Starting phenix.real_space_refine on Sun Feb 18 03:19:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lhf_23338/02_2024/7lhf_23338_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lhf_23338/02_2024/7lhf_23338.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lhf_23338/02_2024/7lhf_23338_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lhf_23338/02_2024/7lhf_23338_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lhf_23338/02_2024/7lhf_23338_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lhf_23338/02_2024/7lhf_23338.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lhf_23338/02_2024/7lhf_23338.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lhf_23338/02_2024/7lhf_23338_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lhf_23338/02_2024/7lhf_23338_updated.pdb" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 28 5.49 5 S 400 5.16 5 C 46224 2.51 5 N 12588 2.21 5 O 12848 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 153": "OE1" <-> "OE2" Residue "A ASP 493": "OD1" <-> "OD2" Residue "A PHE 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 632": "OD1" <-> "OD2" Residue "A ASP 636": "OD1" <-> "OD2" Residue "A PHE 781": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 793": "OD1" <-> "OD2" Residue "A GLU 796": "OE1" <-> "OE2" Residue "A PHE 839": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1097": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1347": "OD1" <-> "OD2" Residue "A PHE 1637": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1745": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2064": "OD1" <-> "OD2" Residue "A GLU 2169": "OE1" <-> "OE2" Residue "A PHE 2188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2206": "OE1" <-> "OE2" Residue "A PHE 2244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2412": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2423": "NH1" <-> "NH2" Residue "A ASP 2551": "OD1" <-> "OD2" Residue "A PHE 2612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2635": "OE1" <-> "OE2" Residue "A ASP 2652": "OD1" <-> "OD2" Residue "A PHE 2675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 632": "OD1" <-> "OD2" Residue "D TYR 735": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 746": "OD1" <-> "OD2" Residue "D PHE 781": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 796": "OE1" <-> "OE2" Residue "D PHE 839": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 969": "OD1" <-> "OD2" Residue "D TYR 988": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1097": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1637": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1745": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 2064": "OD1" <-> "OD2" Residue "D PHE 2188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 2234": "OD1" <-> "OD2" Residue "D PHE 2244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 2360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 2412": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 2423": "NH1" <-> "NH2" Residue "D ASP 2551": "OD1" <-> "OD2" Residue "D PHE 2575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 2612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 2635": "OE1" <-> "OE2" Residue "D ASP 2652": "OD1" <-> "OD2" Residue "D PHE 2675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 13": "OD1" <-> "OD2" Residue "B GLU 153": "OE1" <-> "OE2" Residue "B PHE 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 632": "OD1" <-> "OD2" Residue "B ASP 636": "OD1" <-> "OD2" Residue "B PHE 781": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 796": "OE1" <-> "OE2" Residue "B PHE 839": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 969": "OD1" <-> "OD2" Residue "B GLU 1038": "OE1" <-> "OE2" Residue "B PHE 1311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1637": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1745": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 2064": "OD1" <-> "OD2" Residue "B PHE 2188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 2551": "OD1" <-> "OD2" Residue "B PHE 2612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 2635": "OE1" <-> "OE2" Residue "B ASP 2652": "OD1" <-> "OD2" Residue "B PHE 2675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 13": "OD1" <-> "OD2" Residue "C GLU 439": "OE1" <-> "OE2" Residue "C ASP 493": "OD1" <-> "OD2" Residue "C PHE 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 632": "OD1" <-> "OD2" Residue "C ASP 636": "OD1" <-> "OD2" Residue "C PHE 781": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 839": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 988": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1038": "OE1" <-> "OE2" Residue "C PHE 1311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1637": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1745": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 2064": "OD1" <-> "OD2" Residue "C PHE 2188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 2423": "NH1" <-> "NH2" Residue "C ASP 2551": "OD1" <-> "OD2" Residue "C PHE 2612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 2635": "OE1" <-> "OE2" Residue "C ASP 2652": "OD1" <-> "OD2" Residue "C PHE 2675": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 72092 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 17734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2300, 17734 Classifications: {'peptide': 2300} Incomplete info: {'n_c_alpha_c_only': 2, 'truncation_to_alanine': 37} Link IDs: {'PCIS': 1, 'PTRANS': 67, 'TRANS': 2231} Chain breaks: 13 Unresolved chain link angles: 186 Unresolved non-hydrogen bonds: 911 Unresolved non-hydrogen angles: 1127 Unresolved non-hydrogen dihedrals: 614 Unresolved non-hydrogen chiralities: 77 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 9, 'TYR:plan': 7, 'ASN:plan1': 10, 'TRP:plan': 4, 'ASP:plan': 10, 'PHE:plan': 10, 'GLU:plan': 14, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 385 Chain: "D" Number of atoms: 17734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2300, 17734 Classifications: {'peptide': 2300} Incomplete info: {'n_c_alpha_c_only': 2, 'truncation_to_alanine': 37} Link IDs: {'PCIS': 1, 'PTRANS': 67, 'TRANS': 2231} Chain breaks: 13 Unresolved chain link angles: 186 Unresolved non-hydrogen bonds: 911 Unresolved non-hydrogen angles: 1127 Unresolved non-hydrogen dihedrals: 614 Unresolved non-hydrogen chiralities: 77 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 9, 'TYR:plan': 7, 'ASN:plan1': 10, 'TRP:plan': 4, 'ASP:plan': 10, 'PHE:plan': 10, 'GLU:plan': 14, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 385 Chain: "B" Number of atoms: 17734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2300, 17734 Classifications: {'peptide': 2300} Incomplete info: {'n_c_alpha_c_only': 2, 'truncation_to_alanine': 37} Link IDs: {'PCIS': 1, 'PTRANS': 67, 'TRANS': 2231} Chain breaks: 13 Unresolved chain link angles: 186 Unresolved non-hydrogen bonds: 911 Unresolved non-hydrogen angles: 1127 Unresolved non-hydrogen dihedrals: 614 Unresolved non-hydrogen chiralities: 77 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 9, 'TYR:plan': 7, 'ASN:plan1': 10, 'TRP:plan': 4, 'ASP:plan': 10, 'PHE:plan': 10, 'GLU:plan': 14, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 385 Chain: "C" Number of atoms: 17734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2300, 17734 Classifications: {'peptide': 2300} Incomplete info: {'n_c_alpha_c_only': 2, 'truncation_to_alanine': 37} Link IDs: {'PCIS': 1, 'PTRANS': 67, 'TRANS': 2231} Chain breaks: 13 Unresolved chain link angles: 186 Unresolved non-hydrogen bonds: 911 Unresolved non-hydrogen angles: 1127 Unresolved non-hydrogen dihedrals: 614 Unresolved non-hydrogen chiralities: 77 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 9, 'TYR:plan': 7, 'ASN:plan1': 10, 'TRP:plan': 4, 'ASP:plan': 10, 'PHE:plan': 10, 'GLU:plan': 14, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 385 Chain: "A" Number of atoms: 289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 289 Unusual residues: {' ZN': 1, 'PLX': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 76 Chain: "D" Number of atoms: 289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 289 Unusual residues: {' ZN': 1, 'PLX': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 76 Chain: "B" Number of atoms: 289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 289 Unusual residues: {' ZN': 1, 'PLX': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 76 Chain: "C" Number of atoms: 289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 289 Unusual residues: {' ZN': 1, 'PLX': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 76 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16658 SG CYS A2611 139.100 113.421 110.775 1.00 33.08 S ATOM 34392 SG CYS D2611 126.261 139.101 110.783 1.00 32.54 S ATOM 52126 SG CYS B2611 113.419 100.580 110.772 1.00 32.42 S ATOM 69860 SG CYS C2611 100.582 126.262 110.769 1.00 32.06 S Time building chain proxies: 27.00, per 1000 atoms: 0.37 Number of scatterers: 72092 At special positions: 0 Unit cell: (240.75, 240.75, 196.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 400 16.00 P 28 15.00 O 12848 8.00 N 12588 7.00 C 46224 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=13, symmetry=0 Number of additional bonds: simple=13, symmetry=0 Coordination: Other bonds: Time building additional restraints: 24.03 Conformation dependent library (CDL) restraints added in 9.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2808 " pdb="ZN ZN A2808 " - pdb=" SG CYS A2611 " pdb="ZN ZN A2808 " - pdb=" NE2 HIS A2631 " pdb="ZN ZN A2808 " - pdb=" ND1 HIS A2636 " pdb=" ZN B2808 " pdb="ZN ZN B2808 " - pdb=" SG CYS B2611 " pdb="ZN ZN B2808 " - pdb=" NE2 HIS B2631 " pdb="ZN ZN B2808 " - pdb=" ND1 HIS B2636 " pdb=" ZN C5101 " pdb="ZN ZN C5101 " - pdb=" NE2 HIS C2631 " pdb="ZN ZN C5101 " - pdb=" SG CYS C2611 " pdb="ZN ZN C5101 " - pdb=" ND1 HIS C2636 " pdb=" ZN D5101 " pdb="ZN ZN D5101 " - pdb=" SG CYS D2611 " pdb="ZN ZN D5101 " - pdb=" NE2 HIS D2631 " pdb="ZN ZN D5101 " - pdb=" ND1 HIS D2636 " 18176 Ramachandran restraints generated. 9088 Oldfield, 0 Emsley, 9088 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17584 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 347 helices and 31 sheets defined 46.8% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 20.70 Creating SS restraints... Processing helix chain 'A' and resid 53 through 56 Processing helix chain 'A' and resid 68 through 75 Processing helix chain 'A' and resid 89 through 107 removed outlier: 3.516A pdb=" N GLU A 106 " --> pdb=" O GLN A 102 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN A 107 " --> pdb=" O ASN A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 366 No H-bonds generated for 'chain 'A' and resid 364 through 366' Processing helix chain 'A' and resid 437 through 462 removed outlier: 3.878A pdb=" N ASP A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY A 458 " --> pdb=" O GLY A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 485 removed outlier: 3.558A pdb=" N THR A 474 " --> pdb=" O ARG A 470 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL A 481 " --> pdb=" O LEU A 477 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR A 482 " --> pdb=" O GLU A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 507 No H-bonds generated for 'chain 'A' and resid 504 through 507' Processing helix chain 'A' and resid 509 through 512 No H-bonds generated for 'chain 'A' and resid 509 through 512' Processing helix chain 'A' and resid 515 through 531 removed outlier: 3.596A pdb=" N GLN A 524 " --> pdb=" O PHE A 520 " (cutoff:3.500A) Proline residue: A 526 - end of helix Processing helix chain 'A' and resid 544 through 546 No H-bonds generated for 'chain 'A' and resid 544 through 546' Processing helix chain 'A' and resid 553 through 563 removed outlier: 3.653A pdb=" N ARG A 558 " --> pdb=" O ARG A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 584 removed outlier: 3.802A pdb=" N GLN A 577 " --> pdb=" O TYR A 573 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE A 578 " --> pdb=" O ILE A 574 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N GLY A 579 " --> pdb=" O ALA A 575 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N PHE A 580 " --> pdb=" O LYS A 576 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N MET A 581 " --> pdb=" O GLN A 577 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN A 582 " --> pdb=" O PHE A 578 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N LYS A 583 " --> pdb=" O GLY A 579 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLN A 584 " --> pdb=" O PHE A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 598 removed outlier: 3.598A pdb=" N THR A 596 " --> pdb=" O GLU A 592 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA A 597 " --> pdb=" O ASP A 593 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU A 598 " --> pdb=" O THR A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 609 Processing helix chain 'A' and resid 612 through 616 Processing helix chain 'A' and resid 629 through 638 removed outlier: 4.247A pdb=" N LEU A 637 " --> pdb=" O TYR A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 652 No H-bonds generated for 'chain 'A' and resid 649 through 652' Processing helix chain 'A' and resid 713 through 719 removed outlier: 4.133A pdb=" N GLN A 717 " --> pdb=" O ARG A 713 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP A 718 " --> pdb=" O GLU A 714 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA A 719 " --> pdb=" O LEU A 715 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 713 through 719' Processing helix chain 'A' and resid 724 through 744 removed outlier: 4.648A pdb=" N LEU A 730 " --> pdb=" O ASP A 726 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N SER A 731 " --> pdb=" O ARG A 727 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N CYS A 744 " --> pdb=" O PHE A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 751 No H-bonds generated for 'chain 'A' and resid 749 through 751' Processing helix chain 'A' and resid 754 through 757 No H-bonds generated for 'chain 'A' and resid 754 through 757' Processing helix chain 'A' and resid 761 through 768 removed outlier: 3.850A pdb=" N MET A 768 " --> pdb=" O ILE A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 786 Processing helix chain 'A' and resid 827 through 829 No H-bonds generated for 'chain 'A' and resid 827 through 829' Processing helix chain 'A' and resid 831 through 847 removed outlier: 4.279A pdb=" N GLN A 835 " --> pdb=" O GLU A 831 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N THR A 836 " --> pdb=" O ARG A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 876 removed outlier: 3.651A pdb=" N TYR A 875 " --> pdb=" O ARG A 871 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N PHE A 876 " --> pdb=" O ASN A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 893 removed outlier: 4.399A pdb=" N LYS A 889 " --> pdb=" O LEU A 885 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILE A 890 " --> pdb=" O ARG A 886 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA A 893 " --> pdb=" O LYS A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 1002 removed outlier: 3.824A pdb=" N ASN A 983 " --> pdb=" O GLN A 979 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL A 984 " --> pdb=" O PHE A 980 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ARG A 985 " --> pdb=" O ILE A 981 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU A 986 " --> pdb=" O LEU A 982 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASP A 987 " --> pdb=" O ASN A 983 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE A1001 " --> pdb=" O PHE A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1026 through 1031 removed outlier: 3.681A pdb=" N ASP A1029 " --> pdb=" O GLY A1026 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLU A1031 " --> pdb=" O LEU A1028 " (cutoff:3.500A) Processing helix chain 'A' and resid 1033 through 1035 No H-bonds generated for 'chain 'A' and resid 1033 through 1035' Processing helix chain 'A' and resid 1060 through 1068 Processing helix chain 'A' and resid 1074 through 1086 removed outlier: 3.572A pdb=" N HIS A1086 " --> pdb=" O LEU A1083 " (cutoff:3.500A) Processing helix chain 'A' and resid 1089 through 1100 Processing helix chain 'A' and resid 1110 through 1125 removed outlier: 3.708A pdb=" N ILE A1115 " --> pdb=" O ASN A1111 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ARG A1123 " --> pdb=" O LEU A1119 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N SER A1124 " --> pdb=" O ASP A1120 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ILE A1125 " --> pdb=" O GLN A1121 " (cutoff:3.500A) Processing helix chain 'A' and resid 1173 through 1187 removed outlier: 4.376A pdb=" N LYS A1177 " --> pdb=" O TYR A1173 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N GLU A1178 " --> pdb=" O ARG A1174 " (cutoff:3.500A) Processing helix chain 'A' and resid 1197 through 1203 removed outlier: 4.436A pdb=" N GLN A1202 " --> pdb=" O ARG A1198 " (cutoff:3.500A) Processing helix chain 'A' and resid 1211 through 1219 removed outlier: 3.982A pdb=" N LEU A1215 " --> pdb=" O HIS A1211 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N GLU A1216 " --> pdb=" O ALA A1212 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1244 removed outlier: 3.874A pdb=" N ARG A1235 " --> pdb=" O GLN A1231 " (cutoff:3.500A) Processing helix chain 'A' and resid 1249 through 1261 removed outlier: 4.345A pdb=" N LYS A1257 " --> pdb=" O ALA A1253 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N HIS A1258 " --> pdb=" O LEU A1254 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ILE A1259 " --> pdb=" O LEU A1255 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N ASN A1260 " --> pdb=" O HIS A1256 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU A1261 " --> pdb=" O LYS A1257 " (cutoff:3.500A) Processing helix chain 'A' and resid 1270 through 1274 Processing helix chain 'A' and resid 1292 through 1299 Processing helix chain 'A' and resid 1324 through 1337 removed outlier: 4.267A pdb=" N GLU A1333 " --> pdb=" O MET A1329 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU A1334 " --> pdb=" O VAL A1330 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL A1335 " --> pdb=" O MET A1331 " (cutoff:3.500A) Processing helix chain 'A' and resid 1348 through 1359 removed outlier: 4.623A pdb=" N GLN A1352 " --> pdb=" O ARG A1348 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR A1353 " --> pdb=" O ALA A1349 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG A1359 " --> pdb=" O ILE A1355 " (cutoff:3.500A) Processing helix chain 'A' and resid 1599 through 1631 removed outlier: 4.029A pdb=" N GLN A1605 " --> pdb=" O ILE A1601 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ASP A1606 " --> pdb=" O GLU A1602 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ARG A1614 " --> pdb=" O ALA A1610 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N LEU A1615 " --> pdb=" O LEU A1611 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N ARG A1616 " --> pdb=" O GLU A1612 " (cutoff:3.500A) Proline residue: A1617 - end of helix removed outlier: 3.885A pdb=" N SER A1624 " --> pdb=" O GLN A1620 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL A1625 " --> pdb=" O ALA A1621 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL A1629 " --> pdb=" O VAL A1625 " (cutoff:3.500A) Processing helix chain 'A' and resid 1653 through 1662 removed outlier: 3.686A pdb=" N LYS A1661 " --> pdb=" O ILE A1657 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLN A1662 " --> pdb=" O LYS A1658 " (cutoff:3.500A) Processing helix chain 'A' and resid 1669 through 1683 Processing helix chain 'A' and resid 1728 through 1744 Processing helix chain 'A' and resid 1792 through 1801 removed outlier: 4.413A pdb=" N CYS A1797 " --> pdb=" O ALA A1793 " (cutoff:3.500A) Processing helix chain 'A' and resid 1804 through 1811 Processing helix chain 'A' and resid 1819 through 1832 Processing helix chain 'A' and resid 1837 through 1847 removed outlier: 4.259A pdb=" N SER A1842 " --> pdb=" O THR A1838 " (cutoff:3.500A) Processing helix chain 'A' and resid 1853 through 1871 removed outlier: 3.690A pdb=" N PHE A1860 " --> pdb=" O PHE A1856 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG A1863 " --> pdb=" O VAL A1859 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN A1868 " --> pdb=" O MET A1864 " (cutoff:3.500A) Processing helix chain 'A' and resid 1964 through 1977 Proline residue: A1968 - end of helix removed outlier: 3.563A pdb=" N LEU A1975 " --> pdb=" O PHE A1972 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A1976 " --> pdb=" O LEU A1973 " (cutoff:3.500A) Processing helix chain 'A' and resid 1982 through 1986 removed outlier: 3.817A pdb=" N ASN A1986 " --> pdb=" O ARG A1982 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1982 through 1986' Processing helix chain 'A' and resid 1999 through 2010 Processing helix chain 'A' and resid 2016 through 2018 No H-bonds generated for 'chain 'A' and resid 2016 through 2018' Processing helix chain 'A' and resid 2030 through 2044 removed outlier: 3.797A pdb=" N GLN A2035 " --> pdb=" O ALA A2031 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N CYS A2044 " --> pdb=" O LEU A2040 " (cutoff:3.500A) Processing helix chain 'A' and resid 2049 through 2057 Processing helix chain 'A' and resid 2062 through 2066 removed outlier: 3.780A pdb=" N ILE A2065 " --> pdb=" O GLY A2062 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE A2066 " --> pdb=" O ILE A2063 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2062 through 2066' Processing helix chain 'A' and resid 2068 through 2071 No H-bonds generated for 'chain 'A' and resid 2068 through 2071' Processing helix chain 'A' and resid 2079 through 2099 removed outlier: 4.731A pdb=" N ASP A2083 " --> pdb=" O LYS A2079 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N LEU A2084 " --> pdb=" O LYS A2080 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N GLU A2087 " --> pdb=" O ASP A2083 " (cutoff:3.500A) Processing helix chain 'A' and resid 2106 through 2113 Processing helix chain 'A' and resid 2120 through 2131 removed outlier: 4.026A pdb=" N GLN A2131 " --> pdb=" O LYS A2127 " (cutoff:3.500A) Processing helix chain 'A' and resid 2149 through 2165 removed outlier: 3.777A pdb=" N GLY A2153 " --> pdb=" O PRO A2149 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ARG A2165 " --> pdb=" O HIS A2161 " (cutoff:3.500A) Processing helix chain 'A' and resid 2168 through 2174 removed outlier: 4.084A pdb=" N MET A2173 " --> pdb=" O GLU A2169 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A2174 " --> pdb=" O LEU A2170 " (cutoff:3.500A) Processing helix chain 'A' and resid 2184 through 2191 Processing helix chain 'A' and resid 2221 through 2230 Processing helix chain 'A' and resid 2240 through 2262 removed outlier: 4.075A pdb=" N LEU A2245 " --> pdb=" O ASN A2241 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ALA A2262 " --> pdb=" O LYS A2258 " (cutoff:3.500A) Processing helix chain 'A' and resid 2264 through 2293 removed outlier: 3.721A pdb=" N ASN A2272 " --> pdb=" O TRP A2268 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N MET A2273 " --> pdb=" O CYS A2269 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N SER A2274 " --> pdb=" O ALA A2270 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N PHE A2275 " --> pdb=" O ARG A2271 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TRP A2276 " --> pdb=" O ASN A2272 " (cutoff:3.500A) Processing helix chain 'A' and resid 2309 through 2325 removed outlier: 3.788A pdb=" N ILE A2325 " --> pdb=" O LEU A2321 " (cutoff:3.500A) Processing helix chain 'A' and resid 2333 through 2347 removed outlier: 3.681A pdb=" N ILE A2337 " --> pdb=" O ILE A2333 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE A2346 " --> pdb=" O LEU A2342 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER A2347 " --> pdb=" O ARG A2343 " (cutoff:3.500A) Processing helix chain 'A' and resid 2350 through 2375 removed outlier: 3.774A pdb=" N MET A2370 " --> pdb=" O ILE A2366 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN A2375 " --> pdb=" O SER A2371 " (cutoff:3.500A) Processing helix chain 'A' and resid 2377 through 2380 removed outlier: 3.873A pdb=" N THR A2380 " --> pdb=" O GLY A2377 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2377 through 2380' Processing helix chain 'A' and resid 2384 through 2388 Processing helix chain 'A' and resid 2390 through 2407 Processing helix chain 'A' and resid 2412 through 2423 removed outlier: 4.391A pdb=" N PHE A2418 " --> pdb=" O SER A2414 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ASP A2419 " --> pdb=" O LEU A2415 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ARG A2423 " --> pdb=" O ASP A2419 " (cutoff:3.500A) Processing helix chain 'A' and resid 2426 through 2434 Processing helix chain 'A' and resid 2438 through 2462 Processing helix chain 'A' and resid 2464 through 2466 No H-bonds generated for 'chain 'A' and resid 2464 through 2466' Processing helix chain 'A' and resid 2534 through 2542 Processing helix chain 'A' and resid 2549 through 2551 No H-bonds generated for 'chain 'A' and resid 2549 through 2551' Processing helix chain 'A' and resid 2564 through 2608 Processing helix chain 'A' and resid 2618 through 2620 No H-bonds generated for 'chain 'A' and resid 2618 through 2620' Processing helix chain 'A' and resid 2628 through 2631 No H-bonds generated for 'chain 'A' and resid 2628 through 2631' Processing helix chain 'A' and resid 2638 through 2650 Processing helix chain 'A' and resid 2658 through 2668 Processing helix chain 'A' and resid 2689 through 2735 Processing helix chain 'D' and resid 53 through 56 Processing helix chain 'D' and resid 68 through 75 Processing helix chain 'D' and resid 89 through 107 removed outlier: 3.524A pdb=" N GLU D 106 " --> pdb=" O GLN D 102 