Starting phenix.real_space_refine on Mon Dec 30 07:51:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a3t_15123/12_2024/8a3t_15123.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a3t_15123/12_2024/8a3t_15123.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8a3t_15123/12_2024/8a3t_15123.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a3t_15123/12_2024/8a3t_15123.map" model { file = "/net/cci-nas-00/data/ceres_data/8a3t_15123/12_2024/8a3t_15123.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a3t_15123/12_2024/8a3t_15123.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 3 6.06 5 S 314 5.16 5 C 39451 2.51 5 N 10152 2.21 5 O 11431 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 62 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 61351 Number of models: 1 Model: "" Number of chains: 20 Chain: "F" Number of atoms: 3991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 3991 Classifications: {'peptide': 502} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 14, 'TRANS': 487} Chain breaks: 2 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "J" Number of atoms: 4128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 4128 Classifications: {'peptide': 509} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 12, 'TRANS': 496} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "K" Number of atoms: 4102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 4102 Classifications: {'peptide': 505} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 492} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 284 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "W" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 300 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "H" Number of atoms: 4031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 4031 Classifications: {'peptide': 505} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 14, 'TRANS': 490} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "E" Number of atoms: 1091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1091 Classifications: {'peptide': 130} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain breaks: 4 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1743 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 12, 'TRANS': 206} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 3418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3418 Classifications: {'peptide': 440} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 13, 'TRANS': 426} Chain breaks: 3 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'ARG:plan': 3, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "S" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 45 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Chain: "C" Number of atoms: 10863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1410, 10863 Classifications: {'peptide': 1410} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PCIS': 2, 'PTRANS': 57, 'TRANS': 1350} Chain breaks: 12 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 378 Unresolved non-hydrogen angles: 440 Unresolved non-hydrogen dihedrals: 330 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 10, 'PHE:plan': 4, 'GLU:plan': 15, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 210 Chain: "O" Number of atoms: 5288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 658, 5288 Classifications: {'peptide': 658} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 17, 'TRANS': 640} Chain breaks: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 7, 'ASN:plan1': 1, 'GLN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 57 Chain: "D" Number of atoms: 4524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 560, 4524 Classifications: {'peptide': 560} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 7, 'TRANS': 552} Chain breaks: 2 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'HIS:plan': 1, 'ARG:plan': 5, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 75 Chain: "P" Number of atoms: 4518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 556, 4518 Classifications: {'peptide': 556} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 7, 'TRANS': 548} Chain breaks: 2 Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 58 Chain: "I" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 906 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 107} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 784 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "Q" Number of atoms: 5083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 5083 Classifications: {'peptide': 623} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 602} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "T" Number of atoms: 5337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5337 Classifications: {'peptide': 645} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 622} Chain breaks: 6 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "U" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 912 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain breaks: 1 Chain: "U" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 60720 SG CYS U 52 142.793 78.044 149.272 1.00348.11 S ATOM 60739 SG CYS U 55 142.144 79.339 152.679 1.00343.02 S ATOM 60793 SG CYS U 62 144.299 76.191 152.187 1.00324.62 S ATOM 60841 SG CYS U 69 138.651 60.385 145.898 1.00338.42 S ATOM 61029 SG CYS U 91 138.413 63.099 143.300 1.00351.86 S ATOM 61050 SG CYS U 94 137.764 59.437 142.318 1.00357.58 S ATOM 60643 SG CYS U 41 144.011 71.133 146.041 1.00325.82 S ATOM 60661 SG CYS U 44 145.878 74.426 145.487 1.00332.07 S ATOM 60914 SG CYS U 77 142.278 74.555 146.625 1.00331.34 S Time building chain proxies: 24.34, per 1000 atoms: 0.40 Number of scatterers: 61351 At special positions: 0 Unit cell: (258.06, 212.52, 200.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 3 29.99 S 314 16.00 O 11431 8.00 N 10152 7.00 C 39451 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS J 482 " - pdb=" SG CYS J 506 " distance=2.04 Simple disulfide: pdb=" SG CYS K 482 " - pdb=" SG CYS K 506 " distance=1.93 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.12 Conformation dependent library (CDL) restraints added in 5.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN U 201 " pdb="ZN ZN U 201 " - pdb=" ND1 HIS U 76 " pdb="ZN ZN U 201 " - pdb=" SG CYS U 52 " pdb="ZN ZN U 201 " - pdb=" SG CYS U 55 " pdb="ZN ZN U 201 " - pdb=" SG CYS U 62 " pdb=" ZN U 202 " pdb="ZN ZN U 202 " - pdb=" ND1 HIS U 71 " pdb="ZN ZN U 202 " - pdb=" SG CYS U 69 " pdb="ZN ZN U 202 " - pdb=" SG CYS U 91 " pdb="ZN ZN U 202 " - pdb=" SG CYS U 94 " pdb=" ZN U 203 " pdb="ZN ZN U 203 " - pdb=" ND1 HIS U 74 " pdb="ZN ZN U 203 " - pdb=" SG CYS U 44 " pdb="ZN ZN U 203 " - pdb=" SG CYS U 77 " pdb="ZN ZN U 203 " - pdb=" SG CYS U 41 " Number of angles added : 9 15074 Ramachandran restraints generated. 7537 Oldfield, 0 Emsley, 7537 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14752 Finding SS restraints... Secondary structure from input PDB file: 360 helices and 39 sheets defined 65.5% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.96 Creating SS restraints... Processing helix chain 'F' and resid 24 through 40 Processing helix chain 'F' and resid 44 through 61 removed outlier: 4.358A pdb=" N PHE F 48 " --> pdb=" O SER F 44 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU F 49 " --> pdb=" O THR F 45 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ILE F 59 " --> pdb=" O ALA F 55 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU F 60 " --> pdb=" O GLU F 56 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASP F 61 " --> pdb=" O CYS F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 81 Processing helix chain 'F' and resid 83 through 94 removed outlier: 3.860A pdb=" N ALA F 87 " --> pdb=" O SER F 83 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLN F 89 " --> pdb=" O HIS F 85 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE F 94 " --> pdb=" O ILE F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 113 Processing helix chain 'F' and resid 115 through 132 removed outlier: 3.624A pdb=" N ALA F 119 " --> pdb=" O GLY F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 154 through 168 removed outlier: 3.540A pdb=" N CYS F 158 " --> pdb=" O ALA F 154 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP F 168 " --> pdb=" O TYR F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 184 removed outlier: 4.223A pdb=" N GLY F 173 " --> pdb=" O HIS F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 197 removed outlier: 3.870A pdb=" N MET F 197 " --> pdb=" O ALA F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 209 Processing helix chain 'F' and resid 433 through 450 Processing helix chain 'F' and resid 451 through 462 removed outlier: 3.957A pdb=" N ALA F 455 " --> pdb=" O ASN F 451 " (cutoff:3.500A) Processing helix chain 'F' and resid 464 through 469 Processing helix chain 'F' and resid 471 through 485 Processing helix chain 'F' and resid 488 through 502 Processing helix chain 'F' and resid 509 through 519 Processing helix chain 'F' and resid 522 through 536 Processing helix chain 'F' and resid 539 through 554 removed outlier: 3.586A pdb=" N TRP F 543 " --> pdb=" O LYS F 539 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS F 554 " --> pdb=" O LEU F 550 " (cutoff:3.500A) Processing helix chain 'F' and resid 556 through 570 Processing helix chain 'F' and resid 573 through 587 removed outlier: 3.668A pdb=" N TYR F 577 " --> pdb=" O PHE F 573 " (cutoff:3.500A) Processing helix chain 'F' and resid 589 through 604 Processing helix chain 'F' and resid 607 through 622 removed outlier: 3.567A pdb=" N TYR F 611 " --> pdb=" O HIS F 607 " (cutoff:3.500A) Processing helix chain 'F' and resid 623 through 638 removed outlier: 3.658A pdb=" N ALA F 627 " --> pdb=" O GLN F 623 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE F 637 " --> pdb=" O LYS F 633 " (cutoff:3.500A) Processing helix chain 'F' and resid 641 through 656 Processing helix chain 'F' and resid 657 through 672 removed outlier: 3.695A pdb=" N GLN F 663 " --> pdb=" O GLU F 659 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR F 664 " --> pdb=" O LYS F 660 " (cutoff:3.500A) Processing helix chain 'F' and resid 675 through 690 Processing helix chain 'F' and resid 691 through 706 removed outlier: 3.984A pdb=" N GLN F 697 " --> pdb=" O ASN F 693 " (cutoff:3.500A) Processing helix chain 'F' and resid 709 through 724 removed outlier: 3.795A pdb=" N HIS F 713 " --> pdb=" O ASP F 709 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR F 714 " --> pdb=" O ALA F 710 " (cutoff:3.500A) Processing helix chain 'F' and resid 725 through 740 removed outlier: 3.838A pdb=" N LYS F 731 " --> pdb=" O LYS F 727 " (cutoff:3.500A) Processing helix chain 'F' and resid 743 through 755 removed outlier: 3.505A pdb=" N HIS F 755 " --> pdb=" O LEU F 751 " (cutoff:3.500A) Processing helix chain 'J' and resid 230 through 243 Processing helix chain 'J' and resid 245 through 260 Processing helix chain 'J' and resid 262 through 276 Processing helix chain 'J' and resid 278 through 289 removed outlier: 4.118A pdb=" N ASN J 289 " --> pdb=" O LEU J 285 " (cutoff:3.500A) Processing helix chain 'J' and resid 295 through 309 removed outlier: 3.661A pdb=" N ARG J 299 " --> pdb=" O ASN J 295 " (cutoff:3.500A) Processing helix chain 'J' and resid 311 through 320 Processing helix chain 'J' and resid 356 through 372 removed outlier: 3.561A pdb=" N SER J 360 " --> pdb=" O LYS J 356 " (cutoff:3.500A) Processing helix chain 'J' and resid 374 through 389 removed outlier: 3.581A pdb=" N ASP J 380 " --> pdb=" O ASN J 376 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP J 389 " --> pdb=" O ALA J 385 " (cutoff:3.500A) Processing helix chain 'J' and resid 393 through 402 Processing helix chain 'J' and resid 406 through 417 Processing helix chain 'J' and resid 422 through 424 No H-bonds generated for 'chain 'J' and resid 422 through 424' Processing helix chain 'J' and resid 425 through 436 removed outlier: 4.048A pdb=" N ASN J 436 " --> pdb=" O LEU J 432 " (cutoff:3.500A) Processing helix chain 'J' and resid 442 through 457 removed outlier: 3.840A pdb=" N ILE J 446 " --> pdb=" O ASN J 442 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS J 455 " --> pdb=" O GLU J 451 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TYR J 457 " --> pdb=" O LEU J 453 " (cutoff:3.500A) Processing helix chain 'J' and resid 462 through 476 Processing helix chain 'J' and resid 478 through 491 Processing helix chain 'J' and resid 499 through 511 Processing helix chain 'J' and resid 512 through 527 Processing helix chain 'J' and resid 530 through 543 removed outlier: 4.092A pdb=" N TRP J 534 " --> pdb=" O SER J 530 " (cutoff:3.500A) Processing helix chain 'J' and resid 546 through 561 removed outlier: 4.368A pdb=" N LYS J 552 " --> pdb=" O SER J 548 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR J 553 " --> pdb=" O GLU J 549 " (cutoff:3.500A) Processing helix chain 'J' and resid 564 through 578 removed outlier: 3.592A pdb=" N TRP J 568 " --> pdb=" O PHE J 564 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU J 578 " --> pdb=" O THR J 574 " (cutoff:3.500A) Processing helix chain 'J' and resid 583 through 595 Processing helix chain 'J' and resid 598 through 612 removed outlier: 4.324A pdb=" N LYS J 602 " --> pdb=" O MET J 598 " (cutoff:3.500A) Processing helix chain 'J' and resid 615 through 629 Processing helix chain 'J' and resid 632 through 646 Processing helix chain 'J' and resid 650 through 663 Processing helix chain 'J' and resid 672 through 687 Processing helix chain 'J' and resid 689 through 704 removed outlier: 3.689A pdb=" N ALA J 693 " --> pdb=" O GLU J 689 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS J 695 " --> pdb=" O GLU J 691 " (cutoff:3.500A) Processing helix chain 'J' and resid 707 through 721 removed outlier: 3.716A pdb=" N HIS J 711 " --> pdb=" O ASN J 707 " (cutoff:3.500A) Processing helix chain 'J' and resid 723 through 738 removed outlier: 4.525A pdb=" N ASP J 729 " --> pdb=" O GLN J 725 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N HIS J 730 " --> pdb=" O LYS J 726 " (cutoff:3.500A) Processing helix chain 'J' and resid 741 through 758 Processing helix chain 'K' and resid 230 through 243 Processing helix chain 'K' and resid 245 through 261 Processing helix chain 'K' and resid 262 through 276 Processing helix chain 'K' and resid 278 through 289 removed outlier: 3.697A pdb=" N ALA K 282 " --> pdb=" O GLN K 278 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASN K 289 " --> pdb=" O LEU K 285 " (cutoff:3.500A) Processing helix chain 'K' and resid 290 through 294 removed outlier: 4.011A pdb=" N GLY K 293 " --> pdb=" O ASN K 290 " (cutoff:3.500A) Processing helix chain 'K' and resid 296 through 309 removed outlier: 3.756A pdb=" N TYR K 300 " --> pdb=" O ILE K 296 " (cutoff:3.500A) Processing helix chain 'K' and resid 312 through 320 Processing helix chain 'K' and resid 356 through 372 removed outlier: 3.704A pdb=" N SER K 360 " --> pdb=" O LYS K 356 " (cutoff:3.500A) Processing helix chain 'K' and resid 374 through 389 Processing helix chain 'K' and resid 393 through 402 removed outlier: 4.099A pdb=" N LEU K 399 " --> pdb=" O ALA K 395 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS K 402 " --> pdb=" O MET K 398 " (cutoff:3.500A) Processing helix chain 'K' and resid 406 through 417 Processing helix chain 'K' and resid 419 through 423 Processing helix chain 'K' and resid 425 through 436 removed outlier: 4.360A pdb=" N ASN K 431 " --> pdb=" O GLU K 427 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASN K 436 " --> pdb=" O LEU K 432 " (cutoff:3.500A) Processing helix chain 'K' and resid 442 through 455 removed outlier: 3.637A pdb=" N ILE K 446 " --> pdb=" O ASN K 442 " (cutoff:3.500A) Processing helix chain 'K' and resid 462 through 476 Processing helix chain 'K' and resid 478 through 493 removed outlier: 4.109A pdb=" N ASN K 492 " --> pdb=" O THR K 488 " (cutoff:3.500A) Processing helix chain 'K' and resid 499 through 511 Processing helix chain 'K' and resid 513 through 527 removed outlier: 3.566A pdb=" N GLU K 525 " --> pdb=" O HIS K 521 " (cutoff:3.500A) Processing helix chain 'K' and resid 530 through 544 removed outlier: 4.151A pdb=" N TRP K 534 " --> pdb=" O SER K 530 " (cutoff:3.500A) Processing helix chain 'K' and resid 546 through 561 removed outlier: 3.783A pdb=" N LYS K 552 " --> pdb=" O SER K 548 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER K 557 " --> pdb=" O TYR K 553 " (cutoff:3.500A) Processing helix chain 'K' and resid 564 through 579 removed outlier: 3.710A pdb=" N TRP K 568 " --> pdb=" O PHE K 564 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLY K 579 " --> pdb=" O TYR K 575 " (cutoff:3.500A) Processing helix chain 'K' and resid 581 through 595 removed outlier: 3.782A pdb=" N THR K 586 " --> pdb=" O ASP K 582 " (cutoff:3.500A) Processing helix chain 'K' and resid 598 through 613 removed outlier: 4.201A pdb=" N LYS K 602 " --> pdb=" O MET K 598 " (cutoff:3.500A) Processing helix chain 'K' and resid 614 through 627 removed outlier: 3.853A pdb=" N ALA K 618 " --> pdb=" O SER K 614 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N SER K 620 " --> pdb=" O ASN K 616 " (cutoff:3.500A) Processing helix chain 'K' and resid 632 through 646 removed outlier: 3.571A pdb=" N LEU K 636 " --> pdb=" O ASP K 632 " (cutoff:3.500A) Processing helix chain 'K' and resid 648 through 664 removed outlier: 3.826A pdb=" N ALA K 652 " --> pdb=" O GLU K 648 " (cutoff:3.500A) Processing helix chain 'K' and resid 672 through 687 Processing helix chain 'K' and resid 690 through 704 Processing helix chain 'K' and resid 707 through 721 Processing helix chain 'K' and resid 723 through 738 Processing helix chain 'K' and resid 741 through 758 removed outlier: 3.796A pdb=" N THR K 745 " --> pdb=" O ASN K 741 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ALA K 746 " --> pdb=" O SER K 742 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 35 removed outlier: 3.902A pdb=" N VAL G 16 " --> pdb=" O SER G 12 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLN G 30 " --> pdb=" O GLN G 26 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N GLN G 31 " --> pdb=" O LYS G 27 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LEU G 32 " --> pdb=" O LEU G 28 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'W' and resid 12 through 37 removed outlier: 3.942A pdb=" N VAL W 16 " --> pdb=" O SER W 12 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLN W 30 " --> pdb=" O GLN W 26 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN W 31 " --> pdb=" O LYS W 27 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU W 32 " --> pdb=" O LEU W 28 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASN W 33 " --> pdb=" O LYS W 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 40 Processing helix chain 'H' and resid 43 through 57 Processing helix chain 'H' and resid 64 through 81 removed outlier: 4.024A pdb=" N SER H 68 " --> pdb=" O SER H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 94 removed outlier: 3.726A pdb=" N PHE H 94 " --> pdb=" O ILE H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 98 through 113 Processing helix chain 'H' and resid 115 through 131 removed outlier: 3.897A pdb=" N SER H 125 " --> pdb=" O LEU H 121 " (cutoff:3.500A) Processing helix chain 'H' and resid 152 through 167 removed outlier: 3.936A pdb=" N CYS H 158 " --> pdb=" O ALA H 154 " (cutoff:3.500A) Processing helix chain 'H' and resid 170 through 184 Processing helix chain 'H' and resid 185 through 187 No H-bonds generated for 'chain 'H' and resid 185 through 187' Processing helix chain 'H' and resid 188 through 198 removed outlier: 3.673A pdb=" N GLU H 192 " --> pdb=" O TRP H 188 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 209 Processing helix chain 'H' and resid 433 through 449 Processing helix chain 'H' and resid 451 through 463 removed outlier: 3.629A pdb=" N ILE H 463 " --> pdb=" O PHE H 459 " (cutoff:3.500A) Processing helix chain 'H' and resid 464 through 469 Processing helix chain 'H' and resid 471 through 485 Processing helix chain 'H' and resid 487 through 502 removed outlier: 3.544A pdb=" N SER H 491 " --> pdb=" O ASN H 487 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU H 492 " --> pdb=" O TYR H 488 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LYS H 493 " --> pdb=" O ASP H 489 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TYR H 494 " --> pdb=" O MET H 490 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ARG H 497 " --> pdb=" O LYS H 493 " (cutoff:3.500A) Processing helix chain 'H' and resid 509 through 520 Processing helix chain 'H' and resid 521 through 536 Processing helix chain 'H' and resid 539 through 554 removed outlier: 3.668A pdb=" N TRP H 543 " --> pdb=" O LYS H 539 " (cutoff:3.500A) Processing helix chain 'H' and resid 556 through 570 Processing helix chain 'H' and resid 573 through 587 removed outlier: 3.698A pdb=" N TYR H 577 " --> pdb=" O PHE H 573 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER H 585 " --> pdb=" O GLY H 581 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N SER H 586 " --> pdb=" O HIS H 582 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN H 587 " --> pdb=" O GLU H 583 " (cutoff:3.500A) Processing helix chain 'H' and resid 590 through 604 removed outlier: 3.656A pdb=" N CYS H 603 " --> pdb=" O LYS H 599 " (cutoff:3.500A) Processing helix chain 'H' and resid 608 through 621 removed outlier: 3.534A pdb=" N LEU H 621 " --> pdb=" O SER H 617 " (cutoff:3.500A) Processing helix chain 'H' and resid 623 through 638 removed outlier: 3.634A pdb=" N LYS H 633 " --> pdb=" O LEU H 629 " (cutoff:3.500A) Processing helix chain 'H' and resid 642 through 656 Processing helix chain 'H' and resid 657 through 672 Processing helix chain 'H' and resid 675 through 690 Processing helix chain 'H' and resid 691 through 706 removed outlier: 4.224A pdb=" N GLN H 697 " --> pdb=" O ASN H 693 " (cutoff:3.500A) Processing helix chain 'H' and resid 709 through 724 removed outlier: 3.576A pdb=" N HIS H 713 " --> pdb=" O ASP H 709 " (cutoff:3.500A) Processing helix chain 'H' and resid 725 through 740 Processing helix chain 'H' and resid 743 through 755 removed outlier: 3.670A pdb=" N ILE H 747 " --> pdb=" O GLY H 743 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 123 Processing helix chain 'E' and resid 169 through 178 Processing helix chain 'E' and resid 192 through 207 removed outlier: 3.517A pdb=" N ALA E 202 " --> pdb=" O HIS E 198 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU E 203 " --> pdb=" O GLU E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 216 Processing helix chain 'E' and resid 217 through 240 removed outlier: 3.653A pdb=" N LEU E 221 " --> pdb=" O GLN E 217 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N HIS E 222 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLU E 223 " --> pdb=" O HIS E 219 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU E 224 " --> pdb=" O HIS E 220 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN E 229 " --> pdb=" O TYR E 225 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS E 237 " --> pdb=" O LYS E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 259 removed outlier: 4.045A pdb=" N ARG E 254 " --> pdb=" O ARG E 250 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ARG E 255 " --> pdb=" O ASP E 251 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N HIS E 256 " --> pdb=" O LYS E 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 5 through 14 Processing helix chain 'A' and resid 40 through 47 Processing helix chain 'A' and resid 61 through 79 removed outlier: 3.731A pdb=" N ALA A 79 " --> pdb=" O ILE A 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 74 removed outlier: 3.695A pdb=" N VAL B 70 " --> pdb=" O PHE B 66 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER B 74 " --> pdb=" O VAL B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 111 Processing helix chain 'B' and resid 112 through 118 Processing helix chain 'B' and resid 124 through 132 Processing helix chain 'B' and resid 214 through 226 removed outlier: 3.847A pdb=" N MET B 226 " --> pdb=" O PHE B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 239 Processing helix chain 'B' and resid 557 through 563 removed outlier: 3.531A pdb=" N ALA B 561 " --> pdb=" O LEU B 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 397 removed outlier: 3.683A pdb=" N LYS C 397 " --> pdb=" O SER C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 435 removed outlier: 3.554A pdb=" N