Starting phenix.real_space_refine on Mon Dec 30 15:12:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wa1_37388/12_2024/8wa1_37388.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wa1_37388/12_2024/8wa1_37388.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wa1_37388/12_2024/8wa1_37388.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wa1_37388/12_2024/8wa1_37388.map" model { file = "/net/cci-nas-00/data/ceres_data/8wa1_37388/12_2024/8wa1_37388.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wa1_37388/12_2024/8wa1_37388.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.046 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 50 atoms to isotropic. 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: 8 Type Number sf(0) Gaussians Fe 2 7.16 5 Zn 1 6.06 5 P 27 5.49 5 Mg 1 5.21 5 S 268 5.16 5 C 39610 2.51 5 N 11111 2.21 5 O 11679 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 118 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 62699 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 2190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2190 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 12, 'TRANS': 275} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 76 Chain: "B" Number of atoms: 7604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 998, 7604 Classifications: {'peptide': 998} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PTRANS': 45, 'TRANS': 952} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 345 Unresolved non-hydrogen angles: 434 Unresolved non-hydrogen dihedrals: 286 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 6, 'TRP:plan': 2, 'ASP:plan': 8, 'PHE:plan': 3, 'GLU:plan': 13, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 210 Chain: "C" Number of atoms: 4899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 653, 4899 Classifications: {'peptide': 653} Incomplete info: {'truncation_to_alanine': 115} Link IDs: {'PTRANS': 34, 'TRANS': 618} Chain breaks: 2 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 422 Unresolved non-hydrogen angles: 530 Unresolved non-hydrogen dihedrals: 356 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 5, 'TYR:plan': 4, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 13, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 233 Chain: "D" Number of atoms: 5063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5063 Classifications: {'peptide': 645} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 23, 'TRANS': 621} Chain breaks: 2 Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 71 Chain: "E" Number of atoms: 4563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 700, 4563 Classifications: {'peptide': 700} Incomplete info: {'truncation_to_alanine': 289} Link IDs: {'PTRANS': 18, 'TRANS': 681} Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 1053 Unresolved non-hydrogen angles: 1343 Unresolved non-hydrogen dihedrals: 876 Unresolved non-hydrogen chiralities: 91 Planarities with less than four sites: {'GLN:plan1': 12, 'ASP:plan': 18, 'TYR:plan': 14, 'ASN:plan1': 15, 'TRP:plan': 3, 'HIS:plan': 7, 'PHE:plan': 14, 'GLU:plan': 31, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 595 Chain: "F" Number of atoms: 4259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 4259 Classifications: {'peptide': 544} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PTRANS': 33, 'TRANS': 510} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 341 Unresolved non-hydrogen angles: 429 Unresolved non-hydrogen dihedrals: 296 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 7, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 10, 'PHE:plan': 2, 'GLU:plan': 13, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 199 Chain: "G" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1742 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 11, 'TRANS': 206} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 26 Chain: "H" Number of atoms: 2110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2110 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 17, 'TRANS': 242} Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 11, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 53 Chain: "I" Number of atoms: 2946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2946 Classifications: {'peptide': 376} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 21, 'TRANS': 354} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 6, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 60 Chain: "J" Number of atoms: 3410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3410 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 24, 'TRANS': 396} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "K" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1705 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 187} Chain: "L" Number of atoms: 1776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1776 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 15, 'TRANS': 213} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 51 Chain: "M" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 935 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 109} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "N" Number of atoms: 2995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 2995 Classifications: {'peptide': 537} Incomplete info: {'truncation_to_alanine': 350} Link IDs: {'PTRANS': 23, 'TRANS': 513} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 1206 Unresolved non-hydrogen angles: 1543 Unresolved non-hydrogen dihedrals: 965 Unresolved non-hydrogen chiralities: 127 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 13, 'TYR:plan': 10, 'ASN:plan1': 12, 'ASP:plan': 34, 'PHE:plan': 14, 'GLU:plan': 39, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 648 Chain: "O" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 780 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 92} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "P" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 843 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 96} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "Q" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 82 Classifications: {'DNA': 4} Link IDs: {'rna3p': 3} Chain: "R" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 285 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "S" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 192 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 4} Link IDs: {'rna3p': 8} Chain: "a" Number of atoms: 2358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2358 Classifications: {'peptide': 303} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 13, 'TRANS': 289} Chain breaks: 1 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 52 Chain: "c" Number of atoms: 