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN D 107 " --> pdb=" O ASN D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 366 No H-bonds generated for 'chain 'D' and resid 364 through 366' Processing helix chain 'D' and resid 437 through 462 removed outlier: 3.878A pdb=" N ASP D 442 " --> pdb=" O ALA D 438 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY D 458 " --> pdb=" O GLY D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 467 through 485 removed outlier: 3.547A pdb=" N THR D 474 " --> pdb=" O ARG D 470 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL D 481 " --> pdb=" O LEU D 477 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TYR D 482 " --> pdb=" O GLU D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 504 through 507 No H-bonds generated for 'chain 'D' and resid 504 through 507' Processing helix chain 'D' and resid 509 through 512 No H-bonds generated for 'chain 'D' and resid 509 through 512' Processing helix chain 'D' and resid 515 through 531 removed outlier: 3.615A pdb=" N GLN D 524 " --> pdb=" O PHE D 520 " (cutoff:3.500A) Proline residue: D 526 - end of helix Processing helix chain 'D' and resid 544 through 546 No H-bonds generated for 'chain 'D' and resid 544 through 546' Processing helix chain 'D' and resid 553 through 563 removed outlier: 3.655A pdb=" N ARG D 558 " --> pdb=" O ARG D 554 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 584 removed outlier: 3.788A pdb=" N GLN D 577 " --> pdb=" O TYR D 573 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE D 578 " --> pdb=" O ILE D 574 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N GLY D 579 " --> pdb=" O ALA D 575 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N PHE D 580 " --> pdb=" O LYS D 576 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N MET D 581 " --> pdb=" O GLN D 577 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN D 582 " --> pdb=" O PHE D 578 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N LYS D 583 " --> pdb=" O GLY D 579 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N GLN D 584 " --> pdb=" O PHE D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 591 through 598 removed outlier: 3.595A pdb=" N THR D 596 " --> pdb=" O GLU D 592 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA D 597 " --> pdb=" O ASP D 593 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU D 598 " --> pdb=" O THR D 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 604 through 609 Processing helix chain 'D' and resid 612 through 616 Processing helix chain 'D' and resid 629 through 638 removed outlier: 3.987A pdb=" N LEU D 637 " --> pdb=" O TYR D 633 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 652 No H-bonds generated for 'chain 'D' and resid 649 through 652' Processing helix chain 'D' and resid 713 through 719 removed outlier: 4.155A pdb=" N GLN D 717 " --> pdb=" O ARG D 713 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP D 718 " --> pdb=" O GLU D 714 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA D 719 " --> pdb=" O LEU D 715 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 713 through 719' Processing helix chain 'D' and resid 724 through 743 removed outlier: 4.619A pdb=" N LEU D 730 " --> pdb=" O ASP D 726 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N SER D 731 " --> pdb=" O ARG D 727 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 751 No H-bonds generated for 'chain 'D' and resid 749 through 751' Processing helix chain 'D' and resid 754 through 757 No H-bonds generated for 'chain 'D' and resid 754 through 757' Processing helix chain 'D' and resid 761 through 768 removed outlier: 3.806A pdb=" N MET D 768 " --> pdb=" O ILE D 764 " (cutoff:3.500A) Processing helix chain 'D' and resid 777 through 787 removed outlier: 3.702A pdb=" N HIS D 787 " --> pdb=" O ARG D 783 " (cutoff:3.500A) Processing helix chain 'D' and resid 827 through 829 No H-bonds generated for 'chain 'D' and resid 827 through 829' Processing helix chain 'D' and resid 831 through 847 removed outlier: 4.255A pdb=" N GLN D 835 " --> pdb=" O GLU D 831 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N THR D 836 " --> pdb=" O ARG D 832 " (cutoff:3.500A) Processing helix chain 'D' and resid 860 through 876 removed outlier: 3.628A pdb=" N TYR D 875 " --> pdb=" O ARG D 871 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N PHE D 876 " --> pdb=" O ASN D 872 " (cutoff:3.500A) Processing helix chain 'D' and resid 881 through 893 removed outlier: 4.392A pdb=" N LYS D 889 " --> pdb=" O LEU D 885 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ILE D 890 " --> pdb=" O ARG D 886 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA D 893 " --> pdb=" O LYS D 889 " (cutoff:3.500A) Processing helix chain 'D' and resid 965 through 1002 removed outlier: 3.764A pdb=" N ASN D 983 " --> pdb=" O GLN D 979 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL D 984 " --> pdb=" O PHE D 980 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ARG D 985 " --> pdb=" O ILE D 981 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU D 986 " --> pdb=" O LEU D 982 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASP D 987 " --> pdb=" O ASN D 983 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE D1001 " --> pdb=" O PHE D 997 " (cutoff:3.500A) Processing helix chain 'D' and resid 1026 through 1031 removed outlier: 3.661A pdb=" N ASP D1029 " --> pdb=" O GLY D1026 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLU D1031 " --> pdb=" O LEU D1028 " (cutoff:3.500A) Processing helix chain 'D' and resid 1033 through 1035 No H-bonds generated for 'chain 'D' and resid 1033 through 1035' Processing helix chain 'D' and resid 1060 through 1068 Processing helix chain 'D' and resid 1074 through 1086 removed outlier: 3.533A pdb=" N HIS D1086 " --> pdb=" O LEU D1083 " (cutoff:3.500A) Processing helix chain 'D' and resid 1089 through 1100 Processing helix chain 'D' and resid 1110 through 1125 removed outlier: 3.709A pdb=" N ILE D1115 " --> pdb=" O ASN D1111 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ARG D1123 " --> pdb=" O LEU D1119 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N SER D1124 " --> pdb=" O ASP D1120 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE D1125 " --> pdb=" O GLN D1121 " (cutoff:3.500A) Processing helix chain 'D' and resid 1173 through 1187 removed outlier: 4.365A pdb=" N LYS D1177 " --> pdb=" O TYR D1173 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N GLU D1178 " --> pdb=" O ARG D1174 " (cutoff:3.500A) Processing helix chain 'D' and resid 1197 through 1203 removed outlier: 4.433A pdb=" N GLN D1202 " --> pdb=" O ARG D1198 " (cutoff:3.500A) Processing helix chain 'D' and resid 1211 through 1219 removed outlier: 3.925A pdb=" N LEU D1215 " --> pdb=" O HIS D1211 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N GLU D1216 " --> pdb=" O ALA D1212 " (cutoff:3.500A) Processing helix chain 'D' and resid 1231 through 1244 removed outlier: 3.897A pdb=" N ARG D1235 " --> pdb=" O GLN D1231 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.364A pdb=" N LYS D1257 " --> pdb=" O ALA D1253 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N HIS D1258 " --> pdb=" O LEU D1254 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ILE D1259 " --> pdb=" O LEU D1255 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ASN D1260 " --> pdb=" O HIS D1256 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LEU D1261 " --> pdb=" O LYS D1257 " (cutoff:3.500A) Processing helix chain 'D' and resid 1270 through 1274 Processing helix chain 'D' and resid 1292 through 1299 Processing helix chain 'D' and resid 1324 through 1337 removed outlier: 4.236A pdb=" N GLU D1333 " --> pdb=" O MET D1329 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU D1334 " --> pdb=" O VAL D1330 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL D1335 " --> pdb=" O MET D1331 " (cutoff:3.500A) Processing helix chain 'D' and resid 1348 through 1359 removed outlier: 4.627A pdb=" N GLN D1352 " --> pdb=" O ARG D1348 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR D1353 " --> pdb=" O ALA D1349 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG D1359 " --> pdb=" O ILE D1355 " (cutoff:3.500A) Processing helix chain 'D' and resid 1599 through 1631 removed outlier: 4.023A pdb=" N GLN D1605 " --> pdb=" O ILE D1601 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ASP D1606 " --> pdb=" O GLU D1602 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ARG D1614 " --> pdb=" O ALA D1610 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N LEU D1615 " --> pdb=" O LEU D1611 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ARG D1616 " --> pdb=" O GLU D1612 " (cutoff:3.500A) Proline residue: D1617 - end of helix removed outlier: 3.890A pdb=" N SER D1624 " --> pdb=" O GLN D1620 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N VAL D1625 " --> pdb=" O ALA D1621 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N VAL D1629 " --> pdb=" O VAL D1625 " (cutoff:3.500A) Processing helix chain 'D' and resid 1653 through 1662 removed outlier: 3.684A pdb=" N LYS D1661 " --> pdb=" O ILE D1657 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLN D1662 " --> pdb=" O LYS D1658 " (cutoff:3.500A) Processing helix chain 'D' and resid 1669 through 1683 Processing helix chain 'D' and resid 1728 through 1744 Processing helix chain 'D' and resid 1792 through 1801 removed outlier: 3.519A pdb=" N GLN D1796 " --> pdb=" O LEU D1792 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N CYS D1797 " --> pdb=" O ALA D1793 " (cutoff:3.500A) Processing helix chain 'D' and resid 1804 through 1811 Processing helix chain 'D' and resid 1819 through 1832 Processing helix chain 'D' and resid 1837 through 1847 removed outlier: 4.261A pdb=" N SER D1842 " --> pdb=" O THR D1838 " (cutoff:3.500A) Processing helix chain 'D' and resid 1853 through 1873 removed outlier: 3.674A pdb=" N PHE D1860 " --> pdb=" O PHE D1856 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG D1863 " --> pdb=" O VAL D1859 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN D1868 " --> pdb=" O MET D1864 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN D1869 " --> pdb=" O LYS D1865 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS D1872 " --> pdb=" O GLN D1868 " (cutoff:3.500A) Processing helix chain 'D' and resid 1964 through 1977 Proline residue: D1968 - end of helix removed outlier: 3.555A pdb=" N LEU D1975 " --> pdb=" O PHE D1972 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU D1976 " --> pdb=" O LEU D1973 " (cutoff:3.500A) Processing helix chain 'D' and resid 1982 through 1986 removed outlier: 3.823A pdb=" N ASN D1986 " --> pdb=" O ARG D1982 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1982 through 1986' Processing helix chain 'D' and resid 1999 through 2010 Processing helix chain 'D' and resid 2016 through 2018 No H-bonds generated for 'chain 'D' and resid 2016 through 2018' Processing helix chain 'D' and resid 2030 through 2044 removed outlier: 3.802A pdb=" N GLN D2035 " --> pdb=" O ALA D2031 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N CYS D2044 " --> pdb=" O LEU D2040 " (cutoff:3.500A) Processing helix chain 'D' and resid 2049 through 2057 removed outlier: 3.501A pdb=" N ASN D2053 " --> pdb=" O HIS D2049 " (cutoff:3.500A) Processing helix chain 'D' and resid 2062 through 2066 removed outlier: 3.771A pdb=" N ILE D2065 " --> pdb=" O GLY D2062 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE D2066 " --> pdb=" O ILE D2063 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2062 through 2066' Processing helix chain 'D' and resid 2068 through 2071 No H-bonds generated for 'chain 'D' and resid 2068 through 2071' Processing helix chain 'D' and resid 2079 through 2099 removed outlier: 4.751A pdb=" N ASP D2083 " --> pdb=" O LYS D2079 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N LEU D2084 " --> pdb=" O LYS D2080 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N GLU D2087 " --> pdb=" O ASP D2083 " (cutoff:3.500A) Processing helix chain 'D' and resid 2106 through 2113 Processing helix chain 'D' and resid 2120 through 2131 removed outlier: 4.301A pdb=" N GLN D2131 " --> pdb=" O LYS D2127 " (cutoff:3.500A) Processing helix chain 'D' and resid 2149 through 2165 removed outlier: 3.917A pdb=" N GLY D2153 " --> pdb=" O PRO D2149 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ARG D2165 " --> pdb=" O HIS D2161 " (cutoff:3.500A) Processing helix chain 'D' and resid 2168 through 2174 removed outlier: 3.567A pdb=" N LEU D2174 " --> pdb=" O LEU D2170 " (cutoff:3.500A) Processing helix chain 'D' and resid 2184 through 2191 Processing helix chain 'D' and resid 2221 through 2230 Processing helix chain 'D' and resid 2240 through 2262 removed outlier: 4.086A pdb=" N LEU D2245 " --> pdb=" O ASN D2241 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ALA D2262 " --> pdb=" O LYS D2258 " (cutoff:3.500A) Processing helix chain 'D' and resid 2264 through 2293 removed outlier: 3.717A pdb=" N ASN D2272 " --> pdb=" O TRP D2268 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N MET D2273 " --> pdb=" O CYS D2269 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N SER D2274 " --> pdb=" O ALA D2270 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N PHE D2275 " --> pdb=" O ARG D2271 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TRP D2276 " --> pdb=" O ASN D2272 " (cutoff:3.500A) Processing helix chain 'D' and resid 2309 through 2325 removed outlier: 3.795A pdb=" N ILE D2325 " --> pdb=" O LEU D2321 " (cutoff:3.500A) Processing helix chain 'D' and resid 2333 through 2347 removed outlier: 3.690A pdb=" N ILE D2337 " --> pdb=" O ILE D2333 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE D2346 " --> pdb=" O LEU D2342 " (cutoff:3.500A) Processing helix chain 'D' and resid 2350 through 2375 removed outlier: 3.768A pdb=" N MET D2370 " --> pdb=" O ILE D2366 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN D2375 " --> pdb=" O SER D2371 " (cutoff:3.500A) Processing helix chain 'D' and resid 2377 through 2380 removed outlier: 3.865A pdb=" N THR D2380 " --> pdb=" O GLY D2377 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2377 through 2380' Processing helix chain 'D' and resid 2384 through 2388 Processing helix chain 'D' and resid 2390 through 2407 Processing helix chain 'D' and resid 2412 through 2423 removed outlier: 4.426A pdb=" N PHE D2418 " --> pdb=" O SER D2414 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ASP D2419 " --> pdb=" O LEU D2415 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ARG D2423 " --> pdb=" O ASP D2419 " (cutoff:3.500A) Processing helix chain 'D' and resid 2425 through 2434 Processing helix chain 'D' and resid 2438 through 2462 Processing helix chain 'D' and resid 2464 through 2466 No H-bonds generated for 'chain 'D' and resid 2464 through 2466' Processing helix chain 'D' and resid 2534 through 2542 Processing helix chain 'D' and resid 2549 through 2551 No H-bonds generated for 'chain 'D' and resid 2549 through 2551' Processing helix chain 'D' and resid 2564 through 2608 Processing helix chain 'D' and resid 2618 through 2620 No H-bonds generated for 'chain 'D' and resid 2618 through 2620' Processing helix chain 'D' and resid 2628 through 2631 No H-bonds generated for 'chain 'D' and resid 2628 through 2631' Processing helix chain 'D' and resid 2638 through 2650 Processing helix chain 'D' and resid 2658 through 2668 Processing helix chain 'D' and resid 2689 through 2735 Processing helix chain 'B' and resid 53 through 56 Processing helix chain 'B' and resid 68 through 75 Processing helix chain 'B' and resid 89 through 107 removed outlier: 3.505A pdb=" N GLU B 106 " --> pdb=" O GLN B 102 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN B 107 " --> pdb=" O ASN B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 366 No H-bonds generated for 'chain 'B' and resid 364 through 366' Processing helix chain 'B' and resid 437 through 462 removed outlier: 3.873A pdb=" N ASP B 442 " --> pdb=" O ALA B 438 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY B 458 " --> pdb=" O GLY B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 485 removed outlier: 3.561A pdb=" N THR B 474 " --> pdb=" O ARG B 470 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL B 481 " --> pdb=" O LEU B 477 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR B 482 " --> pdb=" O GLU B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 507 No H-bonds generated for 'chain 'B' and resid 504 through 507' Processing helix chain 'B' and resid 509 through 512 No H-bonds generated for 'chain 'B' and resid 509 through 512' Processing helix chain 'B' and resid 515 through 531 removed outlier: 3.602A pdb=" N GLN B 524 " --> pdb=" O PHE B 520 " (cutoff:3.500A) Proline residue: B 526 - end of helix Processing helix chain 'B' and resid 544 through 546 No H-bonds generated for 'chain 'B' and resid 544 through 546' Processing helix chain 'B' and resid 553 through 563 removed outlier: 3.645A pdb=" N ARG B 558 " --> pdb=" O ARG B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 584 removed outlier: 3.798A pdb=" N GLN B 577 " --> pdb=" O TYR B 573 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE B 578 " --> pdb=" O ILE B 574 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N GLY B 579 " --> pdb=" O ALA B 575 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N PHE B 580 " --> pdb=" O LYS B 576 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N MET B 581 " --> pdb=" O GLN B 577 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN B 582 " --> pdb=" O PHE B 578 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N LYS B 583 " --> pdb=" O GLY B 579 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLN B 584 " --> pdb=" O PHE B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 598 removed outlier: 3.598A pdb=" N THR B 596 " --> pdb=" O GLU B 592 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA B 597 " --> pdb=" O ASP B 593 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU B 598 " --> pdb=" O THR B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 609 Processing helix chain 'B' and resid 612 through 616 Processing helix chain 'B' and resid 629 through 638 removed outlier: 4.090A pdb=" N LEU B 637 " --> pdb=" O TYR B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 653 Processing helix chain 'B' and resid 713 through 719 removed outlier: 4.156A pdb=" N GLN B 717 " --> pdb=" O ARG B 713 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP B 718 " --> pdb=" O GLU B 714 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA B 719 " --> pdb=" O LEU B 715 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 713 through 719' Processing helix chain 'B' and resid 724 through 744 removed outlier: 4.607A pdb=" N LEU B 730 " --> pdb=" O ASP B 726 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N SER B 731 " --> pdb=" O ARG B 727 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N CYS B 744 " --> pdb=" O PHE B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 751 No H-bonds generated for 'chain 'B' and resid 749 through 751' Processing helix chain 'B' and resid 754 through 757 No H-bonds generated for 'chain 'B' and resid 754 through 757' Processing helix chain 'B' and resid 761 through 768 removed outlier: 3.787A pdb=" N MET B 768 " --> pdb=" O ILE B 764 " (cutoff:3.500A) Processing helix chain 'B' and resid 777 through 787 removed outlier: 3.685A pdb=" N HIS B 787 " --> pdb=" O ARG B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 829 No H-bonds generated for 'chain 'B' and resid 827 through 829' Processing helix chain 'B' and resid 831 through 847 removed outlier: 4.280A pdb=" N GLN B 835 " --> pdb=" O GLU B 831 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N THR B 836 " --> pdb=" O ARG B 832 " (cutoff:3.500A) Processing helix chain 'B' and resid 860 through 876 removed outlier: 3.625A pdb=" N TYR B 875 " --> pdb=" O ARG B 871 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N PHE B 876 " --> pdb=" O ASN B 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 881 through 893 removed outlier: 4.407A pdb=" N LYS B 889 " --> pdb=" O LEU B 885 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ILE B 890 " --> pdb=" O ARG B 886 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA B 893 " --> pdb=" O LYS B 889 " (cutoff:3.500A) Processing helix chain 'B' and resid 965 through 1002 removed outlier: 3.820A pdb=" N ASN B 983 " --> pdb=" O GLN B 979 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL B 984 " --> pdb=" O PHE B 980 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG B 985 " --> pdb=" O ILE B 981 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU B 986 " --> pdb=" O LEU B 982 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP B 987 " --> pdb=" O ASN B 983 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N PHE B1001 " --> pdb=" O PHE B 997 " (cutoff:3.500A) Processing helix chain 'B' and resid 1026 through 1031 removed outlier: 3.659A pdb=" N ASP B1029 " --> pdb=" O GLY B1026 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLU B1031 " --> pdb=" O LEU B1028 " (cutoff:3.500A) Processing helix chain 'B' and resid 1033 through 1035 No H-bonds generated for 'chain 'B' and resid 1033 through 1035' Processing helix chain 'B' and resid 1060 through 1068 Processing helix chain 'B' and resid 1074 through 1086 removed outlier: 3.578A pdb=" N HIS B1086 " --> pdb=" O LEU B1083 " (cutoff:3.500A) Processing helix chain 'B' and resid 1089 through 1100 Processing helix chain 'B' and resid 1110 through 1125 removed outlier: 3.715A pdb=" N ILE B1115 " --> pdb=" O ASN B1111 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG B1123 " --> pdb=" O LEU B1119 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N SER B1124 " --> pdb=" O ASP B1120 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ILE B1125 " --> pdb=" O GLN B1121 " (cutoff:3.500A) Processing helix chain 'B' and resid 1173 through 1187 removed outlier: 4.368A pdb=" N LYS B1177 " --> pdb=" O TYR B1173 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N GLU B1178 " --> pdb=" O ARG B1174 " (cutoff:3.500A) Processing helix chain 'B' and resid 1197 through 1203 removed outlier: 4.441A pdb=" N GLN B1202 " --> pdb=" O ARG B1198 " (cutoff:3.500A) Processing helix chain 'B' and resid 1211 through 1219 removed outlier: 3.921A pdb=" N LEU B1215 " --> pdb=" O HIS B1211 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N GLU B1216 " --> pdb=" O ALA B1212 " (cutoff:3.500A) Processing helix chain 'B' and resid 1231 through 1243 removed outlier: 3.913A pdb=" N ARG B1235 " --> pdb=" O GLN B1231 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B1236 " --> pdb=" O GLU B1232 " (cutoff:3.500A) Processing helix chain 'B' and resid 1249 through 1261 removed outlier: 4.331A pdb=" N LYS B1257 " --> pdb=" O ALA B1253 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N HIS B1258 " --> pdb=" O LEU B1254 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ILE B1259 " --> pdb=" O LEU B1255 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ASN B1260 " --> pdb=" O HIS B1256 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LEU B1261 " --> pdb=" O LYS B1257 " (cutoff:3.500A) Processing helix chain 'B' and resid 1270 through 1275 Processing helix chain 'B' and resid 1292 through 1299 Processing helix chain 'B' and resid 1324 through 1337 removed outlier: 4.237A pdb=" N GLU B1333 " --> pdb=" O MET B1329 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU B1334 " --> pdb=" O VAL B1330 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL B1335 " --> pdb=" O MET B1331 " (cutoff:3.500A) Processing helix chain 'B' and resid 1348 through 1360 removed outlier: 4.626A pdb=" N GLN B1352 " --> pdb=" O ARG B1348 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR B1353 " --> pdb=" O ALA B1349 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG B1359 " --> pdb=" O ILE B1355 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER B1360 " --> pdb=" O GLN B1356 " (cutoff:3.500A) Processing helix chain 'B' and resid 1599 through 1631 removed outlier: 4.028A pdb=" N GLN B1605 " --> pdb=" O ILE B1601 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ASP B1606 " --> pdb=" O GLU B1602 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N ARG B1614 " --> pdb=" O ALA B1610 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N LEU B1615 " --> pdb=" O LEU B1611 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ARG B1616 " --> pdb=" O GLU B1612 " (cutoff:3.500A) Proline residue: B1617 - end of helix removed outlier: 3.903A pdb=" N SER B1624 " --> pdb=" O GLN B1620 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N VAL B1625 " --> pdb=" O ALA B1621 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL B1629 " --> pdb=" O VAL B1625 " (cutoff:3.500A) Processing helix chain 'B' and resid 1653 through 1662 removed outlier: 3.630A pdb=" N LYS B1661 " --> pdb=" O ILE B1657 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLN B1662 " --> pdb=" O LYS B1658 " (cutoff:3.500A) Processing helix chain 'B' and resid 1669 through 1683 Processing helix chain 'B' and resid 1728 through 1744 Processing helix chain 'B' and resid 1792 through 1801 removed outlier: 4.393A pdb=" N CYS B1797 " --> pdb=" O ALA B1793 " (cutoff:3.500A) Processing helix chain 'B' and resid 1804 through 1811 Processing helix chain 'B' and resid 1819 through 1832 Processing helix chain 'B' and resid 1837 through 1847 removed outlier: 4.261A pdb=" N SER B1842 " --> pdb=" O THR B1838 " (cutoff:3.500A) Processing helix chain 'B' and resid 1853 through 1873 removed outlier: 3.665A pdb=" N PHE B1860 " --> pdb=" O PHE B1856 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLN B1868 " --> pdb=" O MET B1864 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN B1869 " --> pdb=" O LYS B1865 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE B1871 " --> pdb=" O ALA B1867 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS B1872 " --> pdb=" O GLN B1868 " (cutoff:3.500A) Processing helix