ASP C 434 " --> pdb=" O PRO C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 442 removed outlier: 3.561A pdb=" N LYS C 439 " --> pdb=" O SER C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 460 No H-bonds generated for 'chain 'C' and resid 458 through 460' Processing helix chain 'C' and resid 507 through 513 removed outlier: 3.561A pdb=" N THR C 510 " --> pdb=" O GLU C 507 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LYS C 511 " --> pdb=" O GLU C 508 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N GLN C 512 " --> pdb=" O LEU C 509 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ASN C 513 " --> pdb=" O THR C 510 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 507 through 513' Processing helix chain 'C' and resid 514 through 520 Processing helix chain 'C' and resid 529 through 541 removed outlier: 3.568A pdb=" N CYS C 533 " --> pdb=" O PHE C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 564 Processing helix chain 'C' and resid 571 through 588 removed outlier: 4.038A pdb=" N GLU C 575 " --> pdb=" O GLY C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 601 Processing helix chain 'C' and resid 601 through 606 Processing helix chain 'C' and resid 607 through 616 Processing helix chain 'C' and resid 616 through 639 removed outlier: 3.542A pdb=" N THR C 620 " --> pdb=" O ASP C 616 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N LEU C 624 " --> pdb=" O THR C 620 " (cutoff:3.500A) Proline residue: C 625 - end of helix Processing helix chain 'C' and resid 640 through 643 removed outlier: 6.395A pdb=" N LEU C 643 " --> pdb=" O LEU C 640 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 640 through 643' Processing helix chain 'C' and resid 644 through 663 removed outlier: 3.530A pdb=" N HIS C 648 " --> pdb=" O CYS C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 665 through 671 removed outlier: 3.553A pdb=" N GLN C 669 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 702 through 710 Processing helix chain 'C' and resid 731 through 737 removed outlier: 3.744A pdb=" N GLU C 735 " --> pdb=" O ASP C 731 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG C 737 " --> pdb=" O GLN C 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 753 removed outlier: 3.850A pdb=" N HIS C 753 " --> pdb=" O TYR C 749 " (cutoff:3.500A) Processing helix chain 'C' and resid 760 through 769 removed outlier: 4.446A pdb=" N GLY C 764 " --> pdb=" O ASP C 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 772 through 777 Processing helix chain 'C' and resid 783 through 798 removed outlier: 3.917A pdb=" N LEU C 787 " --> pdb=" O ILE C 783 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASP C 796 " --> pdb=" O LYS C 792 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS C 797 " --> pdb=" O ILE C 793 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU C 798 " --> pdb=" O LEU C 794 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 808 removed outlier: 4.279A pdb=" N LEU C 807 " --> pdb=" O ASN C 804 " (cutoff:3.500A) Processing helix chain 'C' and resid 810 through 826 removed outlier: 3.524A pdb=" N GLN C 814 " --> pdb=" O ARG C 810 " (cutoff:3.500A) Processing helix chain 'C' and resid 859 through 872 removed outlier: 3.818A pdb=" N SER C 872 " --> pdb=" O VAL C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 906 Processing helix chain 'C' and resid 910 through 920 Processing helix chain 'C' and resid 935 through 965 removed outlier: 4.835A pdb=" N GLY C 958 " --> pdb=" O THR C 954 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N VAL C 959 " --> pdb=" O CYS C 955 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLY C 960 " --> pdb=" O THR C 956 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA C 963 " --> pdb=" O VAL C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 1003 through 1021 removed outlier: 3.959A pdb=" N VAL C1007 " --> pdb=" O ALA C1003 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLU C1008 " --> pdb=" O HIS C1004 " (cutoff:3.500A) Processing helix chain 'C' and resid 1030 through 1037 removed outlier: 3.828A pdb=" N ILE C1034 " --> pdb=" O THR C1030 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA C1035 " --> pdb=" O GLY C1031 " (cutoff:3.500A) Processing helix chain 'C' and resid 1043 through 1056 Processing helix chain 'C' and resid 1063 through 1072 removed outlier: 3.886A pdb=" N ILE C1067 " --> pdb=" O GLU C1063 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TYR C1068 " --> pdb=" O GLU C1064 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ASN C1069 " --> pdb=" O TRP C1065 " (cutoff:3.500A) Processing helix chain 'C' and resid 1075 through 1091 Processing helix chain 'C' and resid 1095 through 1106 removed outlier: 4.797A pdb=" N VAL C1101 " --> pdb=" O LYS C1097 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE C1102 " --> pdb=" O LEU C1098 " (cutoff:3.500A) Processing helix chain 'C' and resid 1120 through 1135 Processing helix chain 'C' and resid 1140 through 1153 removed outlier: 4.069A pdb=" N SER C1146 " --> pdb=" O ARG C1142 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL C1152 " --> pdb=" O PHE C1148 " (cutoff:3.500A) Processing helix chain 'C' and resid 1164 through 1179 Processing helix chain 'C' and resid 1212 through 1230 Processing helix chain 'C' and resid 1242 through 1255 removed outlier: 4.653A pdb=" N GLY C1246 " --> pdb=" O ASN C1242 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE C1255 " --> pdb=" O ILE C1251 " (cutoff:3.500A) Processing helix chain 'C' and resid 1260 through 1268 Processing helix chain 'C' and resid 1270 through 1277 removed outlier: 3.665A pdb=" N LYS C1276 " --> pdb=" O LYS C1272 " (cutoff:3.500A) Processing helix chain 'C' and resid 1283 through 1297 removed outlier: 4.138A pdb=" N MET C1287 " --> pdb=" O PRO C1283 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR C1288 " --> pdb=" O GLU C1284 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU C1297 " --> pdb=" O SER C1293 " (cutoff:3.500A) Processing helix chain 'C' and resid 1304 through 1309 removed outlier: 3.640A pdb=" N ILE C1308 " --> pdb=" O ASP C1304 " (cutoff:3.500A) Processing helix chain 'C' and resid 1322 through 1324 No H-bonds generated for 'chain 'C' and resid 1322 through 1324' Processing helix chain 'C' and resid 1325 through 1343 removed outlier: 3.710A pdb=" N TYR C1329 " --> pdb=" O LEU C1325 " (cutoff:3.500A) Processing helix chain 'C' and resid 1349 through 1363 Processing helix chain 'C' and resid 1373 through 1398 Processing helix chain 'C' and resid 1403 through 1415 removed outlier: 3.613A pdb=" N LEU C1407 " --> pdb=" O ASP C1403 " (cutoff:3.500A) Processing helix chain 'C' and resid 1476 through 1505 removed outlier: 3.710A pdb=" N ASP C1486 " --> pdb=" O GLU C1482 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N SER C1496 " --> pdb=" O GLY C1492 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR C1497 " --> pdb=" O LYS C1493 " (cutoff:3.500A) Processing helix chain 'C' and resid 1506 through 1509 Processing helix chain 'C' and resid 1517 through 1528 removed outlier: 3.645A pdb=" N ILE C1521 " --> pdb=" O THR C1517 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA C1522 " --> pdb=" O LEU C1518 " (cutoff:3.500A) Processing helix chain 'C' and resid 1538 through 1543 removed outlier: 3.611A pdb=" N LEU C1541 " --> pdb=" O LEU C1538 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N HIS C1543 " --> pdb=" O GLU C1540 " (cutoff:3.500A) Processing helix chain 'C' and resid 1544 through 1547 removed outlier: 3.554A pdb=" N MET C1547 " --> pdb=" O PHE C1544 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1544 through 1547' Processing helix chain 'C' and resid 1595 through 1599 Processing helix chain 'C' and resid 1621 through 1626 Processing helix chain 'C' and resid 1653 through 1670 Processing helix chain 'C' and resid 1681 through 1690 Processing helix chain 'C' and resid 1693 through 1704 Processing helix chain 'C' and resid 1712 through 1724 Processing helix chain 'C' and resid 1730 through 1744 Processing helix chain 'O' and resid 14 through 30 removed outlier: 3.501A pdb=" N CYS O 19 " --> pdb=" O PRO O 15 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE O 20 " --> pdb=" O TYR O 16 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN O 30 " --> pdb=" O ALA O 26 " (cutoff:3.500A) Processing helix chain 'O' and resid 37 through 49 removed outlier: 4.076A pdb=" N SER O 46 " --> pdb=" O LEU O 42 " (cutoff:3.500A) Proline residue: O 47 - end of helix Processing helix chain 'O' and resid 77 through 87 removed outlier: 3.689A pdb=" N ILE O 84 " --> pdb=" O ASN O 80 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU O 85 " --> pdb=" O ILE O 81 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASP O 87 " --> pdb=" O ARG O 83 " (cutoff:3.500A) Processing helix chain 'O' and resid 90 through 105 removed outlier: 3.541A pdb=" N ILE O 94 " --> pdb=" O ASP O 90 " (cutoff:3.500A) Processing helix chain 'O' and resid 107 through 121 Processing helix chain 'O' and resid 126 through 130 Processing helix chain 'O' and resid 145 through 160 removed outlier: 3.663A pdb=" N PHE O 150 " --> pdb=" O PHE O 146 " (cutoff:3.500A) Processing helix chain 'O' and resid 162 through 182 removed outlier: 3.581A pdb=" N TRP O 170 " --> pdb=" O ARG O 166 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE O 180 " --> pdb=" O PHE O 176 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HIS O 182 " --> pdb=" O THR O 178 " (cutoff:3.500A) Processing helix chain 'O' and resid 183 through 189 removed outlier: 3.525A pdb=" N LEU O 187 " --> pdb=" O THR O 183 " (cutoff:3.500A) Processing helix chain 'O' and resid 193 through 204 removed outlier: 3.613A pdb=" N LEU O 202 " --> pdb=" O VAL O 198 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA O 204 " --> pdb=" O ASN O 200 " (cutoff:3.500A) Processing helix chain 'O' and resid 211 through 224 removed outlier: 3.751A pdb=" N MET O 215 " --> pdb=" O GLU O 211 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE O 218 " --> pdb=" O GLN O 214 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN O 223 " --> pdb=" O PHE O 219 " (cutoff:3.500A) Processing helix chain 'O' and resid 243 through 260 Processing helix chain 'O' and resid 279 through 288 Processing helix chain 'O' and resid 293 through 298 Processing helix chain 'O' and resid 299 through 312 removed outlier: 4.115A pdb=" N ILE O 303 " --> pdb=" O PRO O 299 " (cutoff:3.500A) Processing helix chain 'O' and resid 314 through 333 removed outlier: 3.616A pdb=" N ALA O 318 " --> pdb=" O SER O 314 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER O 330 " --> pdb=" O PHE O 326 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR O 331 " --> pdb=" O ASP O 327 " (cutoff:3.500A) Processing helix chain 'O' and resid 337 through 352 removed outlier: 4.553A pdb=" N LEU O 343 " --> pdb=" O HIS O 339 " (cutoff:3.500A) Processing helix chain 'O' and resid 355 through 373 removed outlier: 3.550A pdb=" N ASN O 360 " --> pdb=" O ASP O 356 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU O 364 " --> pdb=" O ASN O 360 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA O 365 " --> pdb=" O SER O 361 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N THR O 366 " --> pdb=" O PHE O 362 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG O 367 " --> pdb=" O GLU O 363 " (cutoff:3.500A) Processing helix chain 'O' and resid 375 through 392 removed outlier: 3.798A pdb=" N ASN O 379 " --> pdb=" O MET O 375 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU O 380 " --> pdb=" O GLU O 376 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE O 386 " --> pdb=" O MET O 382 " (cutoff:3.500A) Processing helix chain 'O' and resid 393 through 396 Processing helix chain 'O' and resid 402 through 412 removed outlier: 3.632A pdb=" N ILE O 406 " --> pdb=" O THR O 402 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASN O 412 " --> pdb=" O LYS O 408 " (cutoff:3.500A) Processing helix chain 'O' and resid 420 through 436 removed outlier: 3.607A pdb=" N LYS O 427 " --> pdb=" O SER O 423 " (cutoff:3.500A) Processing helix chain 'O' and resid 439 through 457 removed outlier: 3.554A pdb=" N ASN O 457 " --> pdb=" O ILE O 453 " (cutoff:3.500A) Processing helix chain 'O' and resid 462 through 481 removed outlier: 3.512A pdb=" N LEU O 480 " --> pdb=" O PHE O 476 " (cutoff:3.500A) Processing helix chain 'O' and resid 482 through 491 removed outlier: 3.542A pdb=" N VAL O 488 " --> pdb=" O SER O 484 " (cutoff:3.500A) Processing helix chain 'O' and resid 505 through 522 Processing helix chain 'O' and resid 524 through 536 removed outlier: 3.584A pdb=" N LYS O 534 " --> pdb=" O GLN O 530 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU O 536 " --> pdb=" O LEU O 532 " (cutoff:3.500A) Processing helix chain 'O' and resid 541 through 560 removed outlier: 3.603A pdb=" N ASN O 547 " --> pdb=" O ASP O 543 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL O 553 " --> pdb=" O LYS O 549 " (cutoff:3.500A) Processing helix chain 'O' and resid 562 through 579 removed outlier: 3.509A pdb=" N ASN O 570 " --> pdb=" O MET O 566 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLN O 571 " --> pdb=" O ARG O 567 " (cutoff:3.500A) Processing helix chain 'O' and resid 582 through 600 removed outlier: 3.546A pdb=" N GLU O 592 " --> pdb=" O LYS O 588 " (cutoff:3.500A) Processing helix chain 'O' and resid 603 through 605 No H-bonds generated for 'chain 'O' and resid 603 through 605' Processing helix chain 'O' and resid 606 through 621 removed outlier: 3.558A pdb=" N GLU O 616 " --> pdb=" O LYS O 612 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU O 619 " --> pdb=" O ASP O 615 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE O 620 " --> pdb=" O GLU O 616 " (cutoff:3.500A) Processing helix chain 'O' and resid 622 through 640 removed outlier: 3.622A pdb=" N GLN O 639 " --> pdb=" O GLU O 635 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL O 640 " --> pdb=" O VAL O 636 " (cutoff:3.500A) Processing helix chain 'O' and resid 642 through 653 removed outlier: 3.738A pdb=" N ALA O 646 " --> pdb=" O LYS O 642 " (cutoff:3.500A) Processing helix chain 'O' and resid 653 through 658 removed outlier: 3.745A pdb=" N LEU O 658 " --> pdb=" O LEU O 654 " (cutoff:3.500A) Processing helix chain 'O' and resid 663 through 675 Processing helix chain 'D' and resid 5 through 27 removed outlier: 3.623A pdb=" N ILE D 15 " --> pdb=" O HIS D 11 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU D 23 " --> pdb=" O LYS D 19 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU D 24 " --> pdb=" O ALA D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 42 removed outlier: 3.899A pdb=" N SER D 33 " --> pdb=" O LEU D 29 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N TRP D 35 " --> pdb=" O GLY D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 98 removed outlier: 3.520A pdb=" N ASP D 87 " --> pdb=" O GLU D 83 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU D 88 " --> pdb=" O THR D 84 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU D 90 " --> pdb=" O TYR D 86 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASP D 97 " --> pdb=" O SER D 93 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA D 98 " --> pdb=" O THR D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 108 Processing helix chain 'D' and resid 113 through 136 removed outlier: 3.681A pdb=" N LEU D 119 " --> pdb=" O TYR D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 201 removed outlier: 4.017A pdb=" N ILE D 190 " --> pdb=" O ASN D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 227 removed outlier: 3.531A pdb=" N TYR D 219 " --> pdb=" O ALA D 215 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU D 220 " --> pdb=" O LEU D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 245 Processing helix chain 'D' and resid 248 through 259 removed outlier: 3.731A pdb=" N LEU D 259 " --> pdb=" O LEU D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 272 Processing helix chain 'D' and resid 294 through 307 removed outlier: 4.070A pdb=" N GLU D 305 " --> pdb=" O LEU D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 325 Processing helix chain 'D' and resid 328 through 342 removed outlier: 3.504A pdb=" N LYS D 332 " --> pdb=" O PHE D 328 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER D 339 " --> pdb=" O ASN D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 359 removed outlier: 3.552A pdb=" N ASP D 354 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE D 355 " --> pdb=" O ARG D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 377 removed outlier: 3.794A pdb=" N TYR D 369 " --> pdb=" O ASP D 365 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR D 374 " --> pdb=" O SER D 370 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL D 375 " --> pdb=" O ASN D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 393 removed outlier: 3.729A pdb=" N ILE D 392 " --> pdb=" O PHE D 388 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASP D 393 " --> pdb=" O VAL D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 410 removed outlier: 3.591A pdb=" N ILE D 403 " --> pdb=" O THR D 399 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ALA D 404 " --> pdb=" O CYS D 400 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG D 410 " --> pdb=" O TYR D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 427 removed outlier: 4.184A pdb=" N MET D 418 " --> pdb=" O GLU D 414 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR D 419 " --> pdb=" O LYS D 415 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASP D 427 " --> pdb=" O ALA D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 443 removed outlier: 4.399A pdb=" N THR D 435 " --> pdb=" O THR D 431 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU D 436 " --> pdb=" O ASN D 432 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE D 441 " --> pdb=" O MET D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 461 removed outlier: 3.570A pdb=" N ALA D 450 " --> pdb=" O ASN D 446 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU D 452 " --> pdb=" O HIS D 448 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA D 457 " --> pdb=" O CYS D 453 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL D 458 " --> pdb=" O TYR D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 478 removed outlier: 3.546A pdb=" N ALA D 474 " --> pdb=" O GLY D 470 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR D 475 " --> pdb=" O LEU D 471 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU D 478 " --> pdb=" O ALA D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 481 through 483 No H-bonds generated for 'chain 'D' and resid 481 through 483' Processing helix chain 'D' and resid 484 through 495 removed outlier: 3.683A pdb=" N THR D 493 " --> pdb=" O GLN D 489 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU D 494 " --> pdb=" O LYS D 490 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS D 495 " --> pdb=" O ALA D 491 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 512 removed outlier: 3.715A pdb=" N TRP D 502 " --> pdb=" O ASP D 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 529 removed outlier: 4.239A pdb=" N LYS D 520 " --> pdb=" O VAL D 516 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS D 527 " --> pdb=" O LYS D 523 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 534 No H-bonds generated for 'chain 'D' and resid 532 through 534' Processing helix chain 'D' and resid 535 through 550 removed outlier: 3.562A pdb=" N TYR D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR D 546 " --> pdb=" O LEU D 542 " (cutoff:3.500A) Processing helix chain 'D' and resid 551 through 569 removed outlier: 4.201A pdb=" N LYS D 557 " --> pdb=" O GLN D 553 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N PHE D 558 " --> pdb=" O GLU D 554 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLU D 566 " --> pdb=" O CYS D 562 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU D 567 " --> pdb=" O VAL D 563 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 591 removed outlier: 3.839A pdb=" N ALA D 580 " --> pdb=" O GLU D 576 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS D 590 " --> pdb=" O ILE D 586 " (cutoff:3.500A) Processing helix chain 'D' and resid 593 through 604 removed outlier: 3.953A pdb=" N ASP D 599 " --> pdb=" O GLN D 595 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N TYR D 600 " --> pdb=" O LEU D 596 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA D 601 " --> pdb=" O ALA D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 608 through 626 removed outlier: 3.709A pdb=" N GLU D 613 " --> pdb=" O SER D 609 " (cutoff:3.500A) Processing helix chain 'P' and resid 7 through 27 removed outlier: 3.818A pdb=" N HIS P 11 " --> pdb=" O ASP P 7 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU P 24 " --> pdb=" O ALA P 20 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER P 25 " --> pdb=" O ALA P 21 " (cutoff:3.500A) Processing helix chain 'P' and resid 29 through 43 removed outlier: 3.811A pdb=" N ALA P 41 " --> pdb=" O ALA P 37 " (cutoff:3.500A) Processing helix chain 'P' and resid 82 through 98 removed outlier: 3.801A pdb=" N ASP P 87 " --> pdb=" O GLU P 83 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N LEU P 88 " --> pdb=" O THR P 84 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR P 89 " --> pdb=" O GLU P 85 " (cutoff:3.500A) Processing helix chain 'P' and resid 100 through 108 removed outlier: 3.755A pdb=" N CYS P 104 " --> pdb=" O GLU P 100 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL P 105 " --> pdb=" O PHE P 101 " (cutoff:3.500A) Processing helix chain 'P' and resid 116 through 130 removed outlier: 3.549A pdb=" N LYS P 120 " --> pdb=" O LEU P 116 " (cutoff:3.500A) Processing helix chain 'P' and resid 134 through 143 removed outlier: 3.733A pdb=" N LEU P 140 " --> pdb=" O MET P 136 " (cutoff:3.500A) Processing helix chain 'P' and resid 184 through 201 removed outlier: 3.908A pdb=" N SER P 188 " --> pdb=" O GLN P 184 " (cutoff:3.500A) Processing helix chain 'P' and resid 211 through 228 removed outlier: 3.721A pdb=" N ALA P 215 " --> pdb=" O ASP P 211 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU P 216 " --> pdb=" O LEU P 212 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU P 228 " --> pdb=" O ILE P 224 " (cutoff:3.500A) Processing helix chain 'P' and resid 230 through 245 removed outlier: 4.027A pdb=" N SER P 236 " --> pdb=" O SER P 232 " (cutoff:3.500A) Processing helix chain 'P' and resid 248 through 257 removed outlier: 3.854A pdb=" N TRP P 252 " --> pdb=" O ASN P 248 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU P 254 " --> pdb=" O SER P 250 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASP P 257 " --> pdb=" O LEU P 253 " (cutoff:3.500A) Processing helix chain 'P' and resid 262 through 274 removed outlier: 4.108A pdb=" N LEU P 266 " --> pdb=" O VAL P 262 " (cutoff:3.500A) Processing helix chain 'P' and resid 295 through 307 removed outlier: 3.550A pdb=" N GLU P 305 " --> pdb=" O LEU P 301 " (cutoff:3.500A) Processing helix chain 'P' and resid 313 through 324 removed outlier: 3.537A pdb=" N PHE P 320 " --> pdb=" O GLU P 316 " (cutoff:3.500A) Processing helix chain 'P' and resid 328 through 342 removed outlier: 3.874A pdb=" N SER P 339 " --> pdb=" O ASN P 335 " (cutoff:3.500A) Processing helix chain 'P' and resid 344 through 359 removed outlier: 3.765A pdb=" N SER P 350 " --> pdb=" O VAL P 346 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE P 355 " --> pdb=" O ARG P 351 " (cutoff:3.500A) Processing helix chain 'P' and resid 366 through 377 Processing helix chain 'P' and resid 378 through 393 removed outlier: 3.502A pdb=" N TYR P 384 " --> pdb=" O SER P 380 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE P 392 " --> pdb=" O PHE P 388 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP P 393 " --> pdb=" O VAL P 389 " (cutoff:3.500A) Processing helix chain 'P' and resid 396 through 410 removed outlier: 3.524A pdb=" N SER P 408 " --> pdb=" O ALA P 404 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA P 409 " --> pdb=" O ASN P 405 " (cutoff:3.500A) Processing helix chain 'P' and resid 412 through 428 removed outlier: 4.026A pdb=" N ILE P 417 " --> pdb=" O HIS P 413 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N MET P 418 " --> pdb=" O GLU P 414 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TYR P 419 " --> pdb=" O LYS P 415 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU P 426 " --> pdb=" O ARG P 422 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASP P 427 " --> pdb=" O ALA P 423 " (cutoff:3.500A) Processing