Starting phenix.real_space_refine on Sun Mar 24 16:34:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6row_4975/03_2024/6row_4975.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6row_4975/03_2024/6row_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6row_4975/03_2024/6row_4975.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6row_4975/03_2024/6row_4975.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6row_4975/03_2024/6row_4975.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6row_4975/03_2024/6row_4975.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 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 Residue "A GLU 175": "OE1" <-> "OE2" Residue "A GLU 326": "OE1" <-> "OE2" Residue "A PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 494": "OE1" <-> "OE2" Residue "A GLU 754": "OE1" <-> "OE2" Residue "A GLU 829": "OE1" <-> "OE2" Residue "B GLU 221": "OE1" <-> "OE2" Residue "B GLU 326": "OE1" <-> "OE2" Residue "B GLU 566": "OE1" <-> "OE2" Residue "B GLU 593": "OE1" <-> "OE2" Residue "B GLU 728": "OE1" <-> "OE2" Residue "C GLU 140": "OE1" <-> "OE2" Residue "C GLU 590": "OE1" <-> "OE2" Residue "C GLU 657": "OE1" <-> "OE2" Residue "D GLU 140": "OE1" <-> "OE2" Residue "D GLU 745": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/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: {'GLN:plan1': 14, 'ARG:plan': 7, 'TYR:plan': 13, 'ASN:plan1': 15, 'TRP:plan': 4, 'ASP:plan': 16, 'PHE:plan': 18, 'GLU:plan': 12, 'HIS:plan': 2} 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: {'GLN:plan1': 13, 'ARG:plan': 7, 'TYR:plan': 13, 'ASN:plan1': 15, 'TRP:plan': 4, 'ASP:plan': 18, 'PHE:plan': 17, 'GLU:plan': 12, 'HIS:plan': 2} 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: {'GLN:plan1': 5, 'HIS:plan': 4, 'TYR:plan': 8, 'ASN:plan1': 5, 'TRP:plan': 5, 'ASP:plan': 10, 'PHE:plan': 12, 'GLU:plan': 6, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 342 Time building chain proxies: 19.07, per 1000 atoms: 0.44 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 35.02 Conformation dependent library (CDL) restraints added in 4.7 seconds 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: 3.40 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: 15.23 Time building geometry restraints manager: 36.44 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: 80.22 - 91.03: 1 91.03 - 101.84: 111 101.84 - 112.65: 47730 112.65 - 123.47: 25602 123.47 - 134.28: 4186 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 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: 3.170 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: 0.660 Extract box with map and model: 11.800 Check model and map are aligned: 0.620 Set scattering table: 0.380 Process input model: 128.990 Find NCS groups from input model: 2.250 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 151.180 ------------------------------------------------------------------------------- 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 : 0.016 0.195 23286 Z= 1.007 Angle : 1.496 24.164 31501 Z= 0.905 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 : 49.61 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.027 0.004 TRP B 777 HIS 0.018 0.003 HIS D 656 PHE 0.039 0.004 PHE B 374 TYR 0.051 0.004 TYR B 231 ARG 0.014 0.001 ARG A 352 *********************** 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 fitting. rotamer outliers: 0 poor density : 345 time to evaluate : 4.226 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: symmetry clash REVERT: B 304 GLU cc_start: 0.8660 (mm-30) cc_final: 0.7852 (tp30) REVERT: C 231 TYR cc_start: 0.6840 (t80) cc_final: 0.6579 (t80) REVERT: C 511 MET cc_start: 0.8660 (mmm) cc_final: 0.8149 (mmp) REVERT: C 657 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7669 (mm-30) outliers start: 0 outliers final: 0 residues processed: 345 average time/residue: 0.9653 time to fit residues: 475.8601 Evaluate side-chains 237 residues out of total 2685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 3.