chain 'B' and resid 1964 through 1977 removed outlier: 3.517A pdb=" N GLN B1967 " --> pdb=" O THR B1964 " (cutoff:3.500A) Proline residue: B1968 - end of helix removed outlier: 3.559A pdb=" N LEU B1975 " --> pdb=" O PHE B1972 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU B1976 " --> pdb=" O LEU B1973 " (cutoff:3.500A) Processing helix chain 'B' and resid 1982 through 1986 removed outlier: 3.821A pdb=" N ASN B1986 " --> pdb=" O ARG B1982 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1982 through 1986' Processing helix chain 'B' and resid 1999 through 2010 Processing helix chain 'B' and resid 2016 through 2018 No H-bonds generated for 'chain 'B' and resid 2016 through 2018' Processing helix chain 'B' and resid 2030 through 2044 removed outlier: 3.797A pdb=" N GLN B2035 " --> pdb=" O ALA B2031 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N CYS B2044 " --> pdb=" O LEU B2040 " (cutoff:3.500A) Processing helix chain 'B' and resid 2049 through 2057 removed outlier: 3.501A pdb=" N ASN B2053 " --> pdb=" O HIS B2049 " (cutoff:3.500A) Processing helix chain 'B' and resid 2062 through 2066 removed outlier: 3.774A pdb=" N ILE B2065 " --> pdb=" O GLY B2062 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE B2066 " --> pdb=" O ILE B2063 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2062 through 2066' Processing helix chain 'B' and resid 2068 through 2071 No H-bonds generated for 'chain 'B' and resid 2068 through 2071' Processing helix chain 'B' and resid 2079 through 2099 removed outlier: 4.732A pdb=" N ASP B2083 " --> pdb=" O LYS B2079 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N LEU B2084 " --> pdb=" O LYS B2080 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N GLU B2087 " --> pdb=" O ASP B2083 " (cutoff:3.500A) Processing helix chain 'B' and resid 2106 through 2113 Processing helix chain 'B' and resid 2120 through 2131 removed outlier: 4.269A pdb=" N GLN B2131 " --> pdb=" O LYS B2127 " (cutoff:3.500A) Processing helix chain 'B' and resid 2149 through 2165 removed outlier: 3.934A pdb=" N GLY B2153 " --> pdb=" O PRO B2149 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ARG B2165 " --> pdb=" O HIS B2161 " (cutoff:3.500A) Processing helix chain 'B' and resid 2168 through 2174 Processing helix chain 'B' and resid 2184 through 2191 Processing helix chain 'B' and resid 2221 through 2230 Processing helix chain 'B' and resid 2240 through 2262 removed outlier: 4.091A pdb=" N LEU B2245 " --> pdb=" O ASN B2241 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ALA B2262 " --> pdb=" O LYS B2258 " (cutoff:3.500A) Processing helix chain 'B' and resid 2264 through 2293 removed outlier: 3.725A pdb=" N ASN B2272 " --> pdb=" O TRP B2268 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N MET B2273 " --> pdb=" O CYS B2269 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N SER B2274 " --> pdb=" O ALA B2270 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N PHE B2275 " --> pdb=" O ARG B2271 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TRP B2276 " --> pdb=" O ASN B2272 " (cutoff:3.500A) Processing helix chain 'B' and resid 2309 through 2325 removed outlier: 3.785A pdb=" N ILE B2325 " --> pdb=" O LEU B2321 " (cutoff:3.500A) Processing helix chain 'B' and resid 2333 through 2347 removed outlier: 3.683A pdb=" N ILE B2337 " --> pdb=" O ILE B2333 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE B2346 " --> pdb=" O LEU B2342 " (cutoff:3.500A) Processing helix chain 'B' and resid 2350 through 2375 removed outlier: 3.777A pdb=" N MET B2370 " --> pdb=" O ILE B2366 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN B2375 " --> pdb=" O SER B2371 " (cutoff:3.500A) Processing helix chain 'B' and resid 2377 through 2380 removed outlier: 3.863A pdb=" N THR B2380 " --> pdb=" O GLY B2377 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2377 through 2380' Processing helix chain 'B' and resid 2384 through 2388 Processing helix chain 'B' and resid 2390 through 2407 Processing helix chain 'B' and resid 2412 through 2423 removed outlier: 4.392A pdb=" N PHE B2418 " --> pdb=" O SER B2414 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ASP B2419 " --> pdb=" O LEU B2415 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ARG B2423 " --> pdb=" O ASP B2419 " (cutoff:3.500A) Processing helix chain 'B' and resid 2425 through 2434 Processing helix chain 'B' and resid 2438 through 2462 Processing helix chain 'B' and resid 2464 through 2466 No H-bonds generated for 'chain 'B' and resid 2464 through 2466' Processing helix chain 'B' and resid 2534 through 2542 Processing helix chain 'B' and resid 2549 through 2551 No H-bonds generated for 'chain 'B' and resid 2549 through 2551' Processing helix chain 'B' and resid 2564 through 2608 Processing helix chain 'B' and resid 2618 through 2620 No H-bonds generated for 'chain 'B' and resid 2618 through 2620' Processing helix chain 'B' and resid 2628 through 2631 No H-bonds generated for 'chain 'B' and resid 2628 through 2631' Processing helix chain 'B' and resid 2638 through 2650 Processing helix chain 'B' and resid 2658 through 2668 Processing helix chain 'B' and resid 2689 through 2735 Processing helix chain 'C' and resid 53 through 56 Processing helix chain 'C' and resid 68 through 75 Processing helix chain 'C' and resid 89 through 107 removed outlier: 3.506A pdb=" N GLU C 106 " --> pdb=" O GLN C 102 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN C 107 " --> pdb=" O ASN C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 366 No H-bonds generated for 'chain 'C' and resid 364 through 366' Processing helix chain 'C' and resid 437 through 462 removed outlier: 3.819A pdb=" N ASP C 442 " --> pdb=" O ALA C 438 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY C 458 " --> pdb=" O GLY C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 485 removed outlier: 3.551A pdb=" N THR C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL C 481 " --> pdb=" O LEU C 477 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR C 482 " --> pdb=" O GLU C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 507 No H-bonds generated for 'chain 'C' and resid 504 through 507' Processing helix chain 'C' and resid 509 through 512 No H-bonds generated for 'chain 'C' and resid 509 through 512' Processing helix chain 'C' and resid 515 through 531 removed outlier: 3.594A pdb=" N GLN C 524 " --> pdb=" O PHE C 520 " (cutoff:3.500A) Proline residue: C 526 - end of helix Processing helix chain 'C' and resid 544 through 546 No H-bonds generated for 'chain 'C' and resid 544 through 546' Processing helix chain 'C' and resid 553 through 563 removed outlier: 3.657A pdb=" N ARG C 558 " --> pdb=" O ARG C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 584 removed outlier: 3.788A pdb=" N GLN C 577 " --> pdb=" O TYR C 573 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE C 578 " --> pdb=" O ILE C 574 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N GLY C 579 " --> pdb=" O ALA C 575 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N PHE C 580 " --> pdb=" O LYS C 576 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N MET C 581 " --> pdb=" O GLN C 577 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN C 582 " --> pdb=" O PHE C 578 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N LYS C 583 " --> pdb=" O GLY C 579 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLN C 584 " --> pdb=" O PHE C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 591 through 598 removed outlier: 3.600A pdb=" N THR C 596 " --> pdb=" O GLU C 592 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA C 597 " --> pdb=" O ASP C 593 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU C 598 " --> pdb=" O THR C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 609 Processing helix chain 'C' and resid 612 through 616 Processing helix chain 'C' and resid 629 through 638 removed outlier: 4.091A pdb=" N LEU C 637 " --> pdb=" O TYR C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 652 No H-bonds generated for 'chain 'C' and resid 649 through 652' Processing helix chain 'C' and resid 713 through 719 removed outlier: 4.157A pdb=" N GLN C 717 " --> pdb=" O ARG C 713 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP C 718 " --> pdb=" O GLU C 714 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA C 719 " --> pdb=" O LEU C 715 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 713 through 719' Processing helix chain 'C' and resid 724 through 744 removed outlier: 4.651A pdb=" N LEU C 730 " --> pdb=" O ASP C 726 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N SER C 731 " --> pdb=" O ARG C 727 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N CYS C 744 " --> pdb=" O PHE C 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 749 through 751 No H-bonds generated for 'chain 'C' and resid 749 through 751' Processing helix chain 'C' and resid 754 through 757 No H-bonds generated for 'chain 'C' and resid 754 through 757' Processing helix chain 'C' and resid 761 through 768 removed outlier: 3.785A pdb=" N MET C 768 " --> pdb=" O ILE C 764 " (cutoff:3.500A) Processing helix chain 'C' and resid 777 through 787 removed outlier: 3.705A pdb=" N HIS C 787 " --> pdb=" O ARG C 783 " (cutoff:3.500A) Processing helix chain 'C' and resid 827 through 829 No H-bonds generated for 'chain 'C' and resid 827 through 829' Processing helix chain 'C' and resid 831 through 847 removed outlier: 4.280A pdb=" N GLN C 835 " --> pdb=" O GLU C 831 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N THR C 836 " --> pdb=" O ARG C 832 " (cutoff:3.500A) Processing helix chain 'C' and resid 860 through 876 removed outlier: 3.655A pdb=" N TYR C 875 " --> pdb=" O ARG C 871 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N PHE C 876 " --> pdb=" O ASN C 872 " (cutoff:3.500A) Processing helix chain 'C' and resid 881 through 893 removed outlier: 4.402A pdb=" N LYS C 889 " --> pdb=" O LEU C 885 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILE C 890 " --> pdb=" O ARG C 886 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA C 893 " --> pdb=" O LYS C 889 " (cutoff:3.500A) Processing helix chain 'C' and resid 965 through 1002 removed outlier: 3.828A pdb=" N ASN C 983 " --> pdb=" O GLN C 979 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL C 984 " --> pdb=" O PHE C 980 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ARG C 985 " --> pdb=" O ILE C 981 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU C 986 " --> pdb=" O LEU C 982 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASP C 987 " --> pdb=" O ASN C 983 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE C1001 " --> pdb=" O PHE C 997 " (cutoff:3.500A) Processing helix chain 'C' and resid 1026 through 1031 removed outlier: 3.661A pdb=" N ASP C1029 " --> pdb=" O GLY C1026 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU C1031 " --> pdb=" O LEU C1028 " (cutoff:3.500A) Processing helix chain 'C' and resid 1033 through 1035 No H-bonds generated for 'chain 'C' and resid 1033 through 1035' Processing helix chain 'C' and resid 1060 through 1068 Processing helix chain 'C' and resid 1074 through 1086 removed outlier: 3.524A pdb=" N HIS C1086 " --> pdb=" O LEU C1083 " (cutoff:3.500A) Processing helix chain 'C' and resid 1089 through 1100 Processing helix chain 'C' and resid 1110 through 1125 removed outlier: 3.712A pdb=" N ILE C1115 " --> pdb=" O ASN C1111 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG C1123 " --> pdb=" O LEU C1119 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N SER C1124 " --> pdb=" O ASP C1120 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ILE C1125 " --> pdb=" O GLN C1121 " (cutoff:3.500A) Processing helix chain 'C' and resid 1173 through 1187 removed outlier: 4.361A pdb=" N LYS C1177 " --> pdb=" O TYR C1173 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N GLU C1178 " --> pdb=" O ARG C1174 " (cutoff:3.500A) Processing helix chain 'C' and resid 1197 through 1203 removed outlier: 4.433A pdb=" N GLN C1202 " --> pdb=" O ARG C1198 " (cutoff:3.500A) Processing helix chain 'C' and resid 1211 through 1219 removed outlier: 3.918A pdb=" N LEU C1215 " --> pdb=" O HIS C1211 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N GLU C1216 " --> pdb=" O ALA C1212 " (cutoff:3.500A) Processing helix chain 'C' and resid 1231 through 1244 removed outlier: 3.905A pdb=" N ARG C1235 " --> pdb=" O GLN C1231 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU C1236 " --> pdb=" O GLU C1232 " (cutoff:3.500A) Processing helix chain 'C' and resid 1249 through 1261 removed outlier: 4.347A pdb=" N LYS C1257 " --> pdb=" O ALA C1253 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N HIS C1258 " --> pdb=" O LEU C1254 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ILE C1259 " --> pdb=" O LEU C1255 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ASN C1260 " --> pdb=" O HIS C1256 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU C1261 " --> pdb=" O LYS C1257 " (cutoff:3.500A) Processing helix chain 'C' and resid 1270 through 1274 Processing helix chain 'C' and resid 1292 through 1299 Processing helix chain 'C' and resid 1324 through 1337 removed outlier: 4.262A pdb=" N GLU C1333 " --> pdb=" O MET C1329 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU C1334 " --> pdb=" O VAL C1330 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL C1335 " --> pdb=" O MET C1331 " (cutoff:3.500A) Processing helix chain 'C' and resid 1348 through 1360 removed outlier: 4.626A pdb=" N GLN C1352 " --> pdb=" O ARG C1348 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR C1353 " --> pdb=" O ALA C1349 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG C1359 " --> pdb=" O ILE C1355 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER C1360 " --> pdb=" O GLN C1356 " (cutoff:3.500A) Processing helix chain 'C' and resid 1599 through 1631 removed outlier: 4.027A pdb=" N GLN C1605 " --> pdb=" O ILE C1601 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ASP C1606 " --> pdb=" O GLU C1602 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N ARG C1614 " --> pdb=" O ALA C1610 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N LEU C1615 " --> pdb=" O LEU C1611 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ARG C1616 " --> pdb=" O GLU C1612 " (cutoff:3.500A) Proline residue: C1617 - end of helix removed outlier: 3.887A pdb=" N SER C1624 " --> pdb=" O GLN C1620 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N VAL C1625 " --> pdb=" O ALA C1621 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL C1629 " --> pdb=" O VAL C1625 " (cutoff:3.500A) Processing helix chain 'C' and resid 1653 through 1662 removed outlier: 3.627A pdb=" N LYS C1661 " --> pdb=" O ILE C1657 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLN C1662 " --> pdb=" O LYS C1658 " (cutoff:3.500A) Processing helix chain 'C' and resid 1669 through 1683 Processing helix chain 'C' and resid 1728 through 1744 Processing helix chain 'C' and resid 1792 through 1802 removed outlier: 3.514A pdb=" N GLN C1796 " --> pdb=" O LEU C1792 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N CYS C1797 " --> pdb=" O ALA C1793 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU C1802 " --> pdb=" O HIS C1798 " (cutoff:3.500A) Processing helix chain 'C' and resid 1804 through 1811 removed outlier: 3.578A pdb=" N VAL C1808 " --> pdb=" O ALA C1804 " (cutoff:3.500A) Processing helix chain 'C' and resid 1819 through 1832 Processing helix chain 'C' and resid 1837 through 1847 removed outlier: 4.224A pdb=" N SER C1842 " --> pdb=" O THR C1838 " (cutoff:3.500A) Processing helix chain 'C' and resid 1853 through 1873 removed outlier: 3.665A pdb=" N PHE C1860 " --> pdb=" O PHE C1856 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN C1868 " --> pdb=" O MET C1864 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN C1869 " --> pdb=" O LYS C1865 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE C1871 " --> pdb=" O ALA C1867 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS C1872 " --> pdb=" O GLN C1868 " (cutoff:3.500A) Processing helix chain 'C' and resid 1964 through 1977 removed outlier: 3.524A pdb=" N GLN C1967 " --> pdb=" O THR C1964 " (cutoff:3.500A) Proline residue: C1968 - end of helix removed outlier: 3.563A pdb=" N LEU C1975 " --> pdb=" O PHE C1972 " (cutoff:3.500A) Processing helix chain 'C' and resid 1982 through 1986 removed outlier: 3.844A pdb=" N ASN C1986 " --> pdb=" O ARG C1982 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1982 through 1986' Processing helix chain 'C' and resid 1999 through 2010 Processing helix chain 'C' and resid 2016 through 2018 No H-bonds generated for 'chain 'C' and resid 2016 through 2018' Processing helix chain 'C' and resid 2030 through 2044 removed outlier: 3.797A pdb=" N GLN C2035 " --> pdb=" O ALA C2031 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N CYS C2044 " --> pdb=" O LEU C2040 " (cutoff:3.500A) Processing helix chain 'C' and resid 2049 through 2057 Processing helix chain 'C' and resid 2063 through 2066 No H-bonds generated for 'chain 'C' and resid 2063 through 2066' Processing helix chain 'C' and resid 2068 through 2071 No H-bonds generated for 'chain 'C' and resid 2068 through 2071' Processing helix chain 'C' and resid 2079 through 2099 removed outlier: 4.751A pdb=" N ASP C2083 " --> pdb=" O LYS C2079 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N LEU C2084 " --> pdb=" O LYS C2080 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N GLU C2087 " --> pdb=" O ASP C2083 " (cutoff:3.500A) Processing helix chain 'C' and resid 2107 through 2113 Processing helix chain 'C' and resid 2120 through 2131 removed outlier: 3.988A pdb=" N GLN C2131 " --> pdb=" O LYS C2127 " (cutoff:3.500A) Processing helix chain 'C' and resid 2149 through 2165 removed outlier: 3.774A pdb=" N GLY C2153 " --> pdb=" O PRO C2149 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ARG C2165 " --> pdb=" O HIS C2161 " (cutoff:3.500A) Processing helix chain 'C' and resid 2168 through 2173 removed outlier: 4.391A pdb=" N MET C2173 " --> pdb=" O GLU C2169 " (cutoff:3.500A) Processing helix chain 'C' and resid 2184 through 2191 Processing helix chain 'C' and resid 2221 through 2230 Processing helix chain 'C' and resid 2240 through 2262 removed outlier: 4.076A pdb=" N LEU C2245 " --> pdb=" O ASN C2241 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ALA C2262 " --> pdb=" O LYS C2258 " (cutoff:3.500A) Processing helix chain 'C' and resid 2264 through 2293 removed outlier: 3.712A pdb=" N ASN C2272 " --> pdb=" O TRP C2268 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N MET C2273 " --> pdb=" O CYS C2269 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N SER C2274 " --> pdb=" O ALA C2270 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N PHE C2275 " --> pdb=" O ARG C2271 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TRP C2276 " --> pdb=" O ASN C2272 " (cutoff:3.500A) Processing helix chain 'C' and resid 2309 through 2325 removed outlier: 3.786A pdb=" N ILE C2325 " --> pdb=" O LEU C2321 " (cutoff:3.500A) Processing helix chain 'C' and resid 2333 through 2347 removed outlier: 3.679A pdb=" N ILE C2337 " --> pdb=" O ILE C2333 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE C2346 " --> pdb=" O LEU C2342 " (cutoff:3.500A) Processing helix chain 'C' and resid 2350 through 2375 removed outlier: 3.776A pdb=" N MET C2370 " --> pdb=" O ILE C2366 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASN C2375 " --> pdb=" O SER C2371 " (cutoff:3.500A) Processing helix chain 'C' and resid 2384 through 2388 Processing helix chain 'C' and resid 2390 through 2407 Processing helix chain 'C' and resid 2412 through 2423 removed outlier: 4.412A pdb=" N PHE C2418 " --> pdb=" O SER C2414 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ASP C2419 " --> pdb=" O LEU C2415 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ARG C2423 " --> pdb=" O ASP C2419 " (cutoff:3.500A) Processing helix chain 'C' and resid 2425 through 2434 Processing helix chain 'C' and resid 2438 through 2462 Processing helix chain 'C' and resid 2464 through 2466 No H-bonds generated for 'chain 'C' and resid 2464 through 2466' Processing helix chain 'C' and resid 2534 through 2542 Processing helix chain 'C' and resid 2549 through 2551 No H-bonds generated for 'chain 'C' and resid 2549 through 2551' Processing helix chain 'C' and resid 2564 through 2608 Processing helix chain 'C' and resid 2618 through 2620 No H-bonds generated for 'chain 'C' and resid 2618 through 2620' Processing helix chain 'C' and resid 2628 through 2631 No H-bonds generated for 'chain 'C' and resid 2628 through 2631' Processing helix chain 'C' and resid 2638 through 2650 Processing helix chain 'C' and resid 2658 through 2668 Processing helix chain 'C' and resid 2689 through 2735 Processing sheet with id= A, first strand: chain 'A' and resid 27 through 29 Processing sheet with id= B, first strand: chain 'A' and resid 131 through 133 Processing sheet with id= C, first strand: chain 'A' and resid 161 through 165 Processing sheet with id= D, first strand: chain 'A' and resid 431 through 434 removed outlier: 3.540A pdb=" N VAL A 433 " --> pdb=" O ARG A 241 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 368 through 372 Processing sheet with id= F, first strand: chain 'A' and resid 398 through 400 Processing sheet with id= G, first strand: chain 'A' and resid 2193 through 2199 removed outlier: 3.577A pdb=" N PHE A2210 " --> pdb=" O ALA A2194 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 14 through 20 removed outlier: 6.100A pdb=" N SER A 16 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N LEU A 222 " --> pdb=" O SER A 16 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N TYR A 18 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N ILE A 220 " --> pdb=" O TYR A 18 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N GLU A 20 " --> pdb=" O TRP A 218 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N TRP A 218 " --> pdb=" O GLU A 20 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 131 through 133 Processing sheet with id= J, first strand: chain 'D' and resid 161 through 165 Processing sheet with id= K, first strand: chain 'D' and resid 431 through 434 removed outlier: 3.537A pdb=" N VAL D 433 " --> pdb=" O ARG D 241 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 368 through 372 Processing sheet with id= M, first strand: chain 'D' and resid 398 through 400 Processing sheet with id= N, first strand: chain 'D' and resid 2193 through 2199 removed outlier: 3.596A pdb=" N PHE D2210 " --> pdb=" O ALA D2194 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 14 through 20 removed outlier: 6.093A pdb=" N SER D 16 " --> pdb=" O LEU D 222 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LEU D 222 " --> pdb=" O SER D 16 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N TYR D 18 " --> pdb=" O ILE D 220 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ILE D 220 " --> pdb=" O TYR D 18 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N GLU D 20 " --> pdb=" O TRP D 218 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N TRP D 218 " --> pdb=" O GLU D 20 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 27 through 29 Processing sheet with id= Q, first strand: chain 'B' and resid 131 through 133 Processing sheet with id= R, first strand: chain 'B' and resid 161 through 165 Processing sheet with id= S, first strand: chain 'B' and resid 431 through 434 removed outlier: 3.538A pdb=" N VAL B 433 " --> pdb=" O ARG B 241 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 368 through 372 Processing sheet with id= U, first strand: chain 'B' and resid 398 through 400 Processing sheet with id= V, first strand: chain 'B' and resid 2193 through 2199 removed outlier: 3.586A pdb=" N PHE B2210 " --> pdb=" O ALA B2194 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'B' and resid 14 through 20 removed outlier: 6.101A pdb=" N SER B 16 " --> pdb=" O LEU B 222 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N LEU B 222 " --> pdb=" O SER B 16 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N TYR B 18 " --> pdb=" O ILE B 220 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ILE B 220 " --> pdb=" O TYR B 18 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N GLU B 20 " --> pdb=" O TRP B 218 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N TRP B 218 " --> pdb=" O GLU B 20 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 27 through 29 Processing sheet with id= Y, first strand: chain 'C' and resid 131 through 133 Processing sheet with id= Z, first strand: chain 'C' and resid 161 through 165 Processing sheet with id= AA, first strand: chain 'C' and resid 431 through 434 removed outlier: 3.540A pdb=" N VAL C 433 " --> pdb=" O ARG C 241 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'C' and resid 368 through 372 Processing sheet with id= AC, first strand: chain 'C' and resid 398 through 400 Processing sheet with id= AD, first strand: chain 'C' and resid 2193 through 2199 removed outlier: 3.569A pdb=" N PHE C2210 " --> pdb=" O ALA C2194 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'C' and resid 14 through 20 removed outlier: 6.101A pdb=" N SER C 16 " --> pdb=" O LEU C 222 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N LEU C 222 " --> pdb=" O SER C 16 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N TYR C 18 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE C 220 " --> pdb=" O TYR C 18 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N GLU C 20 " --> pdb=" O TRP C 218 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N TRP C 218 " --> pdb=" O GLU C 20 " (cutoff:3.500A) 2615 hydrogen bonds defined for protein. 7572 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: 27.37 Time building geometry restraints manager: 26.