197 removed outlier: 3.832A pdb=" N LEU A 189 " --> pdb=" O SER A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 225 Processing helix chain 'A' and resid 267 through 285 Processing helix chain 'A' and resid 297 through 316 removed outlier: 5.007A pdb=" N ARG A 303 " --> pdb=" O LYS A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 361 Processing helix chain 'A' and resid 382 through 389 Processing helix chain 'A' and resid 390 through 393 removed outlier: 3.914A pdb=" N PHE A 393 " --> pdb=" O ASN A 390 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 390 through 393' Processing helix chain 'A' and resid 401 through 416 removed outlier: 3.510A pdb=" N TYR A 408 " --> pdb=" O PRO A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 474 removed outlier: 3.986A pdb=" N CYS A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 487 Processing helix chain 'A' and resid 489 through 494 Processing helix chain 'A' and resid 494 through 510 removed outlier: 4.811A pdb=" N GLU A 501 " --> pdb=" O LYS A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 533 Processing helix chain 'A' and resid 561 through 567 Processing helix chain 'A' and resid 581 through 594 removed outlier: 3.547A pdb=" N GLY A 588 " --> pdb=" O ILE A 584 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR A 589 " --> pdb=" O LEU A 585 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER A 594 " --> pdb=" O GLU A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 600 removed outlier: 3.958A pdb=" N LYS A 598 " --> pdb=" O PHE A 595 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASN A 599 " --> pdb=" O ARG A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 634 removed outlier: 3.592A pdb=" N THR A 633 " --> pdb=" O GLY A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 649 removed outlier: 3.654A pdb=" N ASN A 646 " --> pdb=" O PRO A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 661 Processing helix chain 'A' and resid 665 through 669 Processing helix chain 'A' and resid 690 through 707 removed outlier: 3.612A pdb=" N CYS A 700 " --> pdb=" O ASP A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 749 removed outlier: 5.433A pdb=" N GLU A 728 " --> pdb=" O HIS A 724 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ALA A 731 " --> pdb=" O GLY A 727 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLN A 737 " --> pdb=" O LEU A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 777 removed outlier: 3.748A pdb=" N ILE A 768 " --> pdb=" O THR A 764 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N TRP A 777 " --> pdb=" O TYR A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 793 removed outlier: 3.714A pdb=" N VAL A 787 " --> pdb=" O GLN A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 797 through 806 removed outlier: 3.584A pdb=" N LEU A 806 " --> pdb=" O VAL A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 816 Processing helix chain 'B' and resid 85 through 97 removed outlier: 3.528A pdb=" N LYS B 89 " --> pdb=" O SER B 85 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN B 90 " --> pdb=" O LYS B 86 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU B 95 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE B 97 " --> pdb=" O ASN B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 121 removed outlier: 3.578A pdb=" N PHE B 112 " --> pdb=" O ASP B 108 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N LYS B 116 " --> pdb=" O PHE B 112 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N PHE B 117 " --> pdb=" O THR B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 150 Processing helix chain 'B' and resid 162 through 175 Processing helix chain 'B' and resid 187 through 195 Processing helix chain 'B' and resid 212 through 225 Processing helix chain 'B' and resid 269 through 277 removed outlier: 3.543A pdb=" N LYS B 274 " --> pdb=" O ASP B 270 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA B 275 " --> pdb=" O ALA B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 282 Processing helix chain 'B' and resid 295 through 314 Processing helix chain 'B' and resid 318 through 322 Processing helix chain 'B' and resid 324 through 329 removed outlier: 3.808A pdb=" N GLN B 328 " --> pdb=" O ASN B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 341 Processing helix chain 'B' and resid 353 through 358 removed outlier: 3.734A pdb=" N ALA B 358 " --> pdb=" O GLY B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 416 removed outlier: 3.631A pdb=" N TYR B 403 " --> pdb=" O GLN B 399 " (cutoff:3.500A) Proline residue: B 404 - end of helix Processing helix chain 'B' and resid 424 through 429 Processing helix chain 'B' and resid 462 through 472 Processing helix chain 'B' and resid 474 through 487 removed outlier: 3.998A pdb=" N THR B 478 " --> pdb=" O MET B 474 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU B 487 " --> pdb=" O VAL B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 510 removed outlier: 3.715A pdb=" N VAL B 492 " --> pdb=" O ASP B 488 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN B 498 " --> pdb=" O GLU B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 532 Processing helix chain 'B' and resid 561 through 567 Processing helix chain 'B' and resid 580 through 597 removed outlier: 3.514A pdb=" N ILE B 584 " --> pdb=" O THR B 580 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG B 597 " --> pdb=" O GLU B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 632 Processing helix chain 'B' and resid 644 through 649 Processing helix chain 'B' and resid 649 through 659 Processing helix chain 'B' and resid 660 through 663 Processing helix chain 'B' and resid 690 through 707 removed outlier: 3.705A pdb=" N CYS B 700 " --> pdb=" O ASP B 696 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL B 701 " --> pdb=" O MET B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 751 removed outlier: 4.552A pdb=" N THR B 725 " --> pdb=" O ASN B 721 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN B 726 " --> pdb=" O GLY B 722 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLY B 727 " --> pdb=" O ALA B 723 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N GLU B 728 " --> pdb=" O HIS B 724 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU B 733 " --> pdb=" O ASN B 729 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU B 736 " --> pdb=" O ASP B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 766 through 777 removed outlier: 3.964A pdb=" N TRP B 770 " --> pdb=" O ASN B 766 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TRP B 777 " --> pdb=" O TYR B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 788 Processing helix chain 'B' and resid 797 through 808 removed outlier: 3.566A pdb=" N ASP B 808 " --> pdb=" O GLN B 804 " (cutoff:3.500A) Processing helix chain 'B' and resid 810 through 816 Processing helix chain 'C' and resid 85 through 99 removed outlier: 4.048A pdb=" N GLY C 98 " --> pdb=" O THR C 94 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU C 99 " --> pdb=" O LEU C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 113 removed outlier: 3.850A pdb=" N PHE C 112 " --> pdb=" O ASP C 108 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR C 113 " --> pdb=" O PHE C 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 108 through 113' Processing helix chain 'C' and resid 115 through 121 Processing helix chain 'C' and resid 134 through 150 Processing helix chain 'C' and resid 161 through 175 Processing helix chain 'C' and resid 176 through 179 Processing helix chain 'C' and resid 180 through 186 removed outlier: 3.867A pdb=" N SER C 185 " --> pdb=" O ASP C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 197 Processing helix chain 'C' and resid 219 through 225 Processing helix chain 'C' and resid 268 through 285 removed outlier: 3.900A pdb=" N ARG C 272 " --> pdb=" O GLU C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 316 Processing helix chain 'C' and resid 336 through 340 Processing helix chain 'C' and resid 354 through 360 removed outlier: 3.635A pdb=" N LEU C 360 " --> pdb=" O TYR C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 415 removed outlier: 4.094A pdb=" N PHE C 415 " --> pdb=" O VAL C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 474 Processing helix chain 'C' and resid 474 through 486 Processing helix chain 'C' and resid 488 through 514 Processing helix chain 'C' and resid 519 through 533 removed outlier: 3.530A pdb=" N MET C 533 " --> pdb=" O LYS C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 567 Processing helix chain 'C' and resid 580 through 597 removed outlier: 4.012A pdb=" N ARG C 597 " --> pdb=" O GLU C 593 " (cutoff:3.500A) Processing helix chain 'C' and resid 642 through 660 removed outlier: 3.804A pdb=" N ASN C 646 " --> pdb=" O PRO C 642 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N SER C 650 " --> pdb=" O ASN C 646 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY C 651 " --> pdb=" O PHE C 647 " (cutoff:3.500A) Processing helix chain 'C' and resid 665 through 669 Processing helix chain 'C' and resid 689 through 690 No H-bonds generated for 'chain 'C' and resid 689 through 690' Processing helix chain 'C' and resid 691 through 706 removed outlier: 4.083A pdb=" N ASN C 706 " --> pdb=" O VAL C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 728 through 746 removed outlier: 4.392A pdb=" N ASP C 732 " --> pdb=" O GLU C 728 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LEU C 733 " --> pdb=" O ASN C 729 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N GLN C 737 " --> pdb=" O LEU C 733 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA C 742 " --> pdb=" O ALA C 738 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR C 743 " --> pdb=" O SER C 739 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS C 744 " --> pdb=" O TYR C 740 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLU C 745 " --> pdb=" O ASN C 741 " (cutoff:3.500A) Processing helix chain 'C' and resid 764 through 776 Processing helix chain 'C' and resid 783 through 789 removed outlier: 4.122A pdb=" N VAL C 787 " --> pdb=" O GLN C 783 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS C 788 " --> pdb=" O SER C 784 " (cutoff:3.500A) Processing helix chain 'C' and resid 799 through 807 removed outlier: 5.046A pdb=" N VAL C 805 " --> pdb=" O ARG C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 808 through 809 No H-bonds generated for 'chain 'C' and resid 808 through 809' Processing helix chain 'C' and resid 810 through 816 removed outlier: 3.614A pdb=" N ASP C 815 " --> pdb=" O PHE C 812 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 99 removed outlier: 3.595A pdb=" N ALA D 91 " --> pdb=" O GLU D 87 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N THR D 94 " --> pdb=" O ASN D 90 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU D 95 " --> pdb=" O ALA D 91 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY D 98 " --> pdb=" O THR D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 121 removed outlier: 5.426A pdb=" N LYS D 116 " --> pdb=" O PHE D 112 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N PHE D 117 " --> pdb=" O THR D 113 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ILE D 121 " --> pdb=" O PHE D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 152 Processing helix chain 'D' and resid 161 through 174 Processing helix chain 'D' and resid 215 through 225 Processing helix chain 'D' and resid 270 through 284 removed outlier: 3.662A pdb=" N VAL D 279 " --> pdb=" O ALA D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 314 removed outlier: 3.519A pdb=" N ARG D 303 " --> pdb=" O LYS D 299 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N MET D 314 " --> pdb=" O GLN D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 322 removed outlier: 3.927A pdb=" N GLU D 321 " --> pdb=" O PRO D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 329 removed outlier: 4.103A pdb=" N GLN D 328 " --> pdb=" O ASN D 324 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N TYR D 329 " --> pdb=" O HIS D 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 324 through 329' Processing helix chain 'D' and resid 353 through 359 Processing helix chain 'D' and resid 382 through 393 removed outlier: 3.874A pdb=" N ASN D 390 " --> pdb=" O MET D 386 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N THR D 391 " --> pdb=" O GLY D 387 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE D 393 " --> pdb=" O LEU D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 416 removed outlier: 4.009A pdb=" N TYR D 408 " --> pdb=" O PRO D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 474 Processing helix chain 'D' and resid 476 through 484 removed outlier: 3.639A pdb=" N ASN D 484 " --> pdb=" O TYR D 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 490 through 510 removed outlier: 3.638A pdb=" N GLU D 494 " --> pdb=" O ASP D 490 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN D 498 " --> pdb=" O GLU D 494 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLN D 499 " --> pdb=" O ASP D 495 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS D 505 " --> pdb=" O GLU D 501 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LYS D 510 " --> pdb=" O THR D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 533 Processing helix chain 'D' and resid 560 through 567 removed outlier: 3.726A pdb=" N ALA D 567 " --> pdb=" O SER D 563 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 596 removed outlier: 3.570A pdb=" N ASN D 591 " --> pdb=" O ARG D 587 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ARG D 592 " --> pdb=" O GLY D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 600 Processing helix chain 'D' and resid 633 through 637 removed outlier: 3.951A pdb=" N TYR D 637 " --> pdb=" O SER D 634 " (cutoff:3.500A) Processing helix chain 'D' and resid 642 through 649 removed outlier: 3.728A pdb=" N ASN D 646 " --> pdb=" O PRO D 642 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 659 Processing helix chain 'D' and resid 660 through 663 Processing helix chain 'D' and resid 665 through 669 Processing helix chain 'D' and resid 691 through 707 removed outlier: 3.666A pdb=" N MET D 697 " --> pdb=" O GLY D 693 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA D 698 " --> pdb=" O PHE D 694 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN D 699 " --> pdb=" O LYS D 695 " (cutoff:3.500A) Processing helix chain 'D' and resid 725 through 751 removed outlier: 3.712A pdb=" N ASN D 741 " --> pdb=" O GLN D 737 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYS D 750 " --> pdb=" O TYR D 746 " (cutoff:3.500A) Processing helix chain 'D' and resid 764 through 776 Processing helix chain 'D' and resid 782 through 791 removed outlier: 3.634A pdb=" N LEU D 791 " --> pdb=" O VAL D 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 797 through 809 removed outlier: 3.544A pdb=" N ILE D 809 " --> pdb=" O VAL D 805 " (cutoff:3.500A) Processing helix chain 'D' and resid 809 through 817 removed outlier: 3.825A pdb=" N ALA D 813 " --> pdb=" O ILE D 809 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 245 Processing helix chain 'E' and resid 328 through 339 Processing helix chain 'E' and resid 373 through 377 Processing helix chain 'E' and resid 404 through 410 Processing helix chain 'F' and resid 227 through 231 Processing helix chain 'F' and resid 237 through 245 removed outlier: 3.997A pdb=" N ASP F 244 " --> pdb=" O GLN F 240 " (cutoff:3.500A) Processing helix chain 'F' and resid 328 through 339 Processing helix chain 'F' and resid 372 through 377 Processing helix chain 'F' and resid 404 through 410 Processing helix chain 'G' and resid 10 through 14 Processing helix chain 'G' and resid 31 through 46 Processing helix chain 'G' and resid 59 through 65 Processing helix chain 'G' and resid 77 through 85 Processing helix chain 'G' and resid 160 through 170 Processing helix chain 'G' and resid 181 through 186 Processing sheet with id=AA1, first strand: chain 'A' and resid 235 through 236 removed outlier: 3.510A pdb=" N ASN A 235 " --> pdb=" O SER A 245 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 534 through 538 removed outlier: 6.382A pdb=" N HIS A 534 " --> pdb=" O LEU A 625 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N LEU A 627 " --> pdb=" O HIS A 534 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ASN A 536 " --> pdb=" O LEU A 627 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER A 624 " --> pdb=" O ALA A 619 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA A 619 " --> pdb=" O SER A 624 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 231 through 236 removed outlier: 4.315A pdb=" N TRP B 233 " --> pdb=" O TYR B 247 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 331 through 332 Processing sheet with id=AA5, first strand: chain 'C' and resid 231 through 236 Processing sheet with id=AA6, first strand: chain 'C' and resid 534 through 536 removed outlier: 6.586A pdb=" N HIS C 534 " --> pdb=" O LEU C 625 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TRP C 617 " --> pdb=" O THR C 626 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 231 through 234 removed outlier: 5.946A pdb=" N TYR D 246 " --> pdb=" O ILE D 379 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 74 through 76 removed outlier: 3.579A pdb=" N ALA E 74 " --> pdb=" O VAL E 87 " (cutoff:3.500A) removed outlier: 9.136A pdb=" N LEU E 223 " --> pdb=" O HIS E 86 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL E 88 " --> pdb=" O LEU E 223 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N LEU E 225 " --> pdb=" O VAL E 88 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ASP E 90 " --> pdb=" O LEU E 225 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ASN E 95 " --> pdb=" O GLY E 224 " (cutoff:3.500A) removed outlier: 10.383A pdb=" N ALA E 94 " --> pdb=" O VAL E 203 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N GLY E 205 " --> pdb=" O ALA E 94 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N LEU E 96 " --> pdb=" O GLY E 205 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ALA E 207 " --> pdb=" O LEU E 96 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE E 98 " --> pdb=" O ALA E 207 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 251 through 253 Processing sheet with id=AB1, first strand: chain 'E' and resid 297 through 298 Processing sheet with id=AB2, first strand: chain 'E' and resid 342 through 343 Processing sheet with id=AB3, first strand: chain 'E' and resid 360 through 364 Processing sheet with id=AB4, first strand: chain 'F' and resid 74 through 75 Processing sheet with id=AB5, first strand: chain 'F' and resid 98 through 99 removed outlier: 6.333A pdb=" N ILE F 98 " --> pdb=" O ALA F 207 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN F 206 " --> pdb=" O PHE F 180 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N PHE F 180 " --> pdb=" O GLN F 206 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'F' and resid 251 through 253 Processing sheet with id=AB7, first strand: chain 'F' and resid 297 through 299 Processing sheet with id=AB8, first strand: chain 'F' and resid 325 through 326 removed outlier: 6.258A pdb=" N MET F 325 " --> pdb=" O MET F 389 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'F' and resid 360 through 364 Processing sheet with id=AC1, first strand: chain 'G' and resid 174 through 175 removed outlier: 3.768A pdb=" N VAL G 204 " --> pdb=" O GLY G 175 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N ILE G 206 " --> pdb=" O ALA G 221 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ALA G 221 " --> pdb=" O ILE G 206 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLY G 208 " --> pdb=" O LEU G 219 " (cutoff:3.500A) 993 hydrogen bonds defined for protein. 2814 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.30 Time building geometry restraints manager: 4.