8166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1176, 8166 Classifications: {'peptide': 1176} Incomplete info: {'truncation_to_alanine': 347} Link IDs: {'PTRANS': 54, 'TRANS': 1121} Chain breaks: 6 Unresolved chain link angles: 19 Unresolved non-hydrogen bonds: 1216 Unresolved non-hydrogen angles: 1540 Unresolved non-hydrogen dihedrals: 1004 Unresolved non-hydrogen chiralities: 109 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 8, 'TYR:plan': 11, 'ASN:plan1': 29, 'TRP:plan': 2, 'ASP:plan': 17, 'PHE:plan': 15, 'GLU:plan': 19, 'ARG:plan': 29} Unresolved non-hydrogen planarities: 636 Chain: "i" Number of atoms: 2937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2937 Classifications: {'peptide': 375} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 20, 'TRANS': 354} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "m" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 855 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 102} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 21 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Time building chain proxies: 26.60, per 1000 atoms: 0.42 Number of scatterers: 62699 At special positions: 0 Unit cell: (227.42, 248.17, 158.53, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 Fe 2 26.01 S 268 16.00 P 27 15.00 Mg 1 11.99 O 11679 8.00 N 11111 7.00 C 39610 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS M 101 " - pdb=" SG CYS M 104 " distance=2.03 Simple disulfide: pdb=" SG CYS m 101 " - pdb=" SG CYS m 104 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.63 Conformation dependent library (CDL) restraints added in 6.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B1101 " pdb="ZN ZN B1101 " - pdb=" NE2 HIS B 536 " 16562 Ramachandran restraints generated. 8281 Oldfield, 0 Emsley, 8281 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15612 Finding SS restraints... Secondary structure from input PDB file: 326 helices and 70 sheets defined 45.9% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.40 Creating SS restraints... Processing helix chain 'A' and resid 40 through 56 removed outlier: 3.989A pdb=" N THR A 44 " --> pdb=" O GLY A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 92 Processing helix chain 'A' and resid 210 through 227 Processing helix chain 'A' and resid 228 through 231 Processing helix chain 'A' and resid 280 through 290 Processing helix chain 'A' and resid 294 through 301 Processing helix chain 'A' and resid 302 through 309 removed outlier: 3.768A pdb=" N ILE A 309 " --> pdb=" O ASP A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 327 Processing helix chain 'B' and resid 16 through 37 removed outlier: 4.964A pdb=" N LEU B 31 " --> pdb=" O ILE B 27 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N THR B 32 " --> pdb=" O ASP B 28 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS B 37 " --> pdb=" O GLU B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 73 removed outlier: 3.611A pdb=" N TYR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 188 Processing helix chain 'B' and resid 192 through 198 Processing helix chain 'B' and resid 200 through 207 removed outlier: 3.873A pdb=" N PHE B 204 " --> pdb=" O TYR B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 256 Processing helix chain 'B' and resid 259 through 270 Processing helix chain 'B' and resid 282 through 298 removed outlier: 3.675A pdb=" N LYS B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE B 298 " --> pdb=" O ILE B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 310 No H-bonds generated for 'chain 'B' and resid 308 through 310' Processing helix chain 'B' and resid 316 through 346 Processing helix chain 'B' and resid 351 through 356 removed outlier: 3.613A pdb=" N LEU B 355 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 372 removed outlier: 3.833A pdb=" N THR B 362 " --> pdb=" O SER B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 390 removed outlier: 3.639A pdb=" N GLN B 386 " --> pdb=" O ASN B 382 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE B 387 " --> pdb=" O PRO B 383 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLY B 390 " --> pdb=" O GLN B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 412 Processing helix chain 'B' and resid 414 through 418 Processing helix chain 'B' and resid 473 through 477 removed outlier: 3.534A pdb=" N TYR B 477 " --> pdb=" O ASP B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 494 Processing helix chain 'B' and resid 525 through 530 Processing helix chain 'B' and resid 533 through 537 Processing helix chain 'B' and resid 538 through 550 removed outlier: 3.830A pdb=" N LEU B 543 " --> pdb=" O ALA B 539 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N MET B 544 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG B 550 " --> pdb=" O SER B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 576 removed outlier: 4.354A pdb=" N GLY B 576 " --> pdb=" O ALA B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 675 through 680 Processing helix chain 'B' and resid 855 through 861 removed outlier: 3.728A pdb=" N SER B 859 " --> pdb=" O LEU B 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 879 removed outlier: 3.736A pdb=" N PHE B 867 " --> pdb=" O VAL B 863 " (cutoff:3.500A) Processing helix chain 'B' and resid 887 through 891 removed outlier: 3.510A pdb=" N TYR B 891 " --> pdb=" O ASP B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 911 Processing helix chain 'B' and resid 913 through 917 removed outlier: 3.508A pdb=" N PHE B 917 " --> pdb=" O PRO B 914 " (cutoff:3.500A) Processing helix chain 'B' and resid 953 through 958 Processing helix chain 'B' and resid 986 through 997 removed outlier: 3.740A pdb=" N ALA B 992 " --> pdb=" O MET B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 998 through 1008 Processing helix chain 'B' and resid 1012 through 1026 removed outlier: 3.716A pdb=" N LEU B1020 " --> pdb=" O ARG B1016 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLY B1021 " --> pdb=" O GLN B1017 " (cutoff:3.500A) Processing helix chain 'B' and resid 1036 through 1049 Processing helix chain 'C' and resid 23 through 30 Processing helix chain 'C' and resid 105 through 110 removed outlier: 3.546A pdb=" N TYR C 109 " --> pdb=" O ARG C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 127 Processing helix chain 'C' and resid 131 through 137 Processing helix chain 'C' and resid 140 through 150 Processing helix chain 'C' and resid 180 through 186 Processing helix chain 'C' and resid 187 through 196 removed outlier: 4.511A pdb=" N ASN C 196 " --> pdb=" O ASP C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 212 removed outlier: 3.876A pdb=" N ARG C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 229 Processing helix chain 'C' and resid 237 through 263 removed outlier: 3.692A pdb=" N ARG C 263 " --> pdb=" O LYS C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 