helix chain 'P' and resid 432 through 444 removed outlier: 3.639A pdb=" N LEU P 436 " --> pdb=" O ASN P 432 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU P 444 " --> pdb=" O GLU P 440 " (cutoff:3.500A) Processing helix chain 'P' and resid 448 through 461 removed outlier: 3.727A pdb=" N ALA P 457 " --> pdb=" O CYS P 453 " (cutoff:3.500A) Processing helix chain 'P' and resid 464 through 478 removed outlier: 3.679A pdb=" N TRP P 468 " --> pdb=" O ASP P 464 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU P 477 " --> pdb=" O GLN P 473 " (cutoff:3.500A) Processing helix chain 'P' and resid 481 through 495 removed outlier: 3.645A pdb=" N LEU P 485 " --> pdb=" O HIS P 481 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N TYR P 486 " --> pdb=" O LEU P 482 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR P 487 " --> pdb=" O TYR P 483 " (cutoff:3.500A) Processing helix chain 'P' and resid 498 through 510 removed outlier: 4.128A pdb=" N TRP P 502 " --> pdb=" O ASP P 498 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN P 503 " --> pdb=" O ARG P 499 " (cutoff:3.500A) Processing helix chain 'P' and resid 511 through 513 No H-bonds generated for 'chain 'P' and resid 511 through 513' Processing helix chain 'P' and resid 514 through 529 removed outlier: 3.944A pdb=" N ALA P 518 " --> pdb=" O ASN P 514 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE P 519 " --> pdb=" O LYS P 515 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS P 520 " --> pdb=" O VAL P 516 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS P 527 " --> pdb=" O LYS P 523 " (cutoff:3.500A) Processing helix chain 'P' and resid 534 through 549 removed outlier: 4.303A pdb=" N ILE P 538 " --> pdb=" O GLN P 534 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR P 540 " --> pdb=" O THR P 536 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG P 541 " --> pdb=" O SER P 537 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU P 549 " --> pdb=" O LEU P 545 " (cutoff:3.500A) Processing helix chain 'P' and resid 551 through 569 removed outlier: 3.683A pdb=" N GLU P 567 " --> pdb=" O VAL P 563 " (cutoff:3.500A) Processing helix chain 'P' and resid 574 through 591 Processing helix chain 'P' and resid 593 through 602 removed outlier: 3.523A pdb=" N TYR P 600 " --> pdb=" O LEU P 596 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N MET P 602 " --> pdb=" O TYR P 598 " (cutoff:3.500A) Processing helix chain 'P' and resid 608 through 626 Processing helix chain 'I' and resid 18 through 24 removed outlier: 3.798A pdb=" N ILE I 22 " --> pdb=" O PRO I 19 " (cutoff:3.500A) Processing helix chain 'I' and resid 26 through 30 removed outlier: 3.620A pdb=" N ASP I 30 " --> pdb=" O TRP I 27 " (cutoff:3.500A) Processing helix chain 'I' and resid 38 through 45 removed outlier: 4.236A pdb=" N THR I 42 " --> pdb=" O VAL I 38 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N MET I 43 " --> pdb=" O ALA I 39 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 90 Processing helix chain 'I' and resid 93 through 100 Processing helix chain 'I' and resid 148 through 160 removed outlier: 3.823A pdb=" N GLN I 152 " --> pdb=" O ARG I 148 " (cutoff:3.500A) Processing helix chain 'N' and resid 8 through 20 removed outlier: 3.643A pdb=" N SER N 20 " --> pdb=" O LYS N 16 " (cutoff:3.500A) Processing helix chain 'N' and resid 85 through 87 No H-bonds generated for 'chain 'N' and resid 85 through 87' Processing helix chain 'N' and resid 95 through 113 Proline residue: N 109 - end of helix removed outlier: 4.027A pdb=" N ARG N 112 " --> pdb=" O LEU N 108 " (cutoff:3.500A) Processing helix chain 'N' and resid 114 through 116 No H-bonds generated for 'chain 'N' and resid 114 through 116' Processing helix chain 'N' and resid 128 through 140 removed outlier: 3.610A pdb=" N ARG N 139 " --> pdb=" O ARG N 135 " (cutoff:3.500A) Processing helix chain 'Q' and resid 45 through 47 No H-bonds generated for 'chain 'Q' and resid 45 through 47' Processing helix chain 'Q' and resid 220 through 226 Processing helix chain 'Q' and resid 226 through 257 removed outlier: 3.617A pdb=" N MET Q 237 " --> pdb=" O LEU Q 233 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS Q 240 " --> pdb=" O ILE Q 236 " (cutoff:3.500A) Processing helix chain 'Q' and resid 257 through 270 removed outlier: 3.788A pdb=" N TYR Q 261 " --> pdb=" O LEU Q 257 " (cutoff:3.500A) Processing helix chain 'Q' and resid 274 through 288 removed outlier: 3.541A pdb=" N LEU Q 278 " --> pdb=" O GLY Q 274 " (cutoff:3.500A) Processing helix chain 'Q' and resid 292 through 301 Processing helix chain 'Q' and resid 303 through 329 removed outlier: 3.573A pdb=" N PHE Q 308 " --> pdb=" O GLY Q 304 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG Q 310 " --> pdb=" O LYS Q 306 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N THR Q 322 " --> pdb=" O ALA Q 318 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN Q 324 " --> pdb=" O GLN Q 320 " (cutoff:3.500A) Processing helix chain 'Q' and resid 329 through 355 removed outlier: 3.513A pdb=" N LEU Q 348 " --> pdb=" O LEU Q 344 " (cutoff:3.500A) Processing helix chain 'Q' and resid 363 through 411 removed outlier: 3.618A pdb=" N TRP Q 400 " --> pdb=" O LYS Q 396 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ASP Q 403 " --> pdb=" O ILE Q 399 " (cutoff:3.500A) Processing helix chain 'Q' and resid 418 through 422 Processing helix chain 'Q' and resid 424 through 437 removed outlier: 3.726A pdb=" N PHE Q 433 " --> pdb=" O LEU Q 429 " (cutoff:3.500A) Processing helix chain 'Q' and resid 438 through 443 removed outlier: 3.712A pdb=" N GLU Q 443 " --> pdb=" O LYS Q 439 " (cutoff:3.500A) Processing helix chain 'Q' and resid 444 through 447 removed outlier: 4.260A pdb=" N ILE Q 447 " --> pdb=" O PRO Q 444 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 444 through 447' Processing helix chain 'Q' and resid 449 through 471 Processing helix chain 'Q' and resid 471 through 480 Processing helix chain 'Q' and resid 558 through 562 removed outlier: 3.716A pdb=" N LYS Q 562 " --> pdb=" O ALA Q 559 " (cutoff:3.500A) Processing helix chain 'Q' and resid 565 through 569 removed outlier: 3.560A pdb=" N SER Q 568 " --> pdb=" O ARG Q 565 " (cutoff:3.500A) Processing helix chain 'Q' and resid 576 through 586 removed outlier: 3.636A pdb=" N LEU Q 580 " --> pdb=" O VAL Q 576 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY Q 584 " --> pdb=" O LEU Q 580 " (cutoff:3.500A) Processing helix chain 'T' and resid 10 through 27 Processing helix chain 'T' and resid 30 through 42 Processing helix chain 'T' and resid 56 through 67 Processing helix chain 'T' and resid 93 through 121 Processing helix chain 'T' and resid 122 through 125 removed outlier: 3.586A pdb=" N ILE T 125 " --> pdb=" O PHE T 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 122 through 125' Processing helix chain 'T' and resid 127 through 145 removed outlier: 3.651A pdb=" N ILE T 131 " --> pdb=" O TYR T 127 " (cutoff:3.500A) Proline residue: T 141 - end of helix removed outlier: 4.392A pdb=" N TYR T 144 " --> pdb=" O PHE T 140 " (cutoff:3.500A) Processing helix chain 'T' and resid 153 through 170 Processing helix chain 'T' and resid 170 through 187 Processing helix chain 'T' and resid 189 through 204 Processing helix chain 'T' and resid 208 through 229 removed outlier: 3.736A pdb=" N LEU T 212 " --> pdb=" O SER T 208 " (cutoff:3.500A) Processing helix chain 'T' and resid 237 through 259 removed outlier: 6.010A pdb=" N SER T 252 " --> pdb=" O ASN T 248 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N GLN T 253 " --> pdb=" O GLN T 249 " (cutoff:3.500A) Processing helix chain 'T' and resid 264 through 293 removed outlier: 5.351A pdb=" N PHE T 288 " --> pdb=" O THR T 284 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ASP T 289 " --> pdb=" O ASN T 285 " (cutoff:3.500A) Processing helix chain 'T' and resid 298 through 309 removed outlier: 3.687A pdb=" N ILE T 308 " --> pdb=" O GLU T 304 " (cutoff:3.500A) Processing helix chain 'T' and resid 311 through 330 Processing helix chain 'T' and resid 336 through 355 Processing helix chain 'T' and resid 358 through 375 Proline residue: T 370 - end of helix Processing helix chain 'T' and resid 377 through 388 Processing helix chain 'T' and resid 390 through 398 removed outlier: 4.204A pdb=" N LYS T 397 " --> pdb=" O GLU T 393 " (cutoff:3.500A) Processing helix chain 'T' and resid 403 through 416 Processing helix chain 'T' and resid 455 through 469 removed outlier: 3.937A pdb=" N LEU T 459 " --> pdb=" O ARG T 455 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR T 460 " --> pdb=" O HIS T 456 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR T 467 " --> pdb=" O ILE T 463 " (cutoff:3.500A) Processing helix chain 'T' and resid 490 through 497 removed outlier: 3.527A pdb=" N VAL T 494 " --> pdb=" O ASN T 490 " (cutoff:3.500A) Processing helix chain 'T' and resid 502 through 520 Processing helix chain 'T' and resid 526 through 544 removed outlier: 3.665A pdb=" N THR T 530 " --> pdb=" O ASP T 526 " (cutoff:3.500A) Processing helix chain 'T' and resid 568 through 576 removed outlier: 4.338A pdb=" N SER T 576 " --> pdb=" O SER T 572 " (cutoff:3.500A) Processing helix chain 'T' and resid 576 through 599 removed outlier: 3.754A pdb=" N ARG T 592 " --> pdb=" O GLU T 588 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLY T 599 " --> pdb=" O HIS T 595 " (cutoff:3.500A) Processing helix chain 'T' and resid 612 through 614 No H-bonds generated for 'chain 'T' and resid 612 through 614' Processing helix chain 'T' and resid 631 through 649 Processing helix chain 'T' and resid 681 through 689 removed outlier: 3.539A pdb=" N GLN T 689 " --> pdb=" O SER T 685 " (cutoff:3.500A) Processing helix chain 'T' and resid 702 through 710 Processing helix chain 'T' and resid 712 through 726 removed outlier: 3.537A pdb=" N HIS T 718 " --> pdb=" O PRO T 714 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TRP T 723 " --> pdb=" O LEU T 719 " (cutoff:3.500A) Processing helix chain 'U' and resid 75 through 83 Processing helix chain 'U' and resid 107 through 109 No H-bonds generated for 'chain 'U' and resid 107 through 109' Processing helix chain 'U' and resid 110 through 128 Processing sheet with id=AA1, first strand: chain 'F' and resid 200 through 201 Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 33 removed outlier: 6.979A pdb=" N LEU A 32 " --> pdb=" O GLU A 171 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL A 155 " --> pdb=" O TYR A 167 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N MET A 169 " --> pdb=" O VAL A 153 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL A 153 " --> pdb=" O MET A 169 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N GLU A 171 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N SER A 151 " --> pdb=" O GLU A 171 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASN A 205 " --> pdb=" O PRO A 150 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N LEU A 152 " --> pdb=" O PRO A 203 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS A 154 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ARG A 199 " --> pdb=" O TYR A 156 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N HIS A 121 " --> pdb=" O PHE A 202 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 82 through 83 removed outlier: 4.315A pdb=" N GLY A 216 " --> pdb=" O PHE A 139 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 113 through 114 removed outlier: 3.629A pdb=" N TRP A 113 " --> pdb=" O LEU A 214 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 132 through 133 Processing sheet with id=AA6, first strand: chain 'B' and resid 60 through 61 Processing sheet with id=AA7, first strand: chain 'B' and resid 253 through 256 removed outlier: 3.890A pdb=" N ARG B 253 " --> pdb=" O TYR B 541 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU B 255 " --> pdb=" O LEU B 539 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU B 539 " --> pdb=" O LEU B 255 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N THR B 538 " --> pdb=" O ALA B 534 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ALA B 534 " --> pdb=" O THR B 538 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ARG B 540 " --> pdb=" O SER B 532 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER B 532 " --> pdb=" O ARG B 540 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N THR B 529 " --> pdb=" O LEU B 523 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N LEU B 523 " --> pdb=" O THR B 529 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL B 531 " --> pdb=" O LEU B 521 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU B 521 " --> pdb=" O VAL B 531 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N GLY B 533 " --> pdb=" O LEU B 519 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 281 removed outlier: 6.817A pdb=" N ILE B 285 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASP B 294 " --> pdb=" O ASP B 289 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 305 through 311 removed outlier: 3.791A pdb=" N VAL B 319 " --> pdb=" O GLU B 327 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU B 327 " --> pdb=" O VAL B 319 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE B 328 " --> pdb=" O ILE B 337 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 347 through 352 removed outlier: 3.601A pdb=" N CYS B 349 " --> pdb=" O GLY B 360 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ILE B 366 " --> pdb=" O THR B 380 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N THR B 380 " --> pdb=" O ILE B 366 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N HIS B 368 " --> pdb=" O PHE B 378 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 388 through 393 removed outlier: 7.000A pdb=" N GLY B 403 " --> pdb=" O CYS B 389 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LEU B 391 " --> pdb=" O ALA B 401 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ALA B 401 " --> pdb=" O LEU B 391 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N TRP B 393 " --> pdb=" O LYS B 399 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N LYS B 399 " --> pdb=" O TRP B 393 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N GLU B 413 " --> pdb=" O PRO B 419 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 433 through 435 removed outlier: 6.876A pdb=" N ASN B 458 " --> pdb=" O LYS B 464 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LYS B 464 " --> pdb=" O ASN B 458 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 474 through 479 removed outlier: 4.292A pdb=" N ASN B 476 " --> pdb=" O SER B 489 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 29 through 30 Processing sheet with id=AB6, first strand: chain 'C' and resid 74 through 75 removed outlier: 3.786A pdb=" N LYS C 74 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 114 through 120 removed outlier: 6.508A pdb=" N GLU C 127 " --> pdb=" O GLY C 115 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ALA C 117 " --> pdb=" O ILE C 125 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE C 125 " --> pdb=" O ALA C 117 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N TRP C 119 " --> pdb=" O GLY C 123 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N GLY C 123 " --> pdb=" O TRP C 119 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL C 124 " --> pdb=" O LEU C 155 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU C 155 " --> pdb=" O VAL C 124 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N TYR C 152 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE C 165 " --> pdb=" O TYR C 152 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU C 164 " --> pdb=" O LYS C 368 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ILE C 370 " --> pdb=" O LEU C 164 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLU C 374 " --> pdb=" O THR C 168 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N PHE C 215 " --> pdb=" O ILE C 375 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N SER C 377 " --> pdb=" O LEU C 213 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU C 213 " --> pdb=" O SER C 377 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL C 212 " --> pdb=" O ASP C 207 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP C 207 " --> pdb=" O VAL C 212 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N VAL C 204 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL C 192 " --> pdb=" O VAL C 204 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 114 through 120 removed outlier: 6.508A pdb=" N GLU C 127 " --> pdb=" O GLY C 115 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ALA C 117 " --> pdb=" O ILE C 125 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE C 125 " --> pdb=" O ALA C 117 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N TRP C 119 " --> pdb=" O GLY C 123 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N GLY C 123 " --> pdb=" O TRP C 119 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL C 124 " --> pdb=" O LEU C 155 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU C 155 " --> pdb=" O VAL C 124 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N TYR C 152 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE C 165 " --> pdb=" O TYR C 152 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU C 164 " --> pdb=" O LYS C 368 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ILE C 370 " --> pdb=" O LEU C 164 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLU C 374 " --> pdb=" O THR C 168 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL C 371 " --> pdb=" O ARG C 219 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 398 through 405 removed outlier: 3.802A pdb=" N ARG C 450 " --> pdb=" O LEU C 425 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 462 through 467 removed outlier: 6.769A pdb=" N ILE C 462 " --> pdb=" O GLY C 481 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLY C 481 " --> pdb=" O ILE C 462 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA C 464 " --> pdb=" O SER C 479 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR C 492 " --> pdb=" O ILE C 476 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN C 482 " --> pdb=" O GLU C 486 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N GLU C 486 " --> pdb=" O GLN C 482 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N TYR C 487 " --> pdb=" O ASN C 504 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N ASN C 504 " --> pdb=" O TYR C 487 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ALA C 489 " --> pdb=" O SER C 502 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N SER C 502 " --> pdb=" O ALA C 489 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 925 through 926 removed outlier: 5.821A pdb=" N THR C 925 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE C 994 " --> pdb=" O SER C 986 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 1155 through 1157 Processing sheet with id=AC4, first strand: chain 'C' and resid 1511 through 1513 Processing sheet with id=AC5, first strand: chain 'C' and resid 1591 through 1592 removed outlier: 4.235A pdb=" N CYS C1591 " --> pdb=" O LEU C1554 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU C1554 " --> pdb=" O CYS C1591 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ILE C1632 " --> pdb=" O CYS C1553 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL C1555 " --> pdb=" O ILE C1632 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ILE C1634 " --> pdb=" O VAL C1555 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LYS C1557 " --> pdb=" O ILE C1634 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'C' and resid 1584 through 1587 removed outlier: 4.325A pdb=" N SER C1601 " --> pdb=" O VAL C1573 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'O' and resid 7 through 9 removed outlier: 6.092A pdb=" N GLY O 8 " --> pdb=" O ILE O 242 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'O' and resid 123 through 124 Processing sheet with id=AC9, first strand: chain 'I' and resid 104 through 105 Processing sheet with id=AD1, first strand: chain 'N' and resid 89 through 90 Processing sheet with id=AD2, first strand: chain 'Q' and resid 11 through 12 removed outlier: 3.697A pdb=" N ASP Q 11 " --> pdb=" O ALA Q 20 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N PHE Q 19 " --> pdb=" O TYR Q 30 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N TYR Q 30 " --> pdb=" O PHE Q 19 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ARG Q 31 " --> pdb=" O ARG Q 37 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ARG Q 37 " --> pdb=" O ARG Q 31 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'Q' and resid 49 through 54 removed outlier: 3.895A pdb=" N ASN Q 51 " --> pdb=" O PHE Q 65 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N THR Q 70 " --> pdb=" O PHE Q 66 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE Q 73 " --> pdb=" O SER Q 84 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER Q 84 " --> pdb=" O ILE Q 73 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ASP Q 75 " --> pdb=" O LEU Q 82 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N LEU Q 82 " --> pdb=" O ASP Q 75 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'Q' and resid 95 through 102 removed outlier: 3.755A pdb=" N LYS Q 95 " --> pdb=" O PHE Q 165 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE Q 165 " --> pdb=" O LYS Q 95 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS Q 171 " --> pdb=" O ASN Q 166 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'Q' and resid 124 through 128 Processing sheet with id=AD6, first strand: chain 'Q' and resid 195 through 202 removed outlier: 6.996A pdb=" N PHE Q 205 " --> pdb=" O VAL Q 201 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N VAL Q 215 " --> pdb=" O LYS Q 485 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LYS Q 485 " --> pdb=" O VAL Q 215 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR Q 217 " --> pdb=" O ASP Q 483 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU Q 481 " --> pdb=" O ASN Q 219 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Q' and resid 496 through 505 removed outlier: 6.977A pdb=" N LEU Q 515 " --> pdb=" O LEU Q 501 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ALA Q 503 " --> pdb=" O VAL Q 513 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL Q 513 " --> pdb=" O ALA Q 503 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N LYS Q 505 " --> pdb=" O TYR Q 511 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N TYR Q 511 " --> pdb=" O LYS Q 505 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY Q 539 " --> pdb=" O TYR Q 514 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'Q' and resid 570 through 571 removed outlier: 3.752A pdb=" N ARG Q 570 " --> pdb=" O VAL Q 644 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL Q 644 " --> pdb=" O ARG Q 570 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'Q' and resid 590 through 591 removed outlier: 4.285A pdb=" N ILE Q 618 " --> pdb=" O PHE Q 627 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N PHE Q 627 " --> pdb=" O ILE Q 618 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'T' and resid 607 through 610 removed outlier: 5.861A pdb=" N LYS T 607 " --> pdb=" O PHE U 12 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N TRP U 14 " --> pdb=" O LYS T 607 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ILE T 609 " --> pdb=" O TRP U 14 " (cutoff:3.500A) removed outlier: 9.088A pdb=" N TRP U 16 " --> pdb=" O ILE T 609 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLU T 664 " --> pdb=" O ASN U 6 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N VAL U 8 " --> pdb=" O LYS T 662 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N LYS T 662 " --> pdb=" O VAL U 8 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N SER U 10 " --> pdb=" O LYS T 660 " (cutoff:3.500A) removed outlier: 8.724A pdb=" N LYS T 660 " --> pdb=" O SER U 10 " (cutoff:3.500A) removed outlier: 9.682A pdb=" N PHE U 12 " --> pdb=" O LYS T 658 " (cutoff:3.500A) removed outlier: 9.343A pdb=" N LYS T 658 " --> pdb=" O PHE U 12 " (cutoff:3.500A) removed outlier: 9.147A pdb=" N TRP U 14 " --> pdb=" O LEU T 656 " (cutoff:3.500A) removed outlier: 9.524A pdb=" N LEU T 656 " --> pdb=" O TRP U 14 " (cutoff:3.500A) removed outlier: 9.742A pdb=" N TRP U 16 " --> pdb=" O LEU T 654 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N LEU T 654 " --> pdb=" O TRP U 16 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'T' and resid 700 through 701 Processing sheet with id=AE3, first strand: chain 'U' and resid 64 through 66 3466 hydrogen bonds defined for protein. 