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.85 - 1.04: 5486 1.04 - 1.24: 17834 1.24 - 1.44: 7315 1.44 - 1.64: 12614 1.64 - 1.84: 193 Bond restraints: 43442 Sorted by residual: bond pdb=" N PRO B 263 " pdb=" CD PRO B 263 " ideal model delta sigma weight residual 1.473 1.278 0.195 1.40e-02 5.10e+03 1.93e+02 bond pdb=" CA PHE C 816 " pdb=" CB PHE C 816 " ideal model delta sigma weight residual 1.524 1.364 0.160 1.62e-02 3.81e+03 9.74e+01 bond pdb=" C ASN B 115 " pdb=" O ASN B 115 " ideal model delta sigma weight residual 1.236 1.125 0.111 1.15e-02 7.56e+03 9.30e+01 bond pdb=" N PRO B 540 " pdb=" CD PRO B 540 " ideal model delta sigma weight residual 1.473 1.597 -0.124 1.40e-02 5.10e+03 7.90e+01 bond pdb=" N ARG G 136 " pdb=" H ARG G 136 " ideal model delta sigma weight residual 0.860 1.025 -0.165 2.00e-02 2.50e+03 6.83e+01 ... (remaining 43437 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.96: 77367 5.96 - 11.91: 245 11.91 - 17.87: 12 17.87 - 23.83: 4 23.83 - 29.78: 2 Bond angle restraints: 77630 Sorted by residual: angle pdb=" N PHE G 96 " pdb=" CA PHE G 96 " pdb=" C PHE G 96 " ideal model delta sigma weight residual 110.64 93.68 16.96 1.48e+00 4.57e-01 1.31e+02 angle pdb=" N SER G 58 " pdb=" CA SER G 58 " pdb=" C SER G 58 " ideal model delta sigma weight residual 110.30 93.84 16.46 1.50e+00 4.44e-01 1.20e+02 angle pdb=" N GLY A 129 " pdb=" CA GLY A 129 " pdb=" HA2 GLY A 129 " ideal model delta sigma weight residual 110.00 80.22 29.78 3.00e+00 1.11e-01 9.86e+01 angle pdb=" C PHE G 96 " pdb=" CA PHE G 96 " pdb=" CB PHE G 96 " ideal model delta sigma weight residual 109.80 121.91 -12.11 1.23e+00 6.61e-01 9.69e+01 angle pdb=" N CYS G 135 " pdb=" CA CYS G 135 " pdb=" C CYS G 135 " ideal model delta sigma weight residual 110.42 96.38 14.04 1.46e+00 4.69e-01 9.25e+01 ... (remaining 77625 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 18812 17.90 - 35.80: 1497 35.80 - 53.70: 483 53.70 - 71.60: 165 71.60 - 89.50: 39 Dihedral angle restraints: 20996 sinusoidal: 10481 harmonic: 10515 Sorted by residual: dihedral pdb=" CA SER D 634 " pdb=" C SER D 634 " pdb=" N PRO D 635 " pdb=" CA PRO D 635 " ideal model delta harmonic sigma weight residual -180.00 -118.49 -61.51 0 5.00e+00 4.00e-02 1.51e+02 dihedral pdb=" CA SER B 634 " pdb=" C SER B 634 " pdb=" N PRO B 635 " pdb=" CA PRO B 635 " ideal model delta harmonic sigma weight residual -180.00 -122.73 -57.27 0 5.00e+00 4.00e-02 1.31e+02 dihedral pdb=" CB CYS A 700 " pdb=" SG CYS A 700 " pdb=" SG CYS A 832 " pdb=" CB CYS A 832 " ideal model delta sinusoidal sigma weight residual 93.00 169.62 -76.62 1 1.00e+01 1.00e-02 7.38e+01 ... (remaining 20993 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 2454 0.069 - 0.139: 842 0.139 - 0.208: 134 0.208 - 0.277: 14 0.277 - 0.346: 5 Chirality restraints: 3449 Sorted by residual: chirality pdb=" CA MET B 314 " pdb=" N MET B 314 " pdb=" C MET B 314 " pdb=" CB MET B 314 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" CA LEU B 262 " pdb=" N LEU B 262 " pdb=" C LEU B 262 " pdb=" CB LEU B 262 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.86e+00 chirality pdb=" CA ALA D 720 " pdb=" N ALA D 720 " pdb=" C ALA D 720 " pdb=" CB ALA D 720 " both_signs ideal model delta sigma weight residual False 2.48 2.17 0.31 2.00e-01 2.50e+01 2.44e+00 ... (remaining 3446 not shown) Planarity restraints: 7081 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 115 " -0.146 2.00e-02 2.50e+03 4.28e-01 2.74e+03 pdb=" CG ASN B 115 " -0.013 2.00e-02 2.50e+03 pdb=" OD1 ASN B 115 " 0.154 2.00e-02 2.50e+03 pdb=" ND2 ASN B 115 " -0.001 2.00e-02 2.50e+03 pdb="HD21 ASN B 115 " 0.728 2.00e-02 2.50e+03 pdb="HD22 ASN B 115 " -0.723 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 407 " -0.255 2.00e-02 2.50e+03 3.44e-01 1.77e+03 pdb=" CG ASN A 407 " 0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN A 407 " 0.247 2.00e-02 2.50e+03 pdb=" ND2 ASN A 407 " 0.000 2.00e-02 2.50e+03 pdb="HD21 ASN A 407 " -0.546 2.00e-02 2.50e+03 pdb="HD22 ASN A 407 " 0.534 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 599 " 0.200 2.00e-02 2.50e+03 2.25e-01 7.57e+02 pdb=" CG ASN A 599 " -0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN A 599 " -0.192 2.00e-02 2.50e+03 pdb=" ND2 ASN A 599 " -0.001 2.00e-02 2.50e+03 pdb="HD21 ASN A 599 " 0.340 2.00e-02 2.50e+03 pdb="HD22 ASN A 599 " -0.332 2.00e-02 2.50e+03 ... (remaining 7078 not shown) Histogram of nonbonded interaction distances: 0.65 - 1.44: 213 1.44 - 2.23: 6380 2.23 - 3.02: 119294 3.02 - 3.81: 164820 3.81 - 4.60: 256226 Warning: very small nonbonded interaction distances. Nonbonded interactions: 546933 Sorted by model distance: nonbonded pdb=" HG CYS C 114 " pdb=" HG CYS C 778 " model vdw 0.652 1.952 nonbonded pdb=" HB2 ASN A 569 " pdb=" HE1 TYR A 589 " model vdw 0.663 2.270 nonbonded pdb=" HE1 MET A 474 " pdb=" HD2 ARG A 586 " model vdw 1.037 2.440 nonbonded pdb="HE22 GLN A 264 " pdb=" HE1 MET A 314 " model vdw 1.042 2.270 nonbonded pdb="HD21 ASN B 583 " pdb="HH21 ARG B 587 " model vdw 1.042 2.100 ... (remaining 546928 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 81 through 122 or (resid 132 and (name N or name CA or nam \ e C or name O or name CB or name OG1 or name CG2 or name HA or name HB or name H \ G1 or name HG21 or name HG22 or name HG23)) or resid 133 through 151 or (resid 1 \ 61 and (name N or name CA or name C or name O or name CB or name CG or name CD o \ r name OE1 or name NE2 or name HA or name HB2 or name HB3 or name HG2 or name HG \ 3 or name HE21 or name HE22)) or resid 162 through 175 or (resid 214 and (name N \ or name CA or name C or name O or name CB or name CG or name CD1 or name CD2 or \ name CE1 or name CE2 or name CZ or name OH or name HA or name HB2 or name HB3 o \ r name HD1 or name HD2 or name HE1 or name HE2 or name HH )) or resid 215 throug \ h 284 or (resid 295 and (name N or name CA or name C or name O or name CB or nam \ e CG or name OD1 or name OD2 or name HA or name HB2 or name HB3)) or resid 296 t \ hrough 334 or (resid 353 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name HA \ or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or name \ HZ )) or resid 354 through 360 or resid 374 through 388 or (resid 407 and (name \ N or name CA or name C or name O or name CB or name CG or name OD1 or name ND2 o \ r name HA or name HB2 or name HB3 or name HD21 or name HD22)) or resid 408 throu \ gh 418 or (resid 462 and (name N or name CA or name C or name O or name CB or na \ me HA or name HB1 or name HB2 or name HB3)) or resid 463 through 485 or (resid 4 \ 86 and (name N or name CA or name C or name O or name CB or name CG or name CD o \ r name NE or name CZ or name NH1 or name NH2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HD2 or name HD3 or name HE or name HH11 or name \ HH12 or name HH21 or name HH22)) or resid 490 through 510 or (resid 522 and (nam \ e N or name CA or name C or name O or name CB or name OG or name HA or name HB2 \ or name HB3 or name HG )) or resid 523 through 628 or (resid 636 and (name N or \ name CA or name C or name O or name CB or name CG or name ND1 or name CD2 or nam \ e CE1 or name NE2 or name HA or name HB2 or name HB3 or name HD2 or name HE1 or \ name HE2)) or resid 637 through 655 or (resid 656 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or res \ id 657 through 669 or (resid 690 and (name N or name CA or name C or name O or n \ ame HA2 or name HA3)) or resid 691 through 708 or (resid 709 and (name N or name \ CA or name C or name O or name CB or name SG or name H or name HA or name HB2 o \ r name HB3)) or resid 710 through 711 or (resid 719 and (name N or name CA or na \ me C or name O or name CB or name SG or name HA or name HB2 or name HB3)) or res \ id 720 through 747 or (resid 754 and (name N or name CA or name C or name O or n \ ame CB or name CG or name CD or name OE1 or name OE2 or name HA or name HB2 or n \ ame HB3 or name HG2 or name HG3)) or resid 755 through 788 or (resid 795 and (na \ me N or name CA or name C or name O or name CB or name CG or name ND1 or name CD \ 2 or name CE1 or name NE2 or name HA or name HB2 or name HB3 or name HD2 or name \ HE1 or name HE2)) or resid 796 through 824 or (resid 825 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 832 through 834 \ )) selection = (chain 'B' and (resid 81 through 175 or (resid 214 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ or name OH or name HA or name HB2 or name HB3 or name HD1 or name \ HD2 or name HE1 or name HE2 or name HH )) or resid 215 through 257 or (resid 26 \ 4 and (name N or name CA or name C or name O or name CB or name CG or name CD or \ name OE1 or name NE2 or name HA or name HB2 or name HB3 or name HG2 or name HG3 \ or name HE21 or name HE22)) or resid 265 through 284 or (resid 295 and (name N \ or name CA or name C or name O or name CB or name CG or name OD1 or name OD2 or \ name HA or name HB2 or name HB3)) or resid 296 through 334 or (resid 353 and (na \ me N or name CA or name C or name O or name CB or name CG or name CD1 or name CD \ 2 or name CE1 or name CE2 or name CZ or name HA or name HB2 or name HB3 or name \ HD1 or name HD2 or name HE1 or name HE2 or name HZ )) or resid 354 through 360 o \ r (resid 374 and (name N or name CA or name C or name O or name CB or name CG or \ name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name HA or name HB2 \ or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or name HZ )) or res \ id 375 through 388 or (resid 407 and (name N or name CA or name C or name O or n \ ame CB or name CG or name OD1 or name ND2 or name HA or name HB2 or name HB3 or \ name HD21 or name HD22)) or resid 408 through 418 or (resid 462 and (name N or n \ ame CA or name C or name O or name CB or name HA or name HB1 or name HB2 or name \ HB3)) or resid 463 through 485 or (resid 486 and (name N or name CA or name C o \ r name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or n \ ame NH2 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 o \ r name HD3 or name HE or name HH11 or name HH12 or name HH21 or name HH22)) or r \ esid 490 through 510 or (resid 522 and (name N or name CA or name C or name O or \ name CB or name OG or name HA or name HB2 or name HB3 or name HG )) or resid 52 \ 3 through 543 or resid 559 through 573 or (resid 580 and (name N or name CA or n \ ame C or name O or name CB or name OG1 or name CG2 or name HA or name HB or name \ HG1 or name HG21 or name HG22 or name HG23)) or resid 581 through 628 or (resid \ 636 and (name N or name CA or name C or name O or name CB or name CG or name ND \ 1 or name CD2 or name CE1 or name NE2 or name HA or name HB2 or name HB3 or name \ HD2 or name HE1 or name HE2)) or resid 637 through 655 or (resid 656 and (name \ N or name CA or name C or name O or name CB or name CG or name ND1 or name CD2 o \ r name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HD2 \ or name HE1)) or resid 657 through 669 or (resid 690 and (name N or name CA or n \ ame C or name O or name HA2 or name HA3)) or resid 691 through 711 or resid 719 \ through 747 or (resid 754 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name OE1 or name OE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3)) or resid 755 through 824 or (resid 825 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 832 thr \ ough 834)) selection = (chain 'C' and (resid 81 through 113 or (resid 114 and (name N or name CA or nam \ e C or name O or name CB or name SG or name H or name HA or name HB2 or name HB3 \ )) or resid 115 through 122 or (resid 132 and (name N or name CA or name C or na \ me O or name CB or name OG1 or name CG2 or name HA or name HB or name HG1 or nam \ e HG21 or name HG22 or name HG23)) or resid 133 through 151 or (resid 161 and (n \ ame N or name CA or name C or name O or name CB or name CG or name CD or name OE \ 1 or name NE2 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name \ HE21 or name HE22)) or resid 162 through 175 or resid 214 through 257 or (resid \ 264 and (name N or name CA or name C or name O or name CB or name CG or name CD \ or name OE1 or name NE2 or name HA or name HB2 or name HB3 or name HG2 or name \ HG3 or name HE21 or name HE22)) or resid 265 through 284 or (resid 295 and (name \ N or name CA or name C or name O or name CB or name CG or name OD1 or name OD2 \ or name HA or name HB2 or name HB3)) or resid 296 through 334 or resid 353 throu \ gh 360 or (resid 374 and (name N or name CA or name C or name O or name CB or na \ me CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name HA or n \ ame HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or name HZ ) \ ) or resid 375 through 485 or (resid 486 and (name N or name CA or name C or nam \ e O or name CB or name CG or name CD or name NE or name CZ or name NH1 or name N \ H2 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or nam \ e HD3 or name HE or name HH11 or name HH12 or name HH21 or name HH22)) or resid \ 490 through 510 or (resid 522 and (name N or name CA or name C or name O or name \ CB or name OG or name HA or name HB2 or name HB3 or name HG )) or resid 523 thr \ ough 543 or resid 559 through 573 or (resid 580 and (name N or name CA or name C \ or name O or name CB or name OG1 or name CG2 or name HA or name HB or name HG1 \ or name HG21 or name HG22 or name HG23)) or resid 581 through 655 or (resid 656 \ and (name N or name CA or name C or name O or name CB or name CG or name ND1 or \ name CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or \ name HD2 or name HE1)) or resid 657 through 669 or (resid 690 and (name N or na \ me CA or name C or name O or name HA2 or name HA3)) or resid 691 through 711 or \ (resid 719 and (name N or name CA or name C or name O or name CB or name SG or n \ ame HA or name HB2 or name HB3)) or resid 720 through 777 or (resid 778 and (nam \ e N or name CA or name C or name O or name CB or name SG or name H or name HA or \ name HB2 or name HB3)) or resid 779 through 788 or (resid 795 and (name N or na \ me CA or name C or name O or name CB or name CG or name ND1 or name CD2 or name \ CE1 or name NE2 or name HA or name HB2 or name HB3 or name HD1 or name HD2 or na \ me HE1)) or resid 796 through 834)) selection = (chain 'D' and (resid 81 through 122 or (resid 132 and (name N or name CA or nam \ e C or name O or name CB or name OG1 or name CG2 or name HA or name HB or name H \ G1 or name HG21 or name HG22 or name HG23)) or resid 133 through 151 or (resid 1 \ 61 and (name N or name CA or name C or name O or name CB or name CG or name CD o \ r name OE1 or name NE2 or name HA or name HB2 or name HB3 or name HG2 or name HG \ 3 or name HE21 or name HE22)) or resid 162 through 257 or (resid 264 and (name N \ or name CA or name C or name O or name CB or name CG or name CD or name OE1 or \ name NE2 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HE21 \ or name HE22)) or resid 265 through 334 or (resid 353 and (name N or name CA or \ name C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or n \ ame CE2 or name CZ or name HA or name HB2 or name HB3 or name HD1 or name HD2 or \ name HE1 or name HE2 or name HZ )) or resid 354 through 388 or (resid 407 and ( \ name N or name CA or name C or name O or name CB or name CG or name OD1 or name \ ND2 or name HA or name HB2 or name HB3 or name HD21 or name HD22)) or resid 408 \ through 418 or (resid 462 and (name N or name CA or name C or name O or name CB \ or name HA or name HB1 or name HB2 or name HB3)) or resid 463 through 573 or res \ id 580 through 628 or (resid 636 and (name N or name CA or name C or name O or n \ ame CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name HA or \ name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or resid 637 through \ 655 or (resid 656 and (name N or name CA or name C or name O or name CB or name \ CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or name \ HB2 or name HB3 or name HD2 or name HE1)) or resid 657 through 669 or resid 690 \ through 708 or (resid 709 and (name N or name CA or name C or name O or name CB \ or name SG or name H or name HA or name HB2 or name HB3)) or resid 710 through 7 \ 11 or (resid 719 and (name N or name CA or name C or name O or name CB or name S \ G or name HA or name HB2 or name HB3)) or resid 720 through 747 or (resid 754 an \ d (name N or name CA or name C or name O or name CB or name CG or name CD or nam \ e OE1 or name OE2 or name HA or name HB2 or name HB3 or name HG2 or name HG3)) o \ r resid 755 through 788 or (resid 795 and (name N or name CA or name C or name O \ or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H \ A or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or resid 796 thr \ ough 824 or (resid 825 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 832 through 834)) } ncs_group { reference = (chain 'E' and (resid 70 through 105 or resid 147 or (resid 148 and (name N or n \ ame CA or name C or name O or name CB or name HA )) or resid 149 through 300 or \ resid 313 through 379 or resid 393 or resid 401 through 427)) selection = (chain 'F' and (resid 70 through 379 or resid 384 or resid 401 through 427)) } 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=0.00 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: 4.090 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: 0.180 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 34.800 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 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 : 0.017 0.669 23305 Z= 0.872 Angle : 1.521 24.164 31539 Z= 0.914 Chirality : 0.068 0.346 3449 Planarity : 0.009 0.159 4172 Dihedral : 14.461 88.680 7995 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 49.50 Ramachandran Plot: Outliers : 0.98 % Allowed : 30.33 % Favored : 68.69 % Rotamer: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.88 % Twisted General : 0.41 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -6.95 (0.10), residues: 2967 helix: -4.45 (0.07), residues: 1325 sheet: -4.47 (0.37), residues: 109 loop : -4.93 (0.11), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 352 TYR 0.051 0.004 TYR B 231 PHE 0.039 0.004 PHE B 374 TRP 0.027 0.004 TRP B 777 HIS 0.018 0.003 HIS D 656 Details of bonding type rmsd covalent geometry : bond 0.01572 (23286) covalent geometry : angle 1.49553 (31501) SS BOND : bond 0.20418 ( 19) SS BOND : angle 8.09955 ( 38) hydrogen bonds : bond 0.20481 ( 993) hydrogen bonds : angle 10.11027 ( 2814) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 825 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue TYR 72 is missing expected H atoms. Skipping. Residue LEU 73 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue THR 77 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue VAL 87 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue SER 93 is missing expected H atoms. Skipping. Residue LEU 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue LYS 148 is missing expected H atoms. Skipping. Residue SER 149 is missing expected H atoms. Skipping. Residue SER 153 is missing expected H atoms. Skipping. Residue THR 154 is missing expected H atoms. Skipping. Residue SER 156 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue SER 158 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 167 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue VAL 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LEU 181 is missing expected H atoms. Skipping. Residue THR 185 is missing expected H atoms. Skipping. Residue VAL 186 is missing expected H atoms. Skipping. Residue LYS 195 is missing expected H atoms. Skipping. Residue THR 196 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue VAL 198 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue THR 202 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue ILE 222 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LEU 225 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue VAL 235 is missing expected H atoms. Skipping. Residue THR 236 is missing expected H atoms. Skipping. Residue LEU 239 is missing expected H atoms. Skipping. Residue ILE 243 is missing expected H atoms. Skipping. Residue LEU 245 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LEU 247 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue ILE 251 is missing expected H atoms. Skipping. Residue THR 253 is missing expected H atoms. Skipping. Residue VAL 254 is missing expected H atoms. Skipping. Residue TYR 255 is missing expected H atoms. Skipping. Residue MET 256 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LEU 259 is missing expected H atoms. Skipping. Residue LYS 262 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue TYR 273 is missing expected H atoms. Skipping. Residue LEU 276 is missing expected H atoms. Skipping. Residue SER 278 is missing expected H atoms. Skipping. Residue VAL 279 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue TYR 287 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue LEU 290 is missing expected H atoms. Skipping. Residue THR 291 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue TYR 295 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue MET 300 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Residue ILE 317 is missing expected H atoms. Skipping. Residue SER 318 is missing expected H atoms. Skipping. Residue THR 320 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue VAL 327 is missing expected H atoms. Skipping. Residue THR 329 is missing expected H atoms. Skipping. Residue ILE 331 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue VAL 335 is missing expected H atoms. Skipping. Residue SER 338 is missing expected H atoms. Skipping. Residue TYR 339 is missing expected H atoms. Skipping. Residue TYR 343 is missing expected H atoms. Skipping. Residue MET 346 is missing expected H atoms. Skipping. Residue ILE 349 is missing expected H atoms. Skipping. Residue TYR 350 is missing expected H atoms. Skipping. Residue THR 351 is missing expected H atoms. Skipping. Residue VAL 352 is missing expected H atoms. Skipping. Residue THR 357 is missing expected H atoms. Skipping. Residue VAL 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue MET 362 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue LYS 367 is missing expected H atoms. Skipping. Residue TYR 369 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue ILE 371 is missing expected H atoms. Skipping. Residue LYS 374 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue VAL 377 is missing expected H atoms. Skipping. Residue LEU 378 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue MET 389 is missing expected H atoms. Skipping. Residue THR 390 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue SER 393 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue LEU 403 is missing expected H atoms. Skipping. Residue ILE 408 is missing expected H atoms. Skipping. Residue TYR 411 is missing expected H atoms. Skipping. Residue ILE 414 is missing expected H atoms. Skipping. Residue MET 417 is missing expected H atoms. Skipping. Residue THR 421 is missing expected H atoms. Skipping. Residue ILE 422 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue TYR 72 is missing expected H atoms. Skipping. Residue LEU 73 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue THR 77 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue VAL 87 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue SER 93 is missing expected H atoms. Skipping. Residue LEU 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LYS 148 is missing expected H atoms. Skipping. Residue SER 149 is missing expected H atoms. Skipping. Residue SER 153 is missing expected H atoms. Skipping. Residue THR 154 is missing expected H atoms. Skipping. Residue SER 156 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue SER 158 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 167 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue VAL 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LEU 181 is missing expected H atoms. Skipping. Residue THR 185 is missing expected H atoms. Skipping. Residue VAL 186 is missing expected H atoms. Skipping. Residue LYS 195 is missing expected H atoms. Skipping. Residue THR 196 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue VAL 198 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue THR 202 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue ILE 222 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LEU 225 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue VAL 235 is missing expected H atoms. Skipping. Residue THR 236 is missing expected H atoms. Skipping. Residue LEU 239 is missing expected H atoms. Skipping. Residue ILE 243 is missing expected H atoms. Skipping. Residue LEU 245 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LEU 247 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue ILE 251 is missing expected H atoms. Skipping. Residue THR 253 is missing expected H atoms. Skipping. Residue VAL 254 is missing expected H atoms. Skipping. Residue TYR 255 is missing expected H atoms. Skipping. Residue MET 256 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LEU 259 is missing expected H atoms. Skipping. Residue LYS 262 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue TYR 273 is missing expected H atoms. Skipping. Residue LEU 276 is missing expected H atoms. Skipping. Residue SER 278 is missing expected H atoms. Skipping. Residue VAL 279 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue TYR 287 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue LEU 290 is missing expected H atoms. Skipping. Residue THR 291 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue TYR 295 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue MET 300 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Residue ILE 317 is missing expected H atoms. Skipping. Residue SER 318 is missing expected H atoms. Skipping. Residue THR 320 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue VAL 327 is missing expected H atoms. Skipping. Residue THR 329 is missing expected H atoms. Skipping. Residue ILE 331 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue VAL 335 is missing expected H atoms. Skipping. Residue SER 338 is missing expected H atoms. Skipping. Residue TYR 339 is missing expected H atoms. Skipping. Residue TYR 343 is missing expected H atoms. Skipping. Residue MET 346 is missing expected H atoms. Skipping. Residue ILE 349 is missing expected H atoms. Skipping. Residue TYR 350 is missing expected H atoms. Skipping. Residue THR 351 is missing expected H atoms. Skipping. Residue VAL 352 is missing expected H atoms. Skipping. Residue THR 357 is missing expected H atoms. Skipping. Residue VAL 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue MET 362 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue LYS 367 is missing expected H atoms. Skipping. Residue TYR 369 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue ILE 371 is missing expected H atoms. Skipping. Residue LYS 374 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue VAL 377 is missing expected H atoms. Skipping. Residue LEU 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue SER 384 is missing expected H atoms. Skipping. Residue MET 386 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue MET 389 is missing expected H atoms. Skipping. Residue THR 390 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue LEU 403 is missing expected H atoms. Skipping. Residue ILE 408 is missing expected H atoms. Skipping. Residue TYR 411 is missing expected H atoms. Skipping. Residue ILE 414 is missing expected H atoms. Skipping. Residue MET 417 is missing expected H atoms. Skipping. Residue THR 421 is missing expected H atoms. Skipping. Residue ILE 422 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue ILE 23 is missing expected H atoms. Skipping. Residue SER 31 is missing expected H atoms. Skipping. Residue VAL 35 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue THR 37 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue SER 42 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue SER 49 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue VAL 55 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue SER 58 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue SER 64 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue THR 78 is missing expected H atoms. Skipping. Residue TYR 84 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue TYR 106 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue ILE 137 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue ILE 163 is missing expected H atoms. Skipping. Residue ILE 167 is missing expected H atoms. Skipping. Residue MET 168 is missing expected H atoms. Skipping. Residue THR 169 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue VAL 174 is missing expected H atoms. Skipping. Residue SER 176 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue THR 181 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue SER 188 is missing expected H atoms. Skipping. Residue ILE 190 is missing expected H atoms. Skipping. Residue TYR 191 is missing expected H atoms. Skipping. Residue VAL 204 is missing expected H atoms. Skipping. Residue ILE 206 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue LYS 211 is missing expected H atoms. Skipping. Residue TYR 217 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue ILE 220 is missing expected H atoms. Skipping. Residue TYR 233 is missing expected H atoms. Skipping. Residue MET 236 is missing expected H atoms. Skipping. Residue ILE 237 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue ILE 249 is missing expected H atoms. Skipping. Residue THR 250 is missing expected H atoms. Skipping. Evaluate side-chains 345 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 345 time to evaluate : 0.940 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash REVERT: B 304 GLU cc_start: 0.8660 (mm-30) cc_final: 0.7851 (tp30) REVERT: C 231 TYR cc_start: 0.6840 (t80) cc_final: 0.6574 (t80) REVERT: C 511 MET cc_start: 0.8660 (mmm) cc_final: 0.8168 (mmp) REVERT: C 657 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7671 (mm-30) outliers start: 0 outliers final: 0 residues processed: 345 average time/residue: 0.3708 time to fit residues: 181.7450 Evaluate side-chains 235 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 GLN A 330 ASN A 407 ASN ** B 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 382 ASN C 536 ASN C 570 ASN C 591 ASN C 640 GLN D 235 ASN D 499 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.068823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.060325 restraints weight = 432194.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.061936 restraints weight = 224742.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.063014 restraints weight = 137773.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.063704 restraints weight = 95002.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.064200 restraints weight = 71110.690| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 23305 Z= 0.252 Angle : 0.800 7.962 31539 Z= 0.438 Chirality : 0.044 0.175 3449 Planarity : 0.007 0.121 4172 Dihedral : 7.384 66.877 3301 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.27 % Allowed : 18.10 % Favored : 81.63 % Rotamer: Outliers : 0.15 % Allowed : 5.77 % Favored : 94.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.44 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.88 (0.11), residues: 2967 helix: -3.37 (0.10), residues: 1402 sheet: -4.20 (0.34), residues: 153 loop : -4.50 (0.13), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 486 TYR 0.023 0.002 TYR A 775 PHE 0.028 0.002 PHE D 265 TRP 0.020 0.002 TRP D 770 HIS 0.008 0.002 HIS D 412 Details of bonding type rmsd covalent geometry : bond 0.00531 (23286) covalent geometry : angle 0.79939 (31501) SS BOND : bond 0.00564 ( 19) SS BOND : angle 1.44610 ( 38) hydrogen bonds : bond 0.06873 ( 993) hydrogen bonds : angle 7.46336 ( 2814) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 825 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue TYR 72 is missing expected H atoms. Skipping. Residue LEU 73 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue THR 77 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue VAL 87 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue SER 93 is missing expected H atoms. Skipping. Residue LEU 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue LYS 148 is missing expected H atoms. Skipping. Residue SER 149 is missing expected H atoms. Skipping. Residue SER 153 is missing expected H atoms. Skipping. Residue THR 154 is missing expected H atoms. Skipping. Residue SER 156 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue SER 158 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 167 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue VAL 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LEU 181 is missing expected H atoms. Skipping. Residue THR 185 is missing expected H atoms. Skipping. Residue VAL 186 is missing expected H atoms. Skipping. Residue LYS 195 is missing expected H atoms. Skipping. Residue THR 196 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue VAL 198 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue THR 202 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue ILE 222 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LEU 225 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue VAL 235 is missing expected H atoms. Skipping. Residue THR 236 is missing expected H atoms. Skipping. Residue LEU 239 is missing expected H atoms. Skipping. Residue ILE 243 is missing expected H atoms. Skipping. Residue LEU 245 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LEU 247 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue ILE 251 is missing expected H atoms. Skipping. Residue THR 253 is missing expected H atoms. Skipping. Residue VAL 254 is missing expected H atoms. Skipping. Residue TYR 255 is missing expected H atoms. Skipping. Residue MET 256 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LEU 259 is missing expected H atoms. Skipping. Residue LYS 262 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue TYR 273 is missing expected H atoms. Skipping. Residue LEU 276 is missing expected H atoms. Skipping. Residue SER 278 is missing expected H atoms. Skipping. Residue VAL 279 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue TYR 287 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue LEU 290 is missing expected H atoms. Skipping. Residue THR 291 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue TYR 295 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue MET 300 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Residue ILE 317 is missing expected H atoms. Skipping. Residue SER 318 is missing expected H atoms. Skipping. Residue THR 320 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue VAL 327 is missing expected H atoms. Skipping. Residue THR 329 is missing expected H atoms. Skipping. Residue ILE 331 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue VAL 335 is missing expected H atoms. Skipping. Residue SER 338 is missing expected H atoms. Skipping. Residue TYR 339 is missing expected H atoms. Skipping. Residue TYR 343 is missing expected H atoms. Skipping. Residue MET 346 is missing expected H atoms. Skipping. Residue ILE 349 is missing expected H atoms. Skipping. Residue TYR 350 is missing expected H atoms. Skipping. Residue THR 351 is missing expected H atoms. Skipping. Residue VAL 352 is missing expected H atoms. Skipping. Residue THR 357 is missing expected H atoms. Skipping. Residue VAL 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue MET 362 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue LYS 367 is missing expected H atoms. Skipping. Residue TYR 369 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue ILE 371 is missing expected H atoms. Skipping. Residue LYS 374 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue VAL 377 is missing expected H atoms. Skipping. Residue LEU 378 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue MET 389 is missing expected H atoms. Skipping. Residue THR 390 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue SER 393 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue LEU 403 is missing expected H atoms. Skipping. Residue ILE 408 is missing expected H atoms. Skipping. Residue TYR 411 is missing expected H atoms. Skipping. Residue ILE 414 is missing expected H atoms. Skipping. Residue MET 417 is missing expected H atoms. Skipping. Residue THR 421 is missing expected H atoms. Skipping. Residue ILE 422 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue TYR 72 is missing expected H atoms. Skipping. Residue LEU 73 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue THR 77 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue VAL 87 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue SER 93 is missing expected H atoms. Skipping. Residue LEU 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LYS 148 is missing expected H atoms. Skipping. Residue SER 149 is missing expected H atoms. Skipping. Residue SER 153 is missing expected H atoms. Skipping. Residue THR 154 is missing expected H atoms. Skipping. Residue SER 156 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue SER 158 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 167 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue VAL 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LEU 181 is missing expected H atoms. Skipping. Residue THR 185 is missing expected H atoms. Skipping. Residue VAL 186 is missing expected H atoms. Skipping. Residue LYS 195 is missing expected H atoms. Skipping. Residue THR 196 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue VAL 198 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue THR 202 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue ILE 222 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LEU 225 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue VAL 235 is missing expected H atoms. Skipping. Residue THR 236 is missing expected H atoms. Skipping. Residue LEU 239 is missing expected H atoms. Skipping. Residue ILE 243 is missing expected H atoms. Skipping. Residue LEU 245 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LEU 247 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue ILE 251 is missing expected H atoms. Skipping. Residue THR 253 is missing expected H atoms. Skipping. Residue VAL 254 is missing expected H atoms. Skipping. Residue TYR 255 is missing expected H atoms. Skipping. Residue MET 256 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LEU 259 is missing expected H atoms. Skipping. Residue LYS 262 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue TYR 273 is missing expected H atoms. Skipping. Residue LEU 276 is missing expected H atoms. Skipping. Residue SER 278 is missing expected H atoms. Skipping. Residue VAL 279 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue TYR 287 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue LEU 290 is missing expected H atoms. Skipping. Residue THR 291 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue TYR 295 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue MET 300 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Residue ILE 317 is missing expected H atoms. Skipping. Residue SER 318 is missing expected H atoms. Skipping. Residue THR 320 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue VAL 327 is missing expected H atoms. Skipping. Residue THR 329 is missing expected H atoms. Skipping. Residue ILE 331 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue VAL 335 is missing expected H atoms. Skipping. Residue SER 338 is missing expected H atoms. Skipping. Residue TYR 339 is missing expected H atoms. Skipping. Residue TYR 343 is missing expected H atoms. Skipping. Residue MET 346 is missing expected H atoms. Skipping. Residue ILE 349 is missing expected H atoms. Skipping. Residue TYR 350 is missing expected H atoms. Skipping. Residue THR 351 is missing expected H atoms. Skipping. Residue VAL 352 is missing expected H atoms. Skipping. Residue THR 357 is missing expected H atoms. Skipping. Residue VAL 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue MET 362 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue LYS 367 is missing expected H atoms. Skipping. Residue TYR 369 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue ILE 371 is missing expected H atoms. Skipping. Residue LYS 374 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue VAL 377 is missing expected H atoms. Skipping. Residue LEU 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue SER 384 is missing expected H atoms. Skipping. Residue MET 386 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue MET 389 is missing expected H atoms. Skipping. Residue THR 390 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue LEU 403 is missing expected H atoms. Skipping. Residue ILE 408 is missing expected H atoms. Skipping. Residue TYR 411 is missing expected H atoms. Skipping. Residue ILE 414 is missing expected H atoms. Skipping. Residue MET 417 is missing expected H atoms. Skipping. Residue THR 421 is missing expected H atoms. Skipping. Residue ILE 422 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue ILE 23 is missing expected H atoms. Skipping. Residue SER 31 is missing expected H atoms. Skipping. Residue VAL 35 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue THR 37 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue SER 42 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue SER 49 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue VAL 55 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue SER 58 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue SER 64 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue THR 78 is missing expected H atoms. Skipping. Residue TYR 84 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue TYR 106 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue ILE 137 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue ILE 163 is missing expected H atoms. Skipping. Residue ILE 167 is missing expected H atoms. Skipping. Residue MET 168 is missing expected H atoms. Skipping. Residue THR 169 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue VAL 174 is missing expected H atoms. Skipping. Residue SER 176 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue THR 181 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue SER 188 is missing expected H atoms. Skipping. Residue ILE 190 is missing expected H atoms. Skipping. Residue TYR 191 is missing expected H atoms. Skipping. Residue VAL 204 is missing expected H atoms. Skipping. Residue ILE 206 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue LYS 211 is missing expected H atoms. Skipping. Residue TYR 217 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue ILE 220 is missing expected H atoms. Skipping. Residue TYR 233 is missing expected H atoms. Skipping. Residue MET 236 is missing expected H atoms. Skipping. Residue ILE 237 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue ILE 249 is missing expected H atoms. Skipping. Residue THR 250 is missing expected H atoms. Skipping. Evaluate side-chains 297 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 294 time to evaluate : 1.093 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: 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: 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: 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: 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 245 SER cc_start: 0.8614 (t) cc_final: 0.8358 (t) REVERT: A 390 ASN cc_start: 0.8917 (t0) cc_final: 0.8532 (t0) REVERT: B 473 TYR cc_start: 0.7836 (m-80) cc_final: 0.7610 (m-80) REVERT: B 659 VAL cc_start: 0.8910 (t) cc_final: 0.8574 (m) REVERT: C 97 PHE cc_start: 0.7217 (t80) cc_final: 0.6431 (t80) REVERT: C 657 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7751 (mm-30) REVERT: D 101 GLU cc_start: 0.8354 (mp0) cc_final: 0.7899 (mp0) REVERT: D 533 MET cc_start: 0.9180 (tmm) cc_final: 0.8905 (tmm) REVERT: D 732 ASP cc_start: 0.8300 (m-30) cc_final: 0.7957 (m-30) REVERT: D 755 MET cc_start: 0.8685 (mmm) cc_final: 0.8078 (mtt) REVERT: D 771 ILE cc_start: 0.9722 (mm) cc_final: 0.9447 (tp) outliers start: 3 outliers final: 1 residues processed: 297 average time/residue: 0.3532 time to fit residues: 151.1628 Evaluate side-chains 212 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 211 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 179 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 246 optimal weight: 1.9990 chunk 134 optimal weight: 0.7980 chunk 239 optimal weight: 0.0770 chunk 243 optimal weight: 0.0050 chunk 35 optimal weight: 0.0050 chunk 112 optimal weight: 4.9990 chunk 302 optimal weight: 0.9990 chunk 197 optimal weight: 5.9990 chunk 131 optimal weight: 5.9990 overall best weight: 0.3768 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 ASN A 407 ASN A 704 GLN B 570 ASN B 724 HIS ** C 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 570 ASN C 591 ASN C 724 HIS D 136 GLN D 222 GLN D 264 GLN ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.070234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.061610 restraints weight = 421385.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.063403 restraints weight = 210624.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.064577 restraints weight = 126073.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.065332 restraints weight = 84957.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.065869 restraints weight = 62303.105| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.4303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23305 Z= 0.144 Angle : 0.654 5.891 31539 Z= 0.351 Chirality : 0.041 0.171 3449 Planarity : 0.006 0.094 4172 Dihedral : 6.436 63.758 3301 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.17 % Allowed : 12.30 % Favored : 87.53 % Rotamer: Outliers : 0.10 % Allowed : 3.25 % Favored : 96.