270 Processing helix chain 'C' and resid 297 through 320 removed outlier: 4.054A pdb=" N SER C 320 " --> pdb=" O LEU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 344 removed outlier: 3.679A pdb=" N VAL C 328 " --> pdb=" O PRO C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 368 Processing helix chain 'C' and resid 372 through 378 Processing helix chain 'C' and resid 406 through 413 removed outlier: 3.921A pdb=" N GLU C 411 " --> pdb=" O GLU C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 424 Processing helix chain 'C' and resid 429 through 439 Processing helix chain 'C' and resid 441 through 452 removed outlier: 3.821A pdb=" N TRP C 445 " --> pdb=" O GLU C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 488 No H-bonds generated for 'chain 'C' and resid 486 through 488' Processing helix chain 'C' and resid 489 through 494 removed outlier: 3.778A pdb=" N PHE C 493 " --> pdb=" O VAL C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 519 Processing helix chain 'C' and resid 540 through 551 removed outlier: 3.613A pdb=" N ILE C 544 " --> pdb=" O GLN C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 591 through 601 Processing helix chain 'C' and resid 663 through 685 removed outlier: 3.579A pdb=" N ILE C 667 " --> pdb=" O THR C 663 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER C 685 " --> pdb=" O SER C 681 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 83 removed outlier: 3.557A pdb=" N GLU D 76 " --> pdb=" O VAL D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 100 Processing helix chain 'D' and resid 104 through 118 removed outlier: 3.674A pdb=" N GLY D 110 " --> pdb=" O ARG D 106 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE D 111 " --> pdb=" O SER D 107 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN D 118 " --> pdb=" O SER D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 134 Processing helix chain 'D' and resid 139 through 154 Processing helix chain 'D' and resid 155 through 169 Processing helix chain 'D' and resid 173 through 187 Processing helix chain 'D' and resid 189 through 204 Processing helix chain 'D' and resid 208 through 223 Processing helix chain 'D' and resid 224 through 238 removed outlier: 3.582A pdb=" N ALA D 228 " --> pdb=" O ASP D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 255 removed outlier: 3.693A pdb=" N VAL D 253 " --> pdb=" O CYS D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 258 No H-bonds generated for 'chain 'D' and resid 256 through 258' Processing helix chain 'D' and resid 261 through 272 removed outlier: 3.672A pdb=" N THR D 266 " --> pdb=" O ILE D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 293 Processing helix chain 'D' and resid 300 through 310 Processing helix chain 'D' and resid 312 through 316 removed outlier: 3.559A pdb=" N LYS D 315 " --> pdb=" O GLU D 312 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG D 316 " --> pdb=" O ASP D 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 312 through 316' Processing helix chain 'D' and resid 320 through 334 Processing helix chain 'D' and resid 336 through 350 removed outlier: 3.541A pdb=" N GLY D 346 " --> pdb=" O ARG D 342 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASN D 349 " --> pdb=" O ARG D 345 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N PHE D 350 " --> pdb=" O GLY D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 358 Processing helix chain 'D' and resid 365 through 378 Processing helix chain 'D' and resid 379 through 393 Processing helix chain 'D' and resid 430 through 440 removed outlier: 3.636A pdb=" N GLY D 440 " --> pdb=" O VAL D 436 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 462 removed outlier: 3.592A pdb=" N ALA D 461 " --> pdb=" O ASP D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 496 Processing helix chain 'D' and resid 505 through 521 removed outlier: 3.796A pdb=" N ILE D 510 " --> pdb=" O GLU D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 593 through 600 removed outlier: 3.574A pdb=" N ILE D 597 " --> pdb=" O LEU D 593 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE D 600 " --> pdb=" O LEU D 596 " (cutoff:3.500A) Processing helix chain 'D' and resid 606 through 615 Processing helix chain 'D' and resid 734 through 746 Processing helix chain 'D' and resid 749 through 753 Processing helix chain 'D' and resid 755 through 760 Processing helix chain 'D' and resid 764 through 770 removed outlier: 4.092A pdb=" N ILE D 768 " --> pdb=" O TRP D 764 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASN D 770 " --> pdb=" O LYS D 766 " (cutoff:3.500A) Processing helix chain 'D' and resid 777 through 795 Processing helix chain 'D' and resid 800 through 814 removed outlier: 3.633A pdb=" N ALA D 814 " --> pdb=" O ALA D 810 " (cutoff:3.500A) Processing helix chain 'D' and resid 817 through 830 removed outlier: 4.418A pdb=" N LEU D 821 " --> pdb=" O PRO D 817 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ASN D 822 " --> pdb=" O SER D 818 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU D 830 " --> pdb=" O THR D 826 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 850 removed outlier: 3.570A pdb=" N TYR D 839 " --> pdb=" O GLY D 835 " (cutoff:3.500A) Processing helix chain 'D' and resid 851 through 866 Processing helix chain 'D' and resid 870 through 885 Processing helix chain 'E' and resid 103 through 114 Processing helix chain 'E' and resid 115 through 128 removed outlier: 3.869A pdb=" N ARG E 128 " --> pdb=" O LYS E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 149 Processing helix chain 'E' and resid 151 through 161 Processing helix chain 'E' and resid 170 through 184 removed outlier: 3.713A pdb=" N TYR E 174 " --> pdb=" O THR E 170 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASN E 184 " --> pdb=" O ALA E 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 200 Processing helix chain 'E' and resid 205 through 219 Processing helix chain 'E' and resid 222 through 236 Processing helix chain 'E' and resid 241 through 256 removed outlier: 3.712A pdb=" N CYS E 252 " --> pdb=" O LEU E 248 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER E 253 " --> pdb=" O LEU E 249 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY E 256 " --> pdb=" O CYS E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 271 removed outlier: 4.326A pdb=" N MET E 268 " --> pdb=" O VAL E 264 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ASN E 269 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA E 271 " --> pdb=" O THR E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 291 removed outlier: 3.705A pdb=" N LYS E 289 " --> pdb=" O ASP E 285 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU E 290 " --> pdb=" O THR E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 306 removed outlier: 3.637A pdb=" N LEU E 300 " --> pdb=" O VAL E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 326 Processing helix chain 'E' and resid 327 through 342 removed outlier: 3.758A pdb=" N GLY E 342 " --> pdb=" O MET E 338 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 361 Processing helix chain 'E' and resid 363 through 376 Processing helix chain 'E' and resid 381 through 396 Processing helix chain 'E' and resid 397 through 411 removed outlier: 3.578A pdb=" N GLU E 410 " --> pdb=" O HIS E 406 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 431 Processing helix chain 'E' and resid 433 through 446 Processing helix chain 'E' and resid 451 through 465 Processing helix chain 'E' and resid 467 through 482 removed outlier: 3.809A pdb=" N GLY E 482 " --> pdb=" O MET E 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 486 through 499 Processing helix chain 'E' and resid 502 through 517 Processing helix chain 'E' and resid 521 through 535 Processing helix chain 'E' and resid 538 through 551 removed outlier: 3.858A pdb=" N ILE E 542 " --> pdb=" O PHE E 538 " (cutoff:3.500A) Processing helix chain 'E' and resid 556 through 570 removed outlier: 3.651A pdb=" N TYR E 567 " --> pdb=" O VAL E 563 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA E 570 " --> pdb=" O VAL E 566 " (cutoff:3.500A) Processing helix chain 'E' and resid 573 through 587 removed outlier: 3.680A pdb=" N GLU E 577 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU E 578 " --> pdb=" O ASP E 574 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LEU E 586 " --> pdb=" O GLU E 582 " (cutoff:3.500A) Processing helix chain 'E' and resid 591 through 605 Processing helix chain 'E' and resid 611 through 621 removed outlier: 4.079A pdb=" N LEU E 615 " --> pdb=" O ALA E 611 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL E 618 " --> pdb=" O LEU E 614 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N MET E 619 " --> pdb=" O LEU E 615 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR E 620 " --> pdb=" O ASN E 616 " (cutoff:3.500A) Processing helix chain 'E' and resid 624 through 635 removed outlier: 4.671A pdb=" N GLN E 632 " --> pdb=" O GLN E 628 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N MET E 633 " --> pdb=" O VAL E 629 " (cutoff:3.500A) Processing helix chain 'E' and resid 640 through 654 removed outlier: 3.671A pdb=" N LEU E 654 " --> pdb=" O VAL E 650 " (cutoff:3.500A) Processing helix chain 'E' and resid 655 through 658 removed outlier: 3.875A pdb=" N GLY E 658 " --> pdb=" O ASN E 655 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 655 through 658' Processing helix chain 'E' and resid 661 through 676 removed outlier: 3.577A pdb=" N TRP E 675 " --> pdb=" O GLU E 671 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LEU E 676 " --> pdb=" O ALA E 672 " (cutoff:3.500A) Processing helix chain 'E' and resid 680 through 693 removed outlier: 4.142A pdb=" N ARG E 684 " --> pdb=" O GLU E 680 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N VAL E 685 " --> pdb=" O ARG E 681 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU E 686 " --> pdb=" O ALA E 682 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG E 692 " --> pdb=" O GLU E 688 " (cutoff:3.500A) Processing helix chain 'E' and resid 714 through 729 Processing helix chain 'E' and resid 730 through 736 removed outlier: 4.231A pdb=" N HIS E 734 " --> pdb=" O GLU E 730 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LYS E 735 " --> pdb=" O GLU E 731 " (cutoff:3.500A) Processing helix chain 'E' and resid 750 through 754 removed outlier: 3.530A pdb=" N GLU E 753 " --> pdb=" O GLY E 750 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LYS E 754 " --> pdb=" O GLN E 751 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 750 through 754' Processing helix chain 'E' and resid 761 through 775 Processing helix chain 'E' and resid 793 through 801 Processing helix chain 'F' and resid 73 through 84 Processing helix chain 'F' and resid 95 through 105 Processing helix chain 'F' and resid 115 through 125 Processing helix chain 'F' and resid 126 through 138 Processing helix chain 'F' and resid 140 through 149 removed outlier: 3.898A pdb=" N PHE F 149 " --> pdb=" O TYR F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 199 removed outlier: 4.556A pdb=" N THR F 195 " --> pdb=" O PHE F 191 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N HIS F 196 " --> pdb=" O ILE F 192 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LYS F 197 " --> pdb=" O ARG F 193 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU F 198 " --> pdb=" O GLU F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 207 through 212 removed outlier: 3.850A pdb=" N MET F 211 " --> pdb=" O LYS F 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 221 through 250 removed outlier: 5.861A pdb=" N ASP F 240 " --> pdb=" O ALA F 236 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ARG F 241 " --> pdb=" O ALA F 237 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 264 Processing helix chain 'F' and resid 270 through 274 Processing helix chain 'F' and resid 311 through 316 Processing helix chain 'F' and resid 372 through 381 Processing helix chain 'F' and resid 405 through 426 removed outlier: 3.500A pdb=" N GLU F 424 " --> pdb=" O LEU F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 431 Processing helix chain 'F' and resid 445 through 450 removed outlier: 3.503A pdb=" N ILE F 450 " --> pdb=" O GLU F 446 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 497 removed outlier: 3.851A pdb=" N ALA F 479 " --> pdb=" O ASP F 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 505 through 540 removed outlier: 3.530A pdb=" N ARG F 531 " --> pdb=" O GLU F 527 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 594 Processing helix chain 'F' and resid 606 through 615 Processing helix chain 'G' and resid 70 through 80 Processing helix chain 'G' and resid 80 through 96 removed outlier: 3.738A pdb=" N LYS G 95 " --> pdb=" O LYS G 91 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN G 96 " --> pdb=" O GLN G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 101 Processing helix chain 'G' and resid 103 through 113 removed outlier: 3.659A pdb=" N ASN G 113 " --> pdb=" O LYS G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 136 removed outlier: 3.552A pdb=" N ALA G 124 " --> pdb=" O GLU G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 157 removed outlier: 3.554A pdb=" N GLN G 151 " --> pdb=" O LEU G 147 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN G 152 " --> pdb=" O GLY G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 174 Processing helix chain 'G' and resid 201 through 205 Processing helix chain 'G' and resid 216 through 221 removed outlier: 4.165A pdb=" N TYR G 220 " --> pdb=" O TRP G 216 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 238 Processing helix chain 'G' and