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 11596 1.31 - 1.44: 18371 1.44 - 1.57: 42599 1.57 - 1.69: 70 1.69 - 1.82: 604 Bond restraints: 73240 Sorted by residual: bond pdb=" C24 PLX D5108 " pdb=" O9 PLX D5108 " ideal model delta sigma weight residual 1.384 1.185 0.199 2.00e-02 2.50e+03 9.88e+01 bond pdb=" C24 PLX B2801 " pdb=" O9 PLX B2801 " ideal model delta sigma weight residual 1.384 1.185 0.199 2.00e-02 2.50e+03 9.85e+01 bond pdb=" C24 PLX A2804 " pdb=" O9 PLX A2804 " ideal model delta sigma weight residual 1.384 1.186 0.198 2.00e-02 2.50e+03 9.84e+01 bond pdb=" C24 PLX C5102 " pdb=" O9 PLX C5102 " ideal model delta sigma weight residual 1.384 1.186 0.198 2.00e-02 2.50e+03 9.81e+01 bond pdb=" C24 PLX B2803 " pdb=" O9 PLX B2803 " ideal model delta sigma weight residual 1.384 1.186 0.198 2.00e-02 2.50e+03 9.78e+01 ... (remaining 73235 not shown) Histogram of bond angle deviations from ideal: 86.14 - 95.78: 5 95.78 - 105.43: 952 105.43 - 115.07: 45144 115.07 - 124.72: 51129 124.72 - 134.36: 1102 Bond angle restraints: 98332 Sorted by residual: angle pdb=" CB LYS A2432 " pdb=" CG LYS A2432 " pdb=" CD LYS A2432 " ideal model delta sigma weight residual 111.30 86.14 25.16 2.30e+00 1.89e-01 1.20e+02 angle pdb=" CB LYS B2432 " pdb=" CG LYS B2432 " pdb=" CD LYS B2432 " ideal model delta sigma weight residual 111.30 92.67 18.63 2.30e+00 1.89e-01 6.56e+01 angle pdb=" CB LYS D2432 " pdb=" CG LYS D2432 " pdb=" CD LYS D2432 " ideal model delta sigma weight residual 111.30 93.61 17.69 2.30e+00 1.89e-01 5.92e+01 angle pdb=" CB LYS C2432 " pdb=" CG LYS C2432 " pdb=" CD LYS C2432 " ideal model delta sigma weight residual 111.30 93.82 17.48 2.30e+00 1.89e-01 5.77e+01 angle pdb=" N LYS A2432 " pdb=" CA LYS A2432 " pdb=" C LYS A2432 " ideal model delta sigma weight residual 113.38 104.18 9.20 1.23e+00 6.61e-01 5.60e+01 ... (remaining 98327 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.00: 44312 35.00 - 69.99: 1159 69.99 - 104.99: 105 104.99 - 139.98: 16 139.98 - 174.98: 20 Dihedral angle restraints: 45612 sinusoidal: 18644 harmonic: 26968 Sorted by residual: dihedral pdb=" CA PHE C1637 " pdb=" C PHE C1637 " pdb=" N PRO C1638 " pdb=" CA PRO C1638 " ideal model delta harmonic sigma weight residual 180.00 136.70 43.30 0 5.00e+00 4.00e-02 7.50e+01 dihedral pdb=" CA PHE B1637 " pdb=" C PHE B1637 " pdb=" N PRO B1638 " pdb=" CA PRO B1638 " ideal model delta harmonic sigma weight residual 180.00 136.72 43.28 0 5.00e+00 4.00e-02 7.49e+01 dihedral pdb=" CA PHE A1637 " pdb=" C PHE A1637 " pdb=" N PRO A1638 " pdb=" CA PRO A1638 " ideal model delta harmonic sigma weight residual 180.00 136.78 43.22 0 5.00e+00 4.00e-02 7.47e+01 ... (remaining 45609 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 10051 0.086 - 0.172: 1108 0.172 - 0.258: 88 0.258 - 0.343: 29 0.343 - 0.429: 4 Chirality restraints: 11280 Sorted by residual: chirality pdb=" CG LEU D1075 " pdb=" CB LEU D1075 " pdb=" CD1 LEU D1075 " pdb=" CD2 LEU D1075 " both_signs ideal model delta sigma weight residual False -2.59 -2.16 -0.43 2.00e-01 2.50e+01 4.61e+00 chirality pdb=" CG LEU A1075 " pdb=" CB LEU A1075 " pdb=" CD1 LEU A1075 " pdb=" CD2 LEU A1075 " both_signs ideal model delta sigma weight residual False -2.59 -2.17 -0.42 2.00e-01 2.50e+01 4.33e+00 chirality pdb=" CG LEU B1075 " pdb=" CB LEU B1075 " pdb=" CD1 LEU B1075 " pdb=" CD2 LEU B1075 " both_signs ideal model delta sigma weight residual False -2.59 -2.17 -0.42 2.00e-01 2.50e+01 4.32e+00 ... (remaining 11277 not shown) Planarity restraints: 12048 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D2423 " -0.530 9.50e-02 1.11e+02 2.37e-01 3.44e+01 pdb=" NE ARG D2423 " 0.031 2.00e-02 2.50e+03 pdb=" CZ ARG D2423 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG D2423 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG D2423 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE C1637 " -0.058 5.00e-02 4.00e+02 8.80e-02 1.24e+01 pdb=" N PRO C1638 " 0.152 5.00e-02 4.00e+02 pdb=" CA PRO C1638 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO C1638 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A1637 " -0.058 5.00e-02 4.00e+02 8.79e-02 1.24e+01 pdb=" N PRO A1638 " 0.152 5.00e-02 4.00e+02 pdb=" CA PRO A1638 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO A1638 " -0.050 5.00e-02 4.00e+02 ... (remaining 12045 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 5358 2.74 - 3.28: 71185 3.28 - 3.82: 114146 3.82 - 4.36: 131510 4.36 - 4.90: 224782 Nonbonded interactions: 546981 Sorted by model distance: nonbonded pdb=" O LEU B1999 " pdb=" OG1 THR B2003 " model vdw 2.200 2.440 nonbonded pdb=" O LEU C1999 " pdb=" OG1 THR C2003 " model vdw 2.201 2.440 nonbonded pdb=" OG SER B 436 " pdb=" OE1 GLU B 439 " model vdw 2.219 2.440 nonbonded pdb=" OG SER A 436 " pdb=" OE1 GLU A 439 " model vdw 2.220 2.440 nonbonded pdb=" OG SER D 436 " pdb=" OE1 GLU D 439 " model vdw 2.221 2.440 ... (remaining 546976 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 6 through 2741 or (resid 2802 and (name C1 or name C10 or \ name C11 or name C12 or name C1A or name C1B or name C1C or name C2 or name C24 \ or name C25 or name C26 or name C27 or name C28 or name C29 or name C3 or name C \ 30 or name C31 or name C32 or name C33 or name C34 or name C4 or name C5 or name \ C6 or name C7 or name C8 or name C9 or name N1 or name O1 or name O2 or name O3 \ or name O4 or name O6 or name O7 or name O8 or name O9 or name P1 )) or (resid \ 2803 and (name C1 or name C10 or name C11 or name C12 or name C1A or name C1B or \ name C1C or name C2 or name C24 or name C25 or name C26 or name C27 or name C28 \ or name C29 or name C3 or name C30 or name C31 or name C32 or name C4 or name C \ 5 or name C6 or name C7 or name C8 or name C9 or name N1 or name O1 or name O2 o \ r name O3 or name O4 or name O6 or name O7 or name O8 or name O9 or name P1 )) o \ r (resid 2804 and (name C1 or name C10 or name C11 or name C12 or name C13 or na \ me C1A or name C1B or name C1C or name C2 or name C24 or name C25 or name C26 or \ name C27 or name C28 or name C29 or name C3 or name C30 or name C31 or name C32 \ or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 or name N1 or \ name O1 or name O2 or name O3 or name O4 or name O6 or name O7 or name O8 or na \ me O9 or name P1 )) or resid 2805 or (resid 2806 and (name C1 or name C10 or nam \ e C11 or name C12 or name C1A or name C1B or name C1C or name C2 or name C24 or \ name C25 or name C26 or name C27 or name C28 or name C29 or name C3 or name C30 \ or name C31 or name C32 or name C4 or name C5 or name C6 or name C7 or name C8 o \ r name C9 or name N1 or name O1 or name O2 or name O3 or name O4 or name O6 or n \ ame O7 or name O8 or name O9 or name P1 )) or (resid 2807 and (name C1 or name C \ 10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C1A or na \ me C1B or name C1C or name C2 or name C24 or name C25 or name C26 or name C27 or \ name C28 or name C29 or name C3 or name C30 or name C31 or name C32 or name C4 \ or name C5 or name C6 or name C7 or name C8 or name C9 or name N1 or name O1 or \ name O2 or name O3 or name O4 or name O6 or name O7 or name O8 or name O9 or nam \ e P1 )))) selection = (chain 'B' and (resid 6 through 2741 or resid 2802 or (resid 2803 and (name C1 o \ r name C10 or name C11 or name C12 or name C1A or name C1B or name C1C or name C \ 2 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 or nam \ e C3 or name C30 or name C31 or name C32 or name C4 or name C5 or name C6 or nam \ e C7 or name C8 or name C9 or name N1 or name O1 or name O2 or name O3 or name O \ 4 or name O6 or name O7 or name O8 or name O9 or name P1 )) or (resid 2804 and ( \ name C1 or name C10 or name C11 or name C12 or name C13 or name C1A or name C1B \ or name C1C or name C2 or name C24 or name C25 or name C26 or name C27 or name C \ 28 or name C29 or name C3 or name C30 or name C31 or name C32 or name C4 or name \ C5 or name C6 or name C7 or name C8 or name C9 or name N1 or name O1 or name O2 \ or name O3 or name O4 or name O6 or name O7 or name O8 or name O9 or name P1 )) \ or (resid 2805 and (name C1 or name C10 or name C11 or name C12 or name C1A or \ name C1B or name C1C or name C2 or name C24 or name C25 or name C26 or name C27 \ or name C28 or name C29 or name C3 or name C30 or name C31 or name C32 or name C \ 33 or name C34 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 \ or name N1 or name O1 or name O2 or name O3 or name O4 or name O6 or name O7 or \ name O8 or name O9 or name P1 )) or (resid 2806 and (name C1 or name C10 or nam \ e C11 or name C12 or name C1A or name C1B or name C1C or name C2 or name C24 or \ name C25 or name C26 or name C27 or name C28 or name C29 or name C3 or name C30 \ or name C31 or name C32 or name C4 or name C5 or name C6 or name C7 or name C8 o \ r name C9 or name N1 or name O1 or name O2 or name O3 or name O4 or name O6 or n \ ame O7 or name O8 or name O9 or name P1 )) or (resid 2807 and (name C1 or name C \ 10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C1A or na \ me C1B or name C1C or name C2 or name C24 or name C25 or name C26 or name C27 or \ name C28 or name C29 or name C3 or name C30 or name C31 or name C32 or name C4 \ or name C5 or name C6 or name C7 or name C8 or name C9 or name N1 or name O1 or \ name O2 or name O3 or name O4 or name O6 or name O7 or name O8 or name O9 or nam \ e P1 )))) selection = (chain 'C' and (resid 6 through 2741 or (resid 5102 and (name C1 or name C10 or \ name C11 or name C12 or name C1A or name C1B or name C1C or name C2 or name C24 \ or name C25 or name C26 or name C27 or name C28 or name C29 or name C3 or name C \ 30 or name C31 or name C32 or name C33 or name C34 or name C4 or name C5 or name \ C6 or name C7 or name C8 or name C9 or name N1 or name O1 or name O2 or name O3 \ or name O4 or name O6 or name O7 or name O8 or name O9 or name P1 )) or (resid \ 5103 and (name C1 or name C10 or name C11 or name C12 or name C1A or name C1B or \ name C1C or name C2 or name C24 or name C25 or name C26 or name C27 or name C28 \ or name C29 or name C3 or name C30 or name C31 or name C32 or name C4 or name C \ 5 or name C6 or name C7 or name C8 or name C9 or name N1 or name O1 or name O2 o \ r name O3 or name O4 or name O6 or name O7 or name O8 or name O9 or name P1 )) o \ r (resid 5104 and (name C1 or name C10 or name C11 or name C12 or name C13 or na \ me C1A or name C1B or name C1C or name C2 or name C24 or name C25 or name C26 or \ name C27 or name C28 or name C29 or name C3 or name C30 or name C31 or name C32 \ or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 or name N1 or \ name O1 or name O2 or name O3 or name O4 or name O6 or name O7 or name O8 or na \ me O9 or name P1 )) or (resid 5105 and (name C1 or name C10 or name C11 or name \ C12 or name C1A or name C1B or name C1C or name C2 or name C24 or name C25 or na \ me C26 or name C27 or name C28 or name C29 or name C3 or name C30 or name C31 or \ name C32 or name C33 or name C34 or name C4 or name C5 or name C6 or name C7 or \ name C8 or name C9 or name N1 or name O1 or name O2 or name O3 or name O4 or na \ me O6 or name O7 or name O8 or name O9 or name P1 )) or (resid 5106 and (name C1 \ or name C10 or name C11 or name C12 or name C1A or name C1B or name C1C or name \ C2 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 or n \ ame C3 or name C30 or name C31 or name C32 or name C4 or name C5 or name C6 or n \ ame C7 or name C8 or name C9 or name N1 or name O1 or name O2 or name O3 or name \ O4 or name O6 or name O7 or name O8 or name O9 or name P1 )) or (resid 5107 and \ (name C1 or name C10 or name C11 or name C12 or name C13 or name C14 or name C1 \ 5 or name C1A or name C1B or name C1C or name C2 or name C24 or name C25 or name \ C26 or name C27 or name C28 or name C29 or name C3 or name C30 or name C31 or n \ ame C32 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 or nam \ e N1 or name O1 or name O2 or name O3 or name O4 or name O6 or name O7 or name O \ 8 or name O9 or name P1 )))) selection = (chain 'D' and (resid 6 through 2741 or (resid 5102 and (name C1 or name C10 or \ name C11 or name C12 or name C1A or name C1B or name C1C or name C2 or name C24 \ or name C25 or name C26 or name C27 or name C28 or name C29 or name C3 or name C \ 30 or name C31 or name C32 or name C33 or name C34 or name C4 or name C5 or name \ C6 or name C7 or name C8 or name C9 or name N1 or name O1 or name O2 or name O3 \ or name O4 or name O6 or name O7 or name O8 or name O9 or name P1 )) or (resid \ 5103 and (name C1 or name C10 or name C11 or name C12 or name C1A or name C1B or \ name C1C or name C2 or name C24 or name C25 or name C26 or name C27 or name C28 \ or name C29 or name C3 or name C30 or name C31 or name C32 or name C4 or name C \ 5 or name C6 or name C7 or name C8 or name C9 or name N1 or name O1 or name O2 o \ r name O3 or name O4 or name O6 or name O7 or name O8 or name O9 or name P1 )) o \ r (resid 5104 and (name C1 or name C10 or name C11 or name C12 or name C13 or na \ me C1A or name C1B or name C1C or name C2 or name C24 or name C25 or name C26 or \ name C27 or name C28 or name C29 or name C3 or name C30 or name C31 or name C32 \ or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 or name N1 or \ name O1 or name O2 or name O3 or name O4 or name O6 or name O7 or name O8 or na \ me O9 or name P1 )) or (resid 5105 and (name C1 or name C10 or name C11 or name \ C12 or name C1A or name C1B or name C1C or name C2 or name C24 or name C25 or na \ me C26 or name C27 or name C28 or name C29 or name C3 or name C30 or name C31 or \ name C32 or name C33 or name C34 or name C4 or name C5 or name C6 or name C7 or \ name C8 or name C9 or name N1 or name O1 or name O2 or name O3 or name O4 or na \ me O6 or name O7 or name O8 or name O9 or name P1 )) or (resid 5106 and (name C1 \ or name C10 or name C11 or name C12 or name C1A or name C1B or name C1C or name \ C2 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 or n \ ame C3 or name C30 or name C31 or name C32 or name C4 or name C5 or name C6 or n \ ame C7 or name C8 or name C9 or name N1 or name O1 or name O2 or name O3 or name \ O4 or name O6 or name O7 or name O8 or name O9 or name P1 )) or (resid 5107 and \ (name C1 or name C10 or name C11 or name C12 or name C13 or name C14 or name C1 \ 5 or name C1A or name C1B or name C1C or name C2 or name C24 or name C25 or name \ C26 or name C27 or name C28 or name C29 or name C3 or name C30 or name C31 or n \ ame C32 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 or nam \ e N1 or name O1 or name O2 or name O3 or name O4 or name O6 or name O7 or name O \ 8 or name O9 or name P1 )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 0.010 Normalize map: mean=0, sd=1: 3.760 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: 0.060 Extract box with map and model: 19.990 Check model and map are aligned: 1.050 Set scattering table: 0.530 Process input model: 157.520 Find NCS groups from input model: 5.230 Set up NCS constraints: 0.430 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:11.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 199.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 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 : 0.007 0.199 73240 Z= 0.466 Angle : 1.173 25.164 98332 Z= 0.562 Chirality : 0.055 0.429 11280 Planarity : 0.006 0.237 12048 Dihedral : 16.619 174.976 28028 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.28 % Favored : 89.65 % Rotamer: Outliers : 0.05 % Allowed : 0.61 % Favored : 99.33 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.12 % 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: -2.92 (0.08), residues: 9088 helix: -1.21 (0.07), residues: 4692 sheet: -1.48 (0.22), residues: 516 loop : -2.91 (0.09), residues: 3880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A2256 HIS 0.029 0.001 HIS B2409 PHE 0.040 0.002 PHE A1311 TYR 0.026 0.002 TYR A 879 ARG 0.012 0.001 ARG A1290 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18176 Ramachandran restraints generated. 9088 Oldfield, 0 Emsley, 9088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18176 Ramachandran restraints generated. 9088 Oldfield, 0 Emsley, 9088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1247 residues out of total 8336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1243 time to evaluate : 6.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET A1365 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1373 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1438 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1447 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET D1365 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1373 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1438 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1447 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET B1365 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1373 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1438 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1447 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET C1365 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1373 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1438 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1447 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 724 LYS cc_start: 0.6778 (mppt) cc_final: 0.6562 (tptp) REVERT: A 732 TYR cc_start: 0.7494 (t80) cc_final: 0.7058 (t80) REVERT: A 1091 GLN cc_start: 0.6875 (tp-100) cc_final: 0.6402 (tp-100) REVERT: A 1243 ASN cc_start: 0.4899 (p0) cc_final: 0.4652 (t0) REVERT: A 1275 HIS cc_start: 0.6901 (m170) cc_final: 0.6380 (m90) REVERT: A 1277 PHE cc_start: 0.7247 (m-10) cc_final: 0.7000 (m-10) REVERT: A 1278 MET cc_start: 0.5423 (pmm) cc_final: 0.3595 (tpt) REVERT: A 1329 MET cc_start: 0.3889 (ppp) cc_final: 0.0985 (tpt) REVERT: A 1740 LEU cc_start: 0.8153 (mt) cc_final: 0.7941 (mm) REVERT: A 1841 HIS cc_start: 0.7472 (t70) cc_final: 0.6924 (t70) REVERT: A 2205 MET cc_start: 0.7929 (mtm) cc_final: 0.7686 (mtp) REVERT: A 2666 MET cc_start: 0.7593 (mmm) cc_final: 0.7369 (mmt) REVERT: D 732 TYR cc_start: 0.7595 (t80) cc_final: 0.7201 (t80) REVERT: D 756 SER cc_start: 0.7504 (t) cc_final: 0.7099 (p) REVERT: D 842 GLU cc_start: 0.8330 (tt0) cc_final: 0.8097 (pt0) REVERT: D 1091 GLN cc_start: 0.6899 (tp-100) cc_final: 0.6419 (tp-100) REVERT: D 1234 MET cc_start: 0.5349 (mmt) cc_final: 0.4891 (mmt) REVERT: D 1275 HIS cc_start: 0.6963 (m170) cc_final: 0.6406 (m90) REVERT: D 1277 PHE cc_start: 0.7038 (m-10) cc_final: 0.6735 (m-10) REVERT: D 1278 MET cc_start: 0.5239 (pmm) cc_final: 0.3413 (tpt) REVERT: D 1329 MET cc_start: 0.3594 (ppp) cc_final: 0.1095 (tpt) REVERT: D 1740 LEU cc_start: 0.8161 (mt) cc_final: 0.7940 (mm) REVERT: D 1841 HIS cc_start: 0.7534 (t70) cc_final: 0.6936 (t70) REVERT: D 1862 ASP cc_start: 0.7718 (p0) cc_final: 0.7137 (p0) REVERT: D 2205 MET cc_start: 0.8254 (mtm) cc_final: 0.8030 (mtp) REVERT: B 700 TRP cc_start: 0.6416 (p90) cc_final: 0.6138 (p90) REVERT: B 732 TYR cc_start: 0.7294 (t80) cc_final: 0.7081 (t80) REVERT: B 842 GLU cc_start: 0.8318 (tt0) cc_final: 0.8077 (pt0) REVERT: B 1234 MET cc_start: 0.5231 (mmt) cc_final: 0.4628 (mmt) REVERT: B 1275 HIS cc_start: 0.6785 (m170) cc_final: 0.6180 (m90) REVERT: B 1278 MET cc_start: 0.5482 (pmm) cc_final: 0.3188 (tpt) REVERT: B 1329 MET cc_start: 0.3613 (ppp) cc_final: 0.1091 (tpt) REVERT: B 1358 MET cc_start: -0.4709 (mtm) cc_final: -0.5190 (mtt) REVERT: B 1740 LEU cc_start: 0.8110 (mt) cc_final: 0.7900 (mm) REVERT: B 1841 HIS cc_start: 0.7438 (t70) cc_final: 0.6928 (t70) REVERT: B 2472 ASP cc_start: 0.6703 (p0) cc_final: 0.6461 (p0) REVERT: B 2666 MET cc_start: 0.7583 (mmm) cc_final: 0.7348 (mmt) REVERT: C 700 TRP cc_start: 0.6303 (p90) cc_final: 0.6021 (p90) REVERT: C 732 TYR cc_start: 0.7577 (t80) cc_final: 0.7187 (t80) REVERT: C 1234 MET cc_start: 0.5291 (mmt) cc_final: 0.4742 (mmt) REVERT: C 1275 HIS cc_start: 0.6980 (m170) cc_final: 0.6430 (m90) REVERT: C 1277 PHE cc_start: 0.7087 (m-10) cc_final: 0.6797 (m-10) REVERT: C 1278 MET cc_start: 0.5424 (pmm) cc_final: 0.3623 (tpt) REVERT: C 1329 MET cc_start: 0.4045 (ppp) cc_final: 0.1143 (tpt) REVERT: C 1740 LEU cc_start: 0.8105 (mt) cc_final: 0.7884 (mm) REVERT: C 1841 HIS cc_start: 0.7434 (t70) cc_final: 0.6946 (t70) REVERT: C 2666 MET cc_start: 0.7638 (mmm) cc_final: 0.7423 (mmt) outliers start: 4 outliers final: 3 residues processed: 1247 average time/residue: 1.6156 time to fit residues: 2644.5327 Evaluate side-chains 649 residues out of total 8336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 646 time to evaluate : 5.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 864 PHE Chi-restraints excluded: chain B residue 864 PHE Chi-restraints excluded: chain C residue 864 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 920 random chunks: chunk 776 optimal weight: 5.9990 chunk 697 optimal weight: 0.8980 chunk 386 optimal weight: 10.0000 chunk 238 optimal weight: 5.9990 chunk 470 optimal weight: 4.9990 chunk 372 optimal weight: 8.9990 chunk 721 optimal weight: 6.9990 chunk 279 optimal weight: 5.9990 chunk 438 optimal weight: 0.9980 chunk 536 optimal weight: 20.0000 chunk 835 optimal weight: 9.9990 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 ASN ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 797 GLN A 860 ASN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 GLN ** A1201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1238 HIS ** A1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1279 ASN ** A1327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2058 HIS A2192 HIS ** A2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 213 ASN D 289 HIS ** D 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 797 GLN D 860 ASN D1091 GLN D1101 GLN ** D1201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1238 HIS ** D1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1279 ASN D1293 GLN D1294 HIS D1327 GLN ** D1742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 ASN ** B 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 860 ASN B1091 GLN B1101 GLN ** B1201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1264 ASN B1279 ASN B1293 GLN B1327 GLN ** B1742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 213 ASN C 289 HIS ** C 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 860 ASN C 872 ASN C1101 GLN ** C1201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1264 ASN C1279 ASN ** C1742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2171 GLN ** C2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 73240 Z= 0.476 Angle : 0.871 11.597 98332 Z= 0.446 Chirality : 0.049 0.252 11280 Planarity : 0.006 0.076 12048 Dihedral : 14.541 153.820 11114 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.59 % Favored : 89.37 % Rotamer: Outliers : 3.01 % Allowed : 15.14 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.08), residues: 9088 helix: -0.69 (0.07), residues: 4668 sheet: -1.79 (0.22), residues: 516 loop : -3.02 (0.09), residues: 3904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP A 160 HIS 0.017 0.002 HIS D2541 PHE 0.024 0.003 PHE D 630 TYR 0.026 0.002 TYR B2129 ARG 0.012 0.001 ARG A2670 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18176 Ramachandran restraints generated. 9088 Oldfield, 0 Emsley, 9088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18176 Ramachandran restraints generated. 9088 Oldfield, 0 Emsley, 9088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 942 residues out of total 8336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 716 time to evaluate : 6.238 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET A1365 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1373 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1438 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1447 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET D1365 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1373 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1438 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1447 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET B1365 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1373 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1438 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1447 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET C1365 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1373 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1438 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1447 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 838 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7427 (pm20) REVERT: A 997 PHE cc_start: 0.6986 (t80) cc_final: 0.6707 (t80) REVERT: A 1097 PHE cc_start: 0.6754 (m-80) cc_final: 0.6150 (m-80) REVERT: A 1275 HIS cc_start: 0.6733 (m170) cc_final: 0.6244 (m90) REVERT: A 1277 PHE cc_start: 0.7668 (m-10) cc_final: 0.7393 (m-10) REVERT: A 1278 MET cc_start: 0.5998 (pmm) cc_final: 0.3837 (tpt) REVERT: A 1683 MET cc_start: 0.7014 (tpp) cc_final: 0.6780 (tpt) REVERT: A 2205 MET cc_start: 0.8166 (mtm) cc_final: 0.7823 (mtp) REVERT: A 2294 PHE cc_start: 0.8420 (OUTLIER) cc_final: 0.7758 (p90) REVERT: A 2386 MET cc_start: 0.7313 (ptt) cc_final: 0.7090 (ppp) REVERT: A 2525 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.7095 (tp30) REVERT: A 2666 MET cc_start: 0.7814 (mmm) cc_final: 0.7522 (mmt) REVERT: D 979 GLN cc_start: 0.7882 (tp40) cc_final: 0.7635 (tm-30) REVERT: D 1097 PHE cc_start: 0.6787 (m-80) cc_final: 0.6151 (m-80) REVERT: D 1275 HIS cc_start: 0.6844 (m170) cc_final: 0.6342 (m90) REVERT: D 1277 PHE cc_start: 0.7604 (m-10) cc_final: 0.7252 (m-10) REVERT: D 1278 MET cc_start: 0.5972 (pmm) cc_final: 0.3903 (tpt) REVERT: D 1295 PHE cc_start: 0.3542 (OUTLIER) cc_final: 0.2893 (m-10) REVERT: D 1605 GLN cc_start: 0.7651 (mm110) cc_final: 0.7391 (mt0) REVERT: D 2205 MET cc_start: 0.8244 (mtm) cc_final: 0.7986 (mtp) REVERT: D 2294 PHE cc_start: 0.8420 (OUTLIER) cc_final: 0.7759 (p90) REVERT: B 1241 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.7349 (mt) REVERT: B 1277 PHE cc_start: 0.7799 (m-10) cc_final: 0.7554 (m-10) REVERT: B 1614 ARG cc_start: 0.4857 (mmm160) cc_final: 0.4655 (mmm160) REVERT: B 1862 ASP cc_start: 0.8069 (p0) cc_final: 0.7850 (p0) REVERT: B 2294 PHE cc_start: 0.8427 (OUTLIER) cc_final: 0.7773 (p90) REVERT: B 2666 MET cc_start: 0.7855 (mmm) cc_final: 0.7581 (mmt) REVERT: B 2706 MET cc_start: 0.6790 (tmm) cc_final: 0.6576 (tpt) REVERT: C 838 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7393 (pm20) REVERT: C 872 ASN cc_start: 0.8659 (OUTLIER) cc_final: 0.8347 (m110) REVERT: C 1095 GLN cc_start: 0.7203 (pt0) cc_final: 0.6883 (pt0) REVERT: C 1275 HIS cc_start: 0.6892 (m170) cc_final: 0.6429 (m90) REVERT: C 1277 PHE cc_start: 0.7651 (m-10) cc_final: 0.7305 (m-10) REVERT: C 1278 MET cc_start: 0.5912 (pmm) cc_final: 0.3805 (tpt) REVERT: C 1605 GLN cc_start: 0.7511 (mm110) cc_final: 0.7282 (mt0) REVERT: C 1813 MET cc_start: 0.7543 (ttt) cc_final: 0.7340 (ttm) REVERT: C 2294 PHE cc_start: 0.8426 (OUTLIER) cc_final: 0.7768 (p90) REVERT: C 2386 MET cc_start: 0.7393 (OUTLIER) cc_final: 0.7192 (ppp) REVERT: C 2666 MET cc_start: 0.7937 (mmm) cc_final: 0.7650 (mmt) REVERT: C 2706 MET cc_start: 0.6667 (tmm) cc_final: 0.6419 (tpt) outliers start: 226 outliers final: 81 residues processed: 880 average time/residue: 1.3711 time to fit residues: 1629.0819 Evaluate side-chains 664 residues out of total 8336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 572 time to evaluate : 6.