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 260 optimal weight: 7.9990 chunk 234 optimal weight: 9.9990 chunk 129 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 242 optimal weight: 8.9990 chunk 93 optimal weight: 5.9990 chunk 147 optimal weight: 0.9990 chunk 180 optimal weight: 1.9990 chunk 280 optimal weight: 10.0000 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 ASN A 407 ASN A 704 GLN ** B 729 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 830 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 235 ASN D 499 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 23286 Z= 0.266 Angle : 0.760 7.409 31501 Z= 0.415 Chirality : 0.044 0.173 3449 Planarity : 0.007 0.119 4172 Dihedral : 7.410 62.858 3301 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 17.41 Ramachandran Plot: Outliers : 0.27 % Allowed : 18.37 % Favored : 81.36 % Rotamer: Outliers : 0.15 % Allowed : 4.95 % Favored : 94.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.44 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.88 (0.11), residues: 2967 helix: -3.40 (0.10), residues: 1394 sheet: -3.96 (0.38), residues: 136 loop : -4.51 (0.12), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 770 HIS 0.007 0.002 HIS D 412 PHE 0.029 0.002 PHE D 265 TYR 0.021 0.002 TYR C 523 ARG 0.011 0.001 ARG D 831 *********************** 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 301 residues out of total 2685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 298 time to evaluate : 3.268 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: A 245 SER cc_start: 0.8391 (t) cc_final: 0.8182 (t) REVERT: B 473 TYR cc_start: 0.7712 (m-80) cc_final: 0.7478 (m-80) REVERT: C 657 GLU cc_start: 0.7689 (mm-30) cc_final: 0.7439 (mm-30) REVERT: D 533 MET cc_start: 0.9131 (tmm) cc_final: 0.8762 (tmm) REVERT: D 732 ASP cc_start: 0.8290 (m-30) cc_final: 0.8080 (m-30) REVERT: D 755 MET cc_start: 0.8560 (mmm) cc_final: 0.8018 (mtt) REVERT: D 771 ILE cc_start: 0.9691 (mm) cc_final: 0.9368 (tp) outliers start: 3 outliers final: 0 residues processed: 301 average time/residue: 0.9449 time to fit residues: 410.3848 Evaluate side-chains 216 residues out of total 2685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 3.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 155 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 233 optimal weight: 2.9990 chunk 191 optimal weight: 0.3980 chunk 77 optimal weight: 0.8980 chunk 281 optimal weight: 40.0000 chunk 303 optimal weight: 30.0000 chunk 250 optimal weight: 40.0000 chunk 278 optimal weight: 0.0980 chunk 95 optimal weight: 0.8980 chunk 225 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 382 ASN A 407 ASN ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 724 HIS ** B 729 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 830 GLN ** 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 570 ASN C 583 ASN C 591 ASN D 136 GLN D 264 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.3969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 23286 Z= 0.202 Angle : 0.641 6.388 31501 Z= 0.346 Chirality : 0.040 0.170 3449 Planarity : 0.006 0.097 4172 Dihedral : 6.515 61.336 3301 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.17 % Allowed : 14.90 % Favored : 84.93 % Rotamer: Outliers : 0.15 % Allowed : 3.01 % Favored : 96.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.44 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.75 (0.13), residues: 2967 helix: -2.37 (0.12), residues: 1396 sheet: -3.80 (0.37), residues: 150 loop : -3.98 (0.14), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 233 HIS 0.006 0.001 HIS B 724 PHE 0.023 0.002 PHE D 265 TYR 0.019 0.002 TYR C 523 ARG 0.011 0.001 ARG A 215 *********************** 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 267 residues out of total 2685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 264 time to evaluate : 3.459 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: B 115 ASN cc_start: 0.7069 (t0) cc_final: 0.6391 (t0) REVERT: B 474 MET cc_start: 0.7599 (tpt) cc_final: 0.7320 (tpt) REVERT: C 97 PHE cc_start: 0.6785 (t80) cc_final: 0.6429 (t80) REVERT: C 657 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7509 (mm-30) REVERT: D 323 ARG cc_start: 0.7836 (mmm160) cc_final: 0.7635 (mtp85) REVERT: D 533 MET cc_start: 0.9155 (tmm) cc_final: 0.8845 (tmm) REVERT: D 732 ASP cc_start: 0.8338 (m-30) cc_final: 0.8113 (m-30) REVERT: D 755 MET cc_start: 0.8398 (mmm) cc_final: 0.8012 (mtt) REVERT: D 771 ILE cc_start: 0.9698 (mm) cc_final: 0.9417 (tp) outliers start: 3 outliers final: 3 residues processed: 267 average time/residue: 0.9129 time to fit residues: 354.0822 Evaluate side-chains 212 residues out of total 2685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 209 time to evaluate : 3.