10239 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: 22.15 Time building geometry restraints manager: 13.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.92 - 1.11: 1 1.11 - 1.30: 10123 1.30 - 1.49: 25715 1.49 - 1.68: 26317 1.68 - 1.87: 476 Bond restraints: 62632 Sorted by residual: bond pdb=" N PRO E 95 " pdb=" CD PRO E 95 " ideal model delta sigma weight residual 1.473 1.801 -0.328 1.40e-02 5.10e+03 5.49e+02 bond pdb=" CB PRO T 650 " pdb=" CG PRO T 650 " ideal model delta sigma weight residual 1.492 0.921 0.571 5.00e-02 4.00e+02 1.31e+02 bond pdb=" CG PRO T 650 " pdb=" CD PRO T 650 " ideal model delta sigma weight residual 1.503 1.286 0.217 3.40e-02 8.65e+02 4.07e+01 bond pdb=" N PRO T 650 " pdb=" CD PRO T 650 " ideal model delta sigma weight residual 1.473 1.531 -0.058 1.40e-02 5.10e+03 1.73e+01 bond pdb=" N PRO T 650 " pdb=" CA PRO T 650 " ideal model delta sigma weight residual 1.467 1.504 -0.037 1.21e-02 6.83e+03 9.17e+00 ... (remaining 62627 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.77: 84778 14.77 - 29.54: 4 29.54 - 44.30: 1 44.30 - 59.07: 0 59.07 - 73.84: 1 Bond angle restraints: 84784 Sorted by residual: angle pdb=" CB PRO T 650 " pdb=" CG PRO T 650 " pdb=" CD PRO T 650 " ideal model delta sigma weight residual 106.10 179.94 -73.84 3.20e+00 9.77e-02 5.32e+02 angle pdb=" N PRO T 650 " pdb=" CD PRO T 650 " pdb=" CG PRO T 650 " ideal model delta sigma weight residual 103.20 75.00 28.20 1.50e+00 4.44e-01 3.53e+02 angle pdb=" CA PRO E 95 " pdb=" N PRO E 95 " pdb=" CD PRO E 95 " ideal model delta sigma weight residual 112.00 88.61 23.39 1.40e+00 5.10e-01 2.79e+02 angle pdb=" CA PRO T 650 " pdb=" CB PRO T 650 " pdb=" CG PRO T 650 " ideal model delta sigma weight residual 104.50 73.70 30.80 1.90e+00 2.77e-01 2.63e+02 angle pdb=" CA PRO T 650 " pdb=" N PRO T 650 " pdb=" CD PRO T 650 " ideal model delta sigma weight residual 112.00 98.85 13.15 1.40e+00 5.10e-01 8.82e+01 ... (remaining 84779 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 33286 17.96 - 35.92: 3516 35.92 - 53.89: 683 53.89 - 71.85: 102 71.85 - 89.81: 39 Dihedral angle restraints: 37626 sinusoidal: 14911 harmonic: 22715 Sorted by residual: dihedral pdb=" CB CYS J 482 " pdb=" SG CYS J 482 " pdb=" SG CYS J 506 " pdb=" CB CYS J 506 " ideal model delta sinusoidal sigma weight residual -86.00 -174.49 88.49 1 1.00e+01 1.00e-02 9.35e+01 dihedral pdb=" CB CYS K 482 " pdb=" SG CYS K 482 " pdb=" SG CYS K 506 " pdb=" CB CYS K 506 " ideal model delta sinusoidal sigma weight residual -86.00 -10.39 -75.61 1 1.00e+01 1.00e-02 7.21e+01 dihedral pdb=" CA PHE F 495 " pdb=" C PHE F 495 " pdb=" N ASN F 496 " pdb=" CA ASN F 496 " ideal model delta harmonic sigma weight residual 180.00 152.19 27.81 0 5.00e+00 4.00e-02 3.09e+01 ... (remaining 37623 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 8907 0.080 - 0.159: 639 0.159 - 0.239: 27 0.239 - 0.319: 6 0.319 - 0.399: 4 Chirality restraints: 9583 Sorted by residual: chirality pdb=" CG LEU T 387 " pdb=" CB LEU T 387 " pdb=" CD1 LEU T 387 " pdb=" CD2 LEU T 387 " both_signs ideal model delta sigma weight residual False -2.59 -2.19 -0.40 2.00e-01 2.50e+01 3.97e+00 chirality pdb=" CG LEU Q 415 " pdb=" CB LEU Q 415 " pdb=" CD1 LEU Q 415 " pdb=" CD2 LEU Q 415 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" CG LEU A 219 " pdb=" CB LEU A 219 " pdb=" CD1 LEU A 219 " pdb=" CD2 LEU A 219 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.12e+00 ... (remaining 9580 not shown) Planarity restraints: 10715 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER E 94 " 0.153 5.00e-02 4.00e+02 1.91e-01 5.85e+01 pdb=" N PRO E 95 " -0.328 5.00e-02 4.00e+02 pdb=" CA PRO E 95 " 0.090 5.00e-02 4.00e+02 pdb=" CD PRO E 95 " 0.085 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET F 536 " -0.093 5.00e-02 4.00e+02 1.37e-01 2.99e+01 pdb=" N PRO F 537 " 0.236 5.00e-02 4.00e+02 pdb=" CA PRO F 537 " -0.072 5.00e-02 4.00e+02 pdb=" CD PRO F 537 " -0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP P 27 " 0.035 2.00e-02 2.50e+03 2.91e-02 2.12e+01 pdb=" CG TRP P 27 " -0.077 2.00e-02 2.50e+03 pdb=" CD1 TRP P 27 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 TRP P 27 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP P 27 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP P 27 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP P 27 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP P 27 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP P 27 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP P 27 " 0.010 2.00e-02 2.50e+03 ... (remaining 10712 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.21: 47 2.21 - 2.89: 23963 2.89 - 3.56: 94435 3.56 - 4.23: 137058 4.23 - 4.90: 236799 Nonbonded interactions: 492302 Sorted by model distance: nonbonded pdb=" O THR D 536 " pdb=" OE2 GLU D 576 " model vdw 1.542 3.040 nonbonded pdb=" OE1 GLN C 463 " pdb=" O SER C 479 " model vdw 1.713 3.040 nonbonded pdb=" C THR D 536 " pdb=" OE2 GLU D 576 " model vdw 1.777 3.270 nonbonded pdb=" OE1 GLN C 463 " pdb=" C SER C 479 " model vdw 1.828 3.270 nonbonded pdb=" CE MET K 242 " pdb=" NE2 GLN K 243 " model vdw 1.848 3.540 ... (remaining 492297 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'D' and (resid 6 through 44 or resid 75 through 143 or (resid 144 and (na \ me N or name CA or name C or name O or name CB )) or resid 145 or (resid 146 and \ (name N or name CA or name C or name O or name CB )) or resid 184 through 198 o \ r (resid 199 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 00 through 201 or (resid 202 and (name N or name CA or name C or name O or name \ CB )) or resid 203 through 340 or (resid 341 and (name N or name CA or name C or \ name O or name CB )) or resid 342 through 343 or (resid 344 and (name N or name \ CA or name C or name O or name CB )) or resid 345 through 349 or (resid 350 and \ (name N or name CA or name C or name O or name CB )) or resid 351 through 439 o \ r (resid 440 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 41 through 555 or (resid 556 and (name N or name CA or name C or name O or name \ CB )) or resid 557 through 575 or (resid 576 and (name N or name CA or name C or \ name O or name CB )) or resid 577 through 607 or (resid 608 and (name N or name \ CA or name C or name O or name CB )) or resid 609 through 626)) selection = (chain 'P' and (resid 6 through 86 or (resid 87 and (name N or name CA or name C \ or name O or name CB )) or resid 88 through 146 or resid 184 through 278 or (re \ sid 279 and (name N or name CA or name C or name O or name CB )) or resid 280 th \ rough 510 or (resid 511 and (name N or name CA or name C or name O or name CB )) \ or resid 512 through 610 or (resid 611 and (name N or name CA or name C or name \ O or name CB )) or resid 612 through 613 or (resid 614 through 616 and (name N \ or name CA or name C or name O or name CB )) or resid 617 through 619 or (resid \ 620 through 621 and (name N or name CA or name C or name O or name CB )) or resi \ d 622 or (resid 623 through 626 and (name N or name CA or name C or name O or na \ me CB )))) } ncs_group { reference = (chain 'F' and (resid 23 through 130 or (resid 131 and (name N or name CA or nam \ e C or name O or name CB )) or resid 143 through 190 or (resid 191 and (name N o \ r name CA or name C or name O or name CB )) or resid 192 through 208 or (resid 2 \ 09 and (name N or name CA or name C or name O or name CB )) or resid 432 through \ 445 or (resid 446 and (name N or name CA or name C or name O or name CB )) or r \ esid 447 through 755)) selection = (chain 'H' and (resid 23 through 55 or (resid 56 and (name N or name CA or name \ C or name O or name CB )) or resid 57 through 60 or (resid 61 through 62 and (na \ me N or name CA or name C or name O or name CB )) or resid 63 through 111 or (re \ sid 112 through 113 and (name N or name CA or name C or name O or name CB )) or \ resid 114 through 131 or resid 143 through 197 or (resid 198 through 199 and (na \ me N or name CA or name C or name O or name CB )) or resid 200 through 453 or (r \ esid 454 through 455 and (name N or name CA or name C or name O or name CB )) or \ resid 456 through 459 or (resid 460 and (name N or name CA or name C or name O \ or name CB )) or resid 461 through 569 or (resid 570 and (name N or name CA or n \ ame C or name O or name CB )) or resid 571 through 755)) } ncs_group { reference = chain 'G' selection = (chain 'W' and resid 1 through 35) } ncs_group { reference = (chain 'J' and (resid 229 through 326 or resid 352 through 508 or (resid 509 and \ (name N or name CA or name C or name O or name CB )) or resid 510 through 748 o \ r (resid 749 and (name N or name CA or name C or name O or name CB )) or resid 7 \ 50 through 757 or (resid 758 and (name N or name CA or name C or name O or name \ CB )))) selection = (chain 'K' and (resid 229 through 231 or (resid 232 and (name N or name CA or na \ me C or name O or name CB )) or resid 233 through 326 or (resid 352 and (name N \ or name CA or name C or name O or name CB )) or resid 353 through 388 or (resid \ 389 and (name N or name CA or name C or name O or name CB )) or resid 390 throug \ h 758)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.480 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: 1.680 Check model and map are aligned: 0.330 Set scattering table: 0.410 Process input model: 107.380 Find NCS groups from input model: 1.840 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 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 : 0.004 0.571 62632 Z= 0.299 Angle : 0.755 73.841 84784 Z= 0.371 Chirality : 0.043 0.399 9583 Planarity : 0.005 0.191 10715 Dihedral : 14.993 89.808 22868 Min Nonbonded Distance : 1.542 Molprobity Statistics. All-atom Clashscore : 18.91 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.90 % Favored : 95.91 % Rotamer: Outliers : 0.10 % Allowed : 14.55 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.10), residues: 7537 helix: 1.23 (0.08), residues: 4521 sheet: 0.17 (0.26), residues: 419 loop : -1.24 (0.12), residues: 2597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.002 TRP P 27 HIS 0.010 0.001 HIS K 732 PHE 0.072 0.002 PHE F 495 TYR 0.050 0.002 TYR J 251 ARG 0.012 0.001 ARG H 635 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15074 Ramachandran restraints generated. 7537 Oldfield, 0 Emsley, 7537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15074 Ramachandran restraints generated. 7537 Oldfield, 0 Emsley, 7537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 6946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 581 time to evaluate : 5.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 542 MET cc_start: 0.8385 (mmm) cc_final: 0.8012 (mmm) REVERT: C 1715 GLU cc_start: 0.8662 (mp0) cc_final: 0.8187 (mp0) outliers start: 7 outliers final: 5 residues processed: 587 average time/residue: 0.5327 time to fit residues: 547.0673 Evaluate side-chains 579 residues out of total 6946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 574 time to evaluate : 5.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 740 ASP Chi-restraints excluded: chain J residue 397 GLU Chi-restraints excluded: chain H residue 599 LYS Chi-restraints excluded: chain P residue 560 MET Chi-restraints excluded: chain Q residue 362 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 758 random chunks: chunk 640 optimal weight: 5.9990 chunk 574 optimal weight: 3.9990 chunk 318 optimal weight: 4.9990 chunk 196 optimal weight: 9.9990 chunk 387 optimal weight: 0.1980 chunk 306 optimal weight: 5.9990 chunk 594 optimal weight: 7.9990 chunk 229 optimal weight: 20.0000 chunk 361 optimal weight: 7.9990 chunk 442 optimal weight: 0.8980 chunk 688 optimal weight: 1.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 184 ASN ** F 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 450 ASN K 583 GLN K 741 ASN ** H 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 638 ASN ** E 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 71 GLN ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 208 ASN ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 458 ASN ** C 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 648 HIS ** C 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1105 HIS ** C1543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 172 ASN ** O 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 ASN ** D 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 534 GLN P 16 GLN I 92 HIS Q 354 GLN Q 355 ASN T 29 ASN ** T 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 62632 Z= 0.265 Angle : 0.646 11.212 84784 Z= 0.335 Chirality : 0.043 0.311 9583 Planarity : 0.004 0.087 10715 Dihedral : 4.424 59.085 8270 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.11 % Favored : 95.71 % Rotamer: Outliers : 1.86 % Allowed : 14.35 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.10), residues: 7537 helix: 1.40 (0.07), residues: 4700 sheet: 0.20 (0.24), residues: 449 loop : -1.29 (0.13), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP P 27 HIS 0.011 0.001 HIS E 256 PHE 0.030 0.002 PHE F 495 TYR 0.022 0.002 TYR P 115 ARG 0.008 0.001 ARG H 635 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15074 Ramachandran restraints generated. 7537 Oldfield, 0 Emsley, 7537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15074 Ramachandran restraints generated. 7537 Oldfield, 0 Emsley, 7537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 781 residues out of total 6946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 656 time to evaluate : 7.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 153 LEU cc_start: 0.7384 (tp) cc_final: 0.7123 (tp) REVERT: F 192 GLU cc_start: 0.9065 (mm-30) cc_final: 0.8560 (mm-30) REVERT: F 490 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.7585 (tpt) REVERT: F 543 TRP cc_start: 0.7969 (m100) cc_final: 0.7334 (m100) REVERT: F 740 ASP cc_start: 0.7444 (t0) cc_final: 0.6699 (t0) REVERT: J 542 MET cc_start: 0.8578 (mmm) cc_final: 0.8282 (mmm) REVERT: J 547 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.8071 (mm) REVERT: J 732 HIS cc_start: 0.8254 (OUTLIER) cc_final: 0.8045 (m170) REVERT: J 735 LEU cc_start: 0.9418 (mp) cc_final: 0.9142 (mp) REVERT: K 396 PHE cc_start: 0.8551 (t80) cc_final: 0.8330 (t80) REVERT: K 542 MET cc_start: 0.9026 (ttp) cc_final: 0.8213 (tmm) REVERT: K 574 THR cc_start: 0.8928 (p) cc_final: 0.8715 (p) REVERT: W 10 GLN cc_start: 0.7766 (tp-100) cc_final: 0.7194 (tp-100) REVERT: H 536 MET cc_start: 0.8177 (mtp) cc_final: 0.7695 (mpp) REVERT: H 619 MET cc_start: 0.4115 (ttt) cc_final: 0.3899 (ttt) REVERT: A 44 LYS cc_start: 0.5176 (tptt) cc_final: 0.4951 (tppt) REVERT: A 131 MET cc_start: 0.7057 (mmt) cc_final: 0.6568 (mpp) REVERT: C 1053 LEU cc_start: 0.8201 (mt) cc_final: 0.7982 (mm) REVERT: C 1133 MET cc_start: 0.8598 (ttm) cc_final: 0.8082 (tpt) REVERT: C 1540 GLU cc_start: 0.8287 (pm20) cc_final: 0.8006 (pm20) REVERT: C 1541 LEU cc_start: 0.8423 (tp) cc_final: 0.8140 (tp) REVERT: C 1715 GLU cc_start: 0.8646 (mp0) cc_final: 0.8295 (mp0) REVERT: O 165 MET cc_start: 0.7365 (tmm) cc_final: 0.6982 (tmm) REVERT: O 386 ILE cc_start: 0.8456 (OUTLIER) cc_final: 0.8154 (mp) REVERT: O 568 LEU cc_start: 0.8912 (tp) cc_final: 0.8678 (tp) REVERT: D 201 TYR cc_start: 0.7487 (t80) cc_final: 0.7190 (t80) REVERT: D 254 GLU cc_start: 0.8996 (mm-30) cc_final: 0.8788 (mm-30) REVERT: D 349 GLU cc_start: 0.8685 (tp30) cc_final: 0.8310 (tm-30) REVERT: D 557 LYS cc_start: 0.8079 (mptt) cc_final: 0.7631 (mptt) REVERT: D 602 MET cc_start: 0.7906 (mmp) cc_final: 0.6460 (ptp) REVERT: P 193 GLU cc_start: 0.8071 (tm-30) cc_final: 0.7770 (tm-30) REVERT: P 240 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8552 (ttmm) REVERT: P 334 TYR cc_start: 0.8289 (t80) cc_final: 0.8060 (t80) REVERT: P 338 ILE cc_start: 0.8827 (mm) cc_final: 0.8461 (mm) REVERT: P 399 THR cc_start: 0.9168 (m) cc_final: 0.8885 (p) REVERT: P 471 LEU cc_start: 0.8641 (mt) cc_final: 0.8390 (tp) REVERT: I 37 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7261 (pt0) REVERT: Q 156 ASN cc_start: 0.8283 (p0) cc_final: 0.7638 (p0) REVERT: Q 453 TYR cc_start: 0.8593 (m-10) cc_final: 0.8233 (m-10) REVERT: Q 463 MET cc_start: 0.8909 (tpt) cc_final: 0.8594 (tpp) REVERT: Q 509 HIS cc_start: 0.7969 (m90) cc_final: 0.7661 (m90) REVERT: T 607 LYS cc_start: 0.5762 (mttt) cc_final: 0.5228 (ttpt) outliers start: 125 outliers final: 60 residues processed: 742 average time/residue: 0.5341 time to fit residues: 692.3252 Evaluate side-chains 633 residues out of total 6946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 567 time to evaluate : 5.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 486 ILE Chi-restraints excluded: chain F residue 490 MET Chi-restraints excluded: chain F residue 520 HIS Chi-restraints excluded: chain F residue 575 TYR Chi-restraints excluded: chain F residue 706 VAL Chi-restraints excluded: chain F residue 748 ILE Chi-restraints excluded: chain J residue 486 CYS Chi-restraints excluded: chain J residue 514 ASN Chi-restraints excluded: chain J residue 547 ILE Chi-restraints excluded: chain J residue 585 LEU Chi-restraints excluded: chain J residue 662 VAL Chi-restraints excluded: chain J residue 732 HIS Chi-restraints excluded: chain J residue 752 LEU Chi-restraints excluded: chain J residue 756 VAL Chi-restraints excluded: chain K residue 287 THR Chi-restraints excluded: chain K residue 361 LEU Chi-restraints excluded: chain K residue 482 CYS Chi-restraints excluded: chain K residue 600 LEU Chi-restraints excluded: chain G residue 13 HIS Chi-restraints excluded: chain G residue 22 ASP Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 644 LEU Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 219 HIS Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 393 TRP Chi-restraints excluded: chain B residue 545 PHE Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain C residue 1504 LEU Chi-restraints excluded: chain C residue 1533 THR Chi-restraints excluded: chain C residue 1604 VAL Chi-restraints excluded: chain O residue 386 ILE Chi-restraints excluded: chain O residue 631 LEU Chi-restraints excluded: chain D residue 77 ASN Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain P residue 240 LYS Chi-restraints excluded: chain P residue 242 LEU Chi-restraints excluded: chain P residue 458 VAL Chi-restraints excluded: chain I residue 37 GLU Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 96 ASP Chi-restraints excluded: chain I residue 107 SER Chi-restraints excluded: chain I residue 162 HIS Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 62 LEU Chi-restraints excluded: chain Q residue 116 ILE Chi-restraints excluded: chain Q residue 297 ASP Chi-restraints excluded: chain Q residue 362 ASP Chi-restraints excluded: chain Q residue 387 LEU Chi-restraints excluded: chain Q residue 411 GLU Chi-restraints excluded: chain Q residue 427 TYR Chi-restraints excluded: chain Q residue 467 ILE Chi-restraints excluded: chain T residue 159 LEU Chi-restraints excluded: chain T residue 300 VAL Chi-restraints excluded: chain T residue 313 LYS Chi-restraints excluded: chain T residue 338 VAL Chi-restraints excluded: chain T residue 341 LEU Chi-restraints excluded: chain T residue 387 LEU Chi-restraints excluded: chain T residue 581 LEU Chi-restraints excluded: chain U residue 100 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 758 random chunks: chunk 382 optimal weight: 0.9990 chunk 213 optimal weight: 5.9990 chunk 572 optimal weight: 2.9990 chunk 468 optimal weight: 0.9980 chunk 189 optimal weight: 1.9990 chunk 689 optimal weight: 9.9990 chunk 744 optimal weight: 9.9990 chunk 614 optimal weight: 0.6980 chunk 683 optimal weight: 20.0000 chunk 235 optimal weight: 8.9990 chunk 553 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 ASN F 580 GLN ** J 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 436 ASN K 741 ASN H 162 ASN ** E 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 71 GLN ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1105 HIS O 224 ASN O 323 HIS ** O 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 ASN ** D 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 448 HIS D 544 GLN P 405 ASN ** T 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 132 GLN ** U 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 62632 Z= 0.183 Angle : 0.577 13.358 84784 Z= 0.296 Chirality : 0.041 0.412 9583 Planarity : 0.003 0.070 10715 Dihedral : 4.263 56.501 8258 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.81 % Favored : 96.01 % Rotamer: Outliers : 2.29 % Allowed : 15.60 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.10), residues: 7537 helix: 1.56 (0.08), residues: 4715 sheet: 0.03 (0.24), residues: 465 loop : -1.27 (0.13), residues: 2357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP I 97 HIS 0.008 0.001 HIS A 213 PHE 0.028 0.001 PHE F 495 TYR 0.022 0.001 TYR K 621 ARG 0.005 0.000 ARG I 14 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15074 Ramachandran restraints generated. 7537 Oldfield, 0 Emsley, 7537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15074 Ramachandran restraints generated. 7537 Oldfield, 0 Emsley, 7537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 818 residues out of total 6946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 664 time to evaluate : 5.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 153 LEU cc_start: 0.7406 (tp) cc_final: 0.7153 (tp) REVERT: F 192 GLU cc_start: 0.9002 (mm-30) cc_final: 0.8564 (mm-30) REVERT: F 490 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.7554 (tpt) REVERT: F 543 TRP cc_start: 0.7976 (m100) cc_final: 0.7429 (m100) REVERT: F 604 ASP cc_start: 0.8803 (t0) cc_final: 0.8328 (t0) REVERT: F 740 ASP cc_start: 0.7365 (t0) cc_final: 0.6766 (t70) REVERT: J 254 ASP cc_start: 0.8419 (t0) cc_final: 0.8124 (t0) REVERT: J 394 GLU cc_start: 0.8235 (tp30) cc_final: 0.7516 (tp30) REVERT: J 480 ASN cc_start: 0.8385 (m-40) cc_final: 0.8160 (p0) REVERT: J 542 MET cc_start: 0.8514 (mmm) cc_final: 0.8203 (mmm) REVERT: J 547 ILE cc_start: 0.8253 (OUTLIER) cc_final: 0.7920 (mm) REVERT: J 575 TYR cc_start: 0.8145 (m-80) cc_final: 0.7836 (m-80) REVERT: J 583 GLN cc_start: 0.7820 (OUTLIER) cc_final: 0.6461 (pp30) REVERT: K 396 PHE cc_start: 0.8468 (t80) cc_final: 0.8248 (t80) REVERT: K 422 PHE cc_start: 0.6964 (m-80) cc_final: 0.5944 (m-80) REVERT: K 542 MET cc_start: 0.8969 (ttp) cc_final: 0.8184 (tmm) REVERT: K 571 PHE cc_start: 0.8887 (t80) cc_final: 0.8542 (t80) REVERT: W 1 MET cc_start: 0.7086 (OUTLIER) cc_final: 0.6856 (mmm) REVERT: W 10 GLN cc_start: 0.8008 (tp-100) cc_final: 0.7596 (tp-100) REVERT: H 536 MET cc_start: 0.8321 (mtp) cc_final: 0.8025 (mpp) REVERT: H 619 MET cc_start: 0.4285 (ttt) cc_final: 0.4082 (ttt) REVERT: H 630 TYR cc_start: 0.8000 (m-80) cc_final: 0.7519 (m-80) REVERT: E 160 MET cc_start: 0.7120 (tpp) cc_final: 0.6769 (tpp) REVERT: A 44 LYS cc_start: 0.5131 (tptt) cc_final: 0.4915 (tppt) REVERT: A 47 TYR cc_start: 0.4783 (t80) cc_final: 0.4541 (t80) REVERT: A 81 MET cc_start: 0.5536 (tpp) cc_final: 0.5163 (tpp) REVERT: A 124 ASP cc_start: 0.7442 (t0) cc_final: 0.6875 (t0) REVERT: A 126 MET cc_start: 0.8366 (tpp) cc_final: 0.7956 (tpp) REVERT: A 195 CYS cc_start: 0.8549 (m) cc_final: 0.7396 (p) REVERT: B 69 ILE cc_start: 0.8077 (OUTLIER) cc_final: 0.7824 (tt) REVERT: B 226 MET cc_start: 0.6302 (OUTLIER) cc_final: 0.5992 (ppp) REVERT: B 281 LEU cc_start: 0.2979 (mt) cc_final: 0.2745 (mt) REVERT: C 800 GLU cc_start: 0.7673 (tm-30) cc_final: 0.7254 (tm-30) REVERT: C 950 MET cc_start: 0.8977 (mmp) cc_final: 0.8730 (mmp) REVERT: C 1098 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.8000 (tt) REVERT: C 1252 MET cc_start: 0.8594 (tmm) cc_final: 0.8001 (tmm) REVERT: C 1540 GLU cc_start: 0.8308 (pm20) cc_final: 0.7940 (pm20) REVERT: C 1606 MET cc_start: 0.6915 (ppp) cc_final: 0.5847 (ppp) REVERT: C 1715 GLU cc_start: 0.8612 (mp0) cc_final: 0.8295 (mp0) REVERT: O 165 MET cc_start: 0.7426 (tmm) cc_final: 0.6855 (tmm) REVERT: O 386 ILE cc_start: 0.8556 (OUTLIER) cc_final: 0.8222 (mm) REVERT: O 568 LEU cc_start: 0.8876 (tp) cc_final: 0.8628 (tp) REVERT: D 349 GLU cc_start: 0.8573 (tp30) cc_final: 0.7989 (tm-30) REVERT: D 557 LYS cc_start: 0.8128 (mptt) cc_final: 0.7662 (mmtm) REVERT: D 602 MET cc_start: 0.7764 (mmp) cc_final: 0.6665 (ptp) REVERT: P 253 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8091 (mm) REVERT: P 317 ASP cc_start: 0.9003 (p0) cc_final: 0.8635 (p0) REVERT: P 334 TYR cc_start: 0.8292 (t80) cc_final: 0.8049 (t80) REVERT: P 338 ILE cc_start: 0.8916 (mm) cc_final: 0.8559 (mm) REVERT: P 399 THR cc_start: 0.9031 (m) cc_final: 0.8826 (p) REVERT: P 432 ASN cc_start: 0.7733 (p0) cc_final: 0.6966 (p0) REVERT: P 602 MET cc_start: 0.3848 (mtm) cc_final: 0.3557 (pmm) REVERT: I 37 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7249 (pt0) REVERT: N 107 ARG cc_start: 0.7500 (ttp80) cc_final: 0.6943 (ttp80) REVERT: Q 156 ASN cc_start: 0.8292 (p0) cc_final: 0.7655 (p0) REVERT: Q 199 ILE cc_start: 0.8655 (OUTLIER) cc_final: 0.8417 (pt) REVERT: Q 299 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8589 (mm) REVERT: Q 509 HIS cc_start: 0.8002 (m90) cc_final: 0.7729 (m90) outliers start: 154 outliers final: 78 residues processed: 768 average time/residue: 0.5280 time to fit residues: 712.1985 Evaluate side-chains 681 residues out of total 6946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 591 time to evaluate : 5.