resid 241 through 253 Processing helix chain 'H' and resid 204 through 213 Processing helix chain 'H' and resid 257 through 268 removed outlier: 3.714A pdb=" N GLU H 268 " --> pdb=" O LYS H 264 " (cutoff:3.500A) Processing helix chain 'H' and resid 269 through 271 No H-bonds generated for 'chain 'H' and resid 269 through 271' Processing helix chain 'H' and resid 280 through 310 removed outlier: 6.209A pdb=" N HIS H 292 " --> pdb=" O ARG H 288 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU H 293 " --> pdb=" O ALA H 289 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N TYR H 294 " --> pdb=" O ARG H 290 " (cutoff:3.500A) Processing helix chain 'H' and resid 310 through 316 Processing helix chain 'H' and resid 317 through 319 No H-bonds generated for 'chain 'H' and resid 317 through 319' Processing helix chain 'H' and resid 327 through 339 Processing helix chain 'H' and resid 341 through 351 Processing helix chain 'H' and resid 354 through 362 Processing helix chain 'H' and resid 363 through 365 No H-bonds generated for 'chain 'H' and resid 363 through 365' Processing helix chain 'H' and resid 371 through 376 Processing helix chain 'H' and resid 378 through 387 removed outlier: 3.689A pdb=" N GLN H 384 " --> pdb=" O ASP H 380 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE H 385 " --> pdb=" O GLN H 381 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N TRP H 386 " --> pdb=" O ILE H 382 " (cutoff:3.500A) Processing helix chain 'H' and resid 393 through 396 removed outlier: 3.516A pdb=" N ASN H 396 " --> pdb=" O PRO H 393 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 393 through 396' Processing helix chain 'H' and resid 418 through 426 Processing helix chain 'H' and resid 431 through 446 Processing helix chain 'I' and resid 149 through 154 Processing helix chain 'I' and resid 156 through 160 Processing helix chain 'I' and resid 165 through 176 removed outlier: 3.766A pdb=" N VAL I 169 " --> pdb=" O PRO I 165 " (cutoff:3.500A) Processing helix chain 'I' and resid 189 through 202 Processing helix chain 'I' and resid 238 through 242 Processing helix chain 'I' and resid 250 through 257 removed outlier: 3.524A pdb=" N LEU I 254 " --> pdb=" O ASN I 250 " (cutoff:3.500A) Processing helix chain 'I' and resid 264 through 269 removed outlier: 3.706A pdb=" N THR I 268 " --> pdb=" O SER I 264 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N SER I 269 " --> pdb=" O GLU I 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 264 through 269' Processing helix chain 'I' and resid 272 through 287 Processing helix chain 'I' and resid 298 through 302 removed outlier: 3.544A pdb=" N ARG I 302 " --> pdb=" O PRO I 299 " (cutoff:3.500A) Processing helix chain 'I' and resid 303 through 311 Processing helix chain 'I' and resid 311 through 317 removed outlier: 3.533A pdb=" N GLN I 317 " --> pdb=" O GLU I 313 " (cutoff:3.500A) Processing helix chain 'I' and resid 325 through 331 Processing helix chain 'I' and resid 333 through 342 removed outlier: 3.598A pdb=" N TYR I 337 " --> pdb=" O ASP I 333 " (cutoff:3.500A) Processing helix chain 'I' and resid 351 through 357 removed outlier: 3.690A pdb=" N THR I 355 " --> pdb=" O ASN I 351 " (cutoff:3.500A) Processing helix chain 'I' and resid 369 through 373 Processing helix chain 'I' and resid 405 through 409 Processing helix chain 'I' and resid 417 through 433 Processing helix chain 'I' and resid 439 through 458 removed outlier: 3.899A pdb=" N PHE I 449 " --> pdb=" O ARG I 445 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA I 450 " --> pdb=" O GLN I 446 " (cutoff:3.500A) Processing helix chain 'I' and resid 469 through 481 Processing helix chain 'J' and resid 99 through 108 removed outlier: 4.085A pdb=" N TYR J 103 " --> pdb=" O ASP J 99 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLY J 106 " --> pdb=" O PHE J 102 " (cutoff:3.500A) Processing helix chain 'J' and resid 148 through 150 No H-bonds generated for 'chain 'J' and resid 148 through 150' Processing helix chain 'J' and resid 170 through 178 removed outlier: 3.822A pdb=" N ASP J 174 " --> pdb=" O HIS J 170 " (cutoff:3.500A) Processing helix chain 'J' and resid 185 through 199 Processing helix chain 'J' and resid 202 through 208 removed outlier: 3.985A pdb=" N LEU J 206 " --> pdb=" O ASN J 202 " (cutoff:3.500A) Processing helix chain 'J' and resid 224 through 231 Processing helix chain 'J' and resid 233 through 255 Processing helix chain 'J' and resid 260 through 265 Processing helix chain 'J' and resid 269 through 283 removed outlier: 3.705A pdb=" N PHE J 273 " --> pdb=" O ASP J 269 " (cutoff:3.500A) Processing helix chain 'J' and resid 352 through 360 removed outlier: 3.529A pdb=" N PHE J 356 " --> pdb=" O LYS J 352 " (cutoff:3.500A) Processing helix chain 'J' and resid 382 through 389 Processing helix chain 'J' and resid 401 through 406 Processing helix chain 'J' and resid 413 through 423 Processing helix chain 'J' and resid 434 through 456 removed outlier: 3.821A pdb=" N PHE J 456 " --> pdb=" O MET J 452 " (cutoff:3.500A) Processing helix chain 'J' and resid 459 through 470 Processing helix chain 'J' and resid 474 through 505 Processing helix chain 'K' and resid 134 through 136 No H-bonds generated for 'chain 'K' and resid 134 through 136' Processing helix chain 'K' and resid 231 through 233 No H-bonds generated for 'chain 'K' and resid 231 through 233' Processing helix chain 'K' and resid 298 through 321 removed outlier: 4.365A pdb=" N LYS K 321 " --> pdb=" O ARG K 317 " (cutoff:3.500A) Processing helix chain 'L' and resid 66 through 90 Processing helix chain 'L' and resid 98 through 106 Processing helix chain 'L' and resid 114 through 131 removed outlier: 4.552A pdb=" N ASN L 118 " --> pdb=" O PRO L 114 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ALA L 119 " --> pdb=" O PRO L 115 " (cutoff:3.500A) Processing helix chain 'L' and resid 142 through 152 removed outlier: 3.605A pdb=" N GLN L 146 " --> pdb=" O GLY L 142 " (cutoff:3.500A) Processing helix chain 'L' and resid 154 through 167 Processing helix chain 'L' and resid 168 through 170 No H-bonds generated for 'chain 'L' and resid 168 through 170' Processing helix chain 'L' and resid 211 through 216 Processing helix chain 'L' and resid 226 through 232 removed outlier: 4.173A pdb=" N TYR L 230 " --> pdb=" O TRP L 226 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU L 232 " --> pdb=" O HIS L 228 " (cutoff:3.500A) Processing helix chain 'L' and resid 237 through 249 removed outlier: 3.827A pdb=" N TYR L 241 " --> pdb=" O ARG L 237 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU L 249 " --> pdb=" O PHE L 245 " (cutoff:3.500A) Processing helix chain 'L' and resid 251 through 282 removed outlier: 3.929A pdb=" N VAL L 255 " --> pdb=" O SER L 251 " (cutoff:3.500A) Processing helix chain 'M' and resid 76 through 86 Processing helix chain 