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 277 optimal weight: 30.0000 chunk 211 optimal weight: 3.9990 chunk 145 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 134 optimal weight: 2.9990 chunk 188 optimal weight: 5.9990 chunk 282 optimal weight: 50.0000 chunk 298 optimal weight: 0.0270 chunk 147 optimal weight: 0.9980 chunk 267 optimal weight: 10.0000 chunk 80 optimal weight: 0.8980 overall best weight: 1.7842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 569 ASN C 570 ASN D 222 GLN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.4510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23286 Z= 0.221 Angle : 0.612 6.362 31501 Z= 0.330 Chirality : 0.039 0.155 3449 Planarity : 0.005 0.089 4172 Dihedral : 6.053 59.974 3301 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.17 % Allowed : 14.69 % Favored : 85.14 % Rotamer: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.44 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.95 (0.14), residues: 2967 helix: -1.66 (0.13), residues: 1390 sheet: -3.48 (0.36), residues: 165 loop : -3.59 (0.15), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 233 HIS 0.004 0.001 HIS B 656 PHE 0.027 0.001 PHE C 607 TYR 0.019 0.002 TYR C 537 ARG 0.004 0.000 ARG B 801 *********************** 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 254 residues out of total 2685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 254 time to evaluate : 3.394 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: A 386 MET cc_start: 0.8453 (mmm) cc_final: 0.8069 (mmm) REVERT: C 589 TYR cc_start: 0.7923 (t80) cc_final: 0.7589 (t80) REVERT: C 657 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7671 (mm-30) REVERT: D 323 ARG cc_start: 0.7920 (mmm160) cc_final: 0.7709 (mtp85) REVERT: D 533 MET cc_start: 0.9187 (tmm) cc_final: 0.8862 (tmm) REVERT: D 732 ASP cc_start: 0.8598 (m-30) cc_final: 0.8345 (m-30) REVERT: D 755 MET cc_start: 0.8373 (mmm) cc_final: 0.8087 (mtt) REVERT: D 771 ILE cc_start: 0.9704 (mm) cc_final: 0.9447 (tp) outliers start: 0 outliers final: 0 residues processed: 254 average time/residue: 0.9026 time to fit residues: 338.1171 Evaluate side-chains 211 residues out of total 2685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 3.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 248 optimal weight: 30.0000 chunk 169 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 222 optimal weight: 0.7980 chunk 123 optimal weight: 0.0980 chunk 254 optimal weight: 20.0000 chunk 206 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 152 optimal weight: 4.9990 chunk 268 optimal weight: 20.0000 chunk 75 optimal weight: 0.3980 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 ASN ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 591 ASN ** B 729 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 591 ASN ** D 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.4818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 23286 Z= 0.238 Angle : 0.607 6.094 31501 Z= 0.329 Chirality : 0.039 0.153 3449 Planarity : 0.005 0.089 4172 Dihedral : 5.808 58.667 3301 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.17 % Allowed : 15.17 % Favored : 84.66 % Rotamer: Outliers : 0.05 % Allowed : 2.13 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.44 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.62 (0.14), residues: 2967 helix: -1.38 (0.13), residues: 1400 sheet: -3.33 (0.36), residues: 175 loop : -3.43 (0.15), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 233 HIS 0.008 0.001 HIS B 238 PHE 0.019 0.001 PHE D 265 TYR 0.027 0.002 TYR B 231 ARG 0.004 0.000 ARG C 586 *********************** 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 248 residues out of total 2685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 247 time to evaluate : 3.272 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: 0.8612 (t) cc_final: 0.8245 (m) REVERT: B 297 MET cc_start: 0.7879 (ttp) cc_final: 0.7537 (ttp) REVERT: B 309 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7391 (mm-30) REVERT: B 474 MET cc_start: 0.7853 (tpt) cc_final: 0.7200 (tpt) REVERT: B 521 GLU cc_start: 0.8970 (pm20) cc_final: 0.8762 (pp20) REVERT: B 659 VAL cc_start: 0.9059 (t) cc_final: 0.8738 (m) REVERT: C 97 PHE cc_start: 0.6746 (t80) cc_final: 0.6542 (t80) REVERT: C 589 TYR cc_start: 0.8045 (t80) cc_final: 0.7644 (t80) REVERT: D 323 ARG cc_start: 0.7956 (mmm160) cc_final: 0.7743 (mtp85) REVERT: D 533 MET cc_start: 0.9124 (tmm) cc_final: 0.8713 (tmm) REVERT: D 755 MET cc_start: 0.8354 (mmm) cc_final: 0.8133 (mtt) REVERT: D 771 ILE cc_start: 0.9704 (mm) cc_final: 0.9483 (tp) outliers start: 1 outliers final: 1 residues processed: 248 average time/residue: 0.8252 time to fit residues: 307.9989 Evaluate side-chains 205 residues out of total 2685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 204 time to evaluate : 3.