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain F residue 486 ILE Chi-restraints excluded: chain F residue 490 MET Chi-restraints excluded: chain F residue 533 MET Chi-restraints excluded: chain F residue 575 TYR Chi-restraints excluded: chain F residue 706 VAL Chi-restraints excluded: chain J residue 296 ILE Chi-restraints excluded: chain J residue 316 LEU Chi-restraints excluded: chain J residue 514 ASN Chi-restraints excluded: chain J residue 547 ILE Chi-restraints excluded: chain J residue 583 GLN Chi-restraints excluded: chain J residue 605 LEU Chi-restraints excluded: chain J residue 607 MET Chi-restraints excluded: chain J residue 662 VAL Chi-restraints excluded: chain J residue 666 LEU Chi-restraints excluded: chain J residue 752 LEU Chi-restraints excluded: chain J residue 756 VAL Chi-restraints excluded: chain K residue 361 LEU Chi-restraints excluded: chain K residue 482 CYS Chi-restraints excluded: chain K residue 600 LEU Chi-restraints excluded: chain K residue 673 THR Chi-restraints excluded: chain K residue 731 LEU Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 13 HIS Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 644 LEU Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 219 HIS Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 393 TRP Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 545 PHE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain C residue 959 VAL Chi-restraints excluded: chain C residue 1090 MET Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1312 VAL Chi-restraints excluded: chain C residue 1325 LEU Chi-restraints excluded: chain C residue 1350 LYS Chi-restraints excluded: chain C residue 1497 THR Chi-restraints excluded: chain C residue 1504 LEU Chi-restraints excluded: chain C residue 1533 THR Chi-restraints excluded: chain C residue 1604 VAL Chi-restraints excluded: chain C residue 1701 THR Chi-restraints excluded: chain O residue 361 SER Chi-restraints excluded: chain O residue 386 ILE Chi-restraints excluded: chain O residue 458 VAL Chi-restraints excluded: chain O residue 631 LEU Chi-restraints excluded: chain D residue 77 ASN Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 480 MET Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain P residue 40 LEU Chi-restraints excluded: chain P residue 253 LEU Chi-restraints excluded: chain I residue 37 GLU Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 96 ASP Chi-restraints excluded: chain I residue 107 SER Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 162 HIS Chi-restraints excluded: chain Q residue 62 LEU Chi-restraints excluded: chain Q residue 116 ILE Chi-restraints excluded: chain Q residue 199 ILE Chi-restraints excluded: chain Q residue 208 CYS Chi-restraints excluded: chain Q residue 297 ASP Chi-restraints excluded: chain Q residue 299 LEU Chi-restraints excluded: chain Q residue 362 ASP Chi-restraints excluded: chain Q residue 387 LEU Chi-restraints excluded: chain Q residue 411 GLU Chi-restraints excluded: chain Q residue 427 TYR Chi-restraints excluded: chain Q residue 457 ILE Chi-restraints excluded: chain Q residue 467 ILE Chi-restraints excluded: chain T residue 280 LEU Chi-restraints excluded: chain T residue 338 VAL Chi-restraints excluded: chain T residue 341 LEU Chi-restraints excluded: chain T residue 387 LEU Chi-restraints excluded: chain T residue 394 LEU Chi-restraints excluded: chain T residue 458 MET Chi-restraints excluded: chain T residue 581 LEU Chi-restraints excluded: chain U residue 100 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 758 random chunks: chunk 681 optimal weight: 30.0000 chunk 518 optimal weight: 0.6980 chunk 357 optimal weight: 0.1980 chunk 76 optimal weight: 2.9990 chunk 329 optimal weight: 8.9990 chunk 463 optimal weight: 0.0870 chunk 692 optimal weight: 5.9990 chunk 732 optimal weight: 10.0000 chunk 361 optimal weight: 9.9990 chunk 655 optimal weight: 5.9990 chunk 197 optimal weight: 9.9990 overall best weight: 1.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 682 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 732 HIS ** J 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 149 HIS ** E 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 71 GLN ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 713 ASN ** C 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 983 ASN C1011 GLN ** C1384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 353 ASN ** O 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 653 ASN ** D 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 571 GLN ** U 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 110 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 62632 Z= 0.220 Angle : 0.582 14.118 84784 Z= 0.298 Chirality : 0.041 0.341 9583 Planarity : 0.003 0.066 10715 Dihedral : 4.236 52.996 8258 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.26 % Favored : 95.57 % Rotamer: Outliers : 3.08 % Allowed : 16.12 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.10), residues: 7537 helix: 1.61 (0.08), residues: 4724 sheet: -0.07 (0.23), residues: 465 loop : -1.28 (0.13), residues: 2348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP P 27 HIS 0.006 0.001 HIS A 213 PHE 0.024 0.001 PHE F 495 TYR 0.024 0.001 TYR D 201 ARG 0.008 0.000 ARG I 14 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15074 Ramachandran restraints generated. 7537 Oldfield, 0 Emsley, 7537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15074 Ramachandran restraints generated. 7537 Oldfield, 0 Emsley, 7537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 842 residues out of total 6946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 207 poor density : 635 time to evaluate : 5.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 153 LEU cc_start: 0.7574 (tp) cc_final: 0.7308 (tp) REVERT: F 187 LEU cc_start: 0.8714 (tp) cc_final: 0.8496 (tp) REVERT: F 192 GLU cc_start: 0.9060 (mm-30) cc_final: 0.8579 (mm-30) REVERT: F 490 MET cc_start: 0.8573 (OUTLIER) cc_final: 0.7595 (tpt) REVERT: F 543 TRP cc_start: 0.8032 (m100) cc_final: 0.7365 (m100) REVERT: F 604 ASP cc_start: 0.8787 (t0) cc_final: 0.8373 (t0) REVERT: F 670 HIS cc_start: 0.8123 (OUTLIER) cc_final: 0.7028 (m170) REVERT: F 740 ASP cc_start: 0.7452 (t0) cc_final: 0.6829 (t0) REVERT: J 254 ASP cc_start: 0.8463 (t0) cc_final: 0.8139 (t0) REVERT: J 394 GLU cc_start: 0.8374 (tp30) cc_final: 0.7606 (tp30) REVERT: J 480 ASN cc_start: 0.8119 (m-40) cc_final: 0.7879 (p0) REVERT: J 542 MET cc_start: 0.8644 (mmm) cc_final: 0.8026 (tpp) REVERT: J 575 TYR cc_start: 0.8255 (m-80) cc_final: 0.7901 (m-80) REVERT: J 583 GLN cc_start: 0.7530 (OUTLIER) cc_final: 0.6044 (pp30) REVERT: K 300 TYR cc_start: 0.8651 (t80) cc_final: 0.8235 (t80) REVERT: K 396 PHE cc_start: 0.8499 (t80) cc_final: 0.8212 (t80) REVERT: K 571 PHE cc_start: 0.9018 (t80) cc_final: 0.8667 (t80) REVERT: K 581 GLN cc_start: 0.7627 (mp10) cc_final: 0.7385 (mp10) REVERT: K 594 PHE cc_start: 0.7993 (OUTLIER) cc_final: 0.7695 (m-80) REVERT: W 10 GLN cc_start: 0.8080 (tp-100) cc_final: 0.7644 (tp-100) REVERT: H 497 ARG cc_start: 0.6763 (OUTLIER) cc_final: 0.6555 (ttp80) REVERT: H 619 MET cc_start: 0.4093 (ttt) cc_final: 0.3881 (ttt) REVERT: A 44 LYS cc_start: 0.5144 (tptt) cc_final: 0.4925 (tppt) REVERT: A 47 TYR cc_start: 0.4756 (t80) cc_final: 0.4525 (t80) REVERT: A 63 GLU cc_start: 0.7830 (tp30) cc_final: 0.7554 (mp0) REVERT: A 124 ASP cc_start: 0.7321 (t0) cc_final: 0.6996 (t0) REVERT: A 126 MET cc_start: 0.8128 (tpp) cc_final: 0.7819 (tpp) REVERT: A 195 CYS cc_start: 0.8735 (m) cc_final: 0.8263 (m) REVERT: B 69 ILE cc_start: 0.8000 (OUTLIER) cc_final: 0.7799 (tt) REVERT: B 118 ASP cc_start: 0.7716 (t0) cc_final: 0.7482 (t0) REVERT: B 226 MET cc_start: 0.6136 (OUTLIER) cc_final: 0.5824 (ppp) REVERT: C 800 GLU cc_start: 0.7501 (tm-30) cc_final: 0.7180 (tm-30) REVERT: C 950 MET cc_start: 0.8946 (mmp) cc_final: 0.8649 (mmp) REVERT: C 1008 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8355 (pm20) REVERT: C 1053 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7653 (mm) REVERT: C 1154 LEU cc_start: 0.8144 (tp) cc_final: 0.7909 (tp) REVERT: C 1252 MET cc_start: 0.8632 (tmm) cc_final: 0.7891 (tmm) REVERT: C 1540 GLU cc_start: 0.8312 (pm20) cc_final: 0.7906 (pm20) REVERT: C 1606 MET cc_start: 0.7088 (ppp) cc_final: 0.5930 (ppp) REVERT: C 1715 GLU cc_start: 0.8706 (mp0) cc_final: 0.8403 (mp0) REVERT: O 165 MET cc_start: 0.7247 (tmm) cc_final: 0.6777 (tmm) REVERT: O 176 PHE cc_start: 0.8198 (OUTLIER) cc_final: 0.7714 (t80) REVERT: O 568 LEU cc_start: 0.8895 (tp) cc_final: 0.8621 (tp) REVERT: D 254 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8210 (mm-30) REVERT: D 256 MET cc_start: 0.8266 (tmm) cc_final: 0.8023 (tmm) REVERT: D 349 GLU cc_start: 0.8580 (tp30) cc_final: 0.7966 (tm-30) REVERT: D 557 LYS cc_start: 0.8157 (mptt) cc_final: 0.7682 (mptt) REVERT: D 602 MET cc_start: 0.7502 (mmp) cc_final: 0.6771 (ptp) REVERT: P 253 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8189 (mm) REVERT: P 317 ASP cc_start: 0.9009 (p0) cc_final: 0.8568 (p0) REVERT: P 334 TYR cc_start: 0.8362 (t80) cc_final: 0.8094 (t80) REVERT: P 338 ILE cc_start: 0.8886 (mm) cc_final: 0.8500 (mm) REVERT: P 432 ASN cc_start: 0.7697 (p0) cc_final: 0.6762 (p0) REVERT: P 567 GLU cc_start: 0.8646 (mt-10) cc_final: 0.8302 (mm-30) REVERT: I 37 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7350 (pt0) REVERT: I 96 ASP cc_start: 0.8768 (OUTLIER) cc_final: 0.8470 (m-30) REVERT: N 107 ARG cc_start: 0.7729 (ttp80) cc_final: 0.7272 (ttp80) REVERT: Q 156 ASN cc_start: 0.8421 (p0) cc_final: 0.7759 (p0) REVERT: Q 299 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8610 (mm) REVERT: Q 453 TYR cc_start: 0.8471 (m-10) cc_final: 0.8133 (m-10) REVERT: Q 509 HIS cc_start: 0.7950 (m90) cc_final: 0.7671 (m90) REVERT: T 121 HIS cc_start: 0.8652 (m90) cc_final: 0.8365 (m90) REVERT: T 309 MET cc_start: 0.7770 (mmm) cc_final: 0.7106 (tpp) REVERT: T 607 LYS cc_start: 0.5810 (mttt) cc_final: 0.5034 (ttpt) REVERT: U 1 MET cc_start: 0.5692 (mmm) cc_final: 0.5129 (mmp) outliers start: 207 outliers final: 118 residues processed: 785 average time/residue: 0.5299 time to fit residues: 728.8904 Evaluate side-chains 706 residues out of total 6946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 574 time to evaluate : 5.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain F residue 81 ASN Chi-restraints excluded: chain F residue 200 THR Chi-restraints excluded: chain F residue 486 ILE Chi-restraints excluded: chain F residue 490 MET Chi-restraints excluded: chain F residue 498 LEU Chi-restraints excluded: chain F residue 520 HIS Chi-restraints excluded: chain F residue 533 MET Chi-restraints excluded: chain F residue 575 TYR Chi-restraints excluded: chain F residue 670 HIS Chi-restraints excluded: chain F residue 748 ILE Chi-restraints excluded: chain J residue 296 ILE Chi-restraints excluded: chain J residue 316 LEU Chi-restraints excluded: chain J residue 482 CYS Chi-restraints excluded: chain J residue 514 ASN Chi-restraints excluded: chain J residue 539 THR Chi-restraints excluded: chain J residue 583 GLN Chi-restraints excluded: chain J residue 585 LEU Chi-restraints excluded: chain J residue 605 LEU Chi-restraints excluded: chain J residue 662 VAL Chi-restraints excluded: chain J residue 666 LEU Chi-restraints excluded: chain J residue 752 LEU Chi-restraints excluded: chain J residue 756 VAL Chi-restraints excluded: chain K residue 361 LEU Chi-restraints excluded: chain K residue 482 CYS Chi-restraints excluded: chain K residue 594 PHE Chi-restraints excluded: chain K residue 600 LEU Chi-restraints excluded: chain K residue 673 THR Chi-restraints excluded: chain K residue 731 LEU Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 13 HIS Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 159 LEU Chi-restraints excluded: chain H residue 497 ARG Chi-restraints excluded: chain H residue 569 LEU Chi-restraints excluded: chain H residue 644 LEU Chi-restraints excluded: chain H residue 706 VAL Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 219 HIS Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 393 TRP Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 545 PHE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 760 ASP Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain C residue 867 ILE Chi-restraints excluded: chain C residue 1008 GLU Chi-restraints excluded: chain C residue 1053 LEU Chi-restraints excluded: chain C residue 1090 MET Chi-restraints excluded: chain C residue 1094 MET Chi-restraints excluded: chain C residue 1143 MET Chi-restraints excluded: chain C residue 1312 VAL Chi-restraints excluded: chain C residue 1325 LEU Chi-restraints excluded: chain C residue 1350 LYS Chi-restraints excluded: chain C residue 1497 THR Chi-restraints excluded: chain C residue 1504 LEU Chi-restraints excluded: chain C residue 1533 THR Chi-restraints excluded: chain C residue 1582 GLU Chi-restraints excluded: chain C residue 1604 VAL Chi-restraints excluded: chain C residue 1614 VAL Chi-restraints excluded: chain C residue 1701 THR Chi-restraints excluded: chain C residue 1731 ILE Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 176 PHE Chi-restraints excluded: chain O residue 344 SER Chi-restraints excluded: chain O residue 361 SER Chi-restraints excluded: chain O residue 458 VAL Chi-restraints excluded: chain O residue 474 VAL Chi-restraints excluded: chain O residue 515 VAL Chi-restraints excluded: chain O residue 559 ILE Chi-restraints excluded: chain O residue 631 LEU Chi-restraints excluded: chain O residue 658 LEU Chi-restraints excluded: chain O residue 671 LEU Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 443 GLU Chi-restraints excluded: chain D residue 480 MET Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain P residue 40 LEU Chi-restraints excluded: chain P residue 112 THR Chi-restraints excluded: chain P residue 242 LEU Chi-restraints excluded: chain P residue 253 LEU Chi-restraints excluded: chain P residue 458 VAL Chi-restraints excluded: chain P residue 480 MET Chi-restraints excluded: chain P residue 516 VAL Chi-restraints excluded: chain P residue 552 LEU Chi-restraints excluded: chain P residue 577 THR Chi-restraints excluded: chain I residue 32 LEU Chi-restraints excluded: chain I residue 37 GLU Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 96 ASP Chi-restraints excluded: chain I residue 103 MET Chi-restraints excluded: chain I residue 107 SER Chi-restraints excluded: chain I residue 155 TYR Chi-restraints excluded: chain I residue 162 HIS Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain Q residue 114 CYS Chi-restraints excluded: chain Q residue 116 ILE Chi-restraints excluded: chain Q residue 208 CYS Chi-restraints excluded: chain Q residue 253 ILE Chi-restraints excluded: chain Q residue 297 ASP Chi-restraints excluded: chain Q residue 299 LEU Chi-restraints excluded: chain Q residue 362 ASP Chi-restraints excluded: chain Q residue 387 LEU Chi-restraints excluded: chain Q residue 411 GLU Chi-restraints excluded: chain Q residue 427 TYR Chi-restraints excluded: chain Q residue 429 LEU Chi-restraints excluded: chain Q residue 467 ILE Chi-restraints excluded: chain T residue 145 VAL Chi-restraints excluded: chain T residue 159 LEU Chi-restraints excluded: chain T residue 300 VAL Chi-restraints excluded: chain T residue 338 VAL Chi-restraints excluded: chain T residue 387 LEU Chi-restraints excluded: chain T residue 394 LEU Chi-restraints excluded: chain T residue 458 MET Chi-restraints excluded: chain T residue 489 THR Chi-restraints excluded: chain T residue 581 LEU Chi-restraints excluded: chain U residue 100 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 758 random chunks: chunk 610 optimal weight: 4.9990 chunk 415 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 545 optimal weight: 8.9990 chunk 302 optimal weight: 4.9990 chunk 625 optimal weight: 5.9990 chunk 506 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 374 optimal weight: 0.0170 chunk 657 optimal weight: 0.9980 chunk 184 optimal weight: 9.9990 overall best weight: 3.4024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 35 GLN ** F 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 682 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 732 HIS ** J 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 HIS ** H 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 71 GLN ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 ASN ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1056 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1105 HIS ** C1384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1536 HIS ** C1543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 77 ASN Q 574 ASN T 113 GLN T 373 GLN T 415 HIS ** U 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 110 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 62632 Z= 0.316 Angle : 0.647 13.589 84784 Z= 0.331 Chirality : 0.043 0.300 9583 Planarity : 0.004 0.064 10715 Dihedral : 4.442 49.140 8258 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.71 % Favored : 95.14 % Rotamer: Outliers : 3.78 % Allowed : 16.73 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.10), residues: 7537 helix: 1.49 (0.07), residues: 4726 sheet: -0.17 (0.23), residues: 453 loop : -1.34 (0.13), residues: 2358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP P 27 HIS 0.007 0.001 HIS I 92 PHE 0.037 0.002 PHE F 495 TYR 0.027 0.002 TYR F 494 ARG 0.009 0.001 ARG I 14 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15074 Ramachandran restraints generated. 7537 Oldfield, 0 Emsley, 7537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15074 Ramachandran restraints generated. 7537 Oldfield, 0 Emsley, 7537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 864 residues out of total 6946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 254 poor density : 610 time to evaluate : 5.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 57 CYS cc_start: 0.7492 (OUTLIER) cc_final: 0.6922 (t) REVERT: F 165 MET cc_start: 0.8189 (mmp) cc_final: 0.7945 (mmp) REVERT: F 192 GLU cc_start: 0.9052 (mm-30) cc_final: 0.8559 (mm-30) REVERT: F 490 MET cc_start: 0.8958 (OUTLIER) cc_final: 0.8074 (tpt) REVERT: F 543 TRP cc_start: 0.8113 (m100) cc_final: 0.7339 (m100) REVERT: F 604 ASP cc_start: 0.8816 (t0) cc_final: 0.8421 (t0) REVERT: F 670 HIS cc_start: 0.8241 (OUTLIER) cc_final: 0.7278 (m170) REVERT: F 682 MET cc_start: 0.8622 (OUTLIER) cc_final: 0.8413 (tpp) REVERT: F 740 ASP cc_start: 0.7805 (t0) cc_final: 0.7324 (t0) REVERT: J 243 GLN cc_start: 0.8853 (tm-30) cc_final: 0.8360 (tm-30) REVERT: J 254 ASP cc_start: 0.8544 (t0) cc_final: 0.8277 (t0) REVERT: J 394 GLU cc_start: 0.8596 (tp30) cc_final: 0.8386 (tp30) REVERT: J 398 MET cc_start: 0.9106 (tpp) cc_final: 0.8864 (tpp) REVERT: J 480 ASN cc_start: 0.8274 (m-40) cc_final: 0.8030 (p0) REVERT: J 542 MET cc_start: 0.8913 (mmm) cc_final: 0.8152 (tpp) REVERT: J 547 ILE cc_start: 0.8295 (OUTLIER) cc_final: 0.7579 (mm) REVERT: J 549 GLU cc_start: 0.8129 (tm-30) cc_final: 0.7645 (tm-30) REVERT: J 575 TYR cc_start: 0.8592 (m-80) cc_final: 0.8329 (m-80) REVERT: J 583 GLN cc_start: 0.7567 (OUTLIER) cc_final: 0.6069 (pp30) REVERT: J 612 MET cc_start: 0.8307 (ppp) cc_final: 0.8084 (ppp) REVERT: K 322 TYR cc_start: 0.7539 (m-10) cc_final: 0.7019 (m-80) REVERT: K 357 MET cc_start: 0.8318 (mmm) cc_final: 0.7760 (tpt) REVERT: K 542 MET cc_start: 0.8634 (ttp) cc_final: 0.8044 (tmm) REVERT: K 581 GLN cc_start: 0.7667 (mp10) cc_final: 0.7427 (mp10) REVERT: G 25 GLU cc_start: 0.7283 (mt-10) cc_final: 0.6838 (pt0) REVERT: W 10 GLN cc_start: 0.8186 (tp-100) cc_final: 0.7724 (tp-100) REVERT: H 123 LEU cc_start: 0.9118 (mt) cc_final: 0.8904 (mp) REVERT: H 160 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7808 (tt) REVERT: H 497 ARG cc_start: 0.6775 (OUTLIER) cc_final: 0.6435 (ttp80) REVERT: H 630 TYR cc_start: 0.7956 (m-80) cc_final: 0.7608 (m-80) REVERT: E 160 MET cc_start: 0.6990 (tpp) cc_final: 0.6775 (tpp) REVERT: A 81 MET cc_start: 0.5600 (tpp) cc_final: 0.5241 (tpp) REVERT: A 126 MET cc_start: 0.8113 (OUTLIER) cc_final: 0.7848 (tpp) REVERT: A 156 TYR cc_start: 0.7710 (m-80) cc_final: 0.7143 (m-10) REVERT: B 109 GLU cc_start: 0.8433 (tm-30) cc_final: 0.8161 (tp30) REVERT: B 226 MET cc_start: 0.6299 (OUTLIER) cc_final: 0.5984 (ppp) REVERT: C 662 MET cc_start: 0.7001 (mtp) cc_final: 0.6708 (ttm) REVERT: C 800 GLU cc_start: 0.7590 (tm-30) cc_final: 0.7301 (tm-30) REVERT: C 807 LEU cc_start: 0.9428 (mp) cc_final: 0.8649 (tt) REVERT: C 950 MET cc_start: 0.9013 (mmp) cc_final: 0.8655 (mmp) REVERT: C 1053 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7815 (mm) REVERT: C 1154 LEU cc_start: 0.8209 (tp) cc_final: 0.7784 (tp) REVERT: C 1252 MET cc_start: 0.8701 (tmm) cc_final: 0.8037 (tmm) REVERT: C 1295 MET cc_start: 0.8667 (mmm) cc_final: 0.8452 (mmm) REVERT: C 1540 GLU cc_start: 0.8332 (pm20) cc_final: 0.7876 (pm20) REVERT: C 1541 LEU cc_start: 0.8533 (tp) cc_final: 0.8309 (tp) REVERT: C 1606 MET cc_start: 0.7047 (ppp) cc_final: 0.5804 (ppp) REVERT: C 1715 GLU cc_start: 0.8743 (mp0) cc_final: 0.8449 (mp0) REVERT: O 68 SER cc_start: 0.9089 (t) cc_final: 0.8757 (p) REVERT: O 165 MET cc_start: 0.7322 (tmm) cc_final: 0.6822 (tmm) REVERT: O 568 LEU cc_start: 0.8931 (tp) cc_final: 0.8633 (tp) REVERT: O 662 PHE cc_start: 0.8871 (OUTLIER) cc_final: 0.7136 (p90) REVERT: D 256 MET cc_start: 0.8290 (tmm) cc_final: 0.8034 (tmm) REVERT: D 322 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8484 (mm) REVERT: D 349 GLU cc_start: 0.8571 (tp30) cc_final: 0.7949 (tm-30) REVERT: D 544 GLN cc_start: 0.8013 (tt0) cc_final: 0.7781 (tt0) REVERT: D 546 TYR cc_start: 0.7686 (OUTLIER) cc_final: 0.7393 (m-10) REVERT: D 560 MET cc_start: 0.7358 (OUTLIER) cc_final: 0.6663 (tmm) REVERT: D 602 MET cc_start: 0.7508 (mmp) cc_final: 0.6649 (ptp) REVERT: P 193 GLU cc_start: 0.8402 (tm-30) cc_final: 0.7913 (tm-30) REVERT: P 253 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8472 (mm) REVERT: P 256 MET cc_start: 0.8728 (mmm) cc_final: 0.8335 (mmm) REVERT: P 317 ASP cc_start: 0.9111 (p0) cc_final: 0.8723 (p0) REVERT: P 338 ILE cc_start: 0.8867 (mm) cc_final: 0.8547 (mm) REVERT: P 432 ASN cc_start: 0.7979 (p0) cc_final: 0.7057 (p0) REVERT: P 452 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7217 (mt-10) REVERT: P 509 TYR cc_start: 0.6600 (t80) cc_final: 0.6179 (t80) REVERT: P 567 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8398 (mp0) REVERT: I 83 ASN cc_start: 0.8499 (t160) cc_final: 0.8231 (m-40) REVERT: I 94 GLU cc_start: 0.8229 (mp0) cc_final: 0.7847 (tm-30) REVERT: I 96 ASP cc_start: 0.8877 (OUTLIER) cc_final: 0.8549 (m-30) REVERT: N 107 ARG cc_start: 0.7962 (ttp80) cc_final: 0.7642 (ttm110) REVERT: Q 299 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8593 (mm) REVERT: Q 453 TYR cc_start: 0.8484 (m-10) cc_final: 0.8154 (m-10) REVERT: Q 509 HIS cc_start: 0.7971 (m90) cc_final: 0.7701 (m90) REVERT: T 106 LEU cc_start: 0.8886 (mt) cc_final: 0.8527 (pp) REVERT: T 159 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7720 (tp) outliers start: 254 outliers final: 148 residues processed: 800 average time/residue: 0.5373 time to fit residues: 754.1267 Evaluate side-chains 711 residues out of total 6946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 544 time to evaluate : 5.