'M' and resid 102 through 118 removed outlier: 4.284A pdb=" N LEU M 106 " --> pdb=" O GLY M 102 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN M 109 " --> pdb=" O ILE M 105 " (cutoff:3.500A) Processing helix chain 'M' and resid 132 through 139 removed outlier: 3.537A pdb=" N ALA M 136 " --> pdb=" O GLU M 132 " (cutoff:3.500A) Processing helix chain 'M' and resid 166 through 177 Processing helix chain 'N' and resid 239 through 246 Processing helix chain 'N' and resid 286 through 298 Processing helix chain 'N' and resid 309 through 313 removed outlier: 3.567A pdb=" N GLU N 312 " --> pdb=" O ASP N 309 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR N 313 " --> pdb=" O ILE N 310 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 309 through 313' Processing helix chain 'N' and resid 324 through 333 removed outlier: 4.450A pdb=" N ALA N 333 " --> pdb=" O LEU N 329 " (cutoff:3.500A) Processing helix chain 'N' and resid 334 through 345 Proline residue: N 340 - end of helix removed outlier: 3.794A pdb=" N THR N 345 " --> pdb=" O SER N 341 " (cutoff:3.500A) Processing helix chain 'N' and resid 354 through 370 removed outlier: 3.765A pdb=" N THR N 358 " --> pdb=" O GLY N 354 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU N 361 " --> pdb=" O THR N 357 " (cutoff:3.500A) Processing helix chain 'N' and resid 397 through 411 removed outlier: 3.597A pdb=" N ASN N 411 " --> pdb=" O LYS N 407 " (cutoff:3.500A) Processing helix chain 'N' and resid 421 through 428 Processing helix chain 'N' and resid 447 through 452 Processing helix chain 'N' and resid 455 through 468 removed outlier: 3.714A pdb=" N MET N 468 " --> pdb=" O LEU N 464 " (cutoff:3.500A) Processing helix chain 'N' and resid 482 through 491 removed outlier: 3.603A pdb=" N ALA N 486 " --> pdb=" O ASP N 482 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN N 491 " --> pdb=" O PHE N 487 " (cutoff:3.500A) Processing helix chain 'N' and resid 542 through 559 removed outlier: 3.733A pdb=" N ALA N 553 " --> pdb=" O LEU N 549 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL N 554 " --> pdb=" O ALA N 550 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL N 558 " --> pdb=" O VAL N 554 " (cutoff:3.500A) Processing helix chain 'N' and resid 561 through 563 No H-bonds generated for 'chain 'N' and resid 561 through 563' Processing helix chain 'N' and resid 564 through 573 removed outlier: 4.538A pdb=" N GLY N 568 " --> pdb=" O ASP N 564 " (cutoff:3.500A) Processing helix chain 'N' and resid 597 through 612 Processing helix chain 'N' and resid 629 through 642 removed outlier: 4.382A pdb=" N ILE N 633 " --> pdb=" O GLY N 629 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA N 635 " --> pdb=" O ARG N 631 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS N 641 " --> pdb=" O ILE N 637 " (cutoff:3.500A) Processing helix chain 'N' and resid 656 through 666 removed outlier: 3.749A pdb=" N ASP N 663 " --> pdb=" O ASP N 659 " (cutoff:3.500A) Processing helix chain 'N' and resid 671 through 681 Processing helix chain 'N' and resid 698 through 709 Processing helix chain 'N' and resid 738 through 756 removed outlier: 3.781A pdb=" N CYS N 742 " --> pdb=" O ASP N 738 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ASP N 750 " --> pdb=" O LEU N 746 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N GLU N 751 " --> pdb=" O GLN N 747 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU N 752 " --> pdb=" O TYR N 748 " (cutoff:3.500A) Processing helix chain 'O' and resid 58 through 69 removed outlier: 3.516A pdb=" N VAL O 62 " --> pdb=" O LEU O 58 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY O 69 " --> pdb=" O ILE O 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 69 through 81 removed outlier: 3.876A pdb=" N THR O 73 " --> pdb=" O GLY O 69 " (cutoff:3.500A) Processing helix chain 'O' and resid 85 through 104 Processing helix chain 'O' and resid 112 through 124 Processing helix chain 'O' and resid 130 through 134 Processing helix chain 'P' and resid 43 through 48 Processing helix chain 'P' and resid 57 through 63 Processing helix chain 'P' and resid 64 through 66 No H-bonds generated for 'chain 'P' and resid 64 through 66' Processing helix chain 'a' and resid 40 through 54 removed outlier: 4.043A pdb=" N THR a 44 " --> pdb=" O GLY a 40 " (cutoff:3.500A) Processing helix chain 'a' and resid 83 through 93 removed outlier: 3.685A pdb=" N GLU a 93 " --> pdb=" O MET a 89 " (cutoff:3.500A) Processing helix chain 'a' and resid 210 through 227 Processing helix chain 'a' and resid 228 through 231 Processing helix chain 'a' and resid 251 through 264 removed outlier: 4.341A pdb=" N LYS a 264 " --> pdb=" O LEU a 260 " (cutoff:3.500A) Processing helix chain 'a' and resid 280 through 290 Processing helix chain 'a' and resid 294 through 301 Processing helix chain 'a' and resid 302 through 309 removed outlier: 3.630A pdb=" N ILE a 309 " --> pdb=" O ASP a 305 " (cutoff:3.500A) Processing helix chain 'a' and resid 313 through 326 removed outlier: 3.842A pdb=" N VAL a 317 " --> pdb=" O ARG a 313 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS a 318 " --> pdb=" O SER a 314 " (cutoff:3.500A) Processing helix chain 'c' and resid 15 through 54 removed outlier: 7.271A pdb=" N MET c 32 " --> pdb=" O ASP c 28 " (cutoff:3.500A) removed outlier: 8.832A pdb=" N ALA c 33 " --> pdb=" O HIS c 29 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR c 34 " --> pdb=" O PHE c 30 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N HIS c 37 " --> pdb=" O ALA c 33 " (cutoff:3.500A) Processing helix chain 'c' and resid 67 through 89 Processing helix chain 'c' and resid 92 through 122 removed outlier: 4.279A pdb=" N ASN c 116 " --> pdb=" O ARG c 112 " (cutoff:3.500A) Proline residue: c 117 - end of helix Processing helix chain 'c' and resid 126 through 135 removed outlier: 3.620A pdb=" N GLY c 135 " --> pdb=" O MET c 131 " (cutoff:3.500A) Processing helix chain 'c' and resid 139 through 148 Processing helix chain 'c' and resid 174 through 211 removed outlier: 3.715A pdb=" N TYR c 183 " --> pdb=" O ILE c 179 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY c 184 " --> pdb=" O ILE c 180 " (cutoff:3.500A) Processing helix chain 'c' and resid 229 through 234 removed outlier: 3.563A pdb=" N ASN c 232 " --> pdb=" O SER c 229 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N MET c 234 " --> pdb=" O ARG c 231 " (cutoff:3.500A) Processing helix chain 'c' and resid 236 through 245 Processing helix chain 'c' and resid 268 through 279 Processing helix chain 'c' and resid 287 through 291 removed outlier: 3.661A pdb=" N CYS c 291 " --> pdb=" O PRO c 288 " (cutoff:3.500A) Processing helix chain 'c' and resid 299 through 303 Processing helix chain 'c' and resid 317 through 328 removed outlier: 3.816A pdb=" N ILE c 321 " --> pdb=" O ALA c 317 " (cutoff:3.500A) Processing