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 100 optimal weight: 5.9990 chunk 268 optimal weight: 20.0000 chunk 59 optimal weight: 10.0000 chunk 175 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 298 optimal weight: 20.0000 chunk 248 optimal weight: 30.0000 chunk 138 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 156 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 ASN ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 491 GLN ** B 729 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 GLN ** C 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 ASN ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.4985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 23286 Z= 0.293 Angle : 0.631 7.592 31501 Z= 0.343 Chirality : 0.039 0.153 3449 Planarity : 0.005 0.089 4172 Dihedral : 5.774 58.595 3301 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.17 % Allowed : 16.25 % Favored : 83.59 % Rotamer: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.44 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.55 (0.14), residues: 2967 helix: -1.35 (0.13), residues: 1406 sheet: -3.35 (0.36), residues: 176 loop : -3.35 (0.16), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 233 HIS 0.009 0.001 HIS D 656 PHE 0.019 0.002 PHE D 265 TYR 0.021 0.002 TYR C 537 ARG 0.005 0.001 ARG B 801 *********************** 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 237 residues out of total 2685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 3.436 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: A 245 SER cc_start: 0.8613 (t) cc_final: 0.8222 (m) REVERT: B 297 MET cc_start: 0.7805 (ttp) cc_final: 0.7459 (ttp) REVERT: C 589 TYR cc_start: 0.8141 (t80) cc_final: 0.7859 (t80) REVERT: D 323 ARG cc_start: 0.7964 (mmm160) cc_final: 0.7738 (mtp85) REVERT: D 533 MET cc_start: 0.9145 (tmm) cc_final: 0.8833 (tmm) REVERT: D 732 ASP cc_start: 0.8538 (m-30) cc_final: 0.8316 (m-30) REVERT: D 755 MET cc_start: 0.8382 (mmm) cc_final: 0.8065 (mtt) outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.8351 time to fit residues: 294.7938 Evaluate side-chains 199 residues out of total 2685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 3.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 288 optimal weight: 8.9990 chunk 33 optimal weight: 6.9990 chunk 170 optimal weight: 4.9990 chunk 218 optimal weight: 5.9990 chunk 169 optimal weight: 0.8980 chunk 251 optimal weight: 30.0000 chunk 166 optimal weight: 2.9990 chunk 297 optimal weight: 10.0000 chunk 186 optimal weight: 6.9990 chunk 181 optimal weight: 5.9990 chunk 137 optimal weight: 2.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 ASN ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN C 640 GLN C 724 HIS ** C 793 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.5124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 23286 Z= 0.335 Angle : 0.663 7.182 31501 Z= 0.361 Chirality : 0.040 0.152 3449 Planarity : 0.005 0.090 4172 Dihedral : 5.854 58.153 3301 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.17 % Allowed : 17.69 % Favored : 82.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.53 (0.14), residues: 2967 helix: -1.41 (0.13), residues: 1400 sheet: -3.39 (0.39), residues: 159 loop : -3.25 (0.16), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 233 HIS 0.011 0.001 HIS D 656 PHE 0.026 0.002 PHE D 265 TYR 0.022 0.002 TYR B 356 ARG 0.005 0.001 ARG B 215 *********************** 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 225 residues out of total 2685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 224 time to evaluate : 3.402 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: A 245 SER cc_start: 0.8653 (t) cc_final: 0.8191 (m) REVERT: B 297 MET cc_start: 0.7839 (ttp) cc_final: 0.7503 (ttp) REVERT: C 589 TYR cc_start: 0.8165 (t80) cc_final: 0.7879 (t80) REVERT: D 533 MET cc_start: 0.9177 (tmm) cc_final: 0.8884 (tmm) REVERT: D 732 ASP cc_start: 0.8509 (m-30) cc_final: 0.8257 (m-30) REVERT: D 755 MET cc_start: 0.8437 (mmm) cc_final: 0.8026 (mtt) REVERT: D 771 ILE cc_start: 0.9738 (mm) cc_final: 0.9488 (tp) REVERT: D 824 MET cc_start: 0.8713 (mmm) cc_final: 0.8446 (mmm) outliers start: 1 outliers final: 0 residues processed: 225 average time/residue: 0.8348 time to fit residues: 281.9840 Evaluate side-chains 197 residues out of total 2685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 3.