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 57 CYS Chi-restraints excluded: chain F residue 81 ASN Chi-restraints excluded: chain F residue 486 ILE Chi-restraints excluded: chain F residue 490 MET Chi-restraints excluded: chain F residue 498 LEU Chi-restraints excluded: chain F residue 520 HIS Chi-restraints excluded: chain F residue 533 MET Chi-restraints excluded: chain F residue 575 TYR Chi-restraints excluded: chain F residue 670 HIS Chi-restraints excluded: chain F residue 682 MET Chi-restraints excluded: chain F residue 703 VAL Chi-restraints excluded: chain F residue 748 ILE Chi-restraints excluded: chain J residue 280 VAL Chi-restraints excluded: chain J residue 296 ILE Chi-restraints excluded: chain J residue 316 LEU Chi-restraints excluded: chain J residue 482 CYS Chi-restraints excluded: chain J residue 483 LEU Chi-restraints excluded: chain J residue 486 CYS Chi-restraints excluded: chain J residue 514 ASN Chi-restraints excluded: chain J residue 539 THR Chi-restraints excluded: chain J residue 547 ILE Chi-restraints excluded: chain J residue 583 GLN Chi-restraints excluded: chain J residue 585 LEU Chi-restraints excluded: chain J residue 605 LEU Chi-restraints excluded: chain J residue 662 VAL Chi-restraints excluded: chain J residue 666 LEU Chi-restraints excluded: chain J residue 752 LEU Chi-restraints excluded: chain J residue 756 VAL Chi-restraints excluded: chain K residue 255 LYS Chi-restraints excluded: chain K residue 287 THR Chi-restraints excluded: chain K residue 297 LEU Chi-restraints excluded: chain K residue 361 LEU Chi-restraints excluded: chain K residue 394 GLU Chi-restraints excluded: chain K residue 586 THR Chi-restraints excluded: chain K residue 673 THR Chi-restraints excluded: chain K residue 731 LEU Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 159 LEU Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain H residue 433 LEU Chi-restraints excluded: chain H residue 497 ARG Chi-restraints excluded: chain H residue 502 GLN Chi-restraints excluded: chain H residue 569 LEU Chi-restraints excluded: chain H residue 706 VAL Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 219 HIS Chi-restraints excluded: chain E residue 229 GLN Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 393 TRP Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain C residue 80 PHE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 760 ASP Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain C residue 867 ILE Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1007 VAL Chi-restraints excluded: chain C residue 1053 LEU Chi-restraints excluded: chain C residue 1312 VAL Chi-restraints excluded: chain C residue 1325 LEU Chi-restraints excluded: chain C residue 1350 LYS Chi-restraints excluded: chain C residue 1497 THR Chi-restraints excluded: chain C residue 1504 LEU Chi-restraints excluded: chain C residue 1533 THR Chi-restraints excluded: chain C residue 1544 PHE Chi-restraints excluded: chain C residue 1604 VAL Chi-restraints excluded: chain C residue 1614 VAL Chi-restraints excluded: chain C residue 1658 LEU Chi-restraints excluded: chain C residue 1701 THR Chi-restraints excluded: chain C residue 1731 ILE Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 256 VAL Chi-restraints excluded: chain O residue 301 ILE Chi-restraints excluded: chain O residue 344 SER Chi-restraints excluded: chain O residue 361 SER Chi-restraints excluded: chain O residue 430 THR Chi-restraints excluded: chain O residue 458 VAL Chi-restraints excluded: chain O residue 474 VAL Chi-restraints excluded: chain O residue 501 LEU Chi-restraints excluded: chain O residue 515 VAL Chi-restraints excluded: chain O residue 559 ILE Chi-restraints excluded: chain O residue 631 LEU Chi-restraints excluded: chain O residue 658 LEU Chi-restraints excluded: chain O residue 662 PHE Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 443 GLU Chi-restraints excluded: chain D residue 480 MET Chi-restraints excluded: chain D residue 492 CYS Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 546 TYR Chi-restraints excluded: chain D residue 560 MET Chi-restraints excluded: chain D residue 565 VAL Chi-restraints excluded: chain P residue 40 LEU Chi-restraints excluded: chain P residue 112 THR Chi-restraints excluded: chain P residue 139 ILE Chi-restraints excluded: chain P residue 242 LEU Chi-restraints excluded: chain P residue 253 LEU Chi-restraints excluded: chain P residue 292 PHE Chi-restraints excluded: chain P residue 305 GLU Chi-restraints excluded: chain P residue 399 THR Chi-restraints excluded: chain P residue 424 LEU Chi-restraints excluded: chain P residue 458 VAL Chi-restraints excluded: chain P residue 480 MET Chi-restraints excluded: chain P residue 516 VAL Chi-restraints excluded: chain P residue 552 LEU Chi-restraints excluded: chain P residue 577 THR Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 96 ASP Chi-restraints excluded: chain I residue 103 MET Chi-restraints excluded: chain I residue 107 SER Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain I residue 162 HIS Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 96 GLU Chi-restraints excluded: chain N residue 100 LEU Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 76 ILE Chi-restraints excluded: chain Q residue 114 CYS Chi-restraints excluded: chain Q residue 116 ILE Chi-restraints excluded: chain Q residue 199 ILE Chi-restraints excluded: chain Q residue 208 CYS Chi-restraints excluded: chain Q residue 224 LEU Chi-restraints excluded: chain Q residue 239 ILE Chi-restraints excluded: chain Q residue 297 ASP Chi-restraints excluded: chain Q residue 299 LEU Chi-restraints excluded: chain Q residue 362 ASP Chi-restraints excluded: chain Q residue 387 LEU Chi-restraints excluded: chain Q residue 411 GLU Chi-restraints excluded: chain Q residue 415 LEU Chi-restraints excluded: chain Q residue 427 TYR Chi-restraints excluded: chain Q residue 429 LEU Chi-restraints excluded: chain Q residue 467 ILE Chi-restraints excluded: chain Q residue 631 THR Chi-restraints excluded: chain Q residue 634 VAL Chi-restraints excluded: chain T residue 145 VAL Chi-restraints excluded: chain T residue 159 LEU Chi-restraints excluded: chain T residue 238 MET Chi-restraints excluded: chain T residue 280 LEU Chi-restraints excluded: chain T residue 300 VAL Chi-restraints excluded: chain T residue 338 VAL Chi-restraints excluded: chain T residue 387 LEU Chi-restraints excluded: chain T residue 394 LEU Chi-restraints excluded: chain T residue 458 MET Chi-restraints excluded: chain T residue 581 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 758 random chunks: chunk 246 optimal weight: 0.0970 chunk 659 optimal weight: 2.9990 chunk 144 optimal weight: 10.0000 chunk 430 optimal weight: 0.0970 chunk 180 optimal weight: 10.0000 chunk 733 optimal weight: 5.9990 chunk 608 optimal weight: 0.9990 chunk 339 optimal weight: 4.9990 chunk 60 optimal weight: 7.9990 chunk 242 optimal weight: 4.9990 chunk 385 optimal weight: 2.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 682 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 732 HIS ** J 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 750 ASN ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 530 ASN ** H 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 64 ASN A 71 GLN ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 HIS B 484 ASN B 503 ASN ** C 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1105 HIS ** C1384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 ASN D 377 GLN D 439 HIS U 110 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 62632 Z= 0.190 Angle : 0.585 12.213 84784 Z= 0.297 Chirality : 0.041 0.281 9583 Planarity : 0.003 0.055 10715 Dihedral : 4.303 48.679 8258 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.15 % Favored : 95.71 % Rotamer: Outliers : 3.00 % Allowed : 18.34 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.10), residues: 7537 helix: 1.60 (0.08), residues: 4737 sheet: -0.21 (0.23), residues: 467 loop : -1.32 (0.13), residues: 2333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP P 27 HIS 0.006 0.001 HIS A 213 PHE 0.028 0.001 PHE F 495 TYR 0.029 0.001 TYR E 236 ARG 0.006 0.000 ARG I 14 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15074 Ramachandran restraints generated. 7537 Oldfield, 0 Emsley, 7537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15074 Ramachandran restraints generated. 7537 Oldfield, 0 Emsley, 7537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 827 residues out of total 6946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 202 poor density : 625 time to evaluate : 6.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 57 CYS cc_start: 0.7549 (OUTLIER) cc_final: 0.6961 (t) REVERT: F 187 LEU cc_start: 0.8559 (tp) cc_final: 0.8246 (tp) REVERT: F 192 GLU cc_start: 0.8999 (mm-30) cc_final: 0.8524 (mm-30) REVERT: F 490 MET cc_start: 0.8799 (OUTLIER) cc_final: 0.7652 (tpt) REVERT: F 543 TRP cc_start: 0.8072 (m100) cc_final: 0.7249 (m100) REVERT: F 604 ASP cc_start: 0.8771 (t0) cc_final: 0.8362 (t0) REVERT: F 670 HIS cc_start: 0.8258 (OUTLIER) cc_final: 0.7110 (m170) REVERT: F 740 ASP cc_start: 0.7765 (t0) cc_final: 0.7248 (t0) REVERT: J 243 GLN cc_start: 0.8819 (tm-30) cc_final: 0.8083 (tm-30) REVERT: J 254 ASP cc_start: 0.8483 (t0) cc_final: 0.8272 (t0) REVERT: J 357 MET cc_start: 0.7960 (tpp) cc_final: 0.7196 (tpp) REVERT: J 394 GLU cc_start: 0.8527 (tp30) cc_final: 0.7808 (tp30) REVERT: J 480 ASN cc_start: 0.8268 (m-40) cc_final: 0.8011 (p0) REVERT: J 542 MET cc_start: 0.8887 (mmm) cc_final: 0.8542 (mmm) REVERT: J 547 ILE cc_start: 0.8174 (OUTLIER) cc_final: 0.7871 (mm) REVERT: J 549 GLU cc_start: 0.8117 (tm-30) cc_final: 0.7526 (tm-30) REVERT: J 551 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7982 (tt0) REVERT: J 612 MET cc_start: 0.7978 (ppp) cc_final: 0.7721 (ppp) REVERT: K 300 TYR cc_start: 0.8738 (t80) cc_final: 0.7625 (t80) REVERT: K 322 TYR cc_start: 0.7407 (m-10) cc_final: 0.6775 (m-80) REVERT: K 420 LYS cc_start: 0.8868 (pptt) cc_final: 0.8463 (ptmm) REVERT: K 464 ASP cc_start: 0.8097 (t0) cc_final: 0.7819 (t0) REVERT: K 542 MET cc_start: 0.8616 (ttp) cc_final: 0.8156 (tmm) REVERT: K 551 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7985 (mm110) REVERT: K 581 GLN cc_start: 0.7435 (mp10) cc_final: 0.7120 (mp10) REVERT: K 594 PHE cc_start: 0.7908 (OUTLIER) cc_final: 0.7703 (t80) REVERT: G 25 GLU cc_start: 0.7268 (mt-10) cc_final: 0.6832 (pt0) REVERT: W 1 MET cc_start: 0.7098 (mmm) cc_final: 0.6856 (mmm) REVERT: H 715 LEU cc_start: 0.5285 (pp) cc_final: 0.4972 (mm) REVERT: E 160 MET cc_start: 0.7099 (tpp) cc_final: 0.6853 (tpp) REVERT: A 44 LYS cc_start: 0.5294 (tptt) cc_final: 0.5055 (tppt) REVERT: A 124 ASP cc_start: 0.7347 (t0) cc_final: 0.7123 (t0) REVERT: A 126 MET cc_start: 0.8070 (tpp) cc_final: 0.7805 (tpp) REVERT: A 156 TYR cc_start: 0.7740 (m-80) cc_final: 0.7233 (m-10) REVERT: B 224 ASP cc_start: 0.8495 (m-30) cc_final: 0.8252 (t0) REVERT: B 226 MET cc_start: 0.6238 (OUTLIER) cc_final: 0.5957 (ppp) REVERT: C 428 LEU cc_start: 0.8326 (mt) cc_final: 0.8120 (mp) REVERT: C 662 MET cc_start: 0.6995 (mtp) cc_final: 0.6742 (ttm) REVERT: C 775 GLU cc_start: 0.6974 (tp30) cc_final: 0.6695 (tp30) REVERT: C 800 GLU cc_start: 0.7702 (tm-30) cc_final: 0.7324 (tm-30) REVERT: C 807 LEU cc_start: 0.9465 (mp) cc_final: 0.8686 (tt) REVERT: C 950 MET cc_start: 0.9007 (mmp) cc_final: 0.8604 (mmp) REVERT: C 1053 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7522 (mm) REVERT: C 1143 MET cc_start: 0.8025 (OUTLIER) cc_final: 0.7807 (tpp) REVERT: C 1154 LEU cc_start: 0.8216 (tp) cc_final: 0.7892 (tp) REVERT: C 1295 MET cc_start: 0.8703 (mmm) cc_final: 0.8351 (mmm) REVERT: C 1540 GLU cc_start: 0.8286 (pm20) cc_final: 0.7834 (pm20) REVERT: C 1606 MET cc_start: 0.6852 (ppp) cc_final: 0.5596 (ppp) REVERT: C 1715 GLU cc_start: 0.8653 (mp0) cc_final: 0.8356 (mp0) REVERT: O 68 SER cc_start: 0.9093 (t) cc_final: 0.8773 (p) REVERT: O 165 MET cc_start: 0.7303 (tmm) cc_final: 0.6745 (tmm) REVERT: O 176 PHE cc_start: 0.8267 (OUTLIER) cc_final: 0.7793 (t80) REVERT: O 248 GLN cc_start: 0.8067 (mm110) cc_final: 0.7807 (tp40) REVERT: O 568 LEU cc_start: 0.8867 (tp) cc_final: 0.8568 (tp) REVERT: O 662 PHE cc_start: 0.8940 (OUTLIER) cc_final: 0.7313 (p90) REVERT: D 214 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8549 (tt) REVERT: D 256 MET cc_start: 0.8281 (tmm) cc_final: 0.8015 (tmm) REVERT: D 349 GLU cc_start: 0.8561 (tp30) cc_final: 0.7989 (tm-30) REVERT: D 443 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8233 (mt-10) REVERT: D 546 TYR cc_start: 0.7657 (OUTLIER) cc_final: 0.7409 (m-10) REVERT: D 557 LYS cc_start: 0.8085 (mptt) cc_final: 0.7868 (mptt) REVERT: D 602 MET cc_start: 0.7235 (mmp) cc_final: 0.6546 (ptp) REVERT: P 193 GLU cc_start: 0.8442 (tm-30) cc_final: 0.7895 (tm-30) REVERT: P 253 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8433 (mm) REVERT: P 256 MET cc_start: 0.8695 (mmm) cc_final: 0.8144 (mmm) REVERT: P 317 ASP cc_start: 0.9042 (p0) cc_final: 0.8684 (p0) REVERT: P 334 TYR cc_start: 0.8330 (t80) cc_final: 0.8073 (t80) REVERT: P 338 ILE cc_start: 0.8877 (mm) cc_final: 0.8520 (mm) REVERT: P 376 MET cc_start: 0.8724 (mmp) cc_final: 0.8333 (mmp) REVERT: P 432 ASN cc_start: 0.7650 (p0) cc_final: 0.6691 (p0) REVERT: P 559 MET cc_start: 0.7122 (mtp) cc_final: 0.6699 (ttm) REVERT: I 96 ASP cc_start: 0.8753 (OUTLIER) cc_final: 0.8544 (m-30) REVERT: Q 295 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8625 (tt) REVERT: Q 299 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8390 (mm) REVERT: Q 453 TYR cc_start: 0.8402 (m-10) cc_final: 0.8027 (m-10) REVERT: T 309 MET cc_start: 0.7776 (mmm) cc_final: 0.7147 (tpp) outliers start: 202 outliers final: 113 residues processed: 779 average time/residue: 0.5402 time to fit residues: 734.6104 Evaluate side-chains 691 residues out of total 6946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 559 time to evaluate : 5.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 57 CYS Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain F residue 81 ASN Chi-restraints excluded: chain F residue 486 ILE Chi-restraints excluded: chain F residue 490 MET Chi-restraints excluded: chain F residue 498 LEU Chi-restraints excluded: chain F residue 533 MET Chi-restraints excluded: chain F residue 575 TYR Chi-restraints excluded: chain F residue 670 HIS Chi-restraints excluded: chain F residue 748 ILE Chi-restraints excluded: chain J residue 291 LEU Chi-restraints excluded: chain J residue 296 ILE Chi-restraints excluded: chain J residue 482 CYS Chi-restraints excluded: chain J residue 483 LEU Chi-restraints excluded: chain J residue 486 CYS Chi-restraints excluded: chain J residue 539 THR Chi-restraints excluded: chain J residue 547 ILE Chi-restraints excluded: chain J residue 551 GLN Chi-restraints excluded: chain J residue 585 LEU Chi-restraints excluded: chain J residue 605 LEU Chi-restraints excluded: chain J residue 617 LEU Chi-restraints excluded: chain J residue 662 VAL Chi-restraints excluded: chain J residue 666 LEU Chi-restraints excluded: chain J residue 752 LEU Chi-restraints excluded: chain K residue 297 LEU Chi-restraints excluded: chain K residue 361 LEU Chi-restraints excluded: chain K residue 394 GLU Chi-restraints excluded: chain K residue 551 GLN Chi-restraints excluded: chain K residue 586 THR Chi-restraints excluded: chain K residue 594 PHE Chi-restraints excluded: chain K residue 600 LEU Chi-restraints excluded: chain K residue 673 THR Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 13 HIS Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 159 LEU Chi-restraints excluded: chain H residue 569 LEU Chi-restraints excluded: chain H residue 601 LEU Chi-restraints excluded: chain H residue 706 VAL Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 219 HIS Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 393 TRP Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 760 ASP Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain C residue 867 ILE Chi-restraints excluded: chain C residue 1053 LEU Chi-restraints excluded: chain C residue 1094 MET Chi-restraints excluded: chain C residue 1143 MET Chi-restraints excluded: chain C residue 1312 VAL Chi-restraints excluded: chain C residue 1325 LEU Chi-restraints excluded: chain C residue 1497 THR Chi-restraints excluded: chain C residue 1504 LEU Chi-restraints excluded: chain C residue 1533 THR Chi-restraints excluded: chain C residue 1604 VAL Chi-restraints excluded: chain C residue 1614 VAL Chi-restraints excluded: chain C residue 1658 LEU Chi-restraints excluded: chain C residue 1701 THR Chi-restraints excluded: chain C residue 1731 ILE Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 176 PHE Chi-restraints excluded: chain O residue 232 THR Chi-restraints excluded: chain O residue 361 SER Chi-restraints excluded: chain O residue 453 ILE Chi-restraints excluded: chain O residue 458 VAL Chi-restraints excluded: chain O residue 501 LEU Chi-restraints excluded: chain O residue 532 LEU Chi-restraints excluded: chain O residue 559 ILE Chi-restraints excluded: chain O residue 631 LEU Chi-restraints excluded: chain O residue 658 LEU Chi-restraints excluded: chain O residue 662 PHE Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 443 GLU Chi-restraints excluded: chain D residue 480 MET Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 546 TYR Chi-restraints excluded: chain P residue 40 LEU Chi-restraints excluded: chain P residue 242 LEU Chi-restraints excluded: chain P residue 253 LEU Chi-restraints excluded: chain P residue 292 PHE Chi-restraints excluded: chain P residue 305 GLU Chi-restraints excluded: chain P residue 399 THR Chi-restraints excluded: chain P residue 458 VAL Chi-restraints excluded: chain P residue 480 MET Chi-restraints excluded: chain P residue 552 LEU Chi-restraints excluded: chain I residue 32 LEU Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 96 ASP Chi-restraints excluded: chain I residue 103 MET Chi-restraints excluded: chain I residue 107 SER Chi-restraints excluded: chain I residue 162 HIS Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 100 LEU Chi-restraints excluded: chain Q residue 116 ILE Chi-restraints excluded: chain Q residue 199 ILE Chi-restraints excluded: chain Q residue 208 CYS Chi-restraints excluded: chain Q residue 253 ILE Chi-restraints excluded: chain Q residue 295 LEU Chi-restraints excluded: chain Q residue 297 ASP Chi-restraints excluded: chain Q residue 299 LEU Chi-restraints excluded: chain Q residue 362 ASP Chi-restraints excluded: chain Q residue 387 LEU Chi-restraints excluded: chain Q residue 390 ASP Chi-restraints excluded: chain Q residue 411 GLU Chi-restraints excluded: chain Q residue 415 LEU Chi-restraints excluded: chain Q residue 427 TYR Chi-restraints excluded: chain Q residue 429 LEU Chi-restraints excluded: chain Q residue 566 LEU Chi-restraints excluded: chain T residue 159 LEU Chi-restraints excluded: chain T residue 300 VAL Chi-restraints excluded: chain T residue 303 LEU Chi-restraints excluded: chain T residue 338 VAL Chi-restraints excluded: chain T residue 387 LEU Chi-restraints excluded: chain T residue 394 LEU Chi-restraints excluded: chain T residue 458 MET Chi-restraints excluded: chain T residue 489 THR Chi-restraints excluded: chain T residue 581 LEU Chi-restraints excluded: chain U residue 100 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 758 random chunks: chunk 707 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 417 optimal weight: 8.9990 chunk 535 optimal weight: 1.9990 chunk 414 optimal weight: 0.9990 chunk 617 optimal weight: 2.9990 chunk 409 optimal weight: 3.9990 chunk 730 optimal weight: 20.0000 chunk 457 optimal weight: 0.7980 chunk 445 optimal weight: 0.7980 chunk 337 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 514 ASN ** J 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 682 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 755 ASN ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 229 GLN ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 ASN B 503 ASN ** C 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1105 HIS ** C1384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 110 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 62632 Z= 0.186 Angle : 0.588 11.671 84784 Z= 0.297 Chirality : 0.041 0.278 9583 Planarity : 0.003 0.054 10715 Dihedral : 4.231 46.696 8258 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.11 % Favored : 95.74 % Rotamer: Outliers : 2.87 % Allowed : 18.77 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.10), residues: 7537 helix: 1.65 (0.08), residues: 4737 sheet: -0.22 (0.23), residues: 472 loop : -1.29 (0.13), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP P 583 HIS 0.006 0.001 HIS K 732 PHE 0.025 0.001 PHE Q 394 TYR 0.018 0.001 TYR H 630 ARG 0.007 0.000 ARG N 137 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15074 Ramachandran restraints generated. 7537 Oldfield, 0 Emsley, 7537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15074 Ramachandran restraints generated. 7537 Oldfield, 0 Emsley, 7537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 803 residues out of total 6946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 193 poor density : 610 time to evaluate : 5.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 45 THR cc_start: 0.5636 (OUTLIER) cc_final: 0.5328 (m) REVERT: F 57 CYS cc_start: 0.7568 (OUTLIER) cc_final: 0.6987 (t) REVERT: F 192 GLU cc_start: 0.8904 (mm-30) cc_final: 0.8485 (mm-30) REVERT: F 490 MET cc_start: 0.8772 (OUTLIER) cc_final: 0.7683 (tpt) REVERT: F 516 LEU cc_start: 0.7374 (OUTLIER) cc_final: 0.7101 (mp) REVERT: F 543 TRP cc_start: 0.8082 (m100) cc_final: 0.7247 (m100) REVERT: F 604 ASP cc_start: 0.8749 (t0) cc_final: 0.8342 (t0) REVERT: F 670 HIS cc_start: 0.8227 (OUTLIER) cc_final: 0.7097 (m170) REVERT: F 740 ASP cc_start: 0.7771 (t0) cc_final: 0.7241 (t0) REVERT: J 390 ILE cc_start: 0.8787 (tp) cc_final: 0.8475 (mt) REVERT: J 394 GLU cc_start: 0.8546 (tp30) cc_final: 0.7845 (tp30) REVERT: J 480 ASN cc_start: 0.8278 (m-40) cc_final: 0.8006 (p0) REVERT: J 509 GLU cc_start: 0.8398 (tp30) cc_final: 0.8191 (tp30) REVERT: J 542 MET cc_start: 0.8875 (mmm) cc_final: 0.8517 (mmm) REVERT: J 547 ILE cc_start: 0.8160 (OUTLIER) cc_final: 0.7820 (mm) REVERT: J 549 GLU cc_start: 0.7992 (tm-30) cc_final: 0.7602 (tm-30) REVERT: J 551 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7974 (tt0) REVERT: J 612 MET cc_start: 0.7977 (ppp) cc_final: 0.7729 (ppp) REVERT: K 322 TYR cc_start: 0.7466 (m-10) cc_final: 0.6859 (m-80) REVERT: K 357 MET cc_start: 0.8253 (mmm) cc_final: 0.7648 (mmm) REVERT: K 397 GLU cc_start: 0.8134 (tp30) cc_final: 0.7620 (tm-30) REVERT: K 420 LYS cc_start: 0.8885 (pptt) cc_final: 0.8499 (ptmm) REVERT: K 464 ASP cc_start: 0.8078 (t0) cc_final: 0.7781 (t0) REVERT: K 542 MET cc_start: 0.8642 (ttp) cc_final: 0.8126 (tmm) REVERT: K 581 GLN cc_start: 0.7401 (mp10) cc_final: 0.7101 (mp10) REVERT: K 594 PHE cc_start: 0.7921 (OUTLIER) cc_final: 0.7690 (t80) REVERT: G 25 GLU cc_start: 0.7280 (mt-10) cc_final: 0.6860 (pt0) REVERT: W 1 MET cc_start: 0.7088 (mmm) cc_final: 0.6867 (mmm) REVERT: A 6 ILE cc_start: 0.7912 (mp) cc_final: 0.7703 (mm) REVERT: A 44 LYS cc_start: 0.5387 (tptt) cc_final: 0.5150 (tppt) REVERT: A 47 TYR cc_start: 0.4595 (t80) cc_final: 0.4356 (t80) REVERT: A 81 MET cc_start: 0.5566 (tpp) cc_final: 0.5256 (tpp) REVERT: A 126 MET cc_start: 0.8091 (OUTLIER) cc_final: 0.7822 (tpp) REVERT: A 156 TYR cc_start: 0.7706 (m-80) cc_final: 0.7242 (m-10) REVERT: B 224 ASP cc_start: 0.8239 (m-30) cc_final: 0.7959 (t0) REVERT: B 226 MET cc_start: 0.6216 (OUTLIER) cc_final: 0.5931 (ppp) REVERT: C 428 LEU cc_start: 0.8308 (mt) cc_final: 0.8093 (mp) REVERT: C 574 MET cc_start: 0.8997 (tpp) cc_final: 0.8747 (tpt) REVERT: C 662 MET cc_start: 0.7005 (mtp) cc_final: 0.6764 (ttm) REVERT: C 760 ASP cc_start: 0.8122 (OUTLIER) cc_final: 0.7583 (p0) REVERT: C 775 GLU cc_start: 0.6981 (tp30) cc_final: 0.6774 (tp30) REVERT: C 800 GLU cc_start: 0.7702 (tm-30) cc_final: 0.7287 (tm-30) REVERT: C 807 LEU cc_start: 0.9428 (mp) cc_final: 0.8677 (tt) REVERT: C 950 MET cc_start: 0.9012 (mmp) cc_final: 0.8576 (mmp) REVERT: C 1053 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7636 (mm) REVERT: C 1097 LYS cc_start: 0.7646 (tppt) cc_final: 0.7388 (ptpt) REVERT: C 1154 LEU cc_start: 0.8262 (tp) cc_final: 0.7847 (tp) REVERT: C 1252 MET cc_start: 0.8642 (ttt) cc_final: 0.7800 (tmm) REVERT: C 1266 MET cc_start: 0.8399 (mpp) cc_final: 0.7886 (pmm) REVERT: C 1267 LEU cc_start: 0.9138 (mp) cc_final: 0.8868 (mp) REVERT: C 1540 GLU cc_start: 0.8293 (pm20) cc_final: 0.7866 (pm20) REVERT: C 1606 MET cc_start: 0.6834 (ppp) cc_final: 0.5845 (ppp) REVERT: C 1715 GLU cc_start: 0.8647 (mp0) cc_final: 0.8356 (mp0) REVERT: O 68 SER cc_start: 0.9077 (t) cc_final: 0.8762 (p) REVERT: O 165 MET cc_start: 0.7280 (tmm) cc_final: 0.6800 (tmm) REVERT: O 176 PHE cc_start: 0.8006 (OUTLIER) cc_final: 0.7544 (t80) REVERT: O 248 GLN cc_start: 0.8043 (mm110) cc_final: 0.7765 (tp40) REVERT: O 568 LEU cc_start: 0.8885 (tp) cc_final: 0.8597 (tp) REVERT: O 662 PHE cc_start: 0.8945 (OUTLIER) cc_final: 0.7320 (p90) REVERT: D 214 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8579 (tt) REVERT: D 253 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8943 (mm) REVERT: D 256 MET cc_start: 0.8338 (tmm) cc_final: 0.8098 (tmm) REVERT: D 349 GLU cc_start: 0.8557 (tp30) cc_final: 0.7989 (tm-30) REVERT: D 443 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8225 (mt-10) REVERT: D 546 TYR cc_start: 0.7649 (OUTLIER) cc_final: 0.7402 (m-10) REVERT: D 557 LYS cc_start: 0.8062 (mptt) cc_final: 0.7861 (mptt) REVERT: D 560 MET cc_start: 0.7076 (OUTLIER) cc_final: 0.6666 (mtt) REVERT: D 602 MET cc_start: 0.7170 (mmp) cc_final: 0.6555 (ptp) REVERT: P 193 GLU cc_start: 0.8468 (tm-30) cc_final: 0.7931 (tm-30) REVERT: P 253 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8431 (mm) REVERT: P 256 MET cc_start: 0.8503 (mmm) cc_final: 0.8024 (mmm) REVERT: P 334 TYR cc_start: 0.8354 (t80) cc_final: 0.8057 (t80) REVERT: P 338 ILE cc_start: 0.8865 (mm) cc_final: 0.8496 (mm) REVERT: P 376 MET cc_start: 0.8681 (mmp) cc_final: 0.8333 (mmp) REVERT: P 432 ASN cc_start: 0.7774 (p0) cc_final: 0.6818 (p0) REVERT: P 559 MET cc_start: 0.7105 (mtp) cc_final: 0.6363 (ttm) REVERT: Q 295 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8629 (tt) REVERT: Q 299 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8393 (mm) REVERT: T 106 LEU cc_start: 0.8885 (mt) cc_final: 0.8534 (pp) REVERT: U 1 MET cc_start: 0.5725 (mmm) cc_final: 0.5029 (mmp) outliers start: 193 outliers final: 132 residues processed: 752 average time/residue: 0.5425 time to fit residues: 715.1333 Evaluate side-chains 721 residues out of total 6946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 567 time to evaluate : 5.