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.44 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.44 (0.13), residues: 2967 helix: -2.09 (0.12), residues: 1397 sheet: -3.85 (0.38), residues: 144 loop : -3.82 (0.14), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 215 TYR 0.024 0.002 TYR B 589 PHE 0.026 0.002 PHE B 816 TRP 0.017 0.001 TRP D 233 HIS 0.016 0.001 HIS A 656 Details of bonding type rmsd covalent geometry : bond 0.00306 (23286) covalent geometry : angle 0.65250 (31501) SS BOND : bond 0.00370 ( 19) SS BOND : angle 1.26793 ( 38) hydrogen bonds : bond 0.05591 ( 993) hydrogen bonds : angle 6.18285 ( 2814) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 825 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue TYR 72 is missing expected H atoms. Skipping. Residue LEU 73 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue THR 77 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue VAL 87 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue SER 93 is missing expected H atoms. Skipping. Residue LEU 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue LYS 148 is missing expected H atoms. Skipping. Residue SER 149 is missing expected H atoms. Skipping. Residue SER 153 is missing expected H atoms. Skipping. Residue THR 154 is missing expected H atoms. Skipping. Residue SER 156 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue SER 158 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 167 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue VAL 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LEU 181 is missing expected H atoms. Skipping. Residue THR 185 is missing expected H atoms. Skipping. Residue VAL 186 is missing expected H atoms. Skipping. Residue LYS 195 is missing expected H atoms. Skipping. Residue THR 196 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue VAL 198 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue THR 202 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue ILE 222 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LEU 225 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue VAL 235 is missing expected H atoms. Skipping. Residue THR 236 is missing expected H atoms. Skipping. Residue LEU 239 is missing expected H atoms. Skipping. Residue ILE 243 is missing expected H atoms. Skipping. Residue LEU 245 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LEU 247 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue ILE 251 is missing expected H atoms. Skipping. Residue THR 253 is missing expected H atoms. Skipping. Residue VAL 254 is missing expected H atoms. Skipping. Residue TYR 255 is missing expected H atoms. Skipping. Residue MET 256 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LEU 259 is missing expected H atoms. Skipping. Residue LYS 262 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue TYR 273 is missing expected H atoms. Skipping. Residue LEU 276 is missing expected H atoms. Skipping. Residue SER 278 is missing expected H atoms. Skipping. Residue VAL 279 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue TYR 287 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue LEU 290 is missing expected H atoms. Skipping. Residue THR 291 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue TYR 295 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue MET 300 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Residue ILE 317 is missing expected H atoms. Skipping. Residue SER 318 is missing expected H atoms. Skipping. Residue THR 320 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue VAL 327 is missing expected H atoms. Skipping. Residue THR 329 is missing expected H atoms. Skipping. Residue ILE 331 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue VAL 335 is missing expected H atoms. Skipping. Residue SER 338 is missing expected H atoms. Skipping. Residue TYR 339 is missing expected H atoms. Skipping. Residue TYR 343 is missing expected H atoms. Skipping. Residue MET 346 is missing expected H atoms. Skipping. Residue ILE 349 is missing expected H atoms. Skipping. Residue TYR 350 is missing expected H atoms. Skipping. Residue THR 351 is missing expected H atoms. Skipping. Residue VAL 352 is missing expected H atoms. Skipping. Residue THR 357 is missing expected H atoms. Skipping. Residue VAL 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue MET 362 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue LYS 367 is missing expected H atoms. Skipping. Residue TYR 369 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue ILE 371 is missing expected H atoms. Skipping. Residue LYS 374 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue VAL 377 is missing expected H atoms. Skipping. Residue LEU 378 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue MET 389 is missing expected H atoms. Skipping. Residue THR 390 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue SER 393 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue LEU 403 is missing expected H atoms. Skipping. Residue ILE 408 is missing expected H atoms. Skipping. Residue TYR 411 is missing expected H atoms. Skipping. Residue ILE 414 is missing expected H atoms. Skipping. Residue MET 417 is missing expected H atoms. Skipping. Residue THR 421 is missing expected H atoms. Skipping. Residue ILE 422 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue TYR 72 is missing expected H atoms. Skipping. Residue LEU 73 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue THR 77 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue VAL 87 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue SER 93 is missing expected H atoms. Skipping. Residue LEU 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LYS 148 is missing expected H atoms. Skipping. Residue SER 149 is missing expected H atoms. Skipping. Residue SER 153 is missing expected H atoms. Skipping. Residue THR 154 is missing expected H atoms. Skipping. Residue SER 156 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue SER 158 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 167 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue VAL 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LEU 181 is missing expected H atoms. Skipping. Residue THR 185 is missing expected H atoms. Skipping. Residue VAL 186 is missing expected H atoms. Skipping. Residue LYS 195 is missing expected H atoms. Skipping. Residue THR 196 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue VAL 198 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue THR 202 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue ILE 222 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LEU 225 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue VAL 235 is missing expected H atoms. Skipping. Residue THR 236 is missing expected H atoms. Skipping. Residue LEU 239 is missing expected H atoms. Skipping. Residue ILE 243 is missing expected H atoms. Skipping. Residue LEU 245 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LEU 247 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue ILE 251 is missing expected H atoms. Skipping. Residue THR 253 is missing expected H atoms. Skipping. Residue VAL 254 is missing expected H atoms. Skipping. Residue TYR 255 is missing expected H atoms. Skipping. Residue MET 256 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LEU 259 is missing expected H atoms. Skipping. Residue LYS 262 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue TYR 273 is missing expected H atoms. Skipping. Residue LEU 276 is missing expected H atoms. Skipping. Residue SER 278 is missing expected H atoms. Skipping. Residue VAL 279 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue TYR 287 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue LEU 290 is missing expected H atoms. Skipping. Residue THR 291 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue TYR 295 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue MET 300 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Residue ILE 317 is missing expected H atoms. Skipping. Residue SER 318 is missing expected H atoms. Skipping. Residue THR 320 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue VAL 327 is missing expected H atoms. Skipping. Residue THR 329 is missing expected H atoms. Skipping. Residue ILE 331 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue VAL 335 is missing expected H atoms. Skipping. Residue SER 338 is missing expected H atoms. Skipping. Residue TYR 339 is missing expected H atoms. Skipping. Residue TYR 343 is missing expected H atoms. Skipping. Residue MET 346 is missing expected H atoms. Skipping. Residue ILE 349 is missing expected H atoms. Skipping. Residue TYR 350 is missing expected H atoms. Skipping. Residue THR 351 is missing expected H atoms. Skipping. Residue VAL 352 is missing expected H atoms. Skipping. Residue THR 357 is missing expected H atoms. Skipping. Residue VAL 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue MET 362 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue LYS 367 is missing expected H atoms. Skipping. Residue TYR 369 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue ILE 371 is missing expected H atoms. Skipping. Residue LYS 374 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue VAL 377 is missing expected H atoms. Skipping. Residue LEU 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue SER 384 is missing expected H atoms. Skipping. Residue MET 386 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue MET 389 is missing expected H atoms. Skipping. Residue THR 390 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue LEU 403 is missing expected H atoms. Skipping. Residue ILE 408 is missing expected H atoms. Skipping. Residue TYR 411 is missing expected H atoms. Skipping. Residue ILE 414 is missing expected H atoms. Skipping. Residue MET 417 is missing expected H atoms. Skipping. Residue THR 421 is missing expected H atoms. Skipping. Residue ILE 422 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue ILE 23 is missing expected H atoms. Skipping. Residue SER 31 is missing expected H atoms. Skipping. Residue VAL 35 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue THR 37 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue SER 42 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue SER 49 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue VAL 55 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue SER 58 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue SER 64 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue THR 78 is missing expected H atoms. Skipping. Residue TYR 84 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue TYR 106 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue ILE 137 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue ILE 163 is missing expected H atoms. Skipping. Residue ILE 167 is missing expected H atoms. Skipping. Residue MET 168 is missing expected H atoms. Skipping. Residue THR 169 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue VAL 174 is missing expected H atoms. Skipping. Residue SER 176 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue THR 181 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue SER 188 is missing expected H atoms. Skipping. Residue ILE 190 is missing expected H atoms. Skipping. Residue TYR 191 is missing expected H atoms. Skipping. Residue VAL 204 is missing expected H atoms. Skipping. Residue ILE 206 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue LYS 211 is missing expected H atoms. Skipping. Residue TYR 217 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue ILE 220 is missing expected H atoms. Skipping. Residue TYR 233 is missing expected H atoms. Skipping. Residue MET 236 is missing expected H atoms. Skipping. Residue ILE 237 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue ILE 249 is missing expected H atoms. Skipping. Residue THR 250 is missing expected H atoms. Skipping. Evaluate side-chains 278 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 276 time to evaluate : 0.900 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: 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: 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: 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: 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 99 LEU cc_start: 0.8888 (mt) cc_final: 0.8663 (mt) REVERT: A 407 ASN cc_start: 0.9275 (t160) cc_final: 0.8954 (t0) REVERT: B 324 ASN cc_start: 0.8395 (t0) cc_final: 0.8097 (p0) REVERT: B 473 TYR cc_start: 0.7565 (m-80) cc_final: 0.7295 (m-80) REVERT: B 474 MET cc_start: 0.7685 (tpt) cc_final: 0.7378 (tpt) REVERT: B 597 ARG cc_start: 0.8125 (mtt180) cc_final: 0.7893 (ttt180) REVERT: B 659 VAL cc_start: 0.8773 (t) cc_final: 0.8458 (m) REVERT: C 97 PHE cc_start: 0.7164 (t80) cc_final: 0.6881 (t80) REVERT: C 657 GLU cc_start: 0.8283 (mm-30) cc_final: 0.7975 (mm-30) REVERT: D 533 MET cc_start: 0.9229 (tmm) cc_final: 0.8982 (tmm) REVERT: D 732 ASP cc_start: 0.8326 (m-30) cc_final: 0.7963 (m-30) REVERT: D 755 MET cc_start: 0.8530 (mmm) cc_final: 0.8074 (mtt) REVERT: D 771 ILE cc_start: 0.9722 (mm) cc_final: 0.9428 (tp) outliers start: 2 outliers final: 1 residues processed: 278 average time/residue: 0.3339 time to fit residues: 136.5833 Evaluate side-chains 214 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 213 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 116 optimal weight: 7.9990 chunk 299 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 chunk 86 optimal weight: 0.0970 chunk 200 optimal weight: 0.6980 chunk 209 optimal weight: 0.6980 chunk 226 optimal weight: 3.9990 chunk 202 optimal weight: 1.9990 chunk 136 optimal weight: 0.8980 chunk 261 optimal weight: 7.9990 chunk 161 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN A 407 ASN ** C 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 569 ASN ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.070373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.061765 restraints weight = 413993.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.063539 restraints weight = 207625.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.064712 restraints weight = 124812.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.065466 restraints weight = 83888.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.065990 restraints weight = 61201.926| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.4832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23305 Z= 0.131 Angle : 0.601 5.740 31539 Z= 0.323 Chirality : 0.039 0.163 3449 Planarity : 0.005 0.083 4172 Dihedral : 5.897 62.994 3301 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.93 % Favored : 87.93 % Rotamer: Outliers : 0.05 % Allowed : 1.31 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.44 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.67 (0.14), residues: 2967 helix: -1.36 (0.13), residues: 1404 sheet: -3.64 (0.39), residues: 148 loop : -3.52 (0.14), residues: 1415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 831 TYR 0.019 0.001 TYR C 356 PHE 0.034 0.001 PHE C 607 TRP 0.013 0.001 TRP A 233 HIS 0.008 0.001 HIS A 656 Details of bonding type rmsd covalent geometry : bond 0.00279 (23286) covalent geometry : angle 0.60040 (31501) SS BOND : bond 0.00268 ( 19) SS BOND : angle 1.00248 ( 38) hydrogen bonds : bond 0.04867 ( 993) hydrogen bonds : angle 5.71036 ( 2814) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 825 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue TYR 72 is missing expected H atoms. Skipping. Residue LEU 73 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue THR 77 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue VAL 87 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue SER 93 is missing expected H atoms. Skipping. Residue LEU 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue LYS 148 is missing expected H atoms. Skipping. Residue SER 149 is missing expected H atoms. Skipping. Residue SER 153 is missing expected H atoms. Skipping. Residue THR 154 is missing expected H atoms. Skipping. Residue SER 156 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue SER 158 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 167 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue VAL 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LEU 181 is missing expected H atoms. Skipping. Residue THR 185 is missing expected H atoms. Skipping. Residue VAL 186 is missing expected H atoms. Skipping. Residue LYS 195 is missing expected H atoms. Skipping. Residue THR 196 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue VAL 198 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue THR 202 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue ILE 222 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LEU 225 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue VAL 235 is missing expected H atoms. Skipping. Residue THR 236 is missing expected H atoms. Skipping. Residue LEU 239 is missing expected H atoms. Skipping. Residue ILE 243 is missing expected H atoms. Skipping. Residue LEU 245 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LEU 247 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue ILE 251 is missing expected H atoms. Skipping. Residue THR 253 is missing expected H atoms. Skipping. Residue VAL 254 is missing expected H atoms. Skipping. Residue TYR 255 is missing expected H atoms. Skipping. Residue MET 256 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LEU 259 is missing expected H atoms. Skipping. Residue LYS 262 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue TYR 273 is missing expected H atoms. Skipping. Residue LEU 276 is missing expected H atoms. Skipping. Residue SER 278 is missing expected H atoms. Skipping. Residue VAL 279 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue TYR 287 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue LEU 290 is missing expected H atoms. Skipping. Residue THR 291 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue TYR 295 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue MET 300 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Residue ILE 317 is missing expected H atoms. Skipping. Residue SER 318 is missing expected H atoms. Skipping. Residue THR 320 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue VAL 327 is missing expected H atoms. Skipping. Residue THR 329 is missing expected H atoms. Skipping. Residue ILE 331 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue VAL 335 is missing expected H atoms. Skipping. Residue SER 338 is missing expected H atoms. Skipping. Residue TYR 339 is missing expected H atoms. Skipping. Residue TYR 343 is missing expected H atoms. Skipping. Residue MET 346 is missing expected H atoms. Skipping. Residue ILE 349 is missing expected H atoms. Skipping. Residue TYR 350 is missing expected H atoms. Skipping. Residue THR 351 is missing expected H atoms. Skipping. Residue VAL 352 is missing expected H atoms. Skipping. Residue THR 357 is missing expected H atoms. Skipping. Residue VAL 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue MET 362 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue LYS 367 is missing expected H atoms. Skipping. Residue TYR 369 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue ILE 371 is missing expected H atoms. Skipping. Residue LYS 374 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue VAL 377 is missing expected H atoms. Skipping. Residue LEU 378 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue MET 389 is missing expected H atoms. Skipping. Residue THR 390 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue SER 393 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue LEU 403 is missing expected H atoms. Skipping. Residue ILE 408 is missing expected H atoms. Skipping. Residue TYR 411 is missing expected H atoms. Skipping. Residue ILE 414 is missing expected H atoms. Skipping. Residue MET 417 is missing expected H atoms. Skipping. Residue THR 421 is missing expected H atoms. Skipping. Residue ILE 422 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue TYR 72 is missing expected H atoms. Skipping. Residue LEU 73 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue THR 77 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue VAL 87 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue SER 93 is missing expected H atoms. Skipping. Residue LEU 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LYS 148 is missing expected H atoms. Skipping. Residue SER 149 is missing expected H atoms. Skipping. Residue SER 153 is missing expected H atoms. Skipping. Residue THR 154 is missing expected H atoms. Skipping. Residue SER 156 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue SER 158 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 167 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue VAL 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LEU 181 is missing expected H atoms. Skipping. Residue THR 185 is missing expected H atoms. Skipping. Residue VAL 186 is missing expected H atoms. Skipping. Residue LYS 195 is missing expected H atoms. Skipping. Residue THR 196 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue VAL 198 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue THR 202 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue ILE 222 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LEU 225 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue VAL 235 is missing expected H atoms. Skipping. Residue THR 236 is missing expected H atoms. Skipping. Residue LEU 239 is missing expected H atoms. Skipping. Residue ILE 243 is missing expected H atoms. Skipping. Residue LEU 245 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LEU 247 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue ILE 251 is missing expected H atoms. Skipping. Residue THR 253 is missing expected H atoms. Skipping. Residue VAL 254 is missing expected H atoms. Skipping. Residue TYR 255 is missing expected H atoms. Skipping. Residue MET 256 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LEU 259 is missing expected H atoms. Skipping. Residue LYS 262 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue TYR 273 is missing expected H atoms. Skipping. Residue LEU 276 is missing expected H atoms. Skipping. Residue SER 278 is missing expected H atoms. Skipping. Residue VAL 279 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue TYR 287 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue LEU 290 is missing expected H atoms. Skipping. Residue THR 291 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue TYR 295 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue MET 300 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Residue ILE 317 is missing expected H atoms. Skipping. Residue SER 318 is missing expected H atoms. Skipping. Residue THR 320 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue VAL 327 is missing expected H atoms. Skipping. Residue THR 329 is missing expected H atoms. Skipping. Residue ILE 331 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue VAL 335 is missing expected H atoms. Skipping. Residue SER 338 is missing expected H atoms. Skipping. Residue TYR 339 is missing expected H atoms. Skipping. Residue TYR 343 is missing expected H atoms. Skipping. Residue MET 346 is missing expected H atoms. Skipping. Residue ILE 349 is missing expected H atoms. Skipping. Residue TYR 350 is missing expected H atoms. Skipping. Residue THR 351 is missing expected H atoms. Skipping. Residue VAL 352 is missing expected H atoms. Skipping. Residue THR 357 is missing expected H atoms. Skipping. Residue VAL 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue MET 362 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue LYS 367 is missing expected H atoms. Skipping. Residue TYR 369 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue ILE 371 is missing expected H atoms. Skipping. Residue LYS 374 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue VAL 377 is missing expected H atoms. Skipping. Residue LEU 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue SER 384 is missing expected H atoms. Skipping. Residue MET 386 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue MET 389 is missing expected H atoms. Skipping. Residue THR 390 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue LEU 403 is missing expected H atoms. Skipping. Residue ILE 408 is missing expected H atoms. Skipping. Residue TYR 411 is missing expected H atoms. Skipping. Residue ILE 414 is missing expected H atoms. Skipping. Residue MET 417 is missing expected H atoms. Skipping. Residue THR 421 is missing expected H atoms. Skipping. Residue ILE 422 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue ILE 23 is missing expected H atoms. Skipping. Residue SER 31 is missing expected H atoms. Skipping. Residue VAL 35 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue THR 37 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue SER 42 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue SER 49 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue VAL 55 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue SER 58 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue SER 64 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue THR 78 is missing expected H atoms. Skipping. Residue TYR 84 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue TYR 106 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue ILE 137 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue ILE 163 is missing expected H atoms. Skipping. Residue ILE 167 is missing expected H atoms. Skipping. Residue MET 168 is missing expected H atoms. Skipping. Residue THR 169 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue VAL 174 is missing expected H atoms. Skipping. Residue SER 176 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue THR 181 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue SER 188 is missing expected H atoms. Skipping. Residue ILE 190 is missing expected H atoms. Skipping. Residue TYR 191 is missing expected H atoms. Skipping. Residue VAL 204 is missing expected H atoms. Skipping. Residue ILE 206 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue LYS 211 is missing expected H atoms. Skipping. Residue TYR 217 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue ILE 220 is missing expected H atoms. Skipping. Residue TYR 233 is missing expected H atoms. Skipping. Residue MET 236 is missing expected H atoms. Skipping. Residue ILE 237 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue ILE 249 is missing expected H atoms. Skipping. Residue THR 250 is missing expected H atoms. Skipping. Evaluate side-chains 255 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 254 time to evaluate : 0.763 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 230 MET cc_start: 0.8700 (ptp) cc_final: 0.8466 (ptp) REVERT: B 239 LYS cc_start: 0.7486 (tttt) cc_final: 0.7150 (tptm) REVERT: B 379 ILE cc_start: 0.9209 (mt) cc_final: 0.8731 (mm) REVERT: B 659 VAL cc_start: 0.8792 (t) cc_final: 0.8503 (m) REVERT: C 97 PHE cc_start: 0.7250 (t80) cc_final: 0.7040 (t80) REVERT: C 657 GLU cc_start: 0.8401 (mm-30) cc_final: 0.8146 (mm-30) REVERT: D 533 MET cc_start: 0.9194 (tmm) cc_final: 0.8981 (tmm) REVERT: D 597 ARG cc_start: 0.8759 (ptp-110) cc_final: 0.8534 (mtt-85) REVERT: D 732 ASP cc_start: 0.8427 (m-30) cc_final: 0.8067 (m-30) REVERT: D 755 MET cc_start: 0.8425 (mmm) cc_final: 0.8056 (mtt) REVERT: D 771 ILE cc_start: 0.9718 (mm) cc_final: 0.9479 (tp) outliers start: 1 outliers final: 1 residues processed: 255 average time/residue: 0.3333 time to fit residues: 125.2318 Evaluate side-chains 205 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 204 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 42 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 200 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 195 optimal weight: 0.6980 chunk 250 optimal weight: 30.0000 chunk 130 optimal weight: 4.9990 chunk 162 optimal weight: 4.9990 chunk 149 optimal weight: 1.9990 chunk 167 optimal weight: 3.9990 chunk 182 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 ASN A 407 ASN A 795 HIS ** B 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 591 ASN C 724 HIS D 115 ASN ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.069840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.061188 restraints weight = 416821.