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 184 optimal weight: 0.1980 chunk 118 optimal weight: 4.9990 chunk 177 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 189 optimal weight: 6.9990 chunk 202 optimal weight: 5.9990 chunk 147 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 234 optimal weight: 30.0000 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 ASN ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 767 GLN ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.5455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23286 Z= 0.173 Angle : 0.567 7.173 31501 Z= 0.303 Chirality : 0.039 0.155 3449 Planarity : 0.005 0.085 4172 Dihedral : 5.503 57.552 3301 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.17 % Allowed : 12.57 % Favored : 87.26 % Rotamer: Outliers : 0.05 % Allowed : 0.34 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.44 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.15), residues: 2967 helix: -0.90 (0.13), residues: 1405 sheet: -3.18 (0.38), residues: 168 loop : -3.07 (0.16), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 233 HIS 0.006 0.001 HIS D 656 PHE 0.017 0.001 PHE D 265 TYR 0.027 0.001 TYR B 482 ARG 0.006 0.000 ARG B 219 *********************** 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 241 residues out of total 2685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 240 time to evaluate : 3.579 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: A 245 SER cc_start: 0.8569 (t) cc_final: 0.8176 (m) REVERT: B 297 MET cc_start: 0.7722 (ttp) cc_final: 0.7417 (ttp) REVERT: B 659 VAL cc_start: 0.9004 (t) cc_final: 0.8711 (m) REVERT: C 314 MET cc_start: 0.9349 (mmm) cc_final: 0.8569 (mmm) REVERT: C 589 TYR cc_start: 0.7934 (t80) cc_final: 0.7699 (t80) REVERT: D 533 MET cc_start: 0.9149 (tmm) cc_final: 0.8881 (tmm) REVERT: D 755 MET cc_start: 0.8329 (mmm) cc_final: 0.7923 (mtt) REVERT: D 771 ILE cc_start: 0.9714 (mm) cc_final: 0.9452 (tp) REVERT: D 824 MET cc_start: 0.8641 (mmm) cc_final: 0.8345 (mmm) outliers start: 1 outliers final: 0 residues processed: 241 average time/residue: 0.8586 time to fit residues: 312.7316 Evaluate side-chains 200 residues out of total 2685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 3.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 270 optimal weight: 50.0000 chunk 285 optimal weight: 0.0000 chunk 260 optimal weight: 20.0000 chunk 277 optimal weight: 7.9990 chunk 167 optimal weight: 0.8980 chunk 120 optimal weight: 6.9990 chunk 217 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 250 optimal weight: 40.0000 chunk 262 optimal weight: 50.0000 chunk 276 optimal weight: 30.0000 overall best weight: 3.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 793 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.5424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 23286 Z= 0.320 Angle : 0.644 7.463 31501 Z= 0.352 Chirality : 0.040 0.167 3449 Planarity : 0.005 0.088 4172 Dihedral : 5.644 57.477 3301 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 0.17 % Allowed : 17.19 % Favored : 82.64 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.44 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.19 (0.15), residues: 2967 helix: -1.09 (0.13), residues: 1405 sheet: -3.29 (0.40), residues: 158 loop : -3.11 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 233 HIS 0.011 0.001 HIS D 656 PHE 0.025 0.002 PHE D 265 TYR 0.025 0.002 TYR B 589 ARG 0.005 0.001 ARG A 352 *********************** 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 215 residues out of total 2685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 3.477 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: A 245 SER cc_start: 0.8677 (t) cc_final: 0.8224 (m) REVERT: B 297 MET cc_start: 0.7790 (ttp) cc_final: 0.7477 (ttp) REVERT: D 533 MET cc_start: 0.9212 (tmm) cc_final: 0.8925 (tmm) REVERT: D 732 ASP cc_start: 0.8487 (m-30) cc_final: 0.8122 (m-30) REVERT: D 755 MET cc_start: 0.8460 (mmm) cc_final: 0.8079 (mtt) REVERT: D 824 MET cc_start: 0.8741 (mmm) cc_final: 0.8410 (mmm) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.7788 time to fit residues: 255.2937 Evaluate side-chains 183 residues out of total 2685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 3.