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 57 CYS Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain F residue 81 ASN Chi-restraints excluded: chain F residue 490 MET Chi-restraints excluded: chain F residue 498 LEU Chi-restraints excluded: chain F residue 516 LEU Chi-restraints excluded: chain F residue 520 HIS Chi-restraints excluded: chain F residue 533 MET Chi-restraints excluded: chain F residue 575 TYR Chi-restraints excluded: chain F residue 670 HIS Chi-restraints excluded: chain F residue 748 ILE Chi-restraints excluded: chain J residue 296 ILE Chi-restraints excluded: chain J residue 482 CYS Chi-restraints excluded: chain J residue 483 LEU Chi-restraints excluded: chain J residue 486 CYS Chi-restraints excluded: chain J residue 514 ASN Chi-restraints excluded: chain J residue 520 SER Chi-restraints excluded: chain J residue 539 THR Chi-restraints excluded: chain J residue 547 ILE Chi-restraints excluded: chain J residue 551 GLN Chi-restraints excluded: chain J residue 585 LEU Chi-restraints excluded: chain J residue 605 LEU Chi-restraints excluded: chain J residue 662 VAL Chi-restraints excluded: chain J residue 666 LEU Chi-restraints excluded: chain J residue 752 LEU Chi-restraints excluded: chain K residue 285 LEU Chi-restraints excluded: chain K residue 297 LEU Chi-restraints excluded: chain K residue 361 LEU Chi-restraints excluded: chain K residue 394 GLU Chi-restraints excluded: chain K residue 523 LEU Chi-restraints excluded: chain K residue 544 LEU Chi-restraints excluded: chain K residue 575 TYR Chi-restraints excluded: chain K residue 586 THR Chi-restraints excluded: chain K residue 594 PHE Chi-restraints excluded: chain K residue 600 LEU Chi-restraints excluded: chain K residue 673 THR Chi-restraints excluded: chain K residue 731 LEU Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 13 HIS Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 159 LEU Chi-restraints excluded: chain H residue 502 GLN Chi-restraints excluded: chain H residue 569 LEU Chi-restraints excluded: chain H residue 601 LEU Chi-restraints excluded: chain H residue 706 VAL Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 219 HIS Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 393 TRP Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 545 PHE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 734 VAL Chi-restraints excluded: chain C residue 760 ASP Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain C residue 867 ILE Chi-restraints excluded: chain C residue 1008 GLU Chi-restraints excluded: chain C residue 1053 LEU Chi-restraints excluded: chain C residue 1094 MET Chi-restraints excluded: chain C residue 1312 VAL Chi-restraints excluded: chain C residue 1325 LEU Chi-restraints excluded: chain C residue 1497 THR Chi-restraints excluded: chain C residue 1504 LEU Chi-restraints excluded: chain C residue 1533 THR Chi-restraints excluded: chain C residue 1555 VAL Chi-restraints excluded: chain C residue 1604 VAL Chi-restraints excluded: chain C residue 1614 VAL Chi-restraints excluded: chain C residue 1658 LEU Chi-restraints excluded: chain C residue 1701 THR Chi-restraints excluded: chain C residue 1731 ILE Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 85 LEU Chi-restraints excluded: chain O residue 176 PHE Chi-restraints excluded: chain O residue 232 THR Chi-restraints excluded: chain O residue 344 SER Chi-restraints excluded: chain O residue 347 THR Chi-restraints excluded: chain O residue 361 SER Chi-restraints excluded: chain O residue 453 ILE Chi-restraints excluded: chain O residue 458 VAL Chi-restraints excluded: chain O residue 474 VAL Chi-restraints excluded: chain O residue 559 ILE Chi-restraints excluded: chain O residue 631 LEU Chi-restraints excluded: chain O residue 658 LEU Chi-restraints excluded: chain O residue 662 PHE Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 443 GLU Chi-restraints excluded: chain D residue 480 MET Chi-restraints excluded: chain D residue 492 CYS Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 546 TYR Chi-restraints excluded: chain D residue 555 CYS Chi-restraints excluded: chain D residue 560 MET Chi-restraints excluded: chain P residue 40 LEU Chi-restraints excluded: chain P residue 242 LEU Chi-restraints excluded: chain P residue 253 LEU Chi-restraints excluded: chain P residue 292 PHE Chi-restraints excluded: chain P residue 305 GLU Chi-restraints excluded: chain P residue 399 THR Chi-restraints excluded: chain P residue 458 VAL Chi-restraints excluded: chain P residue 480 MET Chi-restraints excluded: chain P residue 552 LEU Chi-restraints excluded: chain P residue 577 THR Chi-restraints excluded: chain I residue 32 LEU Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 103 MET Chi-restraints excluded: chain I residue 155 TYR Chi-restraints excluded: chain I residue 162 HIS Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 96 GLU Chi-restraints excluded: chain N residue 100 LEU Chi-restraints excluded: chain N residue 119 PHE Chi-restraints excluded: chain N residue 132 GLU Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 116 ILE Chi-restraints excluded: chain Q residue 208 CYS Chi-restraints excluded: chain Q residue 295 LEU Chi-restraints excluded: chain Q residue 297 ASP Chi-restraints excluded: chain Q residue 299 LEU Chi-restraints excluded: chain Q residue 387 LEU Chi-restraints excluded: chain Q residue 390 ASP Chi-restraints excluded: chain Q residue 411 GLU Chi-restraints excluded: chain Q residue 415 LEU Chi-restraints excluded: chain Q residue 427 TYR Chi-restraints excluded: chain Q residue 429 LEU Chi-restraints excluded: chain Q residue 566 LEU Chi-restraints excluded: chain Q residue 634 VAL Chi-restraints excluded: chain T residue 103 PHE Chi-restraints excluded: chain T residue 159 LEU Chi-restraints excluded: chain T residue 280 LEU Chi-restraints excluded: chain T residue 300 VAL Chi-restraints excluded: chain T residue 303 LEU Chi-restraints excluded: chain T residue 338 VAL Chi-restraints excluded: chain T residue 387 LEU Chi-restraints excluded: chain T residue 458 MET Chi-restraints excluded: chain T residue 489 THR Chi-restraints excluded: chain T residue 581 LEU Chi-restraints excluded: chain U residue 100 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 758 random chunks: chunk 451 optimal weight: 2.9990 chunk 291 optimal weight: 5.9990 chunk 436 optimal weight: 0.9990 chunk 220 optimal weight: 10.0000 chunk 143 optimal weight: 7.9990 chunk 141 optimal weight: 0.0670 chunk 464 optimal weight: 0.3980 chunk 497 optimal weight: 7.9990 chunk 361 optimal weight: 0.0570 chunk 68 optimal weight: 2.9990 chunk 574 optimal weight: 0.9990 overall best weight: 0.5040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 682 HIS ** J 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 146 ASN ** H 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 672 GLN ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1105 HIS C1384 ASN O 323 HIS ** O 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 354 GLN U 110 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 62632 Z= 0.159 Angle : 0.594 12.306 84784 Z= 0.296 Chirality : 0.040 0.265 9583 Planarity : 0.003 0.054 10715 Dihedral : 4.111 25.498 8256 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.82 % Favored : 96.01 % Rotamer: Outliers : 2.41 % Allowed : 19.57 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.10), residues: 7537 helix: 1.68 (0.08), residues: 4733 sheet: -0.20 (0.23), residues: 476 loop : -1.26 (0.13), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP P 583 HIS 0.010 0.001 HIS P 625 PHE 0.026 0.001 PHE F 512 TYR 0.030 0.001 TYR C1135 ARG 0.005 0.000 ARG I 14 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15074 Ramachandran restraints generated. 7537 Oldfield, 0 Emsley, 7537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15074 Ramachandran restraints generated. 7537 Oldfield, 0 Emsley, 7537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 796 residues out of total 6946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 634 time to evaluate : 5.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 57 CYS cc_start: 0.7574 (OUTLIER) cc_final: 0.6985 (t) REVERT: F 165 MET cc_start: 0.8319 (mmp) cc_final: 0.8099 (mmp) REVERT: F 187 LEU cc_start: 0.8526 (tp) cc_final: 0.7991 (mt) REVERT: F 192 GLU cc_start: 0.8866 (mm-30) cc_final: 0.8457 (mm-30) REVERT: F 490 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.7626 (tpt) REVERT: F 543 TRP cc_start: 0.8065 (m100) cc_final: 0.7267 (m100) REVERT: F 604 ASP cc_start: 0.8762 (t0) cc_final: 0.8294 (t0) REVERT: F 670 HIS cc_start: 0.8150 (OUTLIER) cc_final: 0.7052 (m170) REVERT: F 740 ASP cc_start: 0.7715 (t0) cc_final: 0.7153 (t0) REVERT: J 357 MET cc_start: 0.7716 (tpp) cc_final: 0.6889 (tpp) REVERT: J 390 ILE cc_start: 0.8743 (tp) cc_final: 0.8466 (mt) REVERT: J 394 GLU cc_start: 0.8538 (tp30) cc_final: 0.8330 (mm-30) REVERT: J 480 ASN cc_start: 0.8318 (m-40) cc_final: 0.7976 (p0) REVERT: J 509 GLU cc_start: 0.8398 (tp30) cc_final: 0.8193 (tp30) REVERT: J 542 MET cc_start: 0.8831 (mmm) cc_final: 0.8462 (mmm) REVERT: J 547 ILE cc_start: 0.8062 (OUTLIER) cc_final: 0.7745 (mm) REVERT: J 549 GLU cc_start: 0.7962 (tm-30) cc_final: 0.7525 (tm-30) REVERT: J 593 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.8236 (ttt-90) REVERT: K 297 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7584 (mt) REVERT: K 322 TYR cc_start: 0.7441 (m-10) cc_final: 0.6843 (m-80) REVERT: K 397 GLU cc_start: 0.8107 (tp30) cc_final: 0.7612 (tm-30) REVERT: K 420 LYS cc_start: 0.8872 (pptt) cc_final: 0.8500 (ptmm) REVERT: K 542 MET cc_start: 0.8629 (ttp) cc_final: 0.8060 (tmm) REVERT: K 544 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.7163 (mt) REVERT: K 571 PHE cc_start: 0.9132 (t80) cc_final: 0.8813 (t80) REVERT: K 581 GLN cc_start: 0.7375 (mp10) cc_final: 0.7072 (mp10) REVERT: K 594 PHE cc_start: 0.8063 (OUTLIER) cc_final: 0.7771 (t80) REVERT: G 25 GLU cc_start: 0.7239 (mt-10) cc_final: 0.6848 (pt0) REVERT: W 1 MET cc_start: 0.7124 (mmm) cc_final: 0.6812 (mmm) REVERT: H 123 LEU cc_start: 0.8982 (mt) cc_final: 0.8760 (mp) REVERT: E 160 MET cc_start: 0.6991 (tpp) cc_final: 0.5986 (ttm) REVERT: E 179 ARG cc_start: 0.6794 (mmm-85) cc_final: 0.6535 (mmm-85) REVERT: A 12 HIS cc_start: 0.7611 (m90) cc_final: 0.7189 (p-80) REVERT: A 47 TYR cc_start: 0.4506 (t80) cc_final: 0.4181 (t80) REVERT: A 81 MET cc_start: 0.5634 (tpp) cc_final: 0.5314 (tpp) REVERT: A 126 MET cc_start: 0.8004 (OUTLIER) cc_final: 0.7727 (tpp) REVERT: A 156 TYR cc_start: 0.7714 (m-80) cc_final: 0.7270 (m-10) REVERT: A 195 CYS cc_start: 0.8828 (m) cc_final: 0.8497 (m) REVERT: B 109 GLU cc_start: 0.8414 (tm-30) cc_final: 0.8156 (tp30) REVERT: B 226 MET cc_start: 0.6149 (OUTLIER) cc_final: 0.5835 (ppp) REVERT: B 520 HIS cc_start: 0.2148 (OUTLIER) cc_final: 0.1460 (m-70) REVERT: C 428 LEU cc_start: 0.8240 (mt) cc_final: 0.8035 (mp) REVERT: C 574 MET cc_start: 0.8929 (tpp) cc_final: 0.8681 (tpt) REVERT: C 760 ASP cc_start: 0.8128 (OUTLIER) cc_final: 0.7597 (p0) REVERT: C 761 TYR cc_start: 0.8876 (m-80) cc_final: 0.8627 (m-80) REVERT: C 775 GLU cc_start: 0.7298 (tp30) cc_final: 0.7047 (tp30) REVERT: C 800 GLU cc_start: 0.8026 (tm-30) cc_final: 0.7447 (tm-30) REVERT: C 807 LEU cc_start: 0.9403 (mp) cc_final: 0.8655 (tt) REVERT: C 950 MET cc_start: 0.8991 (mmp) cc_final: 0.8530 (mmp) REVERT: C 1053 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7467 (mm) REVERT: C 1097 LYS cc_start: 0.7543 (tppt) cc_final: 0.7280 (ptpt) REVERT: C 1154 LEU cc_start: 0.8277 (tp) cc_final: 0.7855 (tp) REVERT: C 1252 MET cc_start: 0.8373 (ttt) cc_final: 0.7964 (tmm) REVERT: C 1339 MET cc_start: 0.9190 (tmm) cc_final: 0.8893 (ppp) REVERT: C 1503 PHE cc_start: 0.8406 (m-80) cc_final: 0.8204 (m-80) REVERT: C 1540 GLU cc_start: 0.8261 (pm20) cc_final: 0.7833 (pm20) REVERT: C 1606 MET cc_start: 0.6787 (ppp) cc_final: 0.5821 (ppp) REVERT: C 1715 GLU cc_start: 0.8625 (mp0) cc_final: 0.8334 (mp0) REVERT: O 68 SER cc_start: 0.9057 (t) cc_final: 0.8753 (p) REVERT: O 165 MET cc_start: 0.7347 (tmm) cc_final: 0.6778 (tmm) REVERT: O 176 PHE cc_start: 0.8000 (OUTLIER) cc_final: 0.7550 (t80) REVERT: O 248 GLN cc_start: 0.8125 (mm110) cc_final: 0.7754 (tp40) REVERT: O 431 LEU cc_start: 0.8837 (tp) cc_final: 0.8471 (tp) REVERT: O 533 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8699 (mm) REVERT: O 568 LEU cc_start: 0.8840 (tp) cc_final: 0.8580 (tp) REVERT: O 662 PHE cc_start: 0.8925 (OUTLIER) cc_final: 0.7394 (p90) REVERT: D 253 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8924 (mm) REVERT: D 256 MET cc_start: 0.8335 (tmm) cc_final: 0.8100 (tmm) REVERT: D 349 GLU cc_start: 0.8537 (tp30) cc_final: 0.7978 (tm-30) REVERT: D 443 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8201 (mt-10) REVERT: D 546 TYR cc_start: 0.7581 (OUTLIER) cc_final: 0.7381 (m-10) REVERT: D 560 MET cc_start: 0.7032 (tpp) cc_final: 0.6605 (mtt) REVERT: D 602 MET cc_start: 0.6932 (mmp) cc_final: 0.6430 (ptp) REVERT: P 193 GLU cc_start: 0.8506 (tm-30) cc_final: 0.7913 (tm-30) REVERT: P 317 ASP cc_start: 0.8969 (p0) cc_final: 0.8709 (p0) REVERT: P 334 TYR cc_start: 0.8387 (t80) cc_final: 0.8092 (t80) REVERT: P 338 ILE cc_start: 0.8881 (mm) cc_final: 0.8516 (mm) REVERT: P 376 MET cc_start: 0.8527 (mmp) cc_final: 0.8187 (mmp) REVERT: P 432 ASN cc_start: 0.7641 (p0) cc_final: 0.6675 (p0) REVERT: P 559 MET cc_start: 0.6601 (mtp) cc_final: 0.6130 (ttm) REVERT: N 98 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7538 (mm) REVERT: N 107 ARG cc_start: 0.8183 (tmm-80) cc_final: 0.7621 (ttp80) REVERT: Q 299 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8390 (mm) REVERT: T 344 TYR cc_start: 0.8296 (t80) cc_final: 0.8011 (t80) REVERT: U 1 MET cc_start: 0.5777 (mmm) cc_final: 0.5138 (mmp) outliers start: 162 outliers final: 98 residues processed: 757 average time/residue: 0.5409 time to fit residues: 713.8670 Evaluate side-chains 705 residues out of total 6946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 586 time to evaluate : 5.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 57 CYS Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain F residue 81 ASN Chi-restraints excluded: chain F residue 490 MET Chi-restraints excluded: chain F residue 533 MET Chi-restraints excluded: chain F residue 575 TYR Chi-restraints excluded: chain F residue 670 HIS Chi-restraints excluded: chain J residue 296 ILE Chi-restraints excluded: chain J residue 482 CYS Chi-restraints excluded: chain J residue 483 LEU Chi-restraints excluded: chain J residue 490 LEU Chi-restraints excluded: chain J residue 514 ASN Chi-restraints excluded: chain J residue 520 SER Chi-restraints excluded: chain J residue 539 THR Chi-restraints excluded: chain J residue 547 ILE Chi-restraints excluded: chain J residue 585 LEU Chi-restraints excluded: chain J residue 593 ARG Chi-restraints excluded: chain J residue 605 LEU Chi-restraints excluded: chain J residue 662 VAL Chi-restraints excluded: chain J residue 666 LEU Chi-restraints excluded: chain J residue 752 LEU Chi-restraints excluded: chain K residue 297 LEU Chi-restraints excluded: chain K residue 361 LEU Chi-restraints excluded: chain K residue 394 GLU Chi-restraints excluded: chain K residue 523 LEU Chi-restraints excluded: chain K residue 544 LEU Chi-restraints excluded: chain K residue 575 TYR Chi-restraints excluded: chain K residue 586 THR Chi-restraints excluded: chain K residue 594 PHE Chi-restraints excluded: chain K residue 600 LEU Chi-restraints excluded: chain K residue 673 THR Chi-restraints excluded: chain K residue 731 LEU Chi-restraints excluded: chain G residue 13 HIS Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 146 ASN Chi-restraints excluded: chain H residue 159 LEU Chi-restraints excluded: chain H residue 502 GLN Chi-restraints excluded: chain H residue 569 LEU Chi-restraints excluded: chain H residue 601 LEU Chi-restraints excluded: chain H residue 672 GLN Chi-restraints excluded: chain H residue 706 VAL Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 219 HIS Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 393 TRP Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 520 HIS Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 545 PHE Chi-restraints excluded: chain C residue 734 VAL Chi-restraints excluded: chain C residue 760 ASP Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain C residue 1007 VAL Chi-restraints excluded: chain C residue 1053 LEU Chi-restraints excluded: chain C residue 1312 VAL Chi-restraints excluded: chain C residue 1325 LEU Chi-restraints excluded: chain C residue 1497 THR Chi-restraints excluded: chain C residue 1504 LEU Chi-restraints excluded: chain C residue 1533 THR Chi-restraints excluded: chain C residue 1555 VAL Chi-restraints excluded: chain C residue 1604 VAL Chi-restraints excluded: chain C residue 1614 VAL Chi-restraints excluded: chain C residue 1701 THR Chi-restraints excluded: chain C residue 1731 ILE Chi-restraints excluded: chain O residue 85 LEU Chi-restraints excluded: chain O residue 176 PHE Chi-restraints excluded: chain O residue 232 THR Chi-restraints excluded: chain O residue 453 ILE Chi-restraints excluded: chain O residue 458 VAL Chi-restraints excluded: chain O residue 533 LEU Chi-restraints excluded: chain O residue 559 ILE Chi-restraints excluded: chain O residue 631 LEU Chi-restraints excluded: chain O residue 662 PHE Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 443 GLU Chi-restraints excluded: chain D residue 480 MET Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 546 TYR Chi-restraints excluded: chain D residue 574 THR Chi-restraints excluded: chain P residue 112 THR Chi-restraints excluded: chain P residue 242 LEU Chi-restraints excluded: chain P residue 292 PHE Chi-restraints excluded: chain P residue 458 VAL Chi-restraints excluded: chain P residue 552 LEU Chi-restraints excluded: chain P residue 577 THR Chi-restraints excluded: chain I residue 32 LEU Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 103 MET Chi-restraints excluded: chain I residue 107 SER Chi-restraints excluded: chain I residue 162 HIS Chi-restraints excluded: chain N residue 96 GLU Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain N residue 100 LEU Chi-restraints excluded: chain N residue 119 PHE Chi-restraints excluded: chain N residue 132 GLU Chi-restraints excluded: chain Q residue 208 CYS Chi-restraints excluded: chain Q residue 297 ASP Chi-restraints excluded: chain Q residue 299 LEU Chi-restraints excluded: chain Q residue 411 GLU Chi-restraints excluded: chain Q residue 415 LEU Chi-restraints excluded: chain Q residue 427 TYR Chi-restraints excluded: chain Q residue 429 LEU Chi-restraints excluded: chain Q residue 566 LEU Chi-restraints excluded: chain T residue 159 LEU Chi-restraints excluded: chain T residue 300 VAL Chi-restraints excluded: chain T residue 338 VAL Chi-restraints excluded: chain T residue 458 MET Chi-restraints excluded: chain T residue 489 THR Chi-restraints excluded: chain T residue 581 LEU Chi-restraints excluded: chain U residue 100 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 758 random chunks: chunk 664 optimal weight: 6.9990 chunk 699 optimal weight: 20.0000 chunk 638 optimal weight: 2.9990 chunk 680 optimal weight: 3.9990 chunk 409 optimal weight: 0.0040 chunk 296 optimal weight: 6.9990 chunk 534 optimal weight: 1.9990 chunk 208 optimal weight: 3.9990 chunk 615 optimal weight: 1.9990 chunk 643 optimal weight: 1.9990 chunk 678 optimal weight: 4.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 85 HIS F 177 HIS ** J 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 514 ASN ** J 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 682 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 HIS C 753 HIS C1056 ASN C1105 HIS C1265 ASN ** C1543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 110 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 62632 Z= 0.207 Angle : 0.616 16.460 84784 Z= 0.306 Chirality : 0.041 0.284 9583 Planarity : 0.003 0.053 10715 Dihedral : 4.114 24.613 8256 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.21 % Favored : 95.62 % Rotamer: Outliers : 2.45 % Allowed : 19.84 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.10), residues: 7537 helix: 1.71 (0.08), residues: 4744 sheet: -0.13 (0.23), residues: 468 loop : -1.29 (0.13), residues: 2325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP P 583 HIS 0.009 0.001 HIS P 625 PHE 0.027 0.001 PHE Q 394 TYR 0.032 0.001 TYR E 236 ARG 0.016 0.000 ARG N 135 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15074 Ramachandran restraints generated. 7537 Oldfield, 0 Emsley, 7537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15074 Ramachandran restraints generated. 7537 Oldfield, 0 Emsley, 7537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 756 residues out of total 6946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 591 time to evaluate : 5.