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 229 ASN Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 782 CYS Chi-restraints excluded: chain A residue 838 GLU Chi-restraints excluded: chain A residue 1616 ARG Chi-restraints excluded: chain A residue 1625 VAL Chi-restraints excluded: chain A residue 1678 THR Chi-restraints excluded: chain A residue 1983 ASP Chi-restraints excluded: chain A residue 2007 LEU Chi-restraints excluded: chain A residue 2014 THR Chi-restraints excluded: chain A residue 2191 LYS Chi-restraints excluded: chain A residue 2294 PHE Chi-restraints excluded: chain A residue 2408 VAL Chi-restraints excluded: chain A residue 2525 GLU Chi-restraints excluded: chain A residue 2619 ASP Chi-restraints excluded: chain A residue 2657 THR Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 224 MET Chi-restraints excluded: chain D residue 229 ASN Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 488 THR Chi-restraints excluded: chain D residue 493 ASP Chi-restraints excluded: chain D residue 650 GLU Chi-restraints excluded: chain D residue 782 CYS Chi-restraints excluded: chain D residue 1295 PHE Chi-restraints excluded: chain D residue 1625 VAL Chi-restraints excluded: chain D residue 1678 THR Chi-restraints excluded: chain D residue 1983 ASP Chi-restraints excluded: chain D residue 2007 LEU Chi-restraints excluded: chain D residue 2014 THR Chi-restraints excluded: chain D residue 2191 LYS Chi-restraints excluded: chain D residue 2196 ILE Chi-restraints excluded: chain D residue 2294 PHE Chi-restraints excluded: chain D residue 2408 VAL Chi-restraints excluded: chain D residue 2435 THR Chi-restraints excluded: chain D residue 2619 ASP Chi-restraints excluded: chain D residue 2657 THR Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 229 ASN Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 493 ASP Chi-restraints excluded: chain B residue 660 THR Chi-restraints excluded: chain B residue 793 ASP Chi-restraints excluded: chain B residue 1241 LEU Chi-restraints excluded: chain B residue 1299 ILE Chi-restraints excluded: chain B residue 1616 ARG Chi-restraints excluded: chain B residue 1625 VAL Chi-restraints excluded: chain B residue 1678 THR Chi-restraints excluded: chain B residue 1800 ASP Chi-restraints excluded: chain B residue 1983 ASP Chi-restraints excluded: chain B residue 2007 LEU Chi-restraints excluded: chain B residue 2014 THR Chi-restraints excluded: chain B residue 2294 PHE Chi-restraints excluded: chain B residue 2408 VAL Chi-restraints excluded: chain B residue 2435 THR Chi-restraints excluded: chain B residue 2619 ASP Chi-restraints excluded: chain B residue 2657 THR Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 229 ASN Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 660 THR Chi-restraints excluded: chain C residue 793 ASP Chi-restraints excluded: chain C residue 838 GLU Chi-restraints excluded: chain C residue 872 ASN Chi-restraints excluded: chain C residue 1299 ILE Chi-restraints excluded: chain C residue 1625 VAL Chi-restraints excluded: chain C residue 1684 THR Chi-restraints excluded: chain C residue 1983 ASP Chi-restraints excluded: chain C residue 2007 LEU Chi-restraints excluded: chain C residue 2014 THR Chi-restraints excluded: chain C residue 2294 PHE Chi-restraints excluded: chain C residue 2386 MET Chi-restraints excluded: chain C residue 2408 VAL Chi-restraints excluded: chain C residue 2435 THR Chi-restraints excluded: chain C residue 2619 ASP Chi-restraints excluded: chain C residue 2657 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 920 random chunks: chunk 464 optimal weight: 0.0030 chunk 259 optimal weight: 1.9990 chunk 695 optimal weight: 0.6980 chunk 568 optimal weight: 2.9990 chunk 230 optimal weight: 0.6980 chunk 836 optimal weight: 7.9990 chunk 904 optimal weight: 0.6980 chunk 745 optimal weight: 0.0980 chunk 829 optimal weight: 10.0000 chunk 285 optimal weight: 5.9990 chunk 671 optimal weight: 1.9990 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 71 GLN ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 872 ASN A1091 GLN ** A1201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1293 GLN ** A1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 GLN ** D 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 872 ASN D1091 GLN ** D1201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1297 HIS ** D1620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 GLN ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 507 GLN ** B 795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 872 ASN ** B1201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1294 HIS B1297 HIS ** B1742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2236 GLN ** B2361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 GLN ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 ASN ** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1091 GLN ** C1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1293 GLN C1294 HIS C1297 HIS ** C1742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 73240 Z= 0.167 Angle : 0.663 11.884 98332 Z= 0.335 Chirality : 0.042 0.259 11280 Planarity : 0.004 0.079 12048 Dihedral : 13.232 150.992 11108 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.01 % Allowed : 9.50 % Favored : 90.49 % Rotamer: Outliers : 2.73 % Allowed : 19.27 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.09), residues: 9088 helix: -0.10 (0.08), residues: 4664 sheet: -1.29 (0.25), residues: 440 loop : -2.87 (0.09), residues: 3984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D2256 HIS 0.009 0.001 HIS A1297 PHE 0.016 0.001 PHE D 980 TYR 0.043 0.001 TYR C2129 ARG 0.014 0.001 ARG A2670 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18176 Ramachandran restraints generated. 9088 Oldfield, 0 Emsley, 9088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18176 Ramachandran restraints generated. 9088 Oldfield, 0 Emsley, 9088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 881 residues out of total 8336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 676 time to evaluate : 6.094 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "MET A1365 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1373 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1438 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1447 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET D1365 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1373 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1438 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1447 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET B1365 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1373 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1438 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1447 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET C1365 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1373 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1438 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1447 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 251 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7924 (pt) REVERT: A 616 ASP cc_start: 0.8396 (m-30) cc_final: 0.8152 (m-30) REVERT: A 747 ARG cc_start: 0.6542 (tpm170) cc_final: 0.5155 (tpm170) REVERT: A 1095 GLN cc_start: 0.7148 (pt0) cc_final: 0.6847 (pt0) REVERT: A 1097 PHE cc_start: 0.6578 (m-80) cc_final: 0.6142 (m-80) REVERT: A 1275 HIS cc_start: 0.6685 (m170) cc_final: 0.6228 (m90) REVERT: A 1278 MET cc_start: 0.5925 (pmm) cc_final: 0.3931 (tpt) REVERT: A 1297 HIS cc_start: 0.6758 (p90) cc_final: 0.6531 (p-80) REVERT: A 1357 MET cc_start: -0.0556 (OUTLIER) cc_final: -0.1199 (tpt) REVERT: A 2205 MET cc_start: 0.8019 (mtm) cc_final: 0.7730 (mtp) REVERT: A 2294 PHE cc_start: 0.8085 (OUTLIER) cc_final: 0.7428 (p90) REVERT: A 2386 MET cc_start: 0.7280 (OUTLIER) cc_final: 0.7043 (ppp) REVERT: D 616 ASP cc_start: 0.8397 (m-30) cc_final: 0.8161 (m-30) REVERT: D 1091 GLN cc_start: 0.7007 (tp40) cc_final: 0.6645 (tp-100) REVERT: D 1095 GLN cc_start: 0.7513 (pt0) cc_final: 0.7302 (pt0) REVERT: D 1097 PHE cc_start: 0.6645 (m-80) cc_final: 0.6162 (m-80) REVERT: D 1273 MET cc_start: 0.6566 (mpm) cc_final: 0.6266 (mpm) REVERT: D 1275 HIS cc_start: 0.6728 (m170) cc_final: 0.6261 (m90) REVERT: D 1278 MET cc_start: 0.5932 (pmm) cc_final: 0.3943 (tpt) REVERT: B 251 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7936 (pt) REVERT: B 1682 MET cc_start: 0.7584 (ttp) cc_final: 0.7374 (ttt) REVERT: B 1862 ASP cc_start: 0.7870 (p0) cc_final: 0.7573 (p0) REVERT: B 2294 PHE cc_start: 0.8057 (OUTLIER) cc_final: 0.7345 (p90) REVERT: C 616 ASP cc_start: 0.8423 (m-30) cc_final: 0.8176 (m-30) REVERT: C 1091 GLN cc_start: 0.6719 (tp40) cc_final: 0.6222 (tp-100) REVERT: C 1095 GLN cc_start: 0.7305 (pt0) cc_final: 0.7012 (pt0) REVERT: C 1275 HIS cc_start: 0.6626 (m170) cc_final: 0.6170 (m90) REVERT: C 1278 MET cc_start: 0.5893 (pmm) cc_final: 0.3799 (tpt) REVERT: C 1982 ARG cc_start: 0.7497 (tpp-160) cc_final: 0.7209 (tpm170) REVERT: C 2287 MET cc_start: 0.6854 (mtm) cc_final: 0.6625 (mmm) REVERT: C 2386 MET cc_start: 0.7067 (OUTLIER) cc_final: 0.6864 (ppp) REVERT: C 2472 ASP cc_start: 0.6934 (p0) cc_final: 0.6674 (p0) outliers start: 205 outliers final: 52 residues processed: 813 average time/residue: 1.3045 time to fit residues: 1449.5032 Evaluate side-chains 649 residues out of total 8336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 590 time to evaluate : 6.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 793 ASP Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 1314 THR Chi-restraints excluded: chain A residue 1357 MET Chi-restraints excluded: chain A residue 1983 ASP Chi-restraints excluded: chain A residue 2007 LEU Chi-restraints excluded: chain A residue 2014 THR Chi-restraints excluded: chain A residue 2294 PHE Chi-restraints excluded: chain A residue 2386 MET Chi-restraints excluded: chain A residue 2715 GLN Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 488 THR Chi-restraints excluded: chain D residue 602 ASN Chi-restraints excluded: chain D residue 750 LEU Chi-restraints excluded: chain D residue 1240 PHE Chi-restraints excluded: chain D residue 1314 THR Chi-restraints excluded: chain D residue 1625 VAL Chi-restraints excluded: chain D residue 2014 THR Chi-restraints excluded: chain D residue 2434 VAL Chi-restraints excluded: chain D residue 2619 ASP Chi-restraints excluded: chain D residue 2715 GLN Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 602 ASN Chi-restraints excluded: chain B residue 793 ASP Chi-restraints excluded: chain B residue 1251 ASN Chi-restraints excluded: chain B residue 1314 THR Chi-restraints excluded: chain B residue 1625 VAL Chi-restraints excluded: chain B residue 2007 LEU Chi-restraints excluded: chain B residue 2014 THR Chi-restraints excluded: chain B residue 2294 PHE Chi-restraints excluded: chain B residue 2431 ILE Chi-restraints excluded: chain B residue 2434 VAL Chi-restraints excluded: chain B residue 2435 THR Chi-restraints excluded: chain B residue 2715 GLN Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 602 ASN Chi-restraints excluded: chain C residue 750 LEU Chi-restraints excluded: chain C residue 793 ASP Chi-restraints excluded: chain C residue 1314 THR Chi-restraints excluded: chain C residue 1625 VAL Chi-restraints excluded: chain C residue 2014 THR Chi-restraints excluded: chain C residue 2386 MET Chi-restraints excluded: chain C residue 2431 ILE Chi-restraints excluded: chain C residue 2434 VAL Chi-restraints excluded: chain C residue 2619 ASP Chi-restraints excluded: chain C residue 2715 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 920 random chunks: chunk 826 optimal weight: 9.9990 chunk 629 optimal weight: 4.9990 chunk 434 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 399 optimal weight: 7.9990 chunk 562 optimal weight: 0.8980 chunk 839 optimal weight: 4.9990 chunk 889 optimal weight: 2.9990 chunk 438 optimal weight: 0.7980 chunk 796 optimal weight: 10.0000 chunk 239 optimal weight: 8.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 GLN ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 872 ASN A1036 GLN A1091 GLN ** A1201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1297 HIS ** A1742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 270 GLN ** D 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 872 ASN ** D1201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1327 GLN ** D1742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 GLN ** B 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 507 GLN B 872 ASN ** B1201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1327 GLN ** B1742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 HIS C 270 GLN ** C 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 73240 Z= 0.250 Angle : 0.696 14.682 98332 Z= 0.351 Chirality : 0.043 0.273 11280 Planarity : 0.005 0.076 12048 Dihedral : 13.036 151.461 11108 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.98 % Favored : 89.99 % Rotamer: Outliers : 3.81 % Allowed : 20.48 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.09), residues: 9088 helix: -0.04 (0.08), residues: 4704 sheet: -1.67 (0.23), residues: 496 loop : -2.87 (0.09), residues: 3888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D2256 HIS 0.009 0.001 HIS A1297 PHE 0.039 0.002 PHE C 263 TYR 0.043 0.001 TYR A2129 ARG 0.006 0.001 ARG D 701 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18176 Ramachandran restraints generated. 9088 Oldfield, 0 Emsley, 9088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18176 Ramachandran restraints generated. 9088 Oldfield, 0 Emsley, 9088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 911 residues out of total 8336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 286 poor density : 625 time to evaluate : 6.190 Fit side-chains TARDY: cannot create tardy model for: "MET A1365 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1373 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1438 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1447 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET D1365 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1373 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1438 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1447 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET B1365 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1373 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1438 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1447 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET C1365 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1373 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1438 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1447 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 250 PHE cc_start: 0.8292 (OUTLIER) cc_final: 0.8091 (p90) REVERT: A 251 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7945 (pt) REVERT: A 616 ASP cc_start: 0.8430 (m-30) cc_final: 0.8208 (m-30) REVERT: A 745 LEU cc_start: 0.8228 (tp) cc_final: 0.7933 (tt) REVERT: A 747 ARG cc_start: 0.6502 (tpm170) cc_final: 0.5344 (tpm170) REVERT: A 753 ASN cc_start: 0.8489 (OUTLIER) cc_final: 0.7757 (p0) REVERT: A 849 CYS cc_start: 0.7076 (OUTLIER) cc_final: 0.6787 (t) REVERT: A 1091 GLN cc_start: 0.6741 (tp40) cc_final: 0.6082 (tp-100) REVERT: A 1095 GLN cc_start: 0.7144 (pt0) cc_final: 0.6477 (pt0) REVERT: A 1097 PHE cc_start: 0.6560 (m-80) cc_final: 0.6072 (m-80) REVERT: A 1275 HIS cc_start: 0.6567 (m170) cc_final: 0.6204 (m90) REVERT: A 1278 MET cc_start: 0.6109 (pmm) cc_final: 0.4122 (tpt) REVERT: A 1297 HIS cc_start: 0.6548 (p-80) cc_final: 0.6309 (p-80) REVERT: A 2116 MET cc_start: 0.6920 (pmm) cc_final: 0.6582 (ptt) REVERT: A 2205 MET cc_start: 0.8125 (mtm) cc_final: 0.7824 (mtp) REVERT: A 2294 PHE cc_start: 0.8234 (OUTLIER) cc_final: 0.7638 (p90) REVERT: A 2386 MET cc_start: 0.7432 (ptt) cc_final: 0.7220 (ppp) REVERT: A 2606 ILE cc_start: 0.8570 (OUTLIER) cc_final: 0.8126 (tt) REVERT: D 250 PHE cc_start: 0.8180 (OUTLIER) cc_final: 0.7929 (p90) REVERT: D 616 ASP cc_start: 0.8398 (m-30) cc_final: 0.8188 (m-30) REVERT: D 785 MET cc_start: 0.8252 (tpp) cc_final: 0.8005 (tpt) REVERT: D 849 CYS cc_start: 0.7028 (OUTLIER) cc_final: 0.6769 (t) REVERT: D 1091 GLN cc_start: 0.6906 (tp40) cc_final: 0.6609 (tp-100) REVERT: D 1095 GLN cc_start: 0.7266 (pt0) cc_final: 0.7065 (pt0) REVERT: D 1097 PHE cc_start: 0.6594 (m-80) cc_final: 0.6062 (m-80) REVERT: D 1273 MET cc_start: 0.6755 (mpm) cc_final: 0.6507 (mpm) REVERT: D 1275 HIS cc_start: 0.6658 (m170) cc_final: 0.6283 (m90) REVERT: D 1278 MET cc_start: 0.6157 (pmm) cc_final: 0.4255 (tpt) REVERT: D 1295 PHE cc_start: 0.3834 (OUTLIER) cc_final: 0.2872 (m-80) REVERT: D 2294 PHE cc_start: 0.8179 (OUTLIER) cc_final: 0.7478 (p90) REVERT: B 250 PHE cc_start: 0.8254 (OUTLIER) cc_final: 0.8005 (p90) REVERT: B 251 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8019 (pt) REVERT: B 616 ASP cc_start: 0.8463 (m-30) cc_final: 0.8237 (m-30) REVERT: B 745 LEU cc_start: 0.8019 (mt) cc_final: 0.7790 (tt) REVERT: B 976 GLU cc_start: 0.6836 (tp30) cc_final: 0.6551 (mp0) REVERT: B 1097 PHE cc_start: 0.6662 (m-80) cc_final: 0.6344 (m-80) REVERT: B 1682 MET cc_start: 0.7610 (ttp) cc_final: 0.7275 (ttm) REVERT: B 1862 ASP cc_start: 0.7940 (p0) cc_final: 0.7629 (p0) REVERT: B 2294 PHE cc_start: 0.8254 (OUTLIER) cc_final: 0.7549 (p90) REVERT: C 250 PHE cc_start: 0.8166 (OUTLIER) cc_final: 0.7938 (p90) REVERT: C 616 ASP cc_start: 0.8437 (m-30) cc_final: 0.8216 (m-30) REVERT: C 849 CYS cc_start: 0.7149 (OUTLIER) cc_final: 0.6837 (t) REVERT: C 976 GLU cc_start: 0.6770 (tp30) cc_final: 0.6541 (mp0) REVERT: C 1091 GLN cc_start: 0.6844 (tp40) cc_final: 0.6437 (tp-100) REVERT: C 1095 GLN cc_start: 0.7408 (pt0) cc_final: 0.7090 (pt0) REVERT: C 1097 PHE cc_start: 0.6794 (m-80) cc_final: 0.6239 (m-80) REVERT: C 1982 ARG cc_start: 0.7585 (tpp-160) cc_final: 0.7294 (tpm170) REVERT: C 2116 MET cc_start: 0.7024 (pmm) cc_final: 0.6566 (ptt) REVERT: C 2294 PHE cc_start: 0.8194 (OUTLIER) cc_final: 0.7442 (p90) REVERT: C 2386 MET cc_start: 0.7270 (OUTLIER) cc_final: 0.7051 (ppp) outliers start: 286 outliers final: 117 residues processed: 836 average time/residue: 1.2412 time to fit residues: 1443.8909 Evaluate side-chains 703 residues out of total 8336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 569 time to evaluate : 6.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 48 ASN Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 250 PHE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 753 ASN Chi-restraints excluded: chain A residue 793 ASP Chi-restraints excluded: chain A residue 849 CYS Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 1625 VAL Chi-restraints excluded: chain A residue 1983 ASP Chi-restraints excluded: chain A residue 2007 LEU Chi-restraints excluded: chain A residue 2014 THR Chi-restraints excluded: chain A residue 2196 ILE Chi-restraints excluded: chain A residue 2294 PHE Chi-restraints excluded: chain A residue 2363 CYS Chi-restraints excluded: chain A residue 2408 VAL Chi-restraints excluded: chain A residue 2541 HIS Chi-restraints excluded: chain A residue 2549 VAL Chi-restraints excluded: chain A residue 2576 MET Chi-restraints excluded: chain A residue 2605 GLU Chi-restraints excluded: chain A residue 2606 ILE Chi-restraints excluded: chain A residue 2619 ASP Chi-restraints excluded: chain A residue 2650 VAL Chi-restraints excluded: chain A residue 2722 GLN Chi-restraints excluded: chain A residue 2733 ILE Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 48 ASN Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain D residue 250 PHE Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 488 THR Chi-restraints excluded: chain D residue 602 ASN Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 849 CYS Chi-restraints excluded: chain D residue 1240 PHE Chi-restraints excluded: chain D residue 1295 PHE Chi-restraints excluded: chain D residue 1625 VAL Chi-restraints excluded: chain D residue 1983 ASP Chi-restraints excluded: chain D residue 2007 LEU Chi-restraints excluded: chain D residue 2014 THR Chi-restraints excluded: chain D residue 2196 ILE Chi-restraints excluded: chain D residue 2242 ASP Chi-restraints excluded: chain D residue 2294 PHE Chi-restraints excluded: chain D residue 2363 CYS Chi-restraints excluded: chain D residue 2370 MET Chi-restraints excluded: chain D residue 2408 VAL Chi-restraints excluded: chain D residue 2431 ILE Chi-restraints excluded: chain D residue 2434 VAL Chi-restraints excluded: chain D residue 2435 THR Chi-restraints excluded: chain D residue 2549 VAL Chi-restraints excluded: chain D residue 2599 GLU Chi-restraints excluded: chain D residue 2619 ASP Chi-restraints excluded: chain D residue 2650 VAL Chi-restraints excluded: chain D residue 2722 GLN Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 793 ASP Chi-restraints excluded: chain B residue 1625 VAL Chi-restraints excluded: chain B residue 1983 ASP Chi-restraints excluded: chain B residue 2007 LEU Chi-restraints excluded: chain B residue 2014 THR Chi-restraints excluded: chain B residue 2196 ILE Chi-restraints excluded: chain B residue 2201 LEU Chi-restraints excluded: chain B residue 2294 PHE Chi-restraints excluded: chain B residue 2363 CYS Chi-restraints excluded: chain B residue 2370 MET Chi-restraints excluded: chain B residue 2431 ILE Chi-restraints excluded: chain B residue 2434 VAL Chi-restraints excluded: chain B residue 2435 THR Chi-restraints excluded: chain B residue 2541 HIS Chi-restraints excluded: chain B residue 2549 VAL Chi-restraints excluded: chain B residue 2599 GLU Chi-restraints excluded: chain B residue 2619 ASP Chi-restraints excluded: chain B residue 2650 VAL Chi-restraints excluded: chain B residue 2722 GLN Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 48 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 147 MET Chi-restraints excluded: chain C residue 250 PHE Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 793 ASP Chi-restraints excluded: chain C residue 849 CYS Chi-restraints excluded: chain C residue 1625 VAL Chi-restraints excluded: chain C residue 1983 ASP Chi-restraints excluded: chain C residue 2007 LEU Chi-restraints excluded: chain C residue 2014 THR Chi-restraints excluded: chain C residue 2196 ILE Chi-restraints excluded: chain C residue 2294 PHE Chi-restraints excluded: chain C residue 2363 CYS Chi-restraints excluded: chain C residue 2370 MET Chi-restraints excluded: chain C residue 2386 MET Chi-restraints excluded: chain C residue 2408 VAL Chi-restraints excluded: chain C residue 2431 ILE Chi-restraints excluded: chain C residue 2434 VAL Chi-restraints excluded: chain C residue 2435 THR Chi-restraints excluded: chain C residue 2549 VAL Chi-restraints excluded: chain C residue 2576 MET Chi-restraints excluded: chain C residue 2599 GLU Chi-restraints excluded: chain C residue 2619 ASP Chi-restraints excluded: chain C residue 2650 VAL Chi-restraints excluded: chain C residue 2722 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 920 random chunks: chunk 740 optimal weight: 1.9990 chunk 504 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 662 optimal weight: 1.9990 chunk 366 optimal weight: 6.9990 chunk 758 optimal weight: 7.9990 chunk 614 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 454 optimal weight: 6.9990 chunk 798 optimal weight: 6.9990 chunk 224 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 GLN ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 795 GLN A 872 ASN ** A1201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1868 GLN ** A1981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 145 ASN ** D 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 270 GLN ** D 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 795 GLN D 872 ASN ** D1201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1251 ASN ** D1742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 GLN ** B 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 795 GLN B 872 ASN ** B1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 270 GLN ** C 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 795 GLN ** C1201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1986 ASN ** C2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 73240 Z= 0.274 Angle : 0.702 13.590 98332 Z= 0.356 Chirality : 0.044 0.300 11280 Planarity : 0.005 0.077 12048 Dihedral : 13.006 152.930 11108 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.49 % Favored : 89.48 % Rotamer: Outliers : 4.44 % Allowed : 21.67 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.09), residues: 9088 helix: -0.02 (0.08), residues: 4712 sheet: -1.86 (0.22), residues: 544 loop : -2.87 (0.09), residues: 3832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D2256 HIS 0.009 0.001 HIS D 789 PHE 0.047 0.002 PHE B 263 TYR 0.045 0.002 TYR D2129 ARG 0.012 0.001 ARG D 537 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18176 Ramachandran restraints generated. 