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 182 optimal weight: 3.9990 chunk 293 optimal weight: 0.9980 chunk 179 optimal weight: 4.9990 chunk 139 optimal weight: 0.0060 chunk 204 optimal weight: 0.4980 chunk 307 optimal weight: 20.0000 chunk 283 optimal weight: 20.0000 chunk 245 optimal weight: 50.0000 chunk 25 optimal weight: 1.9990 chunk 189 optimal weight: 5.9990 chunk 150 optimal weight: 0.7980 overall best weight: 0.8598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 ASN ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 795 HIS B 570 ASN C 570 ASN C 724 HIS ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 795 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.5722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 23286 Z= 0.161 Angle : 0.557 5.745 31501 Z= 0.296 Chirality : 0.039 0.172 3449 Planarity : 0.005 0.103 4172 Dihedral : 5.319 57.018 3301 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.09 % Favored : 88.78 % Rotamer: Outliers : 0.05 % Allowed : 0.24 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.15), residues: 2967 helix: -0.53 (0.14), residues: 1404 sheet: -3.01 (0.38), residues: 183 loop : -2.94 (0.16), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 233 HIS 0.006 0.001 HIS D 656 PHE 0.015 0.001 PHE B 607 TYR 0.018 0.001 TYR B 740 ARG 0.005 0.000 ARG D 586 ********************** 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 230 residues out of total 2685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 229 time to evaluate : 3.475 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: A 245 SER cc_start: 0.8541 (t) cc_final: 0.8121 (m) REVERT: B 297 MET cc_start: 0.7732 (ttp) cc_final: 0.7426 (ttp) REVERT: B 379 ILE cc_start: 0.9255 (mt) cc_final: 0.8747 (mm) REVERT: B 474 MET cc_start: 0.7761 (tpt) cc_final: 0.7108 (tpt) REVERT: B 521 GLU cc_start: 0.8873 (pm20) cc_final: 0.8626 (pm20) REVERT: D 533 MET cc_start: 0.9156 (tmm) cc_final: 0.8858 (tmm) REVERT: D 732 ASP cc_start: 0.8349 (m-30) cc_final: 0.8109 (m-30) REVERT: D 755 MET cc_start: 0.8286 (mmm) cc_final: 0.7881 (mtt) REVERT: D 771 ILE cc_start: 0.9680 (mm) cc_final: 0.9450 (tp) REVERT: D 824 MET cc_start: 0.8694 (mmm) cc_final: 0.8308 (mmm) outliers start: 1 outliers final: 0 residues processed: 230 average time/residue: 0.8093 time to fit residues: 281.0663 Evaluate side-chains 196 residues out of total 2685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 3.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 194 optimal weight: 0.9980 chunk 261 optimal weight: 20.0000 chunk 75 optimal weight: 0.9990 chunk 226 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 68 optimal weight: 0.4980 chunk 245 optimal weight: 50.0000 chunk 102 optimal weight: 3.9990 chunk 252 optimal weight: 50.0000 chunk 31 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 ASN ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 724 HIS ** D 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3480 r_free = 0.3480 target = 0.068618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.060005 restraints weight = 425716.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.061678 restraints weight = 218944.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.062762 restraints weight = 134390.839| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.5739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 23286 Z= 0.225 Angle : 0.575 5.954 31501 Z= 0.310 Chirality : 0.039 0.152 3449 Planarity : 0.005 0.088 4172 Dihedral : 5.271 56.839 3301 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.17 % Allowed : 14.29 % Favored : 85.54 % Rotamer: Outliers : 0.05 % Allowed : 0.10 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.44 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.15), residues: 2967 helix: -0.53 (0.14), residues: 1408 sheet: -3.12 (0.39), residues: 166 loop : -2.89 (0.16), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 835 HIS 0.008 0.001 HIS D 656 PHE 0.019 0.001 PHE D 265 TYR 0.024 0.002 TYR A 294 ARG 0.003 0.000 ARG B 801 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7383.04 seconds wall clock time: 131 minutes 54.54 seconds (7914.54 seconds total)