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 45 THR cc_start: 0.5765 (OUTLIER) cc_final: 0.5419 (m) REVERT: F 57 CYS cc_start: 0.7545 (OUTLIER) cc_final: 0.6952 (t) REVERT: F 165 MET cc_start: 0.8150 (mmp) cc_final: 0.7917 (mmp) REVERT: F 192 GLU cc_start: 0.8880 (mm-30) cc_final: 0.8386 (mm-30) REVERT: F 490 MET cc_start: 0.8760 (OUTLIER) cc_final: 0.7759 (tpt) REVERT: F 543 TRP cc_start: 0.8101 (m100) cc_final: 0.7262 (m100) REVERT: F 604 ASP cc_start: 0.8779 (t0) cc_final: 0.8314 (t0) REVERT: F 670 HIS cc_start: 0.8129 (OUTLIER) cc_final: 0.7085 (m170) REVERT: F 740 ASP cc_start: 0.7768 (t0) cc_final: 0.7202 (t0) REVERT: J 243 GLN cc_start: 0.8722 (tm-30) cc_final: 0.8339 (tm-30) REVERT: J 357 MET cc_start: 0.7852 (tpp) cc_final: 0.7117 (tpp) REVERT: J 390 ILE cc_start: 0.8767 (tp) cc_final: 0.8542 (mp) REVERT: J 394 GLU cc_start: 0.8573 (tp30) cc_final: 0.7875 (tp30) REVERT: J 480 ASN cc_start: 0.8359 (m-40) cc_final: 0.8002 (p0) REVERT: J 509 GLU cc_start: 0.8406 (tp30) cc_final: 0.8199 (tp30) REVERT: J 542 MET cc_start: 0.8858 (mmm) cc_final: 0.8436 (mmm) REVERT: J 547 ILE cc_start: 0.8175 (OUTLIER) cc_final: 0.7684 (mm) REVERT: J 549 GLU cc_start: 0.8255 (tm-30) cc_final: 0.7966 (tm-30) REVERT: J 682 HIS cc_start: 0.6941 (OUTLIER) cc_final: 0.6497 (t-90) REVERT: K 297 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7583 (mt) REVERT: K 322 TYR cc_start: 0.7466 (m-10) cc_final: 0.6864 (m-80) REVERT: K 357 MET cc_start: 0.8473 (mmm) cc_final: 0.7998 (mmm) REVERT: K 394 GLU cc_start: 0.6743 (OUTLIER) cc_final: 0.5512 (mp0) REVERT: K 397 GLU cc_start: 0.8115 (tp30) cc_final: 0.7586 (tm-30) REVERT: K 420 LYS cc_start: 0.8935 (pptt) cc_final: 0.8571 (ptmm) REVERT: K 542 MET cc_start: 0.8579 (ttp) cc_final: 0.8016 (tmm) REVERT: K 581 GLN cc_start: 0.7393 (mp10) cc_final: 0.7093 (mp10) REVERT: K 594 PHE cc_start: 0.8054 (OUTLIER) cc_final: 0.7754 (t80) REVERT: G 10 GLN cc_start: 0.7915 (pm20) cc_final: 0.7619 (pm20) REVERT: G 25 GLU cc_start: 0.7227 (mt-10) cc_final: 0.6852 (pt0) REVERT: W 1 MET cc_start: 0.7099 (mmm) cc_final: 0.6771 (mmm) REVERT: H 123 LEU cc_start: 0.8987 (mt) cc_final: 0.8756 (mp) REVERT: H 715 LEU cc_start: 0.5218 (pp) cc_final: 0.4919 (mm) REVERT: E 179 ARG cc_start: 0.6806 (mmm-85) cc_final: 0.6575 (mmm-85) REVERT: A 81 MET cc_start: 0.5663 (tpp) cc_final: 0.5344 (tpp) REVERT: A 126 MET cc_start: 0.7996 (OUTLIER) cc_final: 0.7751 (tpp) REVERT: A 156 TYR cc_start: 0.7718 (m-80) cc_final: 0.7294 (m-10) REVERT: B 109 GLU cc_start: 0.8472 (tm-30) cc_final: 0.8204 (tp30) REVERT: B 226 MET cc_start: 0.6281 (OUTLIER) cc_final: 0.6016 (ppp) REVERT: B 520 HIS cc_start: 0.2225 (OUTLIER) cc_final: 0.1570 (m-70) REVERT: C 574 MET cc_start: 0.8933 (tpp) cc_final: 0.8696 (tpt) REVERT: C 760 ASP cc_start: 0.8148 (OUTLIER) cc_final: 0.7594 (p0) REVERT: C 761 TYR cc_start: 0.8905 (m-80) cc_final: 0.8619 (m-80) REVERT: C 800 GLU cc_start: 0.7834 (tm-30) cc_final: 0.7386 (tm-30) REVERT: C 807 LEU cc_start: 0.9413 (mp) cc_final: 0.8668 (tt) REVERT: C 950 MET cc_start: 0.9009 (mmp) cc_final: 0.8571 (mmp) REVERT: C 1053 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7653 (mm) REVERT: C 1064 GLU cc_start: 0.8316 (pm20) cc_final: 0.8113 (pm20) REVERT: C 1154 LEU cc_start: 0.8252 (tp) cc_final: 0.7826 (tp) REVERT: C 1266 MET cc_start: 0.8391 (mpp) cc_final: 0.7897 (pmm) REVERT: C 1540 GLU cc_start: 0.8284 (pm20) cc_final: 0.7848 (pm20) REVERT: C 1606 MET cc_start: 0.6807 (ppp) cc_final: 0.5848 (ppp) REVERT: O 68 SER cc_start: 0.9071 (t) cc_final: 0.8766 (p) REVERT: O 165 MET cc_start: 0.7292 (tmm) cc_final: 0.6801 (tmm) REVERT: O 176 PHE cc_start: 0.7963 (OUTLIER) cc_final: 0.7474 (t80) REVERT: O 248 GLN cc_start: 0.8161 (mm110) cc_final: 0.7763 (tp40) REVERT: O 431 LEU cc_start: 0.8882 (tp) cc_final: 0.8514 (tp) REVERT: O 568 LEU cc_start: 0.8851 (tp) cc_final: 0.8583 (tp) REVERT: O 662 PHE cc_start: 0.8939 (OUTLIER) cc_final: 0.7380 (p90) REVERT: D 253 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8946 (mm) REVERT: D 256 MET cc_start: 0.8310 (tmm) cc_final: 0.8103 (tmm) REVERT: D 349 GLU cc_start: 0.8570 (tp30) cc_final: 0.7995 (tm-30) REVERT: D 443 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8179 (mt-10) REVERT: D 546 TYR cc_start: 0.7636 (OUTLIER) cc_final: 0.7385 (m-10) REVERT: D 560 MET cc_start: 0.7047 (OUTLIER) cc_final: 0.6630 (mtt) REVERT: D 602 MET cc_start: 0.7001 (mmp) cc_final: 0.6497 (ptp) REVERT: P 334 TYR cc_start: 0.8391 (t80) cc_final: 0.8109 (t80) REVERT: P 338 ILE cc_start: 0.8826 (mm) cc_final: 0.8447 (mm) REVERT: P 432 ASN cc_start: 0.7824 (p0) cc_final: 0.6858 (p0) REVERT: N 13 ASP cc_start: 0.9056 (t0) cc_final: 0.8852 (m-30) REVERT: N 98 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7600 (mm) REVERT: N 107 ARG cc_start: 0.8214 (tmm-80) cc_final: 0.7632 (ttp80) REVERT: N 112 ARG cc_start: 0.8384 (mtm-85) cc_final: 0.7980 (mtm-85) REVERT: Q 299 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8435 (mm) REVERT: T 106 LEU cc_start: 0.8873 (mt) cc_final: 0.8517 (pp) REVERT: T 311 ASP cc_start: 0.8084 (t70) cc_final: 0.7804 (t70) REVERT: T 344 TYR cc_start: 0.8330 (t80) cc_final: 0.8053 (t80) REVERT: U 1 MET cc_start: 0.5769 (mmm) cc_final: 0.5143 (mmp) outliers start: 165 outliers final: 123 residues processed: 720 average time/residue: 0.5816 time to fit residues: 738.5283 Evaluate side-chains 719 residues out of total 6946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 574 time to evaluate : 6.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 57 CYS Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain F residue 81 ASN Chi-restraints excluded: chain F residue 490 MET Chi-restraints excluded: chain F residue 533 MET Chi-restraints excluded: chain F residue 575 TYR Chi-restraints excluded: chain F residue 670 HIS Chi-restraints excluded: chain F residue 703 VAL Chi-restraints excluded: chain F residue 748 ILE Chi-restraints excluded: chain J residue 296 ILE Chi-restraints excluded: chain J residue 482 CYS Chi-restraints excluded: chain J residue 483 LEU Chi-restraints excluded: chain J residue 486 CYS Chi-restraints excluded: chain J residue 490 LEU Chi-restraints excluded: chain J residue 514 ASN Chi-restraints excluded: chain J residue 520 SER Chi-restraints excluded: chain J residue 539 THR Chi-restraints excluded: chain J residue 547 ILE Chi-restraints excluded: chain J residue 585 LEU Chi-restraints excluded: chain J residue 605 LEU Chi-restraints excluded: chain J residue 617 LEU Chi-restraints excluded: chain J residue 662 VAL Chi-restraints excluded: chain J residue 666 LEU Chi-restraints excluded: chain J residue 682 HIS Chi-restraints excluded: chain J residue 752 LEU Chi-restraints excluded: chain K residue 297 LEU Chi-restraints excluded: chain K residue 361 LEU Chi-restraints excluded: chain K residue 394 GLU Chi-restraints excluded: chain K residue 413 LEU Chi-restraints excluded: chain K residue 523 LEU Chi-restraints excluded: chain K residue 544 LEU Chi-restraints excluded: chain K residue 575 TYR Chi-restraints excluded: chain K residue 586 THR Chi-restraints excluded: chain K residue 594 PHE Chi-restraints excluded: chain K residue 600 LEU Chi-restraints excluded: chain K residue 673 THR Chi-restraints excluded: chain K residue 731 LEU Chi-restraints excluded: chain G residue 13 HIS Chi-restraints excluded: chain G residue 22 ASP Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 159 LEU Chi-restraints excluded: chain H residue 502 GLN Chi-restraints excluded: chain H residue 569 LEU Chi-restraints excluded: chain H residue 601 LEU Chi-restraints excluded: chain H residue 706 VAL Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 219 HIS Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 393 TRP Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 520 HIS Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 545 PHE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 718 LEU Chi-restraints excluded: chain C residue 734 VAL Chi-restraints excluded: chain C residue 760 ASP Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain C residue 867 ILE Chi-restraints excluded: chain C residue 1007 VAL Chi-restraints excluded: chain C residue 1008 GLU Chi-restraints excluded: chain C residue 1053 LEU Chi-restraints excluded: chain C residue 1056 ASN Chi-restraints excluded: chain C residue 1312 VAL Chi-restraints excluded: chain C residue 1325 LEU Chi-restraints excluded: chain C residue 1497 THR Chi-restraints excluded: chain C residue 1533 THR Chi-restraints excluded: chain C residue 1555 VAL Chi-restraints excluded: chain C residue 1604 VAL Chi-restraints excluded: chain C residue 1614 VAL Chi-restraints excluded: chain C residue 1658 LEU Chi-restraints excluded: chain C residue 1701 THR Chi-restraints excluded: chain C residue 1731 ILE Chi-restraints excluded: chain O residue 85 LEU Chi-restraints excluded: chain O residue 176 PHE Chi-restraints excluded: chain O residue 232 THR Chi-restraints excluded: chain O residue 344 SER Chi-restraints excluded: chain O residue 347 THR Chi-restraints excluded: chain O residue 453 ILE Chi-restraints excluded: chain O residue 458 VAL Chi-restraints excluded: chain O residue 474 VAL Chi-restraints excluded: chain O residue 559 ILE Chi-restraints excluded: chain O residue 631 LEU Chi-restraints excluded: chain O residue 658 LEU Chi-restraints excluded: chain O residue 662 PHE Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 443 GLU Chi-restraints excluded: chain D residue 492 CYS Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 546 TYR Chi-restraints excluded: chain D residue 555 CYS Chi-restraints excluded: chain D residue 560 MET Chi-restraints excluded: chain D residue 574 THR Chi-restraints excluded: chain P residue 112 THR Chi-restraints excluded: chain P residue 242 LEU Chi-restraints excluded: chain P residue 292 PHE Chi-restraints excluded: chain P residue 399 THR Chi-restraints excluded: chain P residue 458 VAL Chi-restraints excluded: chain P residue 552 LEU Chi-restraints excluded: chain P residue 577 THR Chi-restraints excluded: chain I residue 32 LEU Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 103 MET Chi-restraints excluded: chain I residue 107 SER Chi-restraints excluded: chain I residue 162 HIS Chi-restraints excluded: chain N residue 95 ASP Chi-restraints excluded: chain N residue 96 GLU Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain N residue 100 LEU Chi-restraints excluded: chain N residue 119 PHE Chi-restraints excluded: chain N residue 132 GLU Chi-restraints excluded: chain Q residue 208 CYS Chi-restraints excluded: chain Q residue 297 ASP Chi-restraints excluded: chain Q residue 299 LEU Chi-restraints excluded: chain Q residue 390 ASP Chi-restraints excluded: chain Q residue 411 GLU Chi-restraints excluded: chain Q residue 427 TYR Chi-restraints excluded: chain Q residue 429 LEU Chi-restraints excluded: chain Q residue 479 HIS Chi-restraints excluded: chain Q residue 566 LEU Chi-restraints excluded: chain Q residue 634 VAL Chi-restraints excluded: chain T residue 103 PHE Chi-restraints excluded: chain T residue 159 LEU Chi-restraints excluded: chain T residue 238 MET Chi-restraints excluded: chain T residue 300 VAL Chi-restraints excluded: chain T residue 316 THR Chi-restraints excluded: chain T residue 338 VAL Chi-restraints excluded: chain T residue 458 MET Chi-restraints excluded: chain T residue 489 THR Chi-restraints excluded: chain T residue 581 LEU Chi-restraints excluded: chain U residue 100 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 758 random chunks: chunk 447 optimal weight: 9.9990 chunk 719 optimal weight: 0.2980 chunk 439 optimal weight: 0.9980 chunk 341 optimal weight: 9.9990 chunk 500 optimal weight: 0.0670 chunk 755 optimal weight: 20.0000 chunk 695 optimal weight: 20.0000 chunk 601 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 464 optimal weight: 0.9980 chunk 368 optimal weight: 7.9990 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 682 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1105 HIS ** C1543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 110 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.140 62632 Z= 0.210 Angle : 0.682 59.199 84784 Z= 0.361 Chirality : 0.041 0.318 9583 Planarity : 0.004 0.142 10715 Dihedral : 4.115 24.585 8256 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.17 % Favored : 95.66 % Rotamer: Outliers : 2.28 % Allowed : 20.02 % Favored : 77.70 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.10), residues: 7537 helix: 1.72 (0.08), residues: 4740 sheet: -0.16 (0.23), residues: 474 loop : -1.26 (0.13), residues: 2323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP P 583 HIS 0.010 0.001 HIS P 625 PHE 0.028 0.001 PHE Q 394 TYR 0.028 0.001 TYR E 236 ARG 0.005 0.000 ARG N 135 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15074 Ramachandran restraints generated. 7537 Oldfield, 0 Emsley, 7537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15074 Ramachandran restraints generated. 7537 Oldfield, 0 Emsley, 7537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 6946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 577 time to evaluate : 5.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 45 THR cc_start: 0.5763 (OUTLIER) cc_final: 0.5418 (m) REVERT: F 57 CYS cc_start: 0.7545 (OUTLIER) cc_final: 0.6950 (t) REVERT: F 165 MET cc_start: 0.8148 (mmp) cc_final: 0.7908 (mmp) REVERT: F 192 GLU cc_start: 0.8873 (mm-30) cc_final: 0.8382 (mm-30) REVERT: F 490 MET cc_start: 0.8759 (OUTLIER) cc_final: 0.7752 (tpt) REVERT: F 543 TRP cc_start: 0.8099 (m100) cc_final: 0.7256 (m100) REVERT: F 604 ASP cc_start: 0.8783 (t0) cc_final: 0.8369 (t0) REVERT: F 670 HIS cc_start: 0.8126 (OUTLIER) cc_final: 0.7082 (m170) REVERT: F 740 ASP cc_start: 0.7766 (t0) cc_final: 0.7198 (t0) REVERT: J 243 GLN cc_start: 0.8725 (tm-30) cc_final: 0.8339 (tm-30) REVERT: J 357 MET cc_start: 0.7856 (tpp) cc_final: 0.7141 (tpp) REVERT: J 390 ILE cc_start: 0.8764 (tp) cc_final: 0.8540 (mp) REVERT: J 394 GLU cc_start: 0.8479 (tp30) cc_final: 0.7757 (tp30) REVERT: J 480 ASN cc_start: 0.8354 (m-40) cc_final: 0.8000 (p0) REVERT: J 509 GLU cc_start: 0.8404 (tp30) cc_final: 0.8198 (tp30) REVERT: J 542 MET cc_start: 0.8854 (mmm) cc_final: 0.8434 (mmm) REVERT: J 547 ILE cc_start: 0.8161 (OUTLIER) cc_final: 0.7675 (mm) REVERT: J 549 GLU cc_start: 0.8296 (tm-30) cc_final: 0.7946 (tm-30) REVERT: K 297 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7586 (mt) REVERT: K 322 TYR cc_start: 0.7466 (m-10) cc_final: 0.6863 (m-80) REVERT: K 357 MET cc_start: 0.8476 (mmm) cc_final: 0.7999 (mmm) REVERT: K 394 GLU cc_start: 0.6684 (OUTLIER) cc_final: 0.5491 (mp0) REVERT: K 397 GLU cc_start: 0.8111 (tp30) cc_final: 0.7581 (tm-30) REVERT: K 420 LYS cc_start: 0.8934 (pptt) cc_final: 0.8570 (ptmm) REVERT: K 542 MET cc_start: 0.8577 (ttp) cc_final: 0.8007 (tmm) REVERT: K 581 GLN cc_start: 0.7386 (mp10) cc_final: 0.7087 (mp10) REVERT: K 594 PHE cc_start: 0.8053 (OUTLIER) cc_final: 0.7753 (t80) REVERT: G 25 GLU cc_start: 0.7223 (mt-10) cc_final: 0.6849 (pt0) REVERT: W 1 MET cc_start: 0.7093 (mmm) cc_final: 0.6769 (mmm) REVERT: H 123 LEU cc_start: 0.8985 (mt) cc_final: 0.8754 (mp) REVERT: H 715 LEU cc_start: 0.5600 (pp) cc_final: 0.5352 (mm) REVERT: E 179 ARG cc_start: 0.6807 (mmm-85) cc_final: 0.6575 (mmm-85) REVERT: A 81 MET cc_start: 0.5661 (tpp) cc_final: 0.5335 (tpp) REVERT: A 126 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.7725 (tpp) REVERT: A 156 TYR cc_start: 0.7717 (m-80) cc_final: 0.7294 (m-10) REVERT: B 109 GLU cc_start: 0.8463 (tm-30) cc_final: 0.8174 (tp30) REVERT: B 226 MET cc_start: 0.6278 (OUTLIER) cc_final: 0.6016 (ppp) REVERT: B 520 HIS cc_start: 0.2222 (OUTLIER) cc_final: 0.1566 (m-70) REVERT: C 149 LYS cc_start: 0.7700 (pptt) cc_final: 0.6888 (tppt) REVERT: C 574 MET cc_start: 0.8940 (tpp) cc_final: 0.8668 (tpt) REVERT: C 760 ASP cc_start: 0.8147 (OUTLIER) cc_final: 0.7594 (p0) REVERT: C 761 TYR cc_start: 0.8905 (m-80) cc_final: 0.8620 (m-80) REVERT: C 800 GLU cc_start: 0.7833 (tm-30) cc_final: 0.7381 (tm-30) REVERT: C 807 LEU cc_start: 0.9412 (mp) cc_final: 0.8665 (tt) REVERT: C 950 MET cc_start: 0.9007 (mmp) cc_final: 0.8580 (mmp) REVERT: C 1053 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7653 (mm) REVERT: C 1064 GLU cc_start: 0.8314 (pm20) cc_final: 0.8107 (pm20) REVERT: C 1154 LEU cc_start: 0.8245 (tp) cc_final: 0.7820 (tp) REVERT: C 1266 MET cc_start: 0.8371 (mpp) cc_final: 0.7934 (pmm) REVERT: C 1503 PHE cc_start: 0.8374 (m-80) cc_final: 0.8168 (m-80) REVERT: C 1540 GLU cc_start: 0.8284 (pm20) cc_final: 0.7846 (pm20) REVERT: C 1606 MET cc_start: 0.6813 (ppp) cc_final: 0.5854 (ppp) REVERT: O 68 SER cc_start: 0.9070 (t) cc_final: 0.8765 (p) REVERT: O 165 MET cc_start: 0.7288 (tmm) cc_final: 0.6798 (tmm) REVERT: O 176 PHE cc_start: 0.7957 (OUTLIER) cc_final: 0.7470 (t80) REVERT: O 248 GLN cc_start: 0.8158 (mm110) cc_final: 0.7756 (tp40) REVERT: O 431 LEU cc_start: 0.8879 (tp) cc_final: 0.8509 (tp) REVERT: O 568 LEU cc_start: 0.8849 (tp) cc_final: 0.8580 (tp) REVERT: O 662 PHE cc_start: 0.8936 (OUTLIER) cc_final: 0.7377 (p90) REVERT: D 214 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8667 (tt) REVERT: D 253 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8946 (mm) REVERT: D 256 MET cc_start: 0.8300 (tmm) cc_final: 0.8090 (tmm) REVERT: D 349 GLU cc_start: 0.8567 (tp30) cc_final: 0.7993 (tm-30) REVERT: D 443 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8175 (mt-10) REVERT: D 546 TYR cc_start: 0.7631 (OUTLIER) cc_final: 0.7381 (m-10) REVERT: D 560 MET cc_start: 0.7043 (tpp) cc_final: 0.6628 (mtt) REVERT: D 602 MET cc_start: 0.6998 (mmp) cc_final: 0.6498 (ptp) REVERT: P 334 TYR cc_start: 0.8387 (t80) cc_final: 0.8108 (t80) REVERT: P 338 ILE cc_start: 0.8824 (mm) cc_final: 0.8447 (mm) REVERT: P 432 ASN cc_start: 0.7820 (p0) cc_final: 0.6852 (p0) REVERT: N 13 ASP cc_start: 0.9056 (t0) cc_final: 0.8852 (m-30) REVERT: N 98 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7597 (mm) REVERT: N 107 ARG cc_start: 0.8212 (tmm-80) cc_final: 0.7630 (ttp80) REVERT: N 112 ARG cc_start: 0.8380 (mtm-85) cc_final: 0.7979 (mtm-85) REVERT: Q 299 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8434 (mm) REVERT: T 106 LEU cc_start: 0.8872 (mt) cc_final: 0.8515 (pp) REVERT: T 311 ASP cc_start: 0.8073 (t70) cc_final: 0.7801 (t70) REVERT: T 344 TYR cc_start: 0.8331 (t80) cc_final: 0.8056 (t80) REVERT: U 1 MET cc_start: 0.5768 (mmm) cc_final: 0.5143 (mmp) outliers start: 153 outliers final: 126 residues processed: 694 average time/residue: 0.5461 time to fit residues: 668.1653 Evaluate side-chains 716 residues out of total 6946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 569 time to evaluate : 5.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 57 CYS Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain F residue 81 ASN Chi-restraints excluded: chain F residue 490 MET Chi-restraints excluded: chain F residue 495 PHE Chi-restraints excluded: chain F residue 533 MET Chi-restraints excluded: chain F residue 575 TYR Chi-restraints excluded: chain F residue 670 HIS Chi-restraints excluded: chain F residue 703 VAL Chi-restraints excluded: chain J residue 296 ILE Chi-restraints excluded: chain J residue 482 CYS Chi-restraints excluded: chain J residue 483 LEU Chi-restraints excluded: chain J residue 486 CYS Chi-restraints excluded: chain J residue 490 LEU Chi-restraints excluded: chain J residue 520 SER Chi-restraints excluded: chain J residue 539 THR Chi-restraints excluded: chain J residue 547 ILE Chi-restraints excluded: chain J residue 585 LEU Chi-restraints excluded: chain J residue 605 LEU Chi-restraints excluded: chain J residue 617 LEU Chi-restraints excluded: chain J residue 662 VAL Chi-restraints excluded: chain J residue 666 LEU Chi-restraints excluded: chain J residue 752 LEU Chi-restraints excluded: chain K residue 297 LEU Chi-restraints excluded: chain K residue 361 LEU Chi-restraints excluded: chain K residue 394 GLU Chi-restraints excluded: chain K residue 523 LEU Chi-restraints excluded: chain K residue 544 LEU Chi-restraints excluded: chain K residue 575 TYR Chi-restraints excluded: chain K residue 586 THR Chi-restraints excluded: chain K residue 594 PHE Chi-restraints excluded: chain K residue 600 LEU Chi-restraints excluded: chain K residue 673 THR Chi-restraints excluded: chain K residue 731 LEU Chi-restraints excluded: chain G residue 13 HIS Chi-restraints excluded: chain G residue 22 ASP Chi-restraints excluded: chain W residue 9 LEU Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 159 LEU Chi-restraints excluded: chain H residue 502 GLN Chi-restraints excluded: chain H residue 569 LEU Chi-restraints excluded: chain H residue 601 LEU Chi-restraints excluded: chain H residue 706 VAL Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 219 HIS Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 393 TRP Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 520 HIS Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 545 PHE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 718 LEU Chi-restraints excluded: chain C residue 734 VAL Chi-restraints excluded: chain C residue 760 ASP Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain C residue 867 ILE Chi-restraints excluded: chain C residue 1007 VAL Chi-restraints excluded: chain C residue 1008 GLU Chi-restraints excluded: chain C residue 1053 LEU Chi-restraints excluded: chain C residue 1312 VAL Chi-restraints excluded: chain C residue 1325 LEU Chi-restraints excluded: chain C residue 1497 THR Chi-restraints excluded: chain C residue 1504 LEU Chi-restraints excluded: chain C residue 1533 THR Chi-restraints excluded: chain C residue 1555 VAL Chi-restraints excluded: chain C residue 1604 VAL Chi-restraints excluded: chain C residue 1614 VAL Chi-restraints excluded: chain C residue 1658 LEU Chi-restraints excluded: chain C residue 1701 THR Chi-restraints excluded: chain C residue 1731 ILE Chi-restraints excluded: chain O residue 85 LEU Chi-restraints excluded: chain O residue 176 PHE Chi-restraints excluded: chain O residue 232 THR Chi-restraints excluded: chain O residue 347 THR Chi-restraints excluded: chain O residue 453 ILE Chi-restraints excluded: chain O residue 458 VAL Chi-restraints excluded: chain O residue 474 VAL Chi-restraints excluded: chain O residue 559 ILE Chi-restraints excluded: chain O residue 631 LEU Chi-restraints excluded: chain O residue 658 LEU Chi-restraints excluded: chain O residue 662 PHE Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 443 GLU Chi-restraints excluded: chain D residue 492 CYS Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 546 TYR Chi-restraints excluded: chain D residue 555 CYS Chi-restraints excluded: chain D residue 574 THR Chi-restraints excluded: chain P residue 112 THR Chi-restraints excluded: chain P residue 139 ILE Chi-restraints excluded: chain P residue 242 LEU Chi-restraints excluded: chain P residue 292 PHE Chi-restraints excluded: chain P residue 399 THR Chi-restraints excluded: chain P residue 458 VAL Chi-restraints excluded: chain P residue 552 LEU Chi-restraints excluded: chain P residue 577 THR Chi-restraints excluded: chain I residue 32 LEU Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 103 MET Chi-restraints excluded: chain I residue 107 SER Chi-restraints excluded: chain I residue 162 HIS Chi-restraints excluded: chain N residue 95 ASP Chi-restraints excluded: chain N residue 96 GLU Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain N residue 100 LEU Chi-restraints excluded: chain N residue 119 PHE Chi-restraints excluded: chain N residue 132 GLU Chi-restraints excluded: chain Q residue 114 CYS Chi-restraints excluded: chain Q residue 116 ILE Chi-restraints excluded: chain Q residue 199 ILE Chi-restraints excluded: chain Q residue 208 CYS Chi-restraints excluded: chain Q residue 297 ASP Chi-restraints excluded: chain Q residue 299 LEU Chi-restraints excluded: chain Q residue 390 ASP Chi-restraints excluded: chain Q residue 411 GLU Chi-restraints excluded: chain Q residue 427 TYR Chi-restraints excluded: chain Q residue 429 LEU Chi-restraints excluded: chain Q residue 479 HIS Chi-restraints excluded: chain Q residue 566 LEU Chi-restraints excluded: chain Q residue 634 VAL Chi-restraints excluded: chain T residue 103 PHE Chi-restraints excluded: chain T residue 159 LEU Chi-restraints excluded: chain T residue 238 MET Chi-restraints excluded: chain T residue 300 VAL Chi-restraints excluded: chain T residue 316 THR Chi-restraints excluded: chain T residue 325 ASP Chi-restraints excluded: chain T residue 338 VAL Chi-restraints excluded: chain T residue 458 MET Chi-restraints excluded: chain T residue 489 THR Chi-restraints excluded: chain T residue 581 LEU Chi-restraints excluded: chain U residue 100 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 758 random chunks: chunk 477 optimal weight: 0.7980 chunk 640 optimal weight: 9.9990 chunk 184 optimal weight: 8.9990 chunk 554 optimal weight: 0.0980 chunk 88 optimal weight: 0.1980 chunk 167 optimal weight: 4.9990 chunk 602 optimal weight: 2.9990 chunk 252 optimal weight: 0.9980 chunk 618 optimal weight: 0.0370 chunk 76 optimal weight: 0.6980 chunk 110 optimal weight: 9.9990 overall best weight: 0.3658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 682 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1105 HIS ** C1543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 110 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.117546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.084912 restraints weight = 182867.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.086643 restraints weight = 85473.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.087199 restraints weight = 55268.029| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.140 62632 Z= 0.210 Angle : 0.682 59.199 84784 Z= 0.361 Chirality : 0.041 0.318 9583 Planarity : 0.004 0.142 10715 Dihedral : 4.115 24.585 8256 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.17 % Favored : 95.66 % Rotamer: Outliers : 2.19 % Allowed : 20.15 % Favored : 77.66 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.10), residues: 7537 helix: 1.72 (0.08), residues: 4740 sheet: -0.16 (0.23), residues: 474 loop : -1.26 (0.13), residues: 2323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP P 583 HIS 0.010 0.001 HIS P 625 PHE 0.028 0.001 PHE Q 394 TYR 0.028 0.001 TYR E 236 ARG 0.005 0.000 ARG N 135 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11854.09 seconds wall clock time: 210 minutes 47.64 seconds (12647.64 seconds total)