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.062955 restraints weight = 209636.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.064144 restraints weight = 126125.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.064907 restraints weight = 84750.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.065423 restraints weight = 61833.118| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.5066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23305 Z= 0.156 Angle : 0.587 5.678 31539 Z= 0.316 Chirality : 0.039 0.152 3449 Planarity : 0.005 0.082 4172 Dihedral : 5.653 62.158 3301 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.13 % Allowed : 12.23 % Favored : 87.63 % Rotamer: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.44 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.19 (0.14), residues: 2967 helix: -0.91 (0.13), residues: 1390 sheet: -3.43 (0.39), residues: 154 loop : -3.30 (0.15), residues: 1423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 120 TYR 0.017 0.001 TYR C 705 PHE 0.016 0.001 PHE C 595 TRP 0.012 0.001 TRP A 233 HIS 0.007 0.001 HIS A 795 Details of bonding type rmsd covalent geometry : bond 0.00324 (23286) covalent geometry : angle 0.58571 (31501) SS BOND : bond 0.00412 ( 19) SS BOND : angle 1.09507 ( 38) hydrogen bonds : bond 0.04599 ( 993) hydrogen bonds : angle 5.55947 ( 2814) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 825 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue TYR 72 is missing expected H atoms. Skipping. Residue LEU 73 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue THR 77 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue VAL 87 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue SER 93 is missing expected H atoms. Skipping. Residue LEU 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue LYS 148 is missing expected H atoms. Skipping. Residue SER 149 is missing expected H atoms. Skipping. Residue SER 153 is missing expected H atoms. Skipping. Residue THR 154 is missing expected H atoms. Skipping. Residue SER 156 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue SER 158 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 167 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue VAL 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LEU 181 is missing expected H atoms. Skipping. Residue THR 185 is missing expected H atoms. Skipping. Residue VAL 186 is missing expected H atoms. Skipping. Residue LYS 195 is missing expected H atoms. Skipping. Residue THR 196 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue VAL 198 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue THR 202 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue ILE 222 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LEU 225 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue VAL 235 is missing expected H atoms. Skipping. Residue THR 236 is missing expected H atoms. Skipping. Residue LEU 239 is missing expected H atoms. Skipping. Residue ILE 243 is missing expected H atoms. Skipping. Residue LEU 245 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LEU 247 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue ILE 251 is missing expected H atoms. Skipping. Residue THR 253 is missing expected H atoms. Skipping. Residue VAL 254 is missing expected H atoms. Skipping. Residue TYR 255 is missing expected H atoms. Skipping. Residue MET 256 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LEU 259 is missing expected H atoms. Skipping. Residue LYS 262 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue TYR 273 is missing expected H atoms. Skipping. Residue LEU 276 is missing expected H atoms. Skipping. Residue SER 278 is missing expected H atoms. Skipping. Residue VAL 279 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue TYR 287 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue LEU 290 is missing expected H atoms. Skipping. Residue THR 291 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue TYR 295 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue MET 300 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Residue ILE 317 is missing expected H atoms. Skipping. Residue SER 318 is missing expected H atoms. Skipping. Residue THR 320 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue VAL 327 is missing expected H atoms. Skipping. Residue THR 329 is missing expected H atoms. Skipping. Residue ILE 331 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue VAL 335 is missing expected H atoms. Skipping. Residue SER 338 is missing expected H atoms. Skipping. Residue TYR 339 is missing expected H atoms. Skipping. Residue TYR 343 is missing expected H atoms. Skipping. Residue MET 346 is missing expected H atoms. Skipping. Residue ILE 349 is missing expected H atoms. Skipping. Residue TYR 350 is missing expected H atoms. Skipping. Residue THR 351 is missing expected H atoms. Skipping. Residue VAL 352 is missing expected H atoms. Skipping. Residue THR 357 is missing expected H atoms. Skipping. Residue VAL 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue MET 362 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue LYS 367 is missing expected H atoms. Skipping. Residue TYR 369 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue ILE 371 is missing expected H atoms. Skipping. Residue LYS 374 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue VAL 377 is missing expected H atoms. Skipping. Residue LEU 378 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue MET 389 is missing expected H atoms. Skipping. Residue THR 390 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue SER 393 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue LEU 403 is missing expected H atoms. Skipping. Residue ILE 408 is missing expected H atoms. Skipping. Residue TYR 411 is missing expected H atoms. Skipping. Residue ILE 414 is missing expected H atoms. Skipping. Residue MET 417 is missing expected H atoms. Skipping. Residue THR 421 is missing expected H atoms. Skipping. Residue ILE 422 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue TYR 72 is missing expected H atoms. Skipping. Residue LEU 73 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue THR 77 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue VAL 87 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue SER 93 is missing expected H atoms. Skipping. Residue LEU 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LYS 148 is missing expected H atoms. Skipping. Residue SER 149 is missing expected H atoms. Skipping. Residue SER 153 is missing expected H atoms. Skipping. Residue THR 154 is missing expected H atoms. Skipping. Residue SER 156 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue SER 158 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 167 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue VAL 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LEU 181 is missing expected H atoms. Skipping. Residue THR 185 is missing expected H atoms. Skipping. Residue VAL 186 is missing expected H atoms. Skipping. Residue LYS 195 is missing expected H atoms. Skipping. Residue THR 196 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue VAL 198 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue THR 202 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue ILE 222 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LEU 225 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue VAL 235 is missing expected H atoms. Skipping. Residue THR 236 is missing expected H atoms. Skipping. Residue LEU 239 is missing expected H atoms. Skipping. Residue ILE 243 is missing expected H atoms. Skipping. Residue LEU 245 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LEU 247 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue ILE 251 is missing expected H atoms. Skipping. Residue THR 253 is missing expected H atoms. Skipping. Residue VAL 254 is missing expected H atoms. Skipping. Residue TYR 255 is missing expected H atoms. Skipping. Residue MET 256 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LEU 259 is missing expected H atoms. Skipping. Residue LYS 262 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue TYR 273 is missing expected H atoms. Skipping. Residue LEU 276 is missing expected H atoms. Skipping. Residue SER 278 is missing expected H atoms. Skipping. Residue VAL 279 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue TYR 287 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue LEU 290 is missing expected H atoms. Skipping. Residue THR 291 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue TYR 295 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue MET 300 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Residue ILE 317 is missing expected H atoms. Skipping. Residue SER 318 is missing expected H atoms. Skipping. Residue THR 320 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue VAL 327 is missing expected H atoms. Skipping. Residue THR 329 is missing expected H atoms. Skipping. Residue ILE 331 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue VAL 335 is missing expected H atoms. Skipping. Residue SER 338 is missing expected H atoms. Skipping. Residue TYR 339 is missing expected H atoms. Skipping. Residue TYR 343 is missing expected H atoms. Skipping. Residue MET 346 is missing expected H atoms. Skipping. Residue ILE 349 is missing expected H atoms. Skipping. Residue TYR 350 is missing expected H atoms. Skipping. Residue THR 351 is missing expected H atoms. Skipping. Residue VAL 352 is missing expected H atoms. Skipping. Residue THR 357 is missing expected H atoms. Skipping. Residue VAL 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue MET 362 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue LYS 367 is missing expected H atoms. Skipping. Residue TYR 369 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue ILE 371 is missing expected H atoms. Skipping. Residue LYS 374 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue VAL 377 is missing expected H atoms. Skipping. Residue LEU 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue SER 384 is missing expected H atoms. Skipping. Residue MET 386 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue MET 389 is missing expected H atoms. Skipping. Residue THR 390 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue LEU 403 is missing expected H atoms. Skipping. Residue ILE 408 is missing expected H atoms. Skipping. Residue TYR 411 is missing expected H atoms. Skipping. Residue ILE 414 is missing expected H atoms. Skipping. Residue MET 417 is missing expected H atoms. Skipping. Residue THR 421 is missing expected H atoms. Skipping. Residue ILE 422 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue ILE 23 is missing expected H atoms. Skipping. Residue SER 31 is missing expected H atoms. Skipping. Residue VAL 35 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue THR 37 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue SER 42 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue SER 49 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue VAL 55 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue SER 58 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue SER 64 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue THR 78 is missing expected H atoms. Skipping. Residue TYR 84 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue TYR 106 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue ILE 137 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue ILE 163 is missing expected H atoms. Skipping. Residue ILE 167 is missing expected H atoms. Skipping. Residue MET 168 is missing expected H atoms. Skipping. Residue THR 169 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue VAL 174 is missing expected H atoms. Skipping. Residue SER 176 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue THR 181 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue SER 188 is missing expected H atoms. Skipping. Residue ILE 190 is missing expected H atoms. Skipping. Residue TYR 191 is missing expected H atoms. Skipping. Residue VAL 204 is missing expected H atoms. Skipping. Residue ILE 206 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue LYS 211 is missing expected H atoms. Skipping. Residue TYR 217 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue ILE 220 is missing expected H atoms. Skipping. Residue TYR 233 is missing expected H atoms. Skipping. Residue MET 236 is missing expected H atoms. Skipping. Residue ILE 237 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue ILE 249 is missing expected H atoms. Skipping. Residue THR 250 is missing expected H atoms. Skipping. Evaluate side-chains 242 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 1.037 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 SER cc_start: 0.8687 (t) cc_final: 0.8217 (m) REVERT: B 239 LYS cc_start: 0.7684 (tttt) cc_final: 0.7318 (tptm) REVERT: B 297 MET cc_start: 0.8319 (ttp) cc_final: 0.8011 (ttp) REVERT: B 659 VAL cc_start: 0.8743 (t) cc_final: 0.8483 (m) REVERT: C 657 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8272 (mm-30) REVERT: C 824 MET cc_start: 0.7926 (tpp) cc_final: 0.7557 (tpp) REVERT: D 147 LYS cc_start: 0.9615 (mmmt) cc_final: 0.9361 (mmmm) REVERT: D 533 MET cc_start: 0.9193 (tmm) cc_final: 0.8989 (tmm) REVERT: D 732 ASP cc_start: 0.8494 (m-30) cc_final: 0.8286 (m-30) REVERT: D 755 MET cc_start: 0.8444 (mmm) cc_final: 0.8097 (mtt) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.3198 time to fit residues: 115.1353 Evaluate side-chains 199 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 126 optimal weight: 6.9990 chunk 176 optimal weight: 0.6980 chunk 135 optimal weight: 0.7980 chunk 248 optimal weight: 30.0000 chunk 185 optimal weight: 0.5980 chunk 139 optimal weight: 0.0050 chunk 157 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 151 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.8196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN A 407 ASN A 484 ASN A 591 ASN B 570 ASN C 570 ASN C 591 ASN ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.070215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.061466 restraints weight = 418195.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.063253 restraints weight = 210602.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.064434 restraints weight = 127009.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.065204 restraints weight = 85855.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.065741 restraints weight = 62675.126| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.5349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 23305 Z= 0.117 Angle : 0.559 6.009 31539 Z= 0.298 Chirality : 0.039 0.155 3449 Planarity : 0.004 0.078 4172 Dihedral : 5.402 61.391 3301 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.75 % Favored : 89.11 % Rotamer: Outliers : 0.10 % Allowed : 0.97 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.44 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.75 (0.15), residues: 2967 helix: -0.53 (0.14), residues: 1392 sheet: -3.08 (0.38), residues: 170 loop : -3.10 (0.16), residues: 1405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 831 TYR 0.022 0.001 TYR B 231 PHE 0.013 0.001 PHE B 117 TRP 0.012 0.001 TRP A 233 HIS 0.006 0.001 HIS A 656 Details of bonding type rmsd covalent geometry : bond 0.00248 (23286) covalent geometry : angle 0.55823 (31501) SS BOND : bond 0.00408 ( 19) SS BOND : angle 0.93410 ( 38) hydrogen bonds : bond 0.04294 ( 993) hydrogen bonds : angle 5.31303 ( 2814) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 825 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue TYR 72 is missing expected H atoms. Skipping. Residue LEU 73 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue THR 77 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue VAL 87 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue SER 93 is missing expected H atoms. Skipping. Residue LEU 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue LYS 148 is missing expected H atoms. Skipping. Residue SER 149 is missing expected H atoms. Skipping. Residue SER 153 is missing expected H atoms. Skipping. Residue THR 154 is missing expected H atoms. Skipping. Residue SER 156 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue SER 158 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 167 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue VAL 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LEU 181 is missing expected H atoms. Skipping. Residue THR 185 is missing expected H atoms. Skipping. Residue VAL 186 is missing expected H atoms. Skipping. Residue LYS 195 is missing expected H atoms. Skipping. Residue THR 196 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue VAL 198 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue THR 202 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue ILE 222 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LEU 225 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue VAL 235 is missing expected H atoms. Skipping. Residue THR 236 is missing expected H atoms. Skipping. Residue LEU 239 is missing expected H atoms. Skipping. Residue ILE 243 is missing expected H atoms. Skipping. Residue LEU 245 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LEU 247 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue ILE 251 is missing expected H atoms. Skipping. Residue THR 253 is missing expected H atoms. Skipping. Residue VAL 254 is missing expected H atoms. Skipping. Residue TYR 255 is missing expected H atoms. Skipping. Residue MET 256 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LEU 259 is missing expected H atoms. Skipping. Residue LYS 262 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue TYR 273 is missing expected H atoms. Skipping. Residue LEU 276 is missing expected H atoms. Skipping. Residue SER 278 is missing expected H atoms. Skipping. Residue VAL 279 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue TYR 287 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue LEU 290 is missing expected H atoms. Skipping. Residue THR 291 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue TYR 295 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue MET 300 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Residue ILE 317 is missing expected H atoms. Skipping. Residue SER 318 is missing expected H atoms. Skipping. Residue THR 320 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue VAL 327 is missing expected H atoms. Skipping. Residue THR 329 is missing expected H atoms. Skipping. Residue ILE 331 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue VAL 335 is missing expected H atoms. Skipping. Residue SER 338 is missing expected H atoms. Skipping. Residue TYR 339 is missing expected H atoms. Skipping. Residue TYR 343 is missing expected H atoms. Skipping. Residue MET 346 is missing expected H atoms. Skipping. Residue ILE 349 is missing expected H atoms. Skipping. Residue TYR 350 is missing expected H atoms. Skipping. Residue THR 351 is missing expected H atoms. Skipping. Residue VAL 352 is missing expected H atoms. Skipping. Residue THR 357 is missing expected H atoms. Skipping. Residue VAL 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue MET 362 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue LYS 367 is missing expected H atoms. Skipping. Residue TYR 369 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue ILE 371 is missing expected H atoms. Skipping. Residue LYS 374 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue VAL 377 is missing expected H atoms. Skipping. Residue LEU 378 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue MET 389 is missing expected H atoms. Skipping. Residue THR 390 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue SER 393 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue LEU 403 is missing expected H atoms. Skipping. Residue ILE 408 is missing expected H atoms. Skipping. Residue TYR 411 is missing expected H atoms. Skipping. Residue ILE 414 is missing expected H atoms. Skipping. Residue MET 417 is missing expected H atoms. Skipping. Residue THR 421 is missing expected H atoms. Skipping. Residue ILE 422 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue TYR 72 is missing expected H atoms. Skipping. Residue LEU 73 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue THR 77 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue VAL 87 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue SER 93 is missing expected H atoms. Skipping. Residue LEU 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LYS 148 is missing expected H atoms. Skipping. Residue SER 149 is missing expected H atoms. Skipping. Residue SER 153 is missing expected H atoms. Skipping. Residue THR 154 is missing expected H atoms. Skipping. Residue SER 156 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue SER 158 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 167 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue VAL 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LEU 181 is missing expected H atoms. Skipping. Residue THR 185 is missing expected H atoms. Skipping. Residue VAL 186 is missing expected H atoms. Skipping. Residue LYS 195 is missing expected H atoms. Skipping. Residue THR 196 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue VAL 198 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue THR 202 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue ILE 222 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LEU 225 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue VAL 235 is missing expected H atoms. Skipping. Residue THR 236 is missing expected H atoms. Skipping. Residue LEU 239 is missing expected H atoms. Skipping. Residue ILE 243 is missing expected H atoms. Skipping. Residue LEU 245 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LEU 247 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue ILE 251 is missing expected H atoms. Skipping. Residue THR 253 is missing expected H atoms. Skipping. Residue VAL 254 is missing expected H atoms. Skipping. Residue TYR 255 is missing expected H atoms. Skipping. Residue MET 256 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LEU 259 is missing expected H atoms. Skipping. Residue LYS 262 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue TYR 273 is missing expected H atoms. Skipping. Residue LEU 276 is missing expected H atoms. Skipping. Residue SER 278 is missing expected H atoms. Skipping. Residue VAL 279 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue TYR 287 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue LEU 290 is missing expected H atoms. Skipping. Residue THR 291 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue TYR 295 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue MET 300 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Residue ILE 317 is missing expected H atoms. Skipping. Residue SER 318 is missing expected H atoms. Skipping. Residue THR 320 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue VAL 327 is missing expected H atoms. Skipping. Residue THR 329 is missing expected H atoms. Skipping. Residue ILE 331 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue VAL 335 is missing expected H atoms. Skipping. Residue SER 338 is missing expected H atoms. Skipping. Residue TYR 339 is missing expected H atoms. Skipping. Residue TYR 343 is missing expected H atoms. Skipping. Residue MET 346 is missing expected H atoms. Skipping. Residue ILE 349 is missing expected H atoms. Skipping. Residue TYR 350 is missing expected H atoms. Skipping. Residue THR 351 is missing expected H atoms. Skipping. Residue VAL 352 is missing expected H atoms. Skipping. Residue THR 357 is missing expected H atoms. Skipping. Residue VAL 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue MET 362 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue LYS 367 is missing expected H atoms. Skipping. Residue TYR 369 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue ILE 371 is missing expected H atoms. Skipping. Residue LYS 374 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue VAL 377 is missing expected H atoms. Skipping. Residue LEU 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue SER 384 is missing expected H atoms. Skipping. Residue MET 386 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue MET 389 is missing expected H atoms. Skipping. Residue THR 390 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue LEU 403 is missing expected H atoms. Skipping. Residue ILE 408 is missing expected H atoms. Skipping. Residue TYR 411 is missing expected H atoms. Skipping. Residue ILE 414 is missing expected H atoms. Skipping. Residue MET 417 is missing expected H atoms. Skipping. Residue THR 421 is missing expected H atoms. Skipping. Residue ILE 422 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue ILE 23 is missing expected H atoms. Skipping. Residue SER 31 is missing expected H atoms. Skipping. Residue VAL 35 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue THR 37 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue SER 42 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue SER 49 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue VAL 55 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue SER 58 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue SER 64 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue THR 78 is missing expected H atoms. Skipping. Residue TYR 84 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue TYR 106 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue ILE 137 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue ILE 163 is missing expected H atoms. Skipping. Residue ILE 167 is missing expected H atoms. Skipping. Residue MET 168 is missing expected H atoms. Skipping. Residue THR 169 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue VAL 174 is missing expected H atoms. Skipping. Residue SER 176 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue THR 181 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue SER 188 is missing expected H atoms. Skipping. Residue ILE 190 is missing expected H atoms. Skipping. Residue TYR 191 is missing expected H atoms. Skipping. Residue VAL 204 is missing expected H atoms. Skipping. Residue ILE 206 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue LYS 211 is missing expected H atoms. Skipping. Residue TYR 217 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue ILE 220 is missing expected H atoms. Skipping. Residue TYR 233 is missing expected H atoms. Skipping. Residue MET 236 is missing expected H atoms. Skipping. Residue ILE 237 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue ILE 249 is missing expected H atoms. Skipping. Residue THR 250 is missing expected H atoms. Skipping. Evaluate side-chains 248 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 246 time to evaluate : 1.076 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 SER cc_start: 0.8685 (t) cc_final: 0.8235 (m) REVERT: B 243 ARG cc_start: 0.7700 (mmm160) cc_final: 0.7500 (tmm160) REVERT: B 297 MET cc_start: 0.8175 (ttp) cc_final: 0.7891 (ttp) REVERT: B 509 LYS cc_start: 0.9120 (tptp) cc_final: 0.8917 (tptp) REVERT: B 511 MET cc_start: 0.7644 (ptp) cc_final: 0.7036 (ptp) REVERT: C 824 MET cc_start: 0.7936 (tpp) cc_final: 0.7603 (tpp) REVERT: D 147 LYS cc_start: 0.9601 (mmmt) cc_final: 0.9341 (mmmm) REVERT: D 732 ASP cc_start: 0.8462 (m-30) cc_final: 0.8247 (m-30) REVERT: D 755 MET cc_start: 0.8374 (mmm) cc_final: 0.8067 (mtt) outliers start: 2 outliers final: 1 residues processed: 248 average time/residue: 0.3166 time to fit residues: 116.4127 Evaluate side-chains 206 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 205 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 125 optimal weight: 2.9990 chunk 219 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 169 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 58 optimal weight: 0.1980 chunk 32 optimal weight: 5.9990 chunk 258 optimal weight: 0.0170 overall best weight: 0.9822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 ASN C 591 ASN ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.070304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.061592 restraints weight = 417190.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.063327 restraints weight = 214147.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.064480 restraints weight = 131252.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.065227 restraints weight = 89703.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.065741 restraints weight = 66256.708| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.5508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23305 Z= 0.119 Angle : 0.549 6.346 31539 Z= 0.292 Chirality : 0.038 0.161 3449 Planarity : 0.004 0.078 4172 Dihedral : 5.225 61.073 3301 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.92 % Favored : 88.95 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.44 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.45 (0.15), residues: 2967 helix: -0.28 (0.14), residues: 1393 sheet: -3.02 (0.38), residues: 175 loop : -2.94 (0.16), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 801 TYR 0.020 0.001 TYR C 523 PHE 0.016 0.001 PHE C 647 TRP 0.025 0.001 TRP A 835 HIS 0.005 0.001 HIS A 656 Details of bonding type rmsd covalent geometry : bond 0.00254 (23286) covalent geometry : angle 0.54840 (31501) SS BOND : bond 0.00232 ( 19) SS BOND : angle 0.82197 ( 38) hydrogen bonds : bond 0.04132 ( 993) hydrogen bonds : angle 5.15884 ( 2814) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 825 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue TYR 72 is missing expected H atoms. Skipping. Residue LEU 73 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue THR 77 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue VAL 87 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue SER 93 is missing expected H atoms. Skipping. Residue LEU 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue LYS 148 is missing expected H atoms. Skipping. Residue SER 149 is missing expected H atoms. Skipping. Residue SER 153 is missing expected H atoms. Skipping. Residue THR 154 is missing expected H atoms. Skipping. Residue SER 156 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue SER 158 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 167 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue VAL 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LEU 181 is missing expected H atoms. Skipping. Residue THR 185 is missing expected H atoms. Skipping. Residue VAL 186 is missing expected H atoms. Skipping. Residue LYS 195 is missing expected H atoms. Skipping. Residue THR 196 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue VAL 198 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue THR 202 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue ILE 222 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LEU 225 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue VAL 235 is missing expected H atoms. Skipping. Residue THR 236 is missing expected H atoms. Skipping. Residue LEU 239 is missing expected H atoms. Skipping. Residue ILE 243 is missing expected H atoms. Skipping. Residue LEU 245 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LEU 247 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue ILE 251 is missing expected H atoms. Skipping. Residue THR 253 is missing expected H atoms. Skipping. Residue VAL 254 is missing expected H atoms. Skipping. Residue TYR 255 is missing expected H atoms. Skipping. Residue MET 256 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LEU 259 is missing expected H atoms. Skipping. Residue LYS 262 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue TYR 273 is missing expected H atoms. Skipping. Residue LEU 276 is missing expected H atoms. Skipping. Residue SER 278 is missing expected H atoms. Skipping. Residue VAL 279 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue TYR 287 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue LEU 290 is missing expected H atoms. Skipping. Residue THR 291 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue TYR 295 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue MET 300 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Residue ILE 317 is missing expected H atoms. Skipping. Residue SER 318 is missing expected H atoms. Skipping. Residue THR 320 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue VAL 327 is missing expected H atoms. Skipping. Residue THR 329 is missing expected H atoms. Skipping. Residue ILE 331 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue VAL 335 is missing expected H atoms. Skipping. Residue SER 338 is missing expected H atoms. Skipping. Residue TYR 339 is missing expected H atoms. Skipping. Residue TYR 343 is missing expected H atoms. Skipping. Residue MET 346 is missing expected H atoms. Skipping. Residue ILE 349 is missing expected H atoms. Skipping. Residue TYR 350 is missing expected H atoms. Skipping. Residue THR 351 is missing expected H atoms. Skipping. Residue VAL 352 is missing expected H atoms. Skipping. Residue THR 357 is missing expected H atoms. Skipping. Residue VAL 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue MET 362 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue LYS 367 is missing expected H atoms. Skipping. Residue TYR 369 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue ILE 371 is missing expected H atoms. Skipping. Residue LYS 374 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue VAL 377 is missing expected H atoms. Skipping. Residue LEU 378 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue MET 389 is missing expected H atoms. Skipping. Residue THR 390 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue SER 393 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue LEU 403 is missing expected H atoms. Skipping. Residue ILE 408 is missing expected H atoms. Skipping. Residue TYR 411 is missing expected H atoms. Skipping. Residue ILE 414 is missing expected H atoms. Skipping. Residue MET 417 is missing expected H atoms. Skipping. Residue THR 421 is missing expected H atoms. Skipping. Residue ILE 422 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue TYR 72 is missing expected H atoms. Skipping. Residue LEU 73 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue THR 77 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue VAL 87 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue SER 93 is missing expected H atoms. Skipping. Residue LEU 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LYS 148 is missing expected H atoms. Skipping. Residue SER 149 is missing expected H atoms. Skipping. Residue SER 153 is missing expected H atoms. Skipping. Residue THR 154 is missing expected H atoms. Skipping. Residue SER 156 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue SER 158 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 167 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue VAL 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LEU 181 is missing expected H atoms. Skipping. Residue THR 185 is missing expected H atoms. Skipping. Residue VAL 186 is missing expected H atoms. Skipping. Residue LYS 195 is missing expected H atoms. Skipping. Residue THR 196 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue VAL 198 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue THR 202 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue ILE 222 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LEU 225 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue VAL 235 is missing expected H atoms. Skipping. Residue THR 236 is missing expected H atoms. Skipping. Residue LEU 239 is missing expected H atoms. Skipping. Residue ILE 243 is missing expected H atoms. Skipping. Residue LEU 245 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LEU 247 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue ILE 251 is missing expected H atoms. Skipping. Residue THR 253 is missing expected H atoms. Skipping. Residue VAL 254 is missing expected H atoms. Skipping. Residue TYR 255 is missing expected H atoms. Skipping. Residue MET 256 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LEU 259 is missing expected H atoms. Skipping. Residue LYS 262 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue TYR 273 is missing expected H atoms. Skipping. Residue LEU 276 is missing expected H atoms. Skipping. Residue SER 278 is missing expected H atoms. Skipping. Residue VAL 279 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue TYR 287 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue LEU 290 is missing expected H atoms. Skipping. Residue THR 291 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue TYR 295 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue MET 300 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Residue ILE 317 is missing expected H atoms. Skipping. Residue SER 318 is missing expected H atoms. Skipping. Residue THR 320 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue VAL 327 is missing expected H atoms. Skipping. Residue THR 329 is missing expected H atoms. Skipping. Residue ILE 331 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue VAL 335 is missing expected H atoms. Skipping. Residue SER 338 is missing expected H atoms. Skipping. Residue TYR 339 is missing expected H atoms. Skipping. Residue TYR 343 is missing expected H atoms. Skipping. Residue MET 346 is missing expected H atoms. Skipping. Residue ILE 349 is missing expected H atoms. Skipping. Residue TYR 350 is missing expected H atoms. Skipping. Residue THR 351 is missing expected H atoms. Skipping. Residue VAL 352 is missing expected H atoms. Skipping. Residue THR 357 is missing expected H atoms. Skipping. Residue VAL 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue MET 362 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue LYS 367 is missing expected H atoms. Skipping. Residue TYR 369 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue ILE 371 is missing expected H atoms. Skipping. Residue LYS 374 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue VAL 377 is missing expected H atoms. Skipping. Residue LEU 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue SER 384 is missing expected H atoms. Skipping. Residue MET 386 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue MET 389 is missing expected H atoms. Skipping. Residue THR 390 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue LEU 403 is missing expected H atoms. Skipping. Residue ILE 408 is missing expected H atoms. Skipping. Residue TYR 411 is missing expected H atoms. Skipping. Residue ILE 414 is missing expected H atoms. Skipping. Residue MET 417 is missing expected H atoms. Skipping. Residue THR 421 is missing expected H atoms. Skipping. Residue ILE 422 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue ILE 23 is missing expected H atoms. Skipping. Residue SER 31 is missing expected H atoms. Skipping. Residue VAL 35 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue THR 37 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue SER 42 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue SER 49 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue VAL 55 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue SER 58 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue SER 64 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue THR 78 is missing expected H atoms. Skipping. Residue TYR 84 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue TYR 106 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue ILE 137 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue ILE 163 is missing expected H atoms. Skipping. Residue ILE 167 is missing expected H atoms. Skipping. Residue MET 168 is missing expected H atoms. Skipping. Residue THR 169 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue VAL 174 is missing expected H atoms. Skipping. Residue SER 176 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue THR 181 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue SER 188 is missing expected H atoms. Skipping. Residue ILE 190 is missing expected H atoms. Skipping. Residue TYR 191 is missing expected H atoms. Skipping. Residue VAL 204 is missing expected H atoms. Skipping. Residue ILE 206 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue LYS 211 is missing expected H atoms. Skipping. Residue TYR 217 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue ILE 220 is missing expected H atoms. Skipping. Residue TYR 233 is missing expected H atoms. Skipping. Residue MET 236 is missing expected H atoms. Skipping. Residue ILE 237 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue ILE 249 is missing expected H atoms. Skipping. Residue THR 250 is missing expected H atoms. Skipping. Evaluate side-chains 251 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 0.976 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: 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: 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: 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: 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 245 SER cc_start: 0.8697 (t) cc_final: 0.8247 (m) REVERT: A 351 ILE cc_start: 0.9109 (mt) cc_final: 0.8864 (mm) REVERT: B 239 LYS cc_start: 0.7605 (tttt) cc_final: 0.7360 (tppt) REVERT: B 280 MET cc_start: 0.3943 (tpp) cc_final: 0.3408 (mmt) REVERT: B 297 MET cc_start: 0.8176 (ttp) cc_final: 0.7883 (ttp) REVERT: B 379 ILE cc_start: 0.9212 (mt) cc_final: 0.8730 (mm) REVERT: B 474 MET cc_start: 0.7935 (tpt) cc_final: 0.7723 (tpt) REVERT: C 324 ASN cc_start: 0.7471 (t0) cc_final: 0.7074 (t0) REVERT: C 824 MET cc_start: 0.8232 (tpp) cc_final: 0.7870 (tpp) REVERT: D 533 MET cc_start: 0.9143 (tmm) cc_final: 0.8751 (tmm) REVERT: D 732 ASP cc_start: 0.8504 (m-30) cc_final: 0.8242 (m-30) REVERT: D 755 MET cc_start: 0.8316 (mmm) cc_final: 0.8037 (mtt) outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.3302 time to fit residues: 123.0078 Evaluate side-chains 207 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 84 optimal weight: 0.8980 chunk 210 optimal weight: 0.0980 chunk 123 optimal weight: 0.7980 chunk 146 optimal weight: 4.9990 chunk 288 optimal weight: 20.0000 chunk 307 optimal weight: 30.0000 chunk 302 optimal weight: 10.0000 chunk 169 optimal weight: 4.9990 chunk 217 optimal weight: 5.9990 chunk 248 optimal weight: 30.0000 chunk 297 optimal weight: 7.