9088 Oldfield, 0 Emsley, 9088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18176 Ramachandran restraints generated. 9088 Oldfield, 0 Emsley, 9088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 958 residues out of total 8336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 333 poor density : 625 time to evaluate : 6.040 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "MET A1365 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1373 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1438 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1447 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET D1365 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1373 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1438 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1447 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET B1365 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1373 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1438 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1447 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET C1365 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1373 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1438 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1447 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 121 ILE cc_start: 0.7574 (OUTLIER) cc_final: 0.7171 (tp) REVERT: A 250 PHE cc_start: 0.8330 (OUTLIER) cc_final: 0.8108 (p90) REVERT: A 251 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.7974 (pt) REVERT: A 375 LEU cc_start: 0.7153 (OUTLIER) cc_final: 0.6843 (pt) REVERT: A 616 ASP cc_start: 0.8368 (m-30) cc_final: 0.8027 (m-30) REVERT: A 618 PHE cc_start: 0.6090 (OUTLIER) cc_final: 0.5194 (t80) REVERT: A 745 LEU cc_start: 0.8138 (tp) cc_final: 0.7824 (tt) REVERT: A 753 ASN cc_start: 0.8563 (OUTLIER) cc_final: 0.7818 (p0) REVERT: A 838 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.7217 (pm20) REVERT: A 872 ASN cc_start: 0.8583 (OUTLIER) cc_final: 0.8264 (m110) REVERT: A 1091 GLN cc_start: 0.6557 (tp40) cc_final: 0.6186 (tp-100) REVERT: A 1095 GLN cc_start: 0.7084 (pt0) cc_final: 0.6758 (pt0) REVERT: A 1097 PHE cc_start: 0.6417 (m-80) cc_final: 0.5944 (m-80) REVERT: A 1273 MET cc_start: 0.7320 (mmp) cc_final: 0.7116 (mmp) REVERT: A 1275 HIS cc_start: 0.6449 (m170) cc_final: 0.6142 (m90) REVERT: A 1278 MET cc_start: 0.6186 (pmm) cc_final: 0.4207 (tpt) REVERT: A 1297 HIS cc_start: 0.6385 (p-80) cc_final: 0.6085 (p-80) REVERT: A 2042 GLU cc_start: 0.7693 (tp30) cc_final: 0.7492 (tp30) REVERT: A 2116 MET cc_start: 0.7023 (pmm) cc_final: 0.6585 (ptt) REVERT: A 2294 PHE cc_start: 0.8191 (OUTLIER) cc_final: 0.7523 (p90) REVERT: D 250 PHE cc_start: 0.8193 (OUTLIER) cc_final: 0.7975 (p90) REVERT: D 375 LEU cc_start: 0.7220 (OUTLIER) cc_final: 0.6930 (pt) REVERT: D 616 ASP cc_start: 0.8399 (m-30) cc_final: 0.8197 (m-30) REVERT: D 618 PHE cc_start: 0.5994 (OUTLIER) cc_final: 0.5279 (t80) REVERT: D 838 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.7153 (pm20) REVERT: D 1091 GLN cc_start: 0.6798 (tp40) cc_final: 0.6533 (tp-100) REVERT: D 1095 GLN cc_start: 0.7120 (pt0) cc_final: 0.6838 (pt0) REVERT: D 1097 PHE cc_start: 0.6449 (m-80) cc_final: 0.5966 (m-80) REVERT: D 1273 MET cc_start: 0.6922 (mpm) cc_final: 0.6668 (mpm) REVERT: D 1295 PHE cc_start: 0.3879 (OUTLIER) cc_final: 0.2718 (m-80) REVERT: D 1598 ARG cc_start: 0.3896 (OUTLIER) cc_final: 0.3356 (ptp90) REVERT: D 2294 PHE cc_start: 0.8130 (OUTLIER) cc_final: 0.7430 (p90) REVERT: B 250 PHE cc_start: 0.8230 (OUTLIER) cc_final: 0.8004 (p90) REVERT: B 251 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.7997 (pt) REVERT: B 616 ASP cc_start: 0.8407 (m-30) cc_final: 0.8068 (m-30) REVERT: B 745 LEU cc_start: 0.8010 (mt) cc_final: 0.7711 (tt) REVERT: B 849 CYS cc_start: 0.6828 (OUTLIER) cc_final: 0.6593 (t) REVERT: B 1097 PHE cc_start: 0.6821 (m-80) cc_final: 0.6462 (m-80) REVERT: B 1598 ARG cc_start: 0.3815 (OUTLIER) cc_final: 0.3288 (ptp90) REVERT: B 1682 MET cc_start: 0.7533 (ttp) cc_final: 0.7215 (ttm) REVERT: B 1862 ASP cc_start: 0.8076 (p0) cc_final: 0.7816 (p0) REVERT: B 2042 GLU cc_start: 0.7662 (tp30) cc_final: 0.7422 (tp30) REVERT: B 2294 PHE cc_start: 0.8237 (OUTLIER) cc_final: 0.7556 (p90) REVERT: C 578 PHE cc_start: 0.7683 (OUTLIER) cc_final: 0.7474 (t80) REVERT: C 616 ASP cc_start: 0.8374 (m-30) cc_final: 0.8041 (m-30) REVERT: C 618 PHE cc_start: 0.6070 (OUTLIER) cc_final: 0.5102 (t80) REVERT: C 838 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.7072 (pm20) REVERT: C 1095 GLN cc_start: 0.7305 (pt0) cc_final: 0.7052 (pt0) REVERT: C 1097 PHE cc_start: 0.6934 (m-80) cc_final: 0.6540 (m-80) REVERT: C 1598 ARG cc_start: 0.3927 (OUTLIER) cc_final: 0.3387 (ptp90) REVERT: C 1982 ARG cc_start: 0.7545 (tpp-160) cc_final: 0.7249 (tpm170) REVERT: C 2116 MET cc_start: 0.6989 (pmm) cc_final: 0.6518 (ptt) REVERT: C 2287 MET cc_start: 0.7015 (mtm) cc_final: 0.6729 (mmm) REVERT: C 2294 PHE cc_start: 0.8153 (OUTLIER) cc_final: 0.7421 (p90) REVERT: C 2386 MET cc_start: 0.7445 (OUTLIER) cc_final: 0.7232 (ppp) outliers start: 333 outliers final: 152 residues processed: 889 average time/residue: 1.2157 time to fit residues: 1513.3390 Evaluate side-chains 750 residues out of total 8336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 571 time to evaluate : 6.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 250 PHE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 618 PHE Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 724 LYS Chi-restraints excluded: chain A residue 753 ASN Chi-restraints excluded: chain A residue 793 ASP Chi-restraints excluded: chain A residue 838 GLU Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 872 ASN Chi-restraints excluded: chain A residue 1625 VAL Chi-restraints excluded: chain A residue 1983 ASP Chi-restraints excluded: chain A residue 2007 LEU Chi-restraints excluded: chain A residue 2014 THR Chi-restraints excluded: chain A residue 2121 LEU Chi-restraints excluded: chain A residue 2196 ILE Chi-restraints excluded: chain A residue 2242 ASP Chi-restraints excluded: chain A residue 2294 PHE Chi-restraints excluded: chain A residue 2363 CYS Chi-restraints excluded: chain A residue 2408 VAL Chi-restraints excluded: chain A residue 2541 HIS Chi-restraints excluded: chain A residue 2549 VAL Chi-restraints excluded: chain A residue 2576 MET Chi-restraints excluded: chain A residue 2599 GLU Chi-restraints excluded: chain A residue 2605 GLU Chi-restraints excluded: chain A residue 2619 ASP Chi-restraints excluded: chain A residue 2650 VAL Chi-restraints excluded: chain A residue 2656 TYR Chi-restraints excluded: chain A residue 2673 ASP Chi-restraints excluded: chain A residue 2722 GLN Chi-restraints excluded: chain A residue 2733 ILE Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain D residue 250 PHE Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 456 ILE Chi-restraints excluded: chain D residue 488 THR Chi-restraints excluded: chain D residue 618 PHE Chi-restraints excluded: chain D residue 622 VAL Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 753 ASN Chi-restraints excluded: chain D residue 782 CYS Chi-restraints excluded: chain D residue 838 GLU Chi-restraints excluded: chain D residue 849 CYS Chi-restraints excluded: chain D residue 968 MET Chi-restraints excluded: chain D residue 1070 HIS Chi-restraints excluded: chain D residue 1295 PHE Chi-restraints excluded: chain D residue 1598 ARG Chi-restraints excluded: chain D residue 1625 VAL Chi-restraints excluded: chain D residue 1649 SER Chi-restraints excluded: chain D residue 1684 THR Chi-restraints excluded: chain D residue 1800 ASP Chi-restraints excluded: chain D residue 1983 ASP Chi-restraints excluded: chain D residue 2007 LEU Chi-restraints excluded: chain D residue 2014 THR Chi-restraints excluded: chain D residue 2196 ILE Chi-restraints excluded: chain D residue 2294 PHE Chi-restraints excluded: chain D residue 2363 CYS Chi-restraints excluded: chain D residue 2370 MET Chi-restraints excluded: chain D residue 2408 VAL Chi-restraints excluded: chain D residue 2434 VAL Chi-restraints excluded: chain D residue 2435 THR Chi-restraints excluded: chain D residue 2541 HIS Chi-restraints excluded: chain D residue 2549 VAL Chi-restraints excluded: chain D residue 2576 MET Chi-restraints excluded: chain D residue 2599 GLU Chi-restraints excluded: chain D residue 2619 ASP Chi-restraints excluded: chain D residue 2650 VAL Chi-restraints excluded: chain D residue 2657 THR Chi-restraints excluded: chain D residue 2722 GLN Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 660 THR Chi-restraints excluded: chain B residue 793 ASP Chi-restraints excluded: chain B residue 849 CYS Chi-restraints excluded: chain B residue 1251 ASN Chi-restraints excluded: chain B residue 1598 ARG Chi-restraints excluded: chain B residue 1625 VAL Chi-restraints excluded: chain B residue 1800 ASP Chi-restraints excluded: chain B residue 1877 VAL Chi-restraints excluded: chain B residue 1983 ASP Chi-restraints excluded: chain B residue 2007 LEU Chi-restraints excluded: chain B residue 2014 THR Chi-restraints excluded: chain B residue 2196 ILE Chi-restraints excluded: chain B residue 2201 LEU Chi-restraints excluded: chain B residue 2294 PHE Chi-restraints excluded: chain B residue 2363 CYS Chi-restraints excluded: chain B residue 2370 MET Chi-restraints excluded: chain B residue 2419 ASP Chi-restraints excluded: chain B residue 2421 VAL Chi-restraints excluded: chain B residue 2431 ILE Chi-restraints excluded: chain B residue 2434 VAL Chi-restraints excluded: chain B residue 2541 HIS Chi-restraints excluded: chain B residue 2549 VAL Chi-restraints excluded: chain B residue 2599 GLU Chi-restraints excluded: chain B residue 2619 ASP Chi-restraints excluded: chain B residue 2650 VAL Chi-restraints excluded: chain B residue 2656 TYR Chi-restraints excluded: chain B residue 2657 THR Chi-restraints excluded: chain B residue 2673 ASP Chi-restraints excluded: chain B residue 2722 GLN Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 147 MET Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 578 PHE Chi-restraints excluded: chain C residue 618 PHE Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 660 THR Chi-restraints excluded: chain C residue 793 ASP Chi-restraints excluded: chain C residue 838 GLU Chi-restraints excluded: chain C residue 1070 HIS Chi-restraints excluded: chain C residue 1598 ARG Chi-restraints excluded: chain C residue 1625 VAL Chi-restraints excluded: chain C residue 1983 ASP Chi-restraints excluded: chain C residue 2007 LEU Chi-restraints excluded: chain C residue 2014 THR Chi-restraints excluded: chain C residue 2196 ILE Chi-restraints excluded: chain C residue 2294 PHE Chi-restraints excluded: chain C residue 2363 CYS Chi-restraints excluded: chain C residue 2386 MET Chi-restraints excluded: chain C residue 2408 VAL Chi-restraints excluded: chain C residue 2415 LEU Chi-restraints excluded: chain C residue 2431 ILE Chi-restraints excluded: chain C residue 2434 VAL Chi-restraints excluded: chain C residue 2435 THR Chi-restraints excluded: chain C residue 2541 HIS Chi-restraints excluded: chain C residue 2549 VAL Chi-restraints excluded: chain C residue 2576 MET Chi-restraints excluded: chain C residue 2599 GLU Chi-restraints excluded: chain C residue 2619 ASP Chi-restraints excluded: chain C residue 2650 VAL Chi-restraints excluded: chain C residue 2656 TYR Chi-restraints excluded: chain C residue 2673 ASP Chi-restraints excluded: chain C residue 2722 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 920 random chunks: chunk 299 optimal weight: 9.9990 chunk 800 optimal weight: 0.0270 chunk 175 optimal weight: 2.9990 chunk 522 optimal weight: 0.0770 chunk 219 optimal weight: 1.9990 chunk 890 optimal weight: 0.9980 chunk 738 optimal weight: 0.6980 chunk 412 optimal weight: 0.6980 chunk 74 optimal weight: 7.9990 chunk 294 optimal weight: 9.9990 chunk 467 optimal weight: 7.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 GLN ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 795 GLN A 860 ASN ** A1201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 HIS ** D 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 872 ASN ** D1201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 ASN B 270 GLN ** B 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 795 GLN B 872 ASN ** B1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 270 GLN ** C 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 795 GLN C 860 ASN C1091 GLN ** C1201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1986 ASN ** C2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 73240 Z= 0.166 Angle : 0.663 13.261 98332 Z= 0.332 Chirality : 0.041 0.244 11280 Planarity : 0.004 0.078 12048 Dihedral : 12.512 154.163 11108 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.77 % Favored : 90.18 % Rotamer: Outliers : 3.32 % Allowed : 23.61 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.09), residues: 9088 helix: 0.14 (0.08), residues: 4724 sheet: -1.35 (0.25), residues: 440 loop : -2.77 (0.09), residues: 3924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A2256 HIS 0.007 0.001 HIS D 789 PHE 0.038 0.001 PHE B 263 TYR 0.044 0.001 TYR A2129 ARG 0.015 0.000 ARG A 792 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18176 Ramachandran restraints generated. 9088 Oldfield, 0 Emsley, 9088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18176 Ramachandran restraints generated. 9088 Oldfield, 0 Emsley, 9088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 919 residues out of total 8336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 249 poor density : 670 time to evaluate : 6.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET A1365 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1373 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1438 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1447 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET D1365 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1373 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1438 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1447 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET B1365 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1373 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1438 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1447 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET C1365 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1373 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1438 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1447 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 135 ASN cc_start: 0.8498 (OUTLIER) cc_final: 0.8192 (p0) REVERT: A 251 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7957 (pt) REVERT: A 616 ASP cc_start: 0.8335 (m-30) cc_final: 0.7970 (m-30) REVERT: A 745 LEU cc_start: 0.8105 (tp) cc_final: 0.7819 (tt) REVERT: A 789 HIS cc_start: 0.6121 (p90) cc_final: 0.5902 (p90) REVERT: A 997 PHE cc_start: 0.7026 (t80) cc_final: 0.6746 (t80) REVERT: A 1091 GLN cc_start: 0.6517 (tp40) cc_final: 0.6166 (tp-100) REVERT: A 1095 GLN cc_start: 0.7255 (pt0) cc_final: 0.6939 (pt0) REVERT: A 1097 PHE cc_start: 0.6302 (m-80) cc_final: 0.5821 (m-80) REVERT: A 1275 HIS cc_start: 0.6366 (m170) cc_final: 0.6074 (m90) REVERT: A 1278 MET cc_start: 0.6115 (pmm) cc_final: 0.4053 (tpt) REVERT: A 1295 PHE cc_start: 0.3831 (OUTLIER) cc_final: 0.2713 (m-80) REVERT: A 1297 HIS cc_start: 0.6414 (p-80) cc_final: 0.6075 (p-80) REVERT: A 1982 ARG cc_start: 0.7517 (tpp-160) cc_final: 0.7206 (tpm170) REVERT: A 2116 MET cc_start: 0.6895 (pmm) cc_final: 0.6477 (ptt) REVERT: A 2205 MET cc_start: 0.8289 (mtp) cc_final: 0.7860 (mtp) REVERT: A 2294 PHE cc_start: 0.8015 (OUTLIER) cc_final: 0.7308 (p90) REVERT: D 135 ASN cc_start: 0.8542 (OUTLIER) cc_final: 0.8256 (p0) REVERT: D 250 PHE cc_start: 0.8039 (OUTLIER) cc_final: 0.7828 (p90) REVERT: D 578 PHE cc_start: 0.7629 (OUTLIER) cc_final: 0.7243 (t80) REVERT: D 616 ASP cc_start: 0.8242 (m-30) cc_final: 0.7915 (m-30) REVERT: D 1091 GLN cc_start: 0.6768 (tp40) cc_final: 0.6517 (tp-100) REVERT: D 1095 GLN cc_start: 0.7132 (pt0) cc_final: 0.6925 (pt0) REVERT: D 1097 PHE cc_start: 0.6337 (m-80) cc_final: 0.5823 (m-80) REVERT: D 1273 MET cc_start: 0.7017 (mpm) cc_final: 0.6736 (mpm) REVERT: D 1295 PHE cc_start: 0.4066 (OUTLIER) cc_final: 0.2871 (m-80) REVERT: D 1297 HIS cc_start: 0.6126 (p-80) cc_final: 0.5847 (p-80) REVERT: D 1598 ARG cc_start: 0.3946 (OUTLIER) cc_final: 0.3366 (ptp90) REVERT: D 1982 ARG cc_start: 0.7507 (tpp-160) cc_final: 0.7201 (tpm170) REVERT: D 2294 PHE cc_start: 0.7964 (OUTLIER) cc_final: 0.7204 (p90) REVERT: B 135 ASN cc_start: 0.8482 (OUTLIER) cc_final: 0.8227 (p0) REVERT: B 251 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7948 (pt) REVERT: B 261 HIS cc_start: 0.7869 (OUTLIER) cc_final: 0.7613 (p-80) REVERT: B 616 ASP cc_start: 0.8362 (m-30) cc_final: 0.7980 (m-30) REVERT: B 745 LEU cc_start: 0.7959 (mt) cc_final: 0.7741 (tt) REVERT: B 969 ASP cc_start: 0.8168 (t0) cc_final: 0.7955 (p0) REVERT: B 1097 PHE cc_start: 0.6750 (m-80) cc_final: 0.6420 (m-80) REVERT: B 1598 ARG cc_start: 0.3672 (OUTLIER) cc_final: 0.3472 (pmt170) REVERT: B 1682 MET cc_start: 0.7549 (ttp) cc_final: 0.7254 (ttm) REVERT: B 1862 ASP cc_start: 0.7948 (p0) cc_final: 0.7632 (p0) REVERT: B 1982 ARG cc_start: 0.7436 (tpp-160) cc_final: 0.7156 (tpm170) REVERT: B 2294 PHE cc_start: 0.8028 (OUTLIER) cc_final: 0.7276 (p90) REVERT: C 578 PHE cc_start: 0.7625 (OUTLIER) cc_final: 0.7401 (t80) REVERT: C 616 ASP cc_start: 0.8350 (m-30) cc_final: 0.8019 (m-30) REVERT: C 1091 GLN cc_start: 0.6746 (tp40) cc_final: 0.6000 (tp-100) REVERT: C 1095 GLN cc_start: 0.7337 (pt0) cc_final: 0.6882 (pt0) REVERT: C 1097 PHE cc_start: 0.6743 (m-80) cc_final: 0.6408 (m-80) REVERT: C 1982 ARG cc_start: 0.7423 (tpp-160) cc_final: 0.7184 (tpm170) REVERT: C 2116 MET cc_start: 0.6895 (pmm) cc_final: 0.6468 (ptt) REVERT: C 2287 MET cc_start: 0.6903 (mtm) cc_final: 0.6624 (mmm) REVERT: C 2294 PHE cc_start: 0.7961 (OUTLIER) cc_final: 0.7136 (p90) outliers start: 249 outliers final: 104 residues processed: 855 average time/residue: 1.2336 time to fit residues: 1465.5879 Evaluate side-chains 708 residues out of total 8336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 587 time to evaluate : 6.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 724 LYS Chi-restraints excluded: chain A residue 849 CYS Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 999 ARG Chi-restraints excluded: chain A residue 1070 HIS Chi-restraints excluded: chain A residue 1295 PHE Chi-restraints excluded: chain A residue 1625 VAL Chi-restraints excluded: chain A residue 1983 ASP Chi-restraints excluded: chain A residue 2014 THR Chi-restraints excluded: chain A residue 2242 ASP Chi-restraints excluded: chain A residue 2294 PHE Chi-restraints excluded: chain A residue 2422 TYR Chi-restraints excluded: chain A residue 2527 THR Chi-restraints excluded: chain A residue 2599 GLU Chi-restraints excluded: chain A residue 2605 GLU Chi-restraints excluded: chain A residue 2619 ASP Chi-restraints excluded: chain A residue 2650 VAL Chi-restraints excluded: chain A residue 2722 GLN Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 135 ASN Chi-restraints excluded: chain D residue 250 PHE Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 488 THR Chi-restraints excluded: chain D residue 578 PHE Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 724 LYS Chi-restraints excluded: chain D residue 1070 HIS Chi-restraints excluded: chain D residue 1251 ASN Chi-restraints excluded: chain D residue 1295 PHE Chi-restraints excluded: chain D residue 1598 ARG Chi-restraints excluded: chain D residue 1625 VAL Chi-restraints excluded: chain D residue 2007 LEU Chi-restraints excluded: chain D residue 2014 THR Chi-restraints excluded: chain D residue 2121 LEU Chi-restraints excluded: chain D residue 2201 LEU Chi-restraints excluded: chain D residue 2242 ASP Chi-restraints excluded: chain D residue 2294 PHE Chi-restraints excluded: chain D residue 2421 VAL Chi-restraints excluded: chain D residue 2434 VAL Chi-restraints excluded: chain D residue 2435 THR Chi-restraints excluded: chain D residue 2541 HIS Chi-restraints excluded: chain D residue 2599 GLU Chi-restraints excluded: chain D residue 2619 ASP Chi-restraints excluded: chain D residue 2650 VAL Chi-restraints excluded: chain D residue 2722 GLN Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 135 ASN Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 261 HIS Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 650 GLU Chi-restraints excluded: chain B residue 793 ASP Chi-restraints excluded: chain B residue 849 CYS Chi-restraints excluded: chain B residue 1070 HIS Chi-restraints excluded: chain B residue 1251 ASN Chi-restraints excluded: chain B residue 1598 ARG Chi-restraints excluded: chain B residue 1625 VAL Chi-restraints excluded: chain B residue 1877 VAL Chi-restraints excluded: chain B residue 2007 LEU Chi-restraints excluded: chain B residue 2014 THR Chi-restraints excluded: chain B residue 2201 LEU Chi-restraints excluded: chain B residue 2294 PHE Chi-restraints excluded: chain B residue 2408 VAL Chi-restraints excluded: chain B residue 2421 VAL Chi-restraints excluded: chain B residue 2431 ILE Chi-restraints excluded: chain B residue 2434 VAL Chi-restraints excluded: chain B residue 2435 THR Chi-restraints excluded: chain B residue 2599 GLU Chi-restraints excluded: chain B residue 2619 ASP Chi-restraints excluded: chain B residue 2650 VAL Chi-restraints excluded: chain B residue 2722 GLN Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 578 PHE Chi-restraints excluded: chain C residue 660 THR Chi-restraints excluded: chain C residue 724 LYS Chi-restraints excluded: chain C residue 793 ASP Chi-restraints excluded: chain C residue 849 CYS Chi-restraints excluded: chain C residue 1070 HIS Chi-restraints excluded: chain C residue 1625 VAL Chi-restraints excluded: chain C residue 2014 THR Chi-restraints excluded: chain C residue 2201 LEU Chi-restraints excluded: chain C residue 2242 ASP Chi-restraints excluded: chain C residue 2294 PHE Chi-restraints excluded: chain C residue 2408 VAL Chi-restraints excluded: chain C residue 2421 VAL Chi-restraints excluded: chain C residue 2431 ILE Chi-restraints excluded: chain C residue 2434 VAL Chi-restraints excluded: chain C residue 2541 HIS Chi-restraints excluded: chain C residue 2599 GLU Chi-restraints excluded: chain C residue 2619 ASP Chi-restraints excluded: chain C residue 2650 VAL Chi-restraints excluded: chain C residue 2722 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 920 random chunks: chunk 858 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 507 optimal weight: 5.9990 chunk 650 optimal weight: 4.9990 chunk 503 optimal weight: 6.9990 chunk 749 optimal weight: 6.9990 chunk 497 optimal weight: 0.9980 chunk 886 optimal weight: 0.9980 chunk 554 optimal weight: 0.9980 chunk 540 optimal weight: 7.9990 chunk 409 optimal weight: 3.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 795 GLN ** A1201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 244 HIS D 270 GLN ** D 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 872 ASN ** D1201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 795 GLN B 872 ASN B1091 GLN ** B1201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1986 ASN ** B2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 795 GLN ** C1201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1251 ASN ** C1620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 73240 Z= 0.281 Angle : 0.720 12.631 98332 Z= 0.365 Chirality : 0.044 0.241 11280 Planarity : 0.005 0.077 12048 Dihedral : 12.722 158.435 11108 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.57 % Favored : 89.38 % Rotamer: Outliers : 4.16 % Allowed : 24.08 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: -1.81 (0.09), residues: 9088 helix: 0.06 (0.08), residues: 4732 sheet: -1.60 (0.23), residues: 492 loop : -2.83 (0.09), residues: 3864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D2639 HIS 0.009 0.001 HIS D 789 PHE 0.044 0.002 PHE D 263 TYR 0.038 0.002 TYR D2129 ARG 0.012 0.001 ARG A 792 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18176 Ramachandran restraints generated. 9088 Oldfield, 0 Emsley, 9088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18176 Ramachandran restraints generated. 