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 ASN A 407 ASN A 591 ASN A 704 GLN C 795 HIS ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 656 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.069215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.060419 restraints weight = 419484.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.062165 restraints weight = 213754.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.063338 restraints weight = 130601.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.064100 restraints weight = 89058.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.064617 restraints weight = 65625.229| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.5550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 23305 Z= 0.179 Angle : 0.587 7.315 31539 Z= 0.316 Chirality : 0.039 0.208 3449 Planarity : 0.005 0.079 4172 Dihedral : 5.247 60.820 3301 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.13 % Allowed : 12.23 % Favored : 87.63 % Rotamer: Outliers : 0.05 % Allowed : 0.73 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.44 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.47 (0.15), residues: 2967 helix: -0.31 (0.14), residues: 1394 sheet: -3.05 (0.38), residues: 180 loop : -2.91 (0.16), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 84 TYR 0.020 0.002 TYR C 523 PHE 0.015 0.001 PHE D 265 TRP 0.021 0.001 TRP A 88 HIS 0.008 0.001 HIS D 656 Details of bonding type rmsd covalent geometry : bond 0.00370 (23286) covalent geometry : angle 0.58617 (31501) SS BOND : bond 0.00280 ( 19) SS BOND : angle 1.06214 ( 38) hydrogen bonds : bond 0.04205 ( 993) hydrogen bonds : angle 5.29179 ( 2814) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 825 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue TYR 72 is missing expected H atoms. Skipping. Residue LEU 73 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue THR 77 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue VAL 87 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue SER 93 is missing expected H atoms. Skipping. Residue LEU 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue LYS 148 is missing expected H atoms. Skipping. Residue SER 149 is missing expected H atoms. Skipping. Residue SER 153 is missing expected H atoms. Skipping. Residue THR 154 is missing expected H atoms. Skipping. Residue SER 156 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue SER 158 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 167 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue VAL 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LEU 181 is missing expected H atoms. Skipping. Residue THR 185 is missing expected H atoms. Skipping. Residue VAL 186 is missing expected H atoms. Skipping. Residue LYS 195 is missing expected H atoms. Skipping. Residue THR 196 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue VAL 198 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue THR 202 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue ILE 222 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LEU 225 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue VAL 235 is missing expected H atoms. Skipping. Residue THR 236 is missing expected H atoms. Skipping. Residue LEU 239 is missing expected H atoms. Skipping. Residue ILE 243 is missing expected H atoms. Skipping. Residue LEU 245 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LEU 247 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue ILE 251 is missing expected H atoms. Skipping. Residue THR 253 is missing expected H atoms. Skipping. Residue VAL 254 is missing expected H atoms. Skipping. Residue TYR 255 is missing expected H atoms. Skipping. Residue MET 256 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LEU 259 is missing expected H atoms. Skipping. Residue LYS 262 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue TYR 273 is missing expected H atoms. Skipping. Residue LEU 276 is missing expected H atoms. Skipping. Residue SER 278 is missing expected H atoms. Skipping. Residue VAL 279 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue TYR 287 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue LEU 290 is missing expected H atoms. Skipping. Residue THR 291 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue TYR 295 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue MET 300 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Residue ILE 317 is missing expected H atoms. Skipping. Residue SER 318 is missing expected H atoms. Skipping. Residue THR 320 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue VAL 327 is missing expected H atoms. Skipping. Residue THR 329 is missing expected H atoms. Skipping. Residue ILE 331 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue VAL 335 is missing expected H atoms. Skipping. Residue SER 338 is missing expected H atoms. Skipping. Residue TYR 339 is missing expected H atoms. Skipping. Residue TYR 343 is missing expected H atoms. Skipping. Residue MET 346 is missing expected H atoms. Skipping. Residue ILE 349 is missing expected H atoms. Skipping. Residue TYR 350 is missing expected H atoms. Skipping. Residue THR 351 is missing expected H atoms. Skipping. Residue VAL 352 is missing expected H atoms. Skipping. Residue THR 357 is missing expected H atoms. Skipping. Residue VAL 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue MET 362 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue LYS 367 is missing expected H atoms. Skipping. Residue TYR 369 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue ILE 371 is missing expected H atoms. Skipping. Residue LYS 374 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue VAL 377 is missing expected H atoms. Skipping. Residue LEU 378 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue MET 389 is missing expected H atoms. Skipping. Residue THR 390 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue SER 393 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue LEU 403 is missing expected H atoms. Skipping. Residue ILE 408 is missing expected H atoms. Skipping. Residue TYR 411 is missing expected H atoms. Skipping. Residue ILE 414 is missing expected H atoms. Skipping. Residue MET 417 is missing expected H atoms. Skipping. Residue THR 421 is missing expected H atoms. Skipping. Residue ILE 422 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue TYR 72 is missing expected H atoms. Skipping. Residue LEU 73 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue THR 77 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue VAL 87 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue SER 93 is missing expected H atoms. Skipping. Residue LEU 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LYS 148 is missing expected H atoms. Skipping. Residue SER 149 is missing expected H atoms. Skipping. Residue SER 153 is missing expected H atoms. Skipping. Residue THR 154 is missing expected H atoms. Skipping. Residue SER 156 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue SER 158 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 167 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue VAL 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LEU 181 is missing expected H atoms. Skipping. Residue THR 185 is missing expected H atoms. Skipping. Residue VAL 186 is missing expected H atoms. Skipping. Residue LYS 195 is missing expected H atoms. Skipping. Residue THR 196 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue VAL 198 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue THR 202 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue ILE 222 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LEU 225 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue VAL 235 is missing expected H atoms. Skipping. Residue THR 236 is missing expected H atoms. Skipping. Residue LEU 239 is missing expected H atoms. Skipping. Residue ILE 243 is missing expected H atoms. Skipping. Residue LEU 245 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LEU 247 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue ILE 251 is missing expected H atoms. Skipping. Residue THR 253 is missing expected H atoms. Skipping. Residue VAL 254 is missing expected H atoms. Skipping. Residue TYR 255 is missing expected H atoms. Skipping. Residue MET 256 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LEU 259 is missing expected H atoms. Skipping. Residue LYS 262 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue TYR 273 is missing expected H atoms. Skipping. Residue LEU 276 is missing expected H atoms. Skipping. Residue SER 278 is missing expected H atoms. Skipping. Residue VAL 279 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue TYR 287 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue LEU 290 is missing expected H atoms. Skipping. Residue THR 291 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue TYR 295 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue MET 300 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Residue ILE 317 is missing expected H atoms. Skipping. Residue SER 318 is missing expected H atoms. Skipping. Residue THR 320 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue VAL 327 is missing expected H atoms. Skipping. Residue THR 329 is missing expected H atoms. Skipping. Residue ILE 331 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue VAL 335 is missing expected H atoms. Skipping. Residue SER 338 is missing expected H atoms. Skipping. Residue TYR 339 is missing expected H atoms. Skipping. Residue TYR 343 is missing expected H atoms. Skipping. Residue MET 346 is missing expected H atoms. Skipping. Residue ILE 349 is missing expected H atoms. Skipping. Residue TYR 350 is missing expected H atoms. Skipping. Residue THR 351 is missing expected H atoms. Skipping. Residue VAL 352 is missing expected H atoms. Skipping. Residue THR 357 is missing expected H atoms. Skipping. Residue VAL 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue MET 362 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue LYS 367 is missing expected H atoms. Skipping. Residue TYR 369 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue ILE 371 is missing expected H atoms. Skipping. Residue LYS 374 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue VAL 377 is missing expected H atoms. Skipping. Residue LEU 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue SER 384 is missing expected H atoms. Skipping. Residue MET 386 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue MET 389 is missing expected H atoms. Skipping. Residue THR 390 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue LEU 403 is missing expected H atoms. Skipping. Residue ILE 408 is missing expected H atoms. Skipping. Residue TYR 411 is missing expected H atoms. Skipping. Residue ILE 414 is missing expected H atoms. Skipping. Residue MET 417 is missing expected H atoms. Skipping. Residue THR 421 is missing expected H atoms. Skipping. Residue ILE 422 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue ILE 23 is missing expected H atoms. Skipping. Residue SER 31 is missing expected H atoms. Skipping. Residue VAL 35 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue THR 37 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue SER 42 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue SER 49 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue VAL 55 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue SER 58 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue SER 64 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue THR 78 is missing expected H atoms. Skipping. Residue TYR 84 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue TYR 106 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue ILE 137 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue ILE 163 is missing expected H atoms. Skipping. Residue ILE 167 is missing expected H atoms. Skipping. Residue MET 168 is missing expected H atoms. Skipping. Residue THR 169 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue VAL 174 is missing expected H atoms. Skipping. Residue SER 176 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue THR 181 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue SER 188 is missing expected H atoms. Skipping. Residue ILE 190 is missing expected H atoms. Skipping. Residue TYR 191 is missing expected H atoms. Skipping. Residue VAL 204 is missing expected H atoms. Skipping. Residue ILE 206 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue LYS 211 is missing expected H atoms. Skipping. Residue TYR 217 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue ILE 220 is missing expected H atoms. Skipping. Residue TYR 233 is missing expected H atoms. Skipping. Residue MET 236 is missing expected H atoms. Skipping. Residue ILE 237 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue ILE 249 is missing expected H atoms. Skipping. Residue THR 250 is missing expected H atoms. Skipping. Evaluate side-chains 239 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 238 time to evaluate : 1.050 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 SER cc_start: 0.8771 (t) cc_final: 0.8222 (m) REVERT: B 280 MET cc_start: 0.3668 (tpp) cc_final: 0.3145 (mmt) REVERT: B 297 MET cc_start: 0.8168 (ttp) cc_final: 0.7862 (ttp) REVERT: C 134 PHE cc_start: 0.8087 (m-80) cc_final: 0.7607 (m-10) REVERT: C 324 ASN cc_start: 0.7679 (t0) cc_final: 0.7268 (t0) REVERT: C 824 MET cc_start: 0.8579 (tpp) cc_final: 0.8235 (tpp) REVERT: D 533 MET cc_start: 0.9174 (tmm) cc_final: 0.8801 (tmm) REVERT: D 732 ASP cc_start: 0.8327 (m-30) cc_final: 0.8096 (m-30) REVERT: D 755 MET cc_start: 0.8341 (mmm) cc_final: 0.8066 (mtt) outliers start: 1 outliers final: 0 residues processed: 239 average time/residue: 0.3123 time to fit residues: 111.3885 Evaluate side-chains 199 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 115 optimal weight: 4.9990 chunk 280 optimal weight: 50.0000 chunk 298 optimal weight: 0.0030 chunk 281 optimal weight: 40.0000 chunk 101 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 176 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 overall best weight: 1.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 ASN A 729 ASN ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.069698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.060922 restraints weight = 421543.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.062642 restraints weight = 216523.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.063813 restraints weight = 133279.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.064557 restraints weight = 91254.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.065078 restraints weight = 67720.986| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 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 0.038 23305 Z= 0.133 Angle : 0.560 6.561 31539 Z= 0.298 Chirality : 0.039 0.195 3449 Planarity : 0.004 0.083 4172 Dihedral : 5.157 60.289 3301 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.89 % Favored : 88.98 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.44 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.24 (0.15), residues: 2967 helix: -0.09 (0.14), residues: 1394 sheet: -3.06 (0.38), residues: 179 loop : -2.81 (0.16), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 84 TYR 0.031 0.001 TYR B 356 PHE 0.021 0.001 PHE A 109 TRP 0.018 0.001 TRP A 88 HIS 0.004 0.001 HIS A 656 Details of bonding type rmsd covalent geometry : bond 0.00285 (23286) covalent geometry : angle 0.55958 (31501) SS BOND : bond 0.00286 ( 19) SS BOND : angle 0.91626 ( 38) hydrogen bonds : bond 0.04096 ( 993) hydrogen bonds : angle 5.11529 ( 2814) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 825 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue TYR 72 is missing expected H atoms. Skipping. Residue LEU 73 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue THR 77 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue VAL 87 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue SER 93 is missing expected H atoms. Skipping. Residue LEU 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue LYS 148 is missing expected H atoms. Skipping. Residue SER 149 is missing expected H atoms. Skipping. Residue SER 153 is missing expected H atoms. Skipping. Residue THR 154 is missing expected H atoms. Skipping. Residue SER 156 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue SER 158 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 167 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue VAL 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LEU 181 is missing expected H atoms. Skipping. Residue THR 185 is missing expected H atoms. Skipping. Residue VAL 186 is missing expected H atoms. Skipping. Residue LYS 195 is missing expected H atoms. Skipping. Residue THR 196 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue VAL 198 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue THR 202 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue ILE 222 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LEU 225 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue VAL 235 is missing expected H atoms. Skipping. Residue THR 236 is missing expected H atoms. Skipping. Residue LEU 239 is missing expected H atoms. Skipping. Residue ILE 243 is missing expected H atoms. Skipping. Residue LEU 245 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LEU 247 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue ILE 251 is missing expected H atoms. Skipping. Residue THR 253 is missing expected H atoms. Skipping. Residue VAL 254 is missing expected H atoms. Skipping. Residue TYR 255 is missing expected H atoms. Skipping. Residue MET 256 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LEU 259 is missing expected H atoms. Skipping. Residue LYS 262 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue TYR 273 is missing expected H atoms. Skipping. Residue LEU 276 is missing expected H atoms. Skipping. Residue SER 278 is missing expected H atoms. Skipping. Residue VAL 279 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue TYR 287 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue LEU 290 is missing expected H atoms. Skipping. Residue THR 291 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue TYR 295 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue MET 300 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Residue ILE 317 is missing expected H atoms. Skipping. Residue SER 318 is missing expected H atoms. Skipping. Residue THR 320 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue VAL 327 is missing expected H atoms. Skipping. Residue THR 329 is missing expected H atoms. Skipping. Residue ILE 331 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue VAL 335 is missing expected H atoms. Skipping. Residue SER 338 is missing expected H atoms. Skipping. Residue TYR 339 is missing expected H atoms. Skipping. Residue TYR 343 is missing expected H atoms. Skipping. Residue MET 346 is missing expected H atoms. Skipping. Residue ILE 349 is missing expected H atoms. Skipping. Residue TYR 350 is missing expected H atoms. Skipping. Residue THR 351 is missing expected H atoms. Skipping. Residue VAL 352 is missing expected H atoms. Skipping. Residue THR 357 is missing expected H atoms. Skipping. Residue VAL 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue MET 362 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue LYS 367 is missing expected H atoms. Skipping. Residue TYR 369 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue ILE 371 is missing expected H atoms. Skipping. Residue LYS 374 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue VAL 377 is missing expected H atoms. Skipping. Residue LEU 378 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue MET 389 is missing expected H atoms. Skipping. Residue THR 390 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue SER 393 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue LEU 403 is missing expected H atoms. Skipping. Residue ILE 408 is missing expected H atoms. Skipping. Residue TYR 411 is missing expected H atoms. Skipping. Residue ILE 414 is missing expected H atoms. Skipping. Residue MET 417 is missing expected H atoms. Skipping. Residue THR 421 is missing expected H atoms. Skipping. Residue ILE 422 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue TYR 72 is missing expected H atoms. Skipping. Residue LEU 73 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue THR 77 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue VAL 87 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue SER 93 is missing expected H atoms. Skipping. Residue LEU 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LYS 148 is missing expected H atoms. Skipping. Residue SER 149 is missing expected H atoms. Skipping. Residue SER 153 is missing expected H atoms. Skipping. Residue THR 154 is missing expected H atoms. Skipping. Residue SER 156 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue SER 158 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 167 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue VAL 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LEU 181 is missing expected H atoms. Skipping. Residue THR 185 is missing expected H atoms. Skipping. Residue VAL 186 is missing expected H atoms. Skipping. Residue LYS 195 is missing expected H atoms. Skipping. Residue THR 196 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue VAL 198 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue THR 202 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue ILE 222 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LEU 225 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue VAL 235 is missing expected H atoms. Skipping. Residue THR 236 is missing expected H atoms. Skipping. Residue LEU 239 is missing expected H atoms. Skipping. Residue ILE 243 is missing expected H atoms. Skipping. Residue LEU 245 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LEU 247 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue ILE 251 is missing expected H atoms. Skipping. Residue THR 253 is missing expected H atoms. Skipping. Residue VAL 254 is missing expected H atoms. Skipping. Residue TYR 255 is missing expected H atoms. Skipping. Residue MET 256 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LEU 