9088 Oldfield, 0 Emsley, 9088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 919 residues out of total 8336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 312 poor density : 607 time to evaluate : 7.824 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET A1365 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1373 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1438 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1447 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET D1365 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1373 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1438 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1447 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET B1365 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1373 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1438 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1447 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET C1365 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1373 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1438 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1447 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 121 ILE cc_start: 0.7699 (OUTLIER) cc_final: 0.7321 (tp) REVERT: A 135 ASN cc_start: 0.8475 (OUTLIER) cc_final: 0.8208 (p0) REVERT: A 251 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.7999 (pt) REVERT: A 578 PHE cc_start: 0.7831 (OUTLIER) cc_final: 0.7367 (t80) REVERT: A 616 ASP cc_start: 0.8384 (m-30) cc_final: 0.8065 (m-30) REVERT: A 618 PHE cc_start: 0.6468 (OUTLIER) cc_final: 0.5537 (t80) REVERT: A 745 LEU cc_start: 0.8163 (tp) cc_final: 0.7856 (tt) REVERT: A 753 ASN cc_start: 0.8634 (OUTLIER) cc_final: 0.7867 (p0) REVERT: A 806 LEU cc_start: 0.6187 (OUTLIER) cc_final: 0.5934 (tm) REVERT: A 999 ARG cc_start: 0.6405 (OUTLIER) cc_final: 0.6163 (mmm-85) REVERT: A 1091 GLN cc_start: 0.6530 (tp40) cc_final: 0.5957 (tp-100) REVERT: A 1095 GLN cc_start: 0.7098 (pt0) cc_final: 0.6425 (pt0) REVERT: A 1097 PHE cc_start: 0.6448 (m-80) cc_final: 0.5998 (m-80) REVERT: A 1275 HIS cc_start: 0.6413 (m170) cc_final: 0.6155 (m90) REVERT: A 1278 MET cc_start: 0.6283 (pmm) cc_final: 0.4414 (tpt) REVERT: A 1295 PHE cc_start: 0.3889 (OUTLIER) cc_final: 0.2594 (m-80) REVERT: A 1297 HIS cc_start: 0.6314 (p-80) cc_final: 0.6013 (p-80) REVERT: A 2116 MET cc_start: 0.6905 (pmm) cc_final: 0.6547 (ptt) REVERT: A 2205 MET cc_start: 0.8365 (mtp) cc_final: 0.7830 (mtp) REVERT: A 2294 PHE cc_start: 0.8225 (OUTLIER) cc_final: 0.7547 (p90) REVERT: D 135 ASN cc_start: 0.8500 (OUTLIER) cc_final: 0.8256 (p0) REVERT: D 578 PHE cc_start: 0.7700 (OUTLIER) cc_final: 0.7413 (t80) REVERT: D 616 ASP cc_start: 0.8225 (m-30) cc_final: 0.7915 (m-30) REVERT: D 806 LEU cc_start: 0.6084 (OUTLIER) cc_final: 0.5849 (tm) REVERT: D 1097 PHE cc_start: 0.6472 (m-80) cc_final: 0.6005 (m-80) REVERT: D 1273 MET cc_start: 0.7042 (mpm) cc_final: 0.6797 (mpm) REVERT: D 1295 PHE cc_start: 0.4027 (OUTLIER) cc_final: 0.3449 (m-10) REVERT: D 1297 HIS cc_start: 0.6155 (p-80) cc_final: 0.5897 (p-80) REVERT: D 1598 ARG cc_start: 0.3818 (OUTLIER) cc_final: 0.3315 (ptp90) REVERT: D 1982 ARG cc_start: 0.7557 (tpp-160) cc_final: 0.7255 (tpm170) REVERT: D 2294 PHE cc_start: 0.8152 (OUTLIER) cc_final: 0.7518 (p90) REVERT: B 135 ASN cc_start: 0.8529 (OUTLIER) cc_final: 0.8319 (p0) REVERT: B 251 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7975 (pt) REVERT: B 578 PHE cc_start: 0.7799 (OUTLIER) cc_final: 0.7371 (t80) REVERT: B 616 ASP cc_start: 0.8350 (m-30) cc_final: 0.8008 (m-30) REVERT: B 618 PHE cc_start: 0.6326 (OUTLIER) cc_final: 0.5647 (t80) REVERT: B 806 LEU cc_start: 0.6018 (OUTLIER) cc_final: 0.5785 (tm) REVERT: B 1091 GLN cc_start: 0.6806 (tp40) cc_final: 0.6476 (tp-100) REVERT: B 1097 PHE cc_start: 0.6815 (m-80) cc_final: 0.6401 (m-80) REVERT: B 1240 PHE cc_start: 0.5563 (t80) cc_final: 0.5246 (t80) REVERT: B 1598 ARG cc_start: 0.3635 (OUTLIER) cc_final: 0.3199 (ptp90) REVERT: B 1682 MET cc_start: 0.7526 (ttp) cc_final: 0.7192 (ttm) REVERT: B 1862 ASP cc_start: 0.8012 (p0) cc_final: 0.7767 (p0) REVERT: B 2294 PHE cc_start: 0.8231 (OUTLIER) cc_final: 0.7544 (p90) REVERT: C 578 PHE cc_start: 0.7674 (OUTLIER) cc_final: 0.7464 (t80) REVERT: C 616 ASP cc_start: 0.8330 (m-30) cc_final: 0.8015 (m-30) REVERT: C 618 PHE cc_start: 0.6237 (OUTLIER) cc_final: 0.5388 (t80) REVERT: C 806 LEU cc_start: 0.6028 (OUTLIER) cc_final: 0.5801 (tm) REVERT: C 1097 PHE cc_start: 0.6841 (m-80) cc_final: 0.6407 (m-80) REVERT: C 1982 ARG cc_start: 0.7572 (tpp-160) cc_final: 0.7312 (tpm170) REVERT: C 2116 MET cc_start: 0.6945 (pmm) cc_final: 0.6556 (ptt) REVERT: C 2287 MET cc_start: 0.7028 (mtm) cc_final: 0.6743 (mmm) REVERT: C 2294 PHE cc_start: 0.8195 (OUTLIER) cc_final: 0.7463 (p90) outliers start: 312 outliers final: 156 residues processed: 855 average time/residue: 1.2181 time to fit residues: 1454.9132 Evaluate side-chains 753 residues out of total 8336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 570 time to evaluate : 6.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 510 MET Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain A residue 618 PHE Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 724 LYS Chi-restraints excluded: chain A residue 753 ASN Chi-restraints excluded: chain A residue 793 ASP Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 849 CYS Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 999 ARG Chi-restraints excluded: chain A residue 1070 HIS Chi-restraints excluded: chain A residue 1295 PHE Chi-restraints excluded: chain A residue 1625 VAL Chi-restraints excluded: chain A residue 1649 SER Chi-restraints excluded: chain A residue 1800 ASP Chi-restraints excluded: chain A residue 1983 ASP Chi-restraints excluded: chain A residue 2007 LEU Chi-restraints excluded: chain A residue 2014 THR Chi-restraints excluded: chain A residue 2294 PHE Chi-restraints excluded: chain A residue 2363 CYS Chi-restraints excluded: chain A residue 2408 VAL Chi-restraints excluded: chain A residue 2419 ASP Chi-restraints excluded: chain A residue 2527 THR Chi-restraints excluded: chain A residue 2541 HIS Chi-restraints excluded: chain A residue 2549 VAL Chi-restraints excluded: chain A residue 2576 MET Chi-restraints excluded: chain A residue 2599 GLU Chi-restraints excluded: chain A residue 2605 GLU Chi-restraints excluded: chain A residue 2619 ASP Chi-restraints excluded: chain A residue 2650 VAL Chi-restraints excluded: chain A residue 2657 THR Chi-restraints excluded: chain A residue 2673 ASP Chi-restraints excluded: chain A residue 2722 GLN Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 135 ASN Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 456 ILE Chi-restraints excluded: chain D residue 488 THR Chi-restraints excluded: chain D residue 578 PHE Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 724 LYS Chi-restraints excluded: chain D residue 753 ASN Chi-restraints excluded: chain D residue 784 LEU Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 849 CYS Chi-restraints excluded: chain D residue 1070 HIS Chi-restraints excluded: chain D residue 1251 ASN Chi-restraints excluded: chain D residue 1295 PHE Chi-restraints excluded: chain D residue 1598 ARG Chi-restraints excluded: chain D residue 1625 VAL Chi-restraints excluded: chain D residue 1649 SER Chi-restraints excluded: chain D residue 1800 ASP Chi-restraints excluded: chain D residue 2007 LEU Chi-restraints excluded: chain D residue 2014 THR Chi-restraints excluded: chain D residue 2121 LEU Chi-restraints excluded: chain D residue 2201 LEU Chi-restraints excluded: chain D residue 2294 PHE Chi-restraints excluded: chain D residue 2363 CYS Chi-restraints excluded: chain D residue 2408 VAL Chi-restraints excluded: chain D residue 2415 LEU Chi-restraints excluded: chain D residue 2541 HIS Chi-restraints excluded: chain D residue 2549 VAL Chi-restraints excluded: chain D residue 2576 MET Chi-restraints excluded: chain D residue 2599 GLU Chi-restraints excluded: chain D residue 2619 ASP Chi-restraints excluded: chain D residue 2650 VAL Chi-restraints excluded: chain D residue 2656 TYR Chi-restraints excluded: chain D residue 2673 ASP Chi-restraints excluded: chain D residue 2722 GLN Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 135 ASN Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 578 PHE Chi-restraints excluded: chain B residue 618 PHE Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 650 GLU Chi-restraints excluded: chain B residue 660 THR Chi-restraints excluded: chain B residue 724 LYS Chi-restraints excluded: chain B residue 793 ASP Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 849 CYS Chi-restraints excluded: chain B residue 1070 HIS Chi-restraints excluded: chain B residue 1251 ASN Chi-restraints excluded: chain B residue 1598 ARG Chi-restraints excluded: chain B residue 1625 VAL Chi-restraints excluded: chain B residue 1649 SER Chi-restraints excluded: chain B residue 1877 VAL Chi-restraints excluded: chain B residue 1983 ASP Chi-restraints excluded: chain B residue 2007 LEU Chi-restraints excluded: chain B residue 2014 THR Chi-restraints excluded: chain B residue 2201 LEU Chi-restraints excluded: chain B residue 2294 PHE Chi-restraints excluded: chain B residue 2363 CYS Chi-restraints excluded: chain B residue 2408 VAL Chi-restraints excluded: chain B residue 2415 LEU Chi-restraints excluded: chain B residue 2421 VAL Chi-restraints excluded: chain B residue 2422 TYR Chi-restraints excluded: chain B residue 2431 ILE Chi-restraints excluded: chain B residue 2434 VAL Chi-restraints excluded: chain B residue 2435 THR Chi-restraints excluded: chain B residue 2541 HIS Chi-restraints excluded: chain B residue 2549 VAL Chi-restraints excluded: chain B residue 2576 MET Chi-restraints excluded: chain B residue 2599 GLU Chi-restraints excluded: chain B residue 2619 ASP Chi-restraints excluded: chain B residue 2650 VAL Chi-restraints excluded: chain B residue 2722 GLN Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 147 MET Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 578 PHE Chi-restraints excluded: chain C residue 618 PHE Chi-restraints excluded: chain C residue 660 THR Chi-restraints excluded: chain C residue 724 LYS Chi-restraints excluded: chain C residue 793 ASP Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 849 CYS Chi-restraints excluded: chain C residue 970 THR Chi-restraints excluded: chain C residue 1070 HIS Chi-restraints excluded: chain C residue 1625 VAL Chi-restraints excluded: chain C residue 1649 SER Chi-restraints excluded: chain C residue 1983 ASP Chi-restraints excluded: chain C residue 2007 LEU Chi-restraints excluded: chain C residue 2014 THR Chi-restraints excluded: chain C residue 2121 LEU Chi-restraints excluded: chain C residue 2201 LEU Chi-restraints excluded: chain C residue 2294 PHE Chi-restraints excluded: chain C residue 2408 VAL Chi-restraints excluded: chain C residue 2419 ASP Chi-restraints excluded: chain C residue 2431 ILE Chi-restraints excluded: chain C residue 2433 SER Chi-restraints excluded: chain C residue 2434 VAL Chi-restraints excluded: chain C residue 2541 HIS Chi-restraints excluded: chain C residue 2549 VAL Chi-restraints excluded: chain C residue 2599 GLU Chi-restraints excluded: chain C residue 2619 ASP Chi-restraints excluded: chain C residue 2650 VAL Chi-restraints excluded: chain C residue 2657 THR Chi-restraints excluded: chain C residue 2722 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 920 random chunks: chunk 548 optimal weight: 0.8980 chunk 354 optimal weight: 3.9990 chunk 529 optimal weight: 9.9990 chunk 267 optimal weight: 6.9990 chunk 174 optimal weight: 0.0980 chunk 171 optimal weight: 2.9990 chunk 563 optimal weight: 6.9990 chunk 604 optimal weight: 0.9990 chunk 438 optimal weight: 0.9980 chunk 82 optimal weight: 0.6980 chunk 696 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 795 GLN ** A1201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 872 ASN D1091 GLN ** D1201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1250 GLN ** D1620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 860 ASN B 872 ASN ** B1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1986 ASN ** B2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1091 GLN ** C1201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 73240 Z= 0.183 Angle : 0.699 12.737 98332 Z= 0.346 Chirality : 0.042 0.290 11280 Planarity : 0.004 0.078 12048 Dihedral : 12.457 160.425 11108 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.71 % Favored : 90.26 % Rotamer: Outliers : 3.28 % Allowed : 25.55 % Favored : 71.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: -1.66 (0.09), residues: 9088 helix: 0.19 (0.08), residues: 4720 sheet: -1.54 (0.23), residues: 488 loop : -2.76 (0.09), residues: 3880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A2256 HIS 0.007 0.001 HIS A 261 PHE 0.046 0.001 PHE B 839 TYR 0.046 0.001 TYR A2129 ARG 0.011 0.000 ARG A 792 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18176 Ramachandran restraints generated. 9088 Oldfield, 0 Emsley, 9088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18176 Ramachandran restraints generated. 9088 Oldfield, 0 Emsley, 9088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 869 residues out of total 8336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 246 poor density : 623 time to evaluate : 6.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET A1365 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1373 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1438 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1447 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET D1365 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1373 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1438 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1447 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET B1365 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1373 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1438 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1447 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET C1365 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1373 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1438 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1447 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 121 ILE cc_start: 0.7510 (OUTLIER) cc_final: 0.7173 (tp) REVERT: A 135 ASN cc_start: 0.8321 (OUTLIER) cc_final: 0.8062 (p0) REVERT: A 251 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7913 (pt) REVERT: A 578 PHE cc_start: 0.7717 (OUTLIER) cc_final: 0.7315 (t80) REVERT: A 616 ASP cc_start: 0.8262 (m-30) cc_final: 0.7924 (m-30) REVERT: A 708 ARG cc_start: 0.7361 (tmm-80) cc_final: 0.7111 (tmm-80) REVERT: A 745 LEU cc_start: 0.8105 (tp) cc_final: 0.7859 (tt) REVERT: A 753 ASN cc_start: 0.8530 (OUTLIER) cc_final: 0.7866 (p0) REVERT: A 785 MET cc_start: 0.8207 (tpp) cc_final: 0.7987 (tpp) REVERT: A 806 LEU cc_start: 0.6196 (OUTLIER) cc_final: 0.5945 (tm) REVERT: A 1091 GLN cc_start: 0.6559 (tp40) cc_final: 0.5916 (tp-100) REVERT: A 1095 GLN cc_start: 0.7163 (pt0) cc_final: 0.6440 (pt0) REVERT: A 1097 PHE cc_start: 0.6379 (m-80) cc_final: 0.5877 (m-80) REVERT: A 1275 HIS cc_start: 0.6178 (m170) cc_final: 0.5947 (m90) REVERT: A 1278 MET cc_start: 0.6013 (pmm) cc_final: 0.4102 (tpt) REVERT: A 1295 PHE cc_start: 0.4019 (OUTLIER) cc_final: 0.3394 (m-10) REVERT: A 1297 HIS cc_start: 0.6166 (p-80) cc_final: 0.5876 (p-80) REVERT: A 1329 MET cc_start: 0.1655 (ppp) cc_final: 0.1072 (ppp) REVERT: A 1982 ARG cc_start: 0.7510 (tpp-160) cc_final: 0.7233 (tpm170) REVERT: A 2116 MET cc_start: 0.6903 (pmm) cc_final: 0.6582 (ptt) REVERT: A 2205 MET cc_start: 0.8294 (mtp) cc_final: 0.7798 (mtp) REVERT: A 2294 PHE cc_start: 0.8053 (OUTLIER) cc_final: 0.7314 (p90) REVERT: A 2638 MET cc_start: 0.7430 (OUTLIER) cc_final: 0.7227 (ppp) REVERT: D 135 ASN cc_start: 0.8496 (OUTLIER) cc_final: 0.8201 (p0) REVERT: D 578 PHE cc_start: 0.7645 (OUTLIER) cc_final: 0.7263 (t80) REVERT: D 616 ASP cc_start: 0.8191 (m-30) cc_final: 0.7858 (m-30) REVERT: D 806 LEU cc_start: 0.6098 (OUTLIER) cc_final: 0.5879 (tm) REVERT: D 1091 GLN cc_start: 0.6650 (tp40) cc_final: 0.6008 (tp-100) REVERT: D 1095 GLN cc_start: 0.7398 (pt0) cc_final: 0.6836 (pt0) REVERT: D 1097 PHE cc_start: 0.6353 (m-80) cc_final: 0.5830 (m-80) REVERT: D 1273 MET cc_start: 0.7082 (mpm) cc_final: 0.6800 (mpm) REVERT: D 1295 PHE cc_start: 0.4118 (OUTLIER) cc_final: 0.3679 (m-10) REVERT: D 1297 HIS cc_start: 0.6014 (OUTLIER) cc_final: 0.5768 (p-80) REVERT: D 1329 MET cc_start: 0.1792 (ppp) cc_final: 0.1254 (ppp) REVERT: D 1598 ARG cc_start: 0.3827 (OUTLIER) cc_final: 0.3604 (pmt170) REVERT: D 1614 ARG cc_start: 0.5121 (mmp-170) cc_final: 0.4712 (mmm160) REVERT: D 1683 MET cc_start: 0.6664 (tpp) cc_final: 0.6454 (tpt) REVERT: D 1982 ARG cc_start: 0.7475 (tpp-160) cc_final: 0.7180 (tpm170) REVERT: D 2294 PHE cc_start: 0.8010 (OUTLIER) cc_final: 0.7288 (p90) REVERT: B 121 ILE cc_start: 0.7591 (OUTLIER) cc_final: 0.7297 (tp) REVERT: B 135 ASN cc_start: 0.8421 (OUTLIER) cc_final: 0.8206 (p0) REVERT: B 251 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7979 (pt) REVERT: B 578 PHE cc_start: 0.7678 (OUTLIER) cc_final: 0.7301 (t80) REVERT: B 616 ASP cc_start: 0.8270 (m-30) cc_final: 0.7894 (m-30) REVERT: B 618 PHE cc_start: 0.5612 (OUTLIER) cc_final: 0.4937 (t80) REVERT: B 708 ARG cc_start: 0.7573 (tmm-80) cc_final: 0.7355 (tmm-80) REVERT: B 736 GLN cc_start: 0.7618 (OUTLIER) cc_final: 0.7148 (pt0) REVERT: B 806 LEU cc_start: 0.6034 (OUTLIER) cc_final: 0.5807 (tm) REVERT: B 1097 PHE cc_start: 0.6765 (m-80) cc_final: 0.6392 (m-80) REVERT: B 1230 MET cc_start: 0.5684 (tmm) cc_final: 0.5430 (ttm) REVERT: B 1598 ARG cc_start: 0.3715 (OUTLIER) cc_final: 0.3478 (pmt170) REVERT: B 1682 MET cc_start: 0.7557 (ttp) cc_final: 0.7246 (ttm) REVERT: B 1862 ASP cc_start: 0.7999 (p0) cc_final: 0.7711 (p0) REVERT: B 2287 MET cc_start: 0.6867 (mtm) cc_final: 0.6556 (mmm) REVERT: B 2294 PHE cc_start: 0.8081 (OUTLIER) cc_final: 0.7333 (p90) REVERT: C 578 PHE cc_start: 0.7616 (OUTLIER) cc_final: 0.7408 (t80) REVERT: C 616 ASP cc_start: 0.8249 (m-30) cc_final: 0.7900 (m-30) REVERT: C 708 ARG cc_start: 0.7606 (tmm-80) cc_final: 0.7352 (tmm-80) REVERT: C 736 GLN cc_start: 0.7803 (OUTLIER) cc_final: 0.7268 (pt0) REVERT: C 806 LEU cc_start: 0.6036 (OUTLIER) cc_final: 0.5822 (tm) REVERT: C 837 MET cc_start: 0.7562 (mmm) cc_final: 0.7280 (mmm) REVERT: C 1091 GLN cc_start: 0.6868 (tp40) cc_final: 0.6394 (tp-100) REVERT: C 1097 PHE cc_start: 0.6870 (m-80) cc_final: 0.6470 (m-80) REVERT: C 1230 MET cc_start: 0.5554 (tmm) cc_final: 0.5301 (ttm) REVERT: C 1864 MET cc_start: 0.7708 (ptm) cc_final: 0.7477 (ptp) REVERT: C 1982 ARG cc_start: 0.7428 (tpp-160) cc_final: 0.7184 (tpm170) REVERT: C 2116 MET cc_start: 0.6873 (pmm) cc_final: 0.6494 (ptt) REVERT: C 2294 PHE cc_start: 0.8035 (OUTLIER) cc_final: 0.7245 (p90) outliers start: 246 outliers final: 120 residues processed: 819 average time/residue: 1.2103 time to fit residues: 1394.0834 Evaluate side-chains 749 residues out of total 8336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 600 time to evaluate : 6.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 724 LYS Chi-restraints excluded: chain A residue 753 ASN Chi-restraints excluded: chain A residue 793 ASP Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 849 CYS Chi-restraints excluded: chain A residue 1070 HIS Chi-restraints excluded: chain A residue 1295 PHE Chi-restraints excluded: chain A residue 1625 VAL Chi-restraints excluded: chain A residue 1800 ASP Chi-restraints excluded: chain A residue 1983 ASP Chi-restraints excluded: chain A residue 2014 THR Chi-restraints excluded: chain A residue 2294 PHE Chi-restraints excluded: chain A residue 2419 ASP Chi-restraints excluded: chain A residue 2421 VAL Chi-restraints excluded: chain A residue 2527 THR Chi-restraints excluded: chain A residue 2549 VAL Chi-restraints excluded: chain A residue 2599 GLU Chi-restraints excluded: chain A residue 2605 GLU Chi-restraints excluded: chain A residue 2619 ASP Chi-restraints excluded: chain A residue 2638 MET Chi-restraints excluded: chain A residue 2650 VAL Chi-restraints excluded: chain A residue 2722 GLN Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 135 ASN Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 488 THR Chi-restraints excluded: chain D residue 578 PHE Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 724 LYS Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 849 CYS Chi-restraints excluded: chain D residue 1070 HIS Chi-restraints excluded: chain D residue 1295 PHE Chi-restraints excluded: chain D residue 1297 HIS Chi-restraints excluded: chain D residue 1598 ARG Chi-restraints excluded: chain D residue 1625 VAL Chi-restraints excluded: chain D residue 2007 LEU Chi-restraints excluded: chain D residue 2014 THR Chi-restraints excluded: chain D residue 2201 LEU Chi-restraints excluded: chain D residue 2294 PHE Chi-restraints excluded: chain D residue 2419 ASP Chi-restraints excluded: chain D residue 2434 VAL Chi-restraints excluded: chain D residue 2435 THR Chi-restraints excluded: chain D residue 2541 HIS Chi-restraints excluded: chain D residue 2549 VAL Chi-restraints excluded: chain D residue 2599 GLU Chi-restraints excluded: chain D residue 2619 ASP Chi-restraints excluded: chain D residue 2650 VAL Chi-restraints excluded: chain D residue 2722 GLN Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 135 ASN Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 578 PHE Chi-restraints excluded: chain B residue 618 PHE Chi-restraints excluded: chain B residue 650 GLU Chi-restraints excluded: chain B residue 660 THR Chi-restraints excluded: chain B residue 724 LYS Chi-restraints excluded: chain B residue 736 GLN Chi-restraints excluded: chain B residue 793 ASP Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 849 CYS Chi-restraints excluded: chain B residue 1070 HIS Chi-restraints excluded: chain B residue 1251 ASN Chi-restraints excluded: chain B residue 1297 HIS Chi-restraints excluded: chain B residue 1598 ARG Chi-restraints excluded: chain B residue 1625 VAL Chi-restraints excluded: chain B residue 1877 VAL Chi-restraints excluded: chain B residue 2007 LEU Chi-restraints excluded: chain B residue 2014 THR Chi-restraints excluded: chain B residue 2201 LEU Chi-restraints excluded: chain B residue 2294 PHE Chi-restraints excluded: chain B residue 2408 VAL Chi-restraints excluded: chain B residue 2419 ASP Chi-restraints excluded: chain B residue 2421 VAL Chi-restraints excluded: chain B residue 2422 TYR Chi-restraints excluded: chain B residue 2431 ILE Chi-restraints excluded: chain B residue 2434 VAL Chi-restraints excluded: chain B residue 2435 THR Chi-restraints excluded: chain B residue 2549 VAL Chi-restraints excluded: chain B residue 2599 GLU Chi-restraints excluded: chain B residue 2619 ASP Chi-restraints excluded: chain B residue 2650 VAL Chi-restraints excluded: chain B residue 2722 GLN Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 147 MET Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 578 PHE Chi-restraints excluded: chain C residue 660 THR Chi-restraints excluded: chain C residue 724 LYS Chi-restraints excluded: chain C residue 736 GLN Chi-restraints excluded: chain C residue 793 ASP Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 849 CYS Chi-restraints excluded: chain C residue 1070 HIS Chi-restraints excluded: chain C residue 1251 ASN Chi-restraints excluded: chain C residue 1625 VAL Chi-restraints excluded: chain C residue 2014 THR Chi-restraints excluded: chain C residue 2121 LEU Chi-restraints excluded: chain C residue 2201 LEU Chi-restraints excluded: chain C residue 2294 PHE Chi-restraints excluded: chain C residue 2363 CYS Chi-restraints excluded: chain C residue 2408 VAL Chi-restraints excluded: chain C residue 2431 ILE Chi-restraints excluded: chain C residue 2434 VAL Chi-restraints excluded: chain C residue 2435 THR Chi-restraints excluded: chain C residue 2541 HIS Chi-restraints excluded: chain C residue 2549 VAL Chi-restraints excluded: chain C residue 2599 GLU Chi-restraints excluded: chain C residue 2619 ASP Chi-restraints excluded: chain C residue 2650 VAL Chi-restraints excluded: chain C residue 2722 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 920 random chunks: chunk 806 optimal weight: 20.0000 chunk 849 optimal weight: 0.2980 chunk 775 optimal weight: 1.9990 chunk 826 optimal weight: 0.8980 chunk 497 optimal weight: 0.1980 chunk 359 optimal weight: 1.9990 chunk 648 optimal weight: 0.9990 chunk 253 optimal weight: 4.9990 chunk 746 optimal weight: 9.9990 chunk 781 optimal weight: 4.9990 chunk 823 optimal weight: 50.0000 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 795 GLN ** A1201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 270 GLN ** D 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 872 ASN ** D1201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1250 GLN ** D1620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 872 ASN ** B1201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1250 GLN ** B1742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2236 GLN ** B2361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1250 GLN ** C1620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 73240 Z= 0.190 Angle : 0.704 14.692 98332 Z= 0.349 Chirality : 0.042 0.289 11280 Planarity : 0.004 0.077 12048 Dihedral : 12.280 162.593 11108 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.26 % Favored : 89.70 % Rotamer: Outliers : 3.22 % Allowed : 25.89 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.09), residues: 9088 helix: 0.25 (0.08), residues: 4688 sheet: -1.55 (0.23), residues: 488 loop : -2.73 (0.09), residues: 3912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D2256 HIS 0.007 0.001 HIS A 261 PHE 0.044 0.001 PHE B 839 TYR 0.055 0.001 TYR C2129 ARG 0.012 0.000 ARG A1616 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18176 Ramachandran restraints generated. 9088 Oldfield, 0 Emsley, 9088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18176 Ramachandran restraints generated. 9088 Oldfield, 0 Emsley, 9088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 869 residues out of total 8336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 242 poor density : 627 time to evaluate : 6.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET A1365 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1373 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1438 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1447 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET D1365 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1373 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1438 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1447 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET B1365 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1373 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1438 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1447 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET C1365 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1373 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1438 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1447 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 121 ILE cc_start: 0.7439 (OUTLIER) cc_final: 0.7121 (tp) REVERT: A 135 ASN cc_start: 0.8358 (OUTLIER) cc_final: 0.8093 (p0) REVERT: A 251 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7977 (pt) REVERT: A 578 PHE cc_start: 0.7727 (OUTLIER) cc_final: 0.7311 (t80) REVERT: A 616 ASP cc_start: 0.8202 (m-30) cc_final: 0.7801 (m-30) REVERT: A 745 LEU cc_start: 0.8126 (tp) cc_final: 0.7787 (tt) REVERT: A 753 ASN cc_start: 0.8527 (OUTLIER) cc_final: 0.7874 (p0) REVERT: A 806 LEU cc_start: 0.6101 (OUTLIER) cc_final: 0.5880 (tm) REVERT: A 1091 GLN cc_start: 0.6593 (tp40) cc_final: 0.6260 (tp40) REVERT: A 1095 GLN cc_start: 0.7248 (pt0) cc_final: 0.6882 (pt0) REVERT: A 1097 PHE cc_start: 0.6335 (m-80) cc_final: 0.5831 (m-80) REVERT: A 1101 GLN cc_start: 0.6078 (OUTLIER) cc_final: 0.5360 (pp30) REVERT: A 1275 HIS cc_start: 0.6149 (m170) cc_final: 0.5907 (m90) REVERT: A 1278 MET cc_start: 0.6067 (pmm) cc_final: 0.4115 (tpt) REVERT: A 1295 PHE cc_start: 0.4052 (OUTLIER) cc_final: 0.3567 (m-10) REVERT: A 1297 HIS cc_start: 0.6238 (p-80) cc_final: 0.5995 (p-80) REVERT: A 1329 MET cc_start: 0.1653 (ppp) cc_final: 0.1144 (ppp) REVERT: A 1982 ARG cc_start: 0.7519 (tpp-160) cc_final: 0.7301 (tpm170) REVERT: A 2116 MET cc_start: 0.6905 (pmm) cc_final: 0.6605 (ptt) REVERT: A 2205 MET cc_start: 0.8324 (mtp) cc_final: 0.7727 (mtp) REVERT: A 2294 PHE cc_start: 0.8055 (OUTLIER) cc_final: 0.7304 (p90) REVERT: A 2606 ILE cc_start: 0.8411 (tt) cc_final: 0.8079 (tt) REVERT: D 135 ASN cc_start: 0.8455 (OUTLIER) cc_final: 0.8188 (p0) REVERT: D 578 PHE cc_start: 0.7659 (OUTLIER) cc_final: 0.7387 (t80) REVERT: D 616 ASP cc_start: 0.8147 (m-30) cc_final: 0.7736 (m-30) REVERT: D 806 LEU cc_start: 0.6119 (OUTLIER) cc_final: 0.5900 (tm) REVERT: D 1091 GLN cc_start: 0.6524 (tp40) cc_final: 0.6168 (tp-100) REVERT: D 1095 GLN cc_start: 0.7124 (pt0) cc_final: 0.6863 (pt0) REVERT: D 1097 PHE cc_start: 0.6364 (m-80) cc_final: 0.5815 (m-80) REVERT: D 1101 GLN cc_start: 0.6002 (OUTLIER) cc_final: 0.5354 (pp30) REVERT: D 1273 MET cc_start: 0.7101 (mpm) cc_final: 0.6830 (mpm) REVERT: D 1297 HIS cc_start: 0.5849 (OUTLIER) cc_final: 0.5612 (p-80) REVERT: D 1598 ARG cc_start: 0.3904 (OUTLIER) cc_final: 0.3697 (pmt170) REVERT: D 1740 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7756 (mt) REVERT: D 1982 ARG cc_start: 0.7526 (tpp-160) cc_final: 0.7243 (tpm170) REVERT: D 2294 PHE cc_start: 0.7953 (OUTLIER) cc_final: 0.7243 (p90) REVERT: D 2638 MET cc_start: 0.7536 (OUTLIER) cc_final: 0.7331 (ppp) REVERT: B 121 ILE cc_start: 0.7565 (OUTLIER) cc_final: 0.7290 (tp) REVERT: B 135 ASN cc_start: 0.8436 (OUTLIER) cc_final: 0.8199 (p0) REVERT: B 251 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7903 (pt) REVERT: B 578 PHE cc_start: 0.7681 (OUTLIER) cc_final: 0.7298 (t80) REVERT: B 616 ASP cc_start: 0.8265 (m-30) cc_final: 0.7899 (m-30) REVERT: B 618 PHE cc_start: 0.5516 (OUTLIER) cc_final: 0.4947 (t80) REVERT: B 736 GLN cc_start: 0.7611 (OUTLIER) cc_final: 0.7139 (pt0) REVERT: B 806 LEU cc_start: 0.6050 (OUTLIER) cc_final: 0.5826 (tm) REVERT: B 1097 PHE cc_start: 0.6755 (m-80) cc_final: 0.6371 (m-80) REVERT: B 1101 GLN cc_start: 0.6054 (OUTLIER) cc_final: 0.5296 (pp30) REVERT: B 1598 ARG cc_start: 0.3653 (OUTLIER) cc_final: 0.3417 (pmt170) REVERT: B 1682 MET cc_start: 0.7516 (ttp) cc_final: 0.7184 (ttm) REVERT: B 1813 MET cc_start: 0.7674 (tpp) cc_final: 0.7440 (ttm) REVERT: B 1862 ASP cc_start: 0.8061 (p0) cc_final: 0.7786 (p0) REVERT: B 1982 ARG cc_start: 0.7454 (tpp-160) cc_final: 0.7185 (tpm170) REVERT: B 2294 PHE cc_start: 0.8085 (OUTLIER) cc_final: 0.7341 (p90) REVERT: C 578 PHE cc_start: 0.7639 (OUTLIER) cc_final: 0.7429 (t80) REVERT: C 616 ASP cc_start: 0.8188 (m-30) cc_final: 0.7845 (m-30) REVERT: C 708 ARG cc_start: 0.7516 (tmm-80) cc_final: 0.7253 (tmm-80) REVERT: C 736 GLN cc_start: 0.7771 (OUTLIER) cc_final: 0.7208 (pt0) REVERT: C 806 LEU cc_start: 0.6015 (OUTLIER) cc_final: 0.5801 (tm) REVERT: C 837 MET cc_start: 0.7480 (mmm) cc_final: 0.7241 (mmm) REVERT: C 1097 PHE cc_start: 0.6858 (m-80) cc_final: 0.6477 (m-80) REVERT: C 1740 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7722 (mt) REVERT: C 2116 MET cc_start: 0.6875 (OUTLIER) cc_final: 0.6522 (ptt) REVERT: C 2287 MET cc_start: 0.6896 (mtm) cc_final: 0.6598 (mmm) REVERT: C 2294 PHE cc_start: 0.8017 (OUTLIER) cc_final: 0.7219 (p90) REVERT: C 2638 MET cc_start: 0.7495 (OUTLIER) cc_final: 0.7255 (ppp) outliers start: 242 outliers final: 146 residues processed: 812 average time/residue: 1.2125 time to fit residues: 1380.6718 Evaluate side-chains 776 residues out of total 8336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 595 time to evaluate : 6.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 724 LYS Chi-restraints excluded: chain A residue 753 ASN Chi-restraints excluded: chain A residue 793 ASP Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 849 CYS Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 1070 HIS Chi-restraints excluded: chain A residue 1101 GLN Chi-restraints excluded: chain A residue 1295 PHE Chi-restraints excluded: chain A residue 1625 VAL Chi-restraints excluded: chain A residue 1800 ASP Chi-restraints excluded: chain A residue 1983 ASP Chi-restraints excluded: chain A residue 2007 LEU Chi-restraints excluded: chain A residue 2014 THR Chi-restraints excluded: chain A residue 2196 ILE Chi-restraints excluded: chain A residue 2294 PHE Chi-restraints excluded: chain A residue 2363 CYS Chi-restraints excluded: chain A residue 2408 VAL Chi-restraints excluded: chain A residue 2419 ASP Chi-restraints excluded: chain A residue 2421 VAL Chi-restraints excluded: chain A residue 2422 TYR Chi-restraints excluded: chain A residue 2527 THR Chi-restraints excluded: chain A residue 2541 HIS Chi-restraints excluded: chain A residue 2549 VAL Chi-restraints excluded: chain A residue 2599 GLU Chi-restraints excluded: chain A residue 2605 GLU Chi-restraints excluded: chain A residue 2619 ASP Chi-restraints excluded: chain A residue 2650 VAL Chi-restraints excluded: chain A residue 2673 ASP Chi-restraints excluded: chain A residue 2722 GLN Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 135 ASN Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 488 THR Chi-restraints excluded: chain D residue 578 PHE Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 724 LYS Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 849 CYS Chi-restraints excluded: chain D residue 1070 HIS Chi-restraints excluded: chain D residue 1101 GLN Chi-restraints excluded: chain D residue 1251 ASN Chi-restraints excluded: chain D residue 1297 HIS Chi-restraints excluded: chain D residue 1598 ARG Chi-restraints excluded: chain D residue 1625 VAL Chi-restraints excluded: chain D residue 1740 LEU Chi-restraints excluded: chain D residue 2007 LEU Chi-restraints excluded: chain D residue 2014 THR Chi-restraints excluded: chain D residue 2196 ILE Chi-restraints excluded: chain D residue 2201 LEU Chi-restraints excluded: chain D residue 2294 PHE Chi-restraints excluded: chain D residue 2363 CYS Chi-restraints excluded: chain D residue 2408 VAL Chi-restraints excluded: chain D residue 2419 ASP Chi-restraints excluded: chain D residue 2434 VAL Chi-restraints excluded: chain D residue 2435 THR Chi-restraints excluded: chain D residue 2541 HIS Chi-restraints excluded: chain D residue 2549 VAL Chi-restraints excluded: chain D residue 2599 GLU Chi-restraints excluded: chain D residue 2619 ASP Chi-restraints excluded: chain D residue 2638 MET Chi-restraints excluded: chain D residue 2650 VAL Chi-restraints excluded: chain D residue 2722 GLN Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 135 ASN Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 578 PHE Chi-restraints excluded: chain B residue 618 PHE Chi-restraints excluded: chain B residue 660 THR Chi-restraints excluded: chain B residue 736 GLN Chi-restraints excluded: chain B residue 793 ASP Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 849 CYS Chi-restraints excluded: chain B residue 1070 HIS Chi-restraints excluded: chain B residue 1101 GLN Chi-restraints excluded: chain B residue 1251 ASN Chi-restraints excluded: chain B residue 1297 HIS Chi-restraints excluded: chain B residue 1598 ARG Chi-restraints excluded: chain B residue 1625 VAL Chi-restraints excluded: chain B residue 1877 VAL Chi-restraints excluded: chain B residue 2007 LEU Chi-restraints excluded: chain B residue 2014 THR Chi-restraints excluded: chain B residue 2196 ILE Chi-restraints excluded: chain B residue 2201 LEU Chi-restraints excluded: chain B residue 2294 PHE Chi-restraints excluded: chain B residue 2363 CYS Chi-restraints excluded: chain B residue 2408 VAL Chi-restraints excluded: chain B residue 2419 ASP Chi-restraints excluded: chain B residue 2421 VAL Chi-restraints excluded: chain B residue 2422 TYR Chi-restraints excluded: chain B residue 2431 ILE Chi-restraints excluded: chain B residue 2434 VAL Chi-restraints excluded: chain B residue 2435 THR Chi-restraints excluded: chain B residue 2549 VAL Chi-restraints excluded: chain B residue 2599 GLU Chi-restraints excluded: chain B residue 2619 ASP Chi-restraints excluded: chain B residue 2650 VAL Chi-restraints excluded: chain B residue 2673 ASP Chi-restraints excluded: chain B residue 2722 GLN Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 147 MET Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 578 PHE Chi-restraints excluded: chain C residue 660 THR Chi-restraints excluded: chain C residue 724 LYS Chi-restraints excluded: chain C residue 736 GLN Chi-restraints excluded: chain C residue 793 ASP Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 849 CYS Chi-restraints excluded: chain C residue 1070 HIS Chi-restraints excluded: chain C residue 1240 PHE Chi-restraints excluded: chain C residue 1251 ASN Chi-restraints excluded: chain C residue 1297 HIS Chi-restraints excluded: chain C residue 1625 VAL Chi-restraints excluded: chain C residue 1740 LEU Chi-restraints excluded: chain C residue 1966 MET Chi-restraints excluded: chain C residue 2007 LEU Chi-restraints excluded: chain C residue 2014 THR Chi-restraints excluded: chain C residue 2116 MET Chi-restraints excluded: chain C residue 2121 LEU Chi-restraints excluded: chain C residue 2201 LEU Chi-restraints excluded: chain C residue 2294 PHE Chi-restraints excluded: chain C residue 2363 CYS Chi-restraints excluded: chain C residue 2408 VAL Chi-restraints excluded: chain C residue 2431 ILE Chi-restraints excluded: chain C residue 2434 VAL Chi-restraints excluded: chain C residue 2541 HIS Chi-restraints excluded: chain C residue 2549 VAL Chi-restraints excluded: chain C residue 2599 GLU Chi-restraints excluded: chain C residue 2619 ASP Chi-restraints excluded: chain C residue 2638 MET Chi-restraints excluded: chain C residue 2650 VAL Chi-restraints excluded: chain C residue 2722 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 920 random chunks: chunk 542 optimal weight: 4.9990 chunk 873 optimal weight: 3.9990 chunk 533 optimal weight: 8.9990 chunk 414 optimal weight: 2.9990 chunk 607 optimal weight: 9.9990 chunk 916 optimal weight: 8.9990 chunk 843 optimal weight: 3.9990 chunk 729 optimal weight: 0.9990 chunk 75 optimal weight: 0.4980 chunk 563 optimal weight: 6.9990 chunk 447 optimal weight: 0.3980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 GLN ** B 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1250 GLN ** B1742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 270 GLN ** C 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1250 GLN ** C1620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 73240 Z= 0.263 Angle : 0.755 13.897 98332 Z= 0.375 Chirality : 0.044 0.327 11280 Planarity : 0.004 0.077 12048 Dihedral : 12.471 165.892 11108 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.60 % Favored : 89.37 % Rotamer: Outliers : 3.05 % Allowed : 26.19 % Favored : 70.76 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: -1.69 (0.09), residues: 9088 helix: 0.16 (0.08), residues: 4696 sheet: -1.57 (0.23), residues: 492 loop : -2.74 (0.09), residues: 3900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D2639 HIS 0.008 0.001 HIS B2541 PHE 0.045 0.002 PHE B 839 TYR 0.036 0.001 TYR A2129 ARG 0.015 0.001 ARG A1616 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18176 Ramachandran restraints generated. 9088 Oldfield, 0 Emsley, 9088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18176 Ramachandran restraints generated. 9088 Oldfield, 0 Emsley, 9088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 822 residues out of total 8336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 229 poor density : 593 time to evaluate : 6.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET A1365 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1373 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1438 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1447 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET D1365 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1373 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1438 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1447 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET B1365 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1373 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1438 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1447 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET C1365 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1373 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1438 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1447 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1484 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1526 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 121 ILE cc_start: 0.7616 (OUTLIER) cc_final: 0.7266 (tp) REVERT: A 135 ASN cc_start: 0.8303 (OUTLIER) cc_final: 0.8095 (p0) REVERT: A 251 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8004 (pt) REVERT: A 578 PHE cc_start: 0.7819 (OUTLIER) cc_final: 0.7383 (t80) REVERT: A 616 ASP cc_start: 0.8169 (m-30) cc_final: 0.7796 (m-30) REVERT: A 630 PHE cc_start: 0.6187 (t80) cc_final: 0.5924 (t80) REVERT: A 745 LEU cc_start: 0.8178 (tp) cc_final: 0.7825 (tt) REVERT: A 753 ASN cc_start: 0.8615 (OUTLIER) cc_final: 0.7869 (p0) REVERT: A 806 LEU cc_start: 0.6065 (OUTLIER) cc_final: 0.5853 (tm) REVERT: A 1091 GLN cc_start: 0.6623 (tp40) cc_final: 0.6316 (tp40) REVERT: A 1095 GLN cc_start: 0.7136 (pt0) cc_final: 0.6711 (pt0) REVERT: A 1097 PHE cc_start: 0.6497 (m-80) cc_final: 0.5991 (m-80) REVERT: A 1101 GLN cc_start: 0.6175 (OUTLIER) cc_final: 0.5393 (pp30) REVERT: A 1297 HIS cc_start: 0.6281 (p-80) cc_final: 0.6001 (p-80) REVERT: A 1982 ARG cc_start: 0.7521 (tpp-160) cc_final: 0.7252 (tpm170) REVERT: A 2294 PHE cc_start: 0.8158 (OUTLIER) cc_final: 0.7477 (p90) REVERT: D 135 ASN cc_start: 0.8517 (OUTLIER) cc_final: 0.8249 (p0) REVERT: D 578 PHE cc_start: 0.7734 (OUTLIER) cc_final: 0.7444 (t80) REVERT: D 616 ASP cc_start: 0.8114 (m-30) cc_final: 0.7669 (m-30) REVERT: D 806 LEU cc_start: 0.6085 (OUTLIER) cc_final: 0.5870 (tm) REVERT: D 1091 GLN cc_start: 0.6523 (tp40) cc_final: 0.6225 (tp-100) REVERT: D 1095 GLN cc_start: 0.7120 (pt0) cc_final: 0.6896 (pt0) REVERT: D 1097 PHE cc_start: 0.6476 (m-80) cc_final: 0.6006 (m-80) REVERT: D 1101 GLN cc_start: 0.6094 (OUTLIER) cc_final: 0.5388 (pp30) REVERT: D 1273 MET cc_start: 0.7104 (mpm) cc_final: 0.6842 (mpm) REVERT: D 1296 VAL cc_start: 0.4547 (OUTLIER) cc_final: 0.4002 (t) REVERT: D 1598 ARG cc_start: 0.3832 (OUTLIER) cc_final: 0.3599 (pmt170) REVERT: D 1982 ARG cc_start: 0.7537 (tpp-160) cc_final: 0.7257 (tpm170) REVERT: D 2294 PHE cc_start: 0.8115 (OUTLIER) cc_final: 0.7417 (p90) REVERT: B 121 ILE cc_start: 0.7682 (OUTLIER) cc_final: 0.7352 (tp) REVERT: B 135 ASN cc_start: 0.8448 (OUTLIER) cc_final: 0.8209 (p0) REVERT: B 251 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8030 (pt) REVERT: B 578 PHE cc_start: 0.7773 (OUTLIER) cc_final: 0.7356 (t80) REVERT: B 616 ASP cc_start: 0.8256 (m-30) cc_final: 0.7904 (m-30) REVERT: B 618 PHE cc_start: 0.5783 (OUTLIER) cc_final: 0.5166 (t80) REVERT: B 806 LEU cc_start: 0.5957 (OUTLIER) cc_final: 0.5737 (tm) REVERT: B 1097 PHE cc_start: 0.6686 (m-80) cc_final: 0.6305 (m-80) REVERT: B 1101 GLN cc_start: 0.6175 (OUTLIER) cc_final: 0.5357 (pp30) REVERT: B 1598 ARG cc_start: 0.3762 (OUTLIER) cc_final: 0.3488 (pmt170) REVERT: B 1682 MET cc_start: 0.7551 (ttp) cc_final: 0.7343 (ttt) REVERT: B 1683 MET cc_start: 0.6079 (tpt) cc_final: 0.5831 (tpt) REVERT: B 1862 ASP cc_start: 0.8024 (p0) cc_final: 0.7757 (p0) REVERT: B 1982 ARG cc_start: 0.7552 (tpp-160) cc_final: 0.7302 (tpm170) REVERT: B 2294 PHE cc_start: 0.8212 (OUTLIER) cc_final: 0.7466 (p90) REVERT: C 616 ASP cc_start: 0.8174 (m-30) cc_final: 0.7828 (m-30) REVERT: C 736 GLN cc_start: 0.7758 (OUTLIER) cc_final: 0.7239 (pt0) REVERT: C 747 ARG cc_start: 0.6835 (tpm170) cc_final: 0.5486 (tpm170) REVERT: C 806 LEU cc_start: 0.5993 (OUTLIER) cc_final: 0.5779 (tm) REVERT: C 837 MET cc_start: 0.7454 (mmm) cc_final: 0.7210 (mmm) REVERT: C 1097 PHE cc_start: 0.6777 (m-80) cc_final: 0.6367 (m-80) REVERT: C 2287 MET cc_start: 0.7000 (mtm) cc_final: 0.6672 (mmm) REVERT: C 2294 PHE cc_start: 0.8155 (OUTLIER) cc_final: 0.7410 (p90) REVERT: C 2606 ILE cc_start: 0.8556 (tt) cc_final: 0.8181 (tt) outliers start: 229 outliers final: 153 residues processed: 778 average time/residue: 1.1987 time to fit residues: 1308.6458 Evaluate side-chains 755 residues out of total 8336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 575 time to evaluate : 6.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 724 LYS Chi-restraints excluded: chain A residue 753 ASN Chi-restraints excluded: chain A residue 782 CYS Chi-restraints excluded: chain A residue 793 ASP Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 849 CYS Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 1070 HIS Chi-restraints excluded: chain A residue 1101 GLN Chi-restraints excluded: chain A residue 1625 VAL Chi-restraints excluded: chain A residue 1800 ASP Chi-restraints excluded: chain A residue 1983 ASP Chi-restraints excluded: chain A residue 2007 LEU Chi-restraints excluded: chain A residue 2014 THR Chi-restraints excluded: chain A residue 2196 ILE Chi-restraints excluded: chain A residue 2201 LEU Chi-restraints excluded: chain A residue 2294 PHE Chi-restraints excluded: chain A residue 2363 CYS Chi-restraints excluded: chain A residue 2408 VAL Chi-restraints excluded: chain A residue 2419 ASP Chi-restraints excluded: chain A residue 2422 TYR Chi-restraints excluded: chain A residue 2527 THR Chi-restraints excluded: chain A residue 2541 HIS Chi-restraints excluded: chain A residue 2549 VAL Chi-restraints excluded: chain A residue 2599 GLU Chi-restraints excluded: chain A residue 2605 GLU Chi-restraints excluded: chain A residue 2619 ASP Chi-restraints excluded: chain A residue 2650 VAL Chi-restraints excluded: chain A residue 2673 ASP Chi-restraints excluded: chain A residue 2722 GLN Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 135 ASN Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 488 THR Chi-restraints excluded: chain D residue 578 PHE Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 849 CYS Chi-restraints excluded: chain D residue 1070 HIS Chi-restraints excluded: chain D residue 1101 GLN Chi-restraints excluded: chain D residue 1240 PHE Chi-restraints excluded: chain D residue 1296 VAL Chi-restraints excluded: chain D residue 1598 ARG Chi-restraints excluded: chain D residue 1625 VAL Chi-restraints excluded: chain D residue 2007 LEU Chi-restraints excluded: chain D residue 2014 THR Chi-restraints excluded: chain D residue 2196 ILE Chi-restraints excluded: chain D residue 2201 LEU Chi-restraints excluded: chain D residue 2294 PHE Chi-restraints excluded: chain D residue 2363 CYS Chi-restraints excluded: chain D residue 2408 VAL Chi-restraints excluded: chain D residue 2419 ASP Chi-restraints excluded: chain D residue 2434 VAL Chi-restraints excluded: chain D residue 2435 THR Chi-restraints excluded: chain D residue 2541 HIS Chi-restraints excluded: chain D residue 2549 VAL Chi-restraints excluded: chain D residue 2599 GLU Chi-restraints excluded: chain D residue 2619 ASP Chi-restraints excluded: chain D residue 2650 VAL Chi-restraints excluded: chain D residue 2656 TYR Chi-restraints excluded: chain D residue 2722 GLN Chi-restraints excluded: chain D residue 2733 ILE Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 135 ASN Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 578 PHE Chi-restraints excluded: chain B residue 618 PHE Chi-restraints excluded: chain B residue 660 THR Chi-restraints excluded: chain B residue 724 LYS Chi-restraints excluded: chain B residue 793 ASP Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 849 CYS Chi-restraints excluded: chain B residue 1070 HIS Chi-restraints excluded: chain B residue 1101 GLN Chi-restraints excluded: chain B residue 1251 ASN Chi-restraints excluded: chain B residue 1297 HIS Chi-restraints excluded: chain B residue 1598 ARG Chi-restraints excluded: chain B residue 1625 VAL Chi-restraints excluded: chain B residue 1877 VAL Chi-restraints excluded: chain B residue 2007 LEU Chi-restraints excluded: chain B residue 2014 THR Chi-restraints excluded: chain B residue 2196 ILE Chi-restraints excluded: chain B residue 2201 LEU Chi-restraints excluded: chain B residue 2294 PHE Chi-restraints excluded: chain B residue 2363 CYS Chi-restraints excluded: chain B residue 2370 MET Chi-restraints excluded: chain B residue 2408 VAL Chi-restraints excluded: chain B residue 2419 ASP Chi-restraints excluded: chain B residue 2421 VAL Chi-restraints excluded: chain B residue 2422 TYR Chi-restraints excluded: chain B residue 2431 ILE Chi-restraints excluded: chain B residue 2434 VAL Chi-restraints excluded: chain B residue 2435 THR Chi-restraints excluded: chain B residue 2541 HIS Chi-restraints excluded: chain B residue 2549 VAL Chi-restraints excluded: chain B residue 2599 GLU Chi-restraints excluded: chain B residue 2619 ASP Chi-restraints excluded: chain B residue 2650 VAL Chi-restraints excluded: chain B residue 2673 ASP Chi-restraints excluded: chain B residue 2722 GLN Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 147 MET Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 580 PHE Chi-restraints excluded: chain C residue 660 THR Chi-restraints excluded: chain C residue 724 LYS Chi-restraints excluded: chain C residue 736 GLN Chi-restraints excluded: chain C residue 793 ASP Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 849 CYS Chi-restraints excluded: chain C residue 1070 HIS Chi-restraints excluded: chain C residue 1251 ASN Chi-restraints excluded: chain C residue 1297 HIS Chi-restraints excluded: chain C residue 1625 VAL Chi-restraints excluded: chain C residue 1966 MET Chi-restraints excluded: chain C residue 2007 LEU Chi-restraints excluded: chain C residue 2014 THR Chi-restraints excluded: chain C residue 2121 LEU Chi-restraints excluded: chain C residue 2201 LEU Chi-restraints excluded: chain C residue 2294 PHE Chi-restraints excluded: chain C residue 2363 CYS Chi-restraints excluded: chain C residue 2408 VAL Chi-restraints excluded: chain C residue 2421 VAL Chi-restraints excluded: chain C residue 2431 ILE Chi-restraints excluded: chain C residue 2434 VAL Chi-restraints excluded: chain C residue 2541 HIS Chi-restraints excluded: chain C residue 2549 VAL Chi-restraints excluded: chain C residue 2599 GLU Chi-restraints excluded: chain C residue 2619 ASP Chi-restraints excluded: chain C residue 2650 VAL Chi-restraints excluded: chain C residue 2722 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 920 random chunks: chunk 579 optimal weight: 20.0000 chunk 777 optimal weight: 3.9990 chunk 223 optimal weight: 0.6980 chunk 672 optimal weight: 2.9990 chunk 107 optimal weight: 10.0000 chunk 202 optimal weight: 2.9990 chunk 731 optimal weight: 0.6980 chunk 305 optimal weight: 0.0770 chunk 750 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 134 optimal weight: 0.7980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 872 ASN ** D1201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 872 ASN ** C1201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2715 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 = 0.4380 r_free = 0.4380 target = 0.154016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.109292 restraints weight = 147702.345| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 2.99 r_work: 0.3631 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 73240 Z= 0.182 Angle : 0.718 13.776 98332 Z= 0.354 Chirality : 0.042 0.332 11280 Planarity : 0.004 0.077 12048 Dihedral : 12.192 169.040 11108 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.20 % Favored : 89.77 % Rotamer: Outliers : 2.54 % Allowed : 26.82 % Favored : 70.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 2.65 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.09), residues: 9088 helix: 0.28 (0.08), residues: 4692 sheet: -1.47 (0.23), residues: 488 loop : -2.70 (0.09), residues: 3908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B2256 HIS 0.006 0.001 HIS A 261 PHE 0.043 0.001 PHE B 839 TYR 0.044 0.001 TYR D2129 ARG 0.017 0.000 ARG A1616 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23255.69 seconds wall clock time: 406 minutes 25.17 seconds (24385.17 seconds total)