259 is missing expected H atoms. Skipping. Residue LYS 262 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue TYR 273 is missing expected H atoms. Skipping. Residue LEU 276 is missing expected H atoms. Skipping. Residue SER 278 is missing expected H atoms. Skipping. Residue VAL 279 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue TYR 287 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue LEU 290 is missing expected H atoms. Skipping. Residue THR 291 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue TYR 295 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue MET 300 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Residue ILE 317 is missing expected H atoms. Skipping. Residue SER 318 is missing expected H atoms. Skipping. Residue THR 320 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue VAL 327 is missing expected H atoms. Skipping. Residue THR 329 is missing expected H atoms. Skipping. Residue ILE 331 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue VAL 335 is missing expected H atoms. Skipping. Residue SER 338 is missing expected H atoms. Skipping. Residue TYR 339 is missing expected H atoms. Skipping. Residue TYR 343 is missing expected H atoms. Skipping. Residue MET 346 is missing expected H atoms. Skipping. Residue ILE 349 is missing expected H atoms. Skipping. Residue TYR 350 is missing expected H atoms. Skipping. Residue THR 351 is missing expected H atoms. Skipping. Residue VAL 352 is missing expected H atoms. Skipping. Residue THR 357 is missing expected H atoms. Skipping. Residue VAL 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue MET 362 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue LYS 367 is missing expected H atoms. Skipping. Residue TYR 369 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue ILE 371 is missing expected H atoms. Skipping. Residue LYS 374 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue VAL 377 is missing expected H atoms. Skipping. Residue LEU 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue SER 384 is missing expected H atoms. Skipping. Residue MET 386 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue MET 389 is missing expected H atoms. Skipping. Residue THR 390 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue LEU 403 is missing expected H atoms. Skipping. Residue ILE 408 is missing expected H atoms. Skipping. Residue TYR 411 is missing expected H atoms. Skipping. Residue ILE 414 is missing expected H atoms. Skipping. Residue MET 417 is missing expected H atoms. Skipping. Residue THR 421 is missing expected H atoms. Skipping. Residue ILE 422 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue ILE 23 is missing expected H atoms. Skipping. Residue SER 31 is missing expected H atoms. Skipping. Residue VAL 35 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue THR 37 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue SER 42 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue SER 49 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue VAL 55 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue SER 58 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue SER 64 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue THR 78 is missing expected H atoms. Skipping. Residue TYR 84 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue TYR 106 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue ILE 137 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue ILE 163 is missing expected H atoms. Skipping. Residue ILE 167 is missing expected H atoms. Skipping. Residue MET 168 is missing expected H atoms. Skipping. Residue THR 169 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue VAL 174 is missing expected H atoms. Skipping. Residue SER 176 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue THR 181 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue SER 188 is missing expected H atoms. Skipping. Residue ILE 190 is missing expected H atoms. Skipping. Residue TYR 191 is missing expected H atoms. Skipping. Residue VAL 204 is missing expected H atoms. Skipping. Residue ILE 206 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue LYS 211 is missing expected H atoms. Skipping. Residue TYR 217 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue ILE 220 is missing expected H atoms. Skipping. Residue TYR 233 is missing expected H atoms. Skipping. Residue MET 236 is missing expected H atoms. Skipping. Residue ILE 237 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue ILE 249 is missing expected H atoms. Skipping. Residue THR 250 is missing expected H atoms. Skipping. Evaluate side-chains 237 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.731 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: 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: 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: 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: 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 245 SER cc_start: 0.8771 (t) cc_final: 0.8190 (m) REVERT: B 239 LYS cc_start: 0.7660 (tppt) cc_final: 0.7406 (tptm) REVERT: B 280 MET cc_start: 0.3975 (tpp) cc_final: 0.3449 (mmt) REVERT: B 297 MET cc_start: 0.8117 (ttp) cc_final: 0.7821 (ttp) REVERT: C 314 MET cc_start: 0.9359 (mmm) cc_final: 0.8796 (mmm) REVERT: C 324 ASN cc_start: 0.7558 (t0) cc_final: 0.7129 (t0) REVERT: C 824 MET cc_start: 0.8542 (tpp) cc_final: 0.8175 (tpp) REVERT: D 533 MET cc_start: 0.9185 (tmm) cc_final: 0.8806 (tmm) REVERT: D 732 ASP cc_start: 0.8367 (m-30) cc_final: 0.8118 (m-30) REVERT: D 755 MET cc_start: 0.8387 (mmm) cc_final: 0.8025 (mtt) outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.3216 time to fit residues: 112.7045 Evaluate side-chains 207 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 170 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 284 optimal weight: 20.0000 chunk 8 optimal weight: 2.9990 chunk 211 optimal weight: 0.2980 chunk 217 optimal weight: 5.9990 chunk 38 optimal weight: 0.0050 chunk 164 optimal weight: 4.9990 chunk 261 optimal weight: 30.0000 chunk 194 optimal weight: 0.6980 chunk 240 optimal weight: 20.0000 overall best weight: 0.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 ASN A 591 ASN B 491 GLN C 623 ASN ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.070034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.061351 restraints weight = 419426.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.063080 restraints weight = 216402.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.064239 restraints weight = 132480.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.064988 restraints weight = 90581.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.065507 restraints weight = 66789.356| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.5921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 23305 Z= 0.115 Angle : 0.541 7.126 31539 Z= 0.287 Chirality : 0.038 0.189 3449 Planarity : 0.004 0.085 4172 Dihedral : 4.999 60.008 3301 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.68 % Favored : 89.18 % Rotamer: Outliers : 0.10 % Allowed : 0.24 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.44 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.98 (0.16), residues: 2967 helix: 0.13 (0.14), residues: 1402 sheet: -3.06 (0.38), residues: 179 loop : -2.69 (0.16), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 84 TYR 0.022 0.001 TYR B 356 PHE 0.019 0.001 PHE A 109 TRP 0.018 0.001 TRP A 835 HIS 0.004 0.001 HIS C 795 Details of bonding type rmsd covalent geometry : bond 0.00246 (23286) covalent geometry : angle 0.54094 (31501) SS BOND : bond 0.00221 ( 19) SS BOND : angle 0.75452 ( 38) hydrogen bonds : bond 0.03884 ( 993) hydrogen bonds : angle 4.94498 ( 2814) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 825 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue TYR 72 is missing expected H atoms. Skipping. Residue LEU 73 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue THR 77 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue VAL 87 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue SER 93 is missing expected H atoms. Skipping. Residue LEU 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue LYS 148 is missing expected H atoms. Skipping. Residue SER 149 is missing expected H atoms. Skipping. Residue SER 153 is missing expected H atoms. Skipping. Residue THR 154 is missing expected H atoms. Skipping. Residue SER 156 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue SER 158 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 167 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue VAL 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LEU 181 is missing expected H atoms. Skipping. Residue THR 185 is missing expected H atoms. Skipping. Residue VAL 186 is missing expected H atoms. Skipping. Residue LYS 195 is missing expected H atoms. Skipping. Residue THR 196 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue VAL 198 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue THR 202 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue ILE 222 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LEU 225 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue VAL 235 is missing expected H atoms. Skipping. Residue THR 236 is missing expected H atoms. Skipping. Residue LEU 239 is missing expected H atoms. Skipping. Residue ILE 243 is missing expected H atoms. Skipping. Residue LEU 245 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LEU 247 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue ILE 251 is missing expected H atoms. Skipping. Residue THR 253 is missing expected H atoms. Skipping. Residue VAL 254 is missing expected H atoms. Skipping. Residue TYR 255 is missing expected H atoms. Skipping. Residue MET 256 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LEU 259 is missing expected H atoms. Skipping. Residue LYS 262 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue TYR 273 is missing expected H atoms. Skipping. Residue LEU 276 is missing expected H atoms. Skipping. Residue SER 278 is missing expected H atoms. Skipping. Residue VAL 279 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue TYR 287 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue LEU 290 is missing expected H atoms. Skipping. Residue THR 291 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue TYR 295 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue MET 300 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Residue ILE 317 is missing expected H atoms. Skipping. Residue SER 318 is missing expected H atoms. Skipping. Residue THR 320 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue VAL 327 is missing expected H atoms. Skipping. Residue THR 329 is missing expected H atoms. Skipping. Residue ILE 331 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue VAL 335 is missing expected H atoms. Skipping. Residue SER 338 is missing expected H atoms. Skipping. Residue TYR 339 is missing expected H atoms. Skipping. Residue TYR 343 is missing expected H atoms. Skipping. Residue MET 346 is missing expected H atoms. Skipping. Residue ILE 349 is missing expected H atoms. Skipping. Residue TYR 350 is missing expected H atoms. Skipping. Residue THR 351 is missing expected H atoms. Skipping. Residue VAL 352 is missing expected H atoms. Skipping. Residue THR 357 is missing expected H atoms. Skipping. Residue VAL 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue MET 362 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue LYS 367 is missing expected H atoms. Skipping. Residue TYR 369 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue ILE 371 is missing expected H atoms. Skipping. Residue LYS 374 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue VAL 377 is missing expected H atoms. Skipping. Residue LEU 378 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue MET 389 is missing expected H atoms. Skipping. Residue THR 390 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue SER 393 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue LEU 403 is missing expected H atoms. Skipping. Residue ILE 408 is missing expected H atoms. Skipping. Residue TYR 411 is missing expected H atoms. Skipping. Residue ILE 414 is missing expected H atoms. Skipping. Residue MET 417 is missing expected H atoms. Skipping. Residue THR 421 is missing expected H atoms. Skipping. Residue ILE 422 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue TYR 72 is missing expected H atoms. Skipping. Residue LEU 73 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue THR 77 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue VAL 87 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue SER 93 is missing expected H atoms. Skipping. Residue LEU 96 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LYS 148 is missing expected H atoms. Skipping. Residue SER 149 is missing expected H atoms. Skipping. Residue SER 153 is missing expected H atoms. Skipping. Residue THR 154 is missing expected H atoms. Skipping. Residue SER 156 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue SER 158 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 167 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue VAL 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LEU 181 is missing expected H atoms. Skipping. Residue THR 185 is missing expected H atoms. Skipping. Residue VAL 186 is missing expected H atoms. Skipping. Residue LYS 195 is missing expected H atoms. Skipping. Residue THR 196 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue VAL 198 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue THR 202 is missing expected H atoms. Skipping. Residue VAL 203 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue ILE 222 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LEU 225 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue VAL 235 is missing expected H atoms. Skipping. Residue THR 236 is missing expected H atoms. Skipping. Residue LEU 239 is missing expected H atoms. Skipping. Residue ILE 243 is missing expected H atoms. Skipping. Residue LEU 245 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LEU 247 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue ILE 251 is missing expected H atoms. Skipping. Residue THR 253 is missing expected H atoms. Skipping. Residue VAL 254 is missing expected H atoms. Skipping. Residue TYR 255 is missing expected H atoms. Skipping. Residue MET 256 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LEU 259 is missing expected H atoms. Skipping. Residue LYS 262 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue TYR 273 is missing expected H atoms. Skipping. Residue LEU 276 is missing expected H atoms. Skipping. Residue SER 278 is missing expected H atoms. Skipping. Residue VAL 279 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue TYR 287 is missing expected H atoms. Skipping. Residue VAL 288 is missing expected H atoms. Skipping. Residue LEU 290 is missing expected H atoms. Skipping. Residue THR 291 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue TYR 295 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue MET 300 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Residue ILE 317 is missing expected H atoms. Skipping. Residue SER 318 is missing expected H atoms. Skipping. Residue THR 320 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue SER 323 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue VAL 327 is missing expected H atoms. Skipping. Residue THR 329 is missing expected H atoms. Skipping. Residue ILE 331 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue VAL 335 is missing expected H atoms. Skipping. Residue SER 338 is missing expected H atoms. Skipping. Residue TYR 339 is missing expected H atoms. Skipping. Residue TYR 343 is missing expected H atoms. Skipping. Residue MET 346 is missing expected H atoms. Skipping. Residue ILE 349 is missing expected H atoms. Skipping. Residue TYR 350 is missing expected H atoms. Skipping. Residue THR 351 is missing expected H atoms. Skipping. Residue VAL 352 is missing expected H atoms. Skipping. Residue THR 357 is missing expected H atoms. Skipping. Residue VAL 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue MET 362 is missing expected H atoms. Skipping. Residue THR 363 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue LYS 367 is missing expected H atoms. Skipping. Residue TYR 369 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue ILE 371 is missing expected H atoms. Skipping. Residue LYS 374 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue VAL 377 is missing expected H atoms. Skipping. Residue LEU 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue SER 384 is missing expected H atoms. Skipping. Residue MET 386 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue MET 389 is missing expected H atoms. Skipping. Residue THR 390 is missing expected H atoms. Skipping. Residue ILE 402 is missing expected H atoms. Skipping. Residue LEU 403 is missing expected H atoms. Skipping. Residue ILE 408 is missing expected H atoms. Skipping. Residue TYR 411 is missing expected H atoms. Skipping. Residue ILE 414 is missing expected H atoms. Skipping. Residue MET 417 is missing expected H atoms. Skipping. Residue THR 421 is missing expected H atoms. Skipping. Residue ILE 422 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue ILE 23 is missing expected H atoms. Skipping. Residue SER 31 is missing expected H atoms. Skipping. Residue VAL 35 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue THR 37 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue SER 42 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue SER 49 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue VAL 55 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue SER 58 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue SER 64 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue THR 78 is missing expected H atoms. Skipping. Residue TYR 84 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue TYR 106 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue ILE 137 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue ILE 163 is missing expected H atoms. Skipping. Residue ILE 167 is missing expected H atoms. Skipping. Residue MET 168 is missing expected H atoms. Skipping. Residue THR 169 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue VAL 174 is missing expected H atoms. Skipping. Residue SER 176 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue THR 181 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue SER 188 is missing expected H atoms. Skipping. Residue ILE 190 is missing expected H atoms. Skipping. Residue TYR 191 is missing expected H atoms. Skipping. Residue VAL 204 is missing expected H atoms. Skipping. Residue ILE 206 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue LYS 211 is missing expected H atoms. Skipping. Residue TYR 217 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue ILE 220 is missing expected H atoms. Skipping. Residue TYR 233 is missing expected H atoms. Skipping. Residue MET 236 is missing expected H atoms. Skipping. Residue ILE 237 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue ILE 249 is missing expected H atoms. Skipping. Residue THR 250 is missing expected H atoms. Skipping. Evaluate side-chains 240 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 238 time to evaluate : 1.083 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: 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: 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: 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: 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 245 SER cc_start: 0.8762 (t) cc_final: 0.8237 (m) REVERT: A 351 ILE cc_start: 0.9135 (mt) cc_final: 0.8884 (mm) REVERT: B 280 MET cc_start: 0.3821 (tpp) cc_final: 0.3306 (mmt) REVERT: B 297 MET cc_start: 0.8057 (ttp) cc_final: 0.7762 (ttp) REVERT: B 379 ILE cc_start: 0.9219 (mt) cc_final: 0.8706 (mm) REVERT: C 324 ASN cc_start: 0.7455 (t0) cc_final: 0.7078 (t0) REVERT: C 824 MET cc_start: 0.8509 (tpp) cc_final: 0.8068 (tpp) REVERT: D 217 MET cc_start: 0.8233 (ptt) cc_final: 0.8032 (ptp) REVERT: D 533 MET cc_start: 0.9117 (tmm) cc_final: 0.8722 (tmm) REVERT: D 586 ARG cc_start: 0.8677 (ptm160) cc_final: 0.8282 (mtp85) REVERT: D 732 ASP cc_start: 0.8343 (m-30) cc_final: 0.8070 (m-30) REVERT: D 755 MET cc_start: 0.8246 (mmm) cc_final: 0.7903 (mtt) outliers start: 2 outliers final: 0 residues processed: 240 average time/residue: 0.3325 time to fit residues: 118.3818 Evaluate side-chains 198 residues out of total 2685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 113 optimal weight: 0.2980 chunk 16 optimal weight: 5.9990 chunk 14 optimal weight: 0.4980 chunk 135 optimal weight: 0.9980 chunk 214 optimal weight: 0.6980 chunk 297 optimal weight: 8.9990 chunk 285 optimal weight: 40.0000 chunk 207 optimal weight: 6.9990 chunk 90 optimal weight: 0.5980 chunk 301 optimal weight: 9.9990 chunk 282 optimal weight: 40.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 ASN ** A 729 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN A 822 GLN C 536 ASN ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.070314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.061568 restraints weight = 418492.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.063282 restraints weight = 215278.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.064454 restraints weight = 132289.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.065193 restraints weight = 90270.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.065724 restraints weight = 66869.807| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.6106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 23305 Z= 0.104 Angle : 0.532 6.836 31539 Z= 0.282 Chirality : 0.038 0.164 3449 Planarity : 0.004 0.084 4172 Dihedral : 4.884 59.101 3301 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.27 % Favored : 90.63 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.44 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.82 (0.16), residues: 2967 helix: 0.28 (0.14), residues: 1404 sheet: -2.98 (0.38), residues: 179 loop : -2.63 (0.16), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 84 TYR 0.020 0.001 TYR C 705 PHE 0.018 0.001 PHE A 816 TRP 0.017 0.001 TRP A 835 HIS 0.003 0.001 HIS A 656 Details of bonding type rmsd covalent geometry : bond 0.00229 (23286) covalent geometry : angle 0.53121 (31501) SS BOND : bond 0.00227 ( 19) SS BOND : angle 0.79445 ( 38) hydrogen bonds : bond 0.03800 ( 993) hydrogen bonds : angle 4.84300 ( 2814) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4909.60 seconds wall clock time: 84 minutes 48.45 seconds (5088.45 seconds total)