helix chain 'c' and resid 329 through 332 Processing helix chain 'c' and resid 485 through 492 removed outlier: 3.883A pdb=" N SER c 490 " --> pdb=" O LEU c 486 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE c 491 " --> pdb=" O VAL c 487 " (cutoff:3.500A) Processing helix chain 'c' and resid 563 through 568 Processing helix chain 'c' and resid 616 through 620 removed outlier: 3.522A pdb=" N TYR c 619 " --> pdb=" O ASP c 616 " (cutoff:3.500A) Processing helix chain 'c' and resid 907 through 916 removed outlier: 3.527A pdb=" N ILE c 916 " --> pdb=" O SER c 912 " (cutoff:3.500A) Processing helix chain 'c' and resid 1004 through 1009 removed outlier: 3.683A pdb=" N TYR c1008 " --> pdb=" O LEU c1004 " (cutoff:3.500A) Processing helix chain 'c' and resid 1146 through 1154 Processing helix chain 'c' and resid 1157 through 1162 Processing helix chain 'c' and resid 1162 through 1176 Processing helix chain 'c' and resid 1182 through 1212 removed outlier: 4.048A pdb=" N PHE c1186 " --> pdb=" O ILE c1182 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LEU c1187 " --> pdb=" O PRO c1183 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ILE c1188 " --> pdb=" O TRP c1184 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLN c1212 " --> pdb=" O VAL c1208 " (cutoff:3.500A) Processing helix chain 'c' and resid 1217 through 1229 removed outlier: 4.019A pdb=" N LEU c1221 " --> pdb=" O HIS c1217 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE c1224 " --> pdb=" O HIS c1220 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN c1227 " --> pdb=" O ILE c1223 " (cutoff:3.500A) Processing helix chain 'c' and resid 1251 through 1261 Processing helix chain 'c' and resid 1273 through 1280 Processing helix chain 'c' and resid 1292 through 1304 Processing helix chain 'c' and resid 1311 through 1319 removed outlier: 3.619A pdb=" N ASN c1315 " --> pdb=" O GLY c1311 " (cutoff:3.500A) Processing helix chain 'c' and resid 1324 through 1328 Processing helix chain 'i' and resid 269 through 274 Processing helix chain 'i' and resid 302 through 309 Processing helix chain 'i' and resid 326 through 337 Processing helix chain 'i' and resid 350 through 363 Processing helix chain 'i' and resid 405 through 409 Processing helix chain 'i' and resid 410 through 416 removed outlier: 3.597A pdb=" N LEU i 414 " --> pdb=" O ASN i 410 " (cutoff:3.500A) Processing helix chain 'i' and resid 425 through 428 removed outlier: 3.556A pdb=" N LEU i 428 " --> pdb=" O PHE i 425 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 425 through 428' Processing helix chain 'i' and resid 429 through 446 Processing helix chain 'i' and resid 457 through 462 removed outlier: 3.794A pdb=" N GLU i 462 " --> pdb=" O PRO i 459 " (cutoff:3.500A) Processing helix chain 'i' and resid 463 through 471 Processing helix chain 'i' and resid 485 through 492 Processing helix chain 'i' and resid 514 through 519 removed outlier: 3.625A pdb=" N ILE i 518 " --> pdb=" O PRO i 514 " (cutoff:3.500A) Processing helix chain 'i' and resid 520 through 522 No H-bonds generated for 'chain 'i' and resid 520 through 522' Processing helix chain 'i' and resid 559 through 563 removed outlier: 4.279A pdb=" N ASP i 563 " --> pdb=" O TYR i 560 " (cutoff:3.500A) Processing helix chain 'i' and resid 564 through 582 removed outlier: 4.048A pdb=" N GLY i 568 " --> pdb=" O MET i 564 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN i 582 " --> pdb=" O MET i 578 " (cutoff:3.500A) Processing helix chain 'i' and resid 583 through 586 Processing helix chain 'i' and resid 588 through 614 Processing helix chain 'i' and resid 634 through 639 Processing helix chain 'm' and resid 76 through 86 Processing helix chain 'm' and resid 101 through 118 removed outlier: 3.781A pdb=" N ILE m 105 " --> pdb=" O CYS m 101 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU m 106 " --> pdb=" O GLY m 102 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLN m 109 " --> pdb=" O ILE m 105 " (cutoff:3.500A) Processing helix chain 'm' and resid 132 through 139 removed outlier: 3.732A pdb=" N ALA m 136 " --> pdb=" O GLU m 132 " (cutoff:3.500A) Processing helix chain 'm' and resid 166 through 177 Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 24 removed outlier: 6.191A pdb=" N CYS A 17 " --> pdb=" O ILE A 33 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ILE A 33 " --> pdb=" O CYS A 17 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU A 19 " --> pdb=" O ARG A 31 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP A 23 " --> pdb=" O LEU A 27 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU A 27 " --> pdb=" O ASP A 23 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N MET O 146 " --> pdb=" O GLY A 190 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 67 removed outlier: 6.500A pdb=" N GLN A 150 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N VAL A 65 " --> pdb=" O GLY A 148 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N GLY A 148 " --> pdb=" O VAL A 65 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N SER A 67 " --> pdb=" O CYS A 146 " (cutoff:3.500A) removed outlier: 9.036A pdb=" N CYS A 146 " --> pdb=" O SER A 67 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 96 through 97 Processing sheet with id=AA4, first strand: chain 'B' and resid 41 through 42 removed outlier: 3.612A pdb=" N ILE B 41 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU B 49 " --> pdb=" O ILE B 87 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N SER B 83 " --> pdb=" O PHE B 53 " (cutoff:3.500A) removed outlier: 8.986A pdb=" N GLU B 55 " --> pdb=" O TYR B 81 " (cutoff:3.500A) removed outlier: 10.445A pdb=" N TYR B 81 " --> pdb=" O GLU B 55 " (cutoff:3.500A) removed outlier: 9.744A pdb=" N TYR B 57 " --> pdb=" O GLU B 79 " (cutoff:3.500A) removed outlier: 11.179A pdb=" N GLU B 79 " --> pdb=" O TYR B 57 " (cutoff:3.500A) removed outlier: 10.403A pdb=" N LEU B 59 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 11.920A pdb=" N SER B 77 " --> pdb=" O LEU B 59 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N SER B 78 " --> pdb=" O ASN B 103 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ASN B 103 " --> pdb=" O SER B 78 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N LEU B 80 " --> pdb=" O ILE B 101 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 113 through 115 Processing sheet with id=AA6, first strand: chain 'B' and resid 312 through 315 removed outlier: 6.705A pdb=" N ASN B 124 " --> pdb=" O SER B 394 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 135 through 138 removed outlier: 3.926A pdb=" N TYR B 146 " --> pdb=" O ILE B 162 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 443 through 444 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 466 through 469 current: chain 'B' and resid 515 through 516 Processing sheet with id=AA9, first strand: chain 'B' and resid 496 through 501 Processing sheet with id=AB1, first strand: chain 'B' and resid 563 through 564 Processing sheet with id=AB2, first strand: chain 'B' and resid 579 through 580 removed outlier: 6.735A pdb=" N ALA B 579 " --> pdb=" O LEU B 638 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 602 through 607 removed outlier: 7.265A pdb=" N LYS B 594 " --> pdb=" O THR B 590 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N THR B 590 " --> pdb=" O LYS B 594 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N LEU B 596 " --> pdb=" O VAL B 588 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 612 through 613 Processing sheet with id=AB5, first strand: chain 'B' and resid 644 through 645 Processing sheet with id=AB6, first strand: chain 'B' and resid 653 through 654 removed outlier: 7.408A pdb=" N VAL B 671 " --> pdb=" O SER B 831 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE B 833 " --> pdb=" O VAL B 671 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE B 673 " --> pdb=" O ILE B 833 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU B 672 " --> pdb=" O VAL B 851 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ALA B 658 " --> pdb=" O PHE B 852 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ILE B 941 " --> pdb=" O TYR B 659 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 685 through 694 removed outlier: 3.600A pdb=" N ILE B 693 " --> pdb=" O ILE B 804 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE B 804 " --> pdb=" O ILE B 693 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASP B 787 " --> pdb=" O TYR B 807 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LEU B 809 " --> pdb=" O VAL B 785 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N VAL B 785 " --> pdb=" O LEU B 809 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 737 through 739 removed outlier: 6.400A pdb=" N LEU B 775 " --> pdb=" O LEU B 738 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 984 through 985 Processing sheet with id=AC1, first strand: chain 'B' and resid 1065 through 1066 removed outlier: 4.173A pdb=" N HIS C 14 " --> pdb=" O VAL B1058 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 33 through 34 Processing sheet with id=AC3, first strand: chain 'C' and resid 112 through 121 removed outlier: 3.652A pdb=" N LEU C 116 " --> pdb=" O CYS C 274 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N CYS C 274 " --> pdb=" O LEU C 116 " (cutoff:3.500A) removed outlier: 11.013A pdb=" N CYS C 118 " --> pdb=" O VAL C 272 " (cutoff:3.500A) removed outlier: 10.517A pdb=" N VAL C 272 " --> pdb=" O CYS C 118 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 401 through 405 removed outlier: 3.565A pdb=" N GLY C 387 " --> pdb=" O VAL C 504 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ILE C 483 " --> pdb=" O ARG C 388 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL C 390 " --> pdb=" O ILE C 483 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N LEU C 485 " --> pdb=" O VAL C 390 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL C 392 " --> pdb=" O LEU C 485 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 588 through 589 removed outlier: 4.351A pdb=" N ILE C 658 " --> pdb=" O TRP C 614 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU C 629 " --> pdb=" O ILE C 641 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL K 263 " --> pdb=" O ILE K 290 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE H 193 " --> pdb=" O VAL K 264 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 699 through 701 removed outlier: 6.469A pdb=" N TRP E 706 " --> pdb=" O SER E 744 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N VAL E 746 " --> pdb=" O TRP E 706 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL E 708 " --> pdb=" O VAL E 746 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 92 through 93 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 92 through 93 current: chain 'F' and resid 292 through 296 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 303 through 306 current: chain 'F' and resid 342 through 346 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 342 through 346 current: chain 'c' and resid 1034 through 1035 WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 1034 through 1035 current: chain 'c' and resid 1089 through 1095 removed outlier: 5.793A pdb=" N VAL c1091 " --> pdb=" O ARG c1102 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ARG c1102 " --> pdb=" O VAL c1091 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 162 through 163 removed outlier: 4.301A pdb=" N MET F 162 " --> pdb=" O HIS c1000 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 365 through 366 Processing sheet with id=AD1, first strand: chain 'F' and resid 465 through 468 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 465 through 468 current: chain 'c' and resid 574 through 578 WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 574 through 578 current: chain 'c' and resid 851 through 859 removed outlier: 3.648A pdb=" N PHE c 867 " --> pdb=" O VAL c 856 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 600 through 605 removed outlier: 6.217A pdb=" N LEU c 837 " --> pdb=" O ILE c 610 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N ILE c 610 " --> pdb=" O LEU c 837 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 190 through 197 removed outlier: 3.785A pdb=" N ARG G 190 " --> pdb=" O LYS G 185 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLY G 178 " --> pdb=" O ASP G 214 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N ASP G 214 " --> pdb=" O GLY G 178 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE G 180 " --> pdb=" O GLY G 212 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLY G 212 " --> pdb=" O ILE G 180 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU G 182 " --> pdb=" O LEU G 210 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 216 through 217 Processing sheet with id=AD5, first strand: chain 'I' and resid 209 through 212 removed outlier: 3.595A pdb=" N ASP I 212 " --> pdb=" O VAL I 186 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N LEU I 118 " --> pdb=" O ILE I 259 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N HIS I 261 " --> pdb=" O LEU I 118 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ILE I 120 " --> pdb=" O HIS I 261 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N ASN I 263 " --> pdb=" O ILE I 120 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N PHE I 122 " --> pdb=" O ASN I 263 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N PHE I 260 " --> pdb=" O PHE I 291 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ASP I 293 " --> pdb=" O PHE I 260 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N PHE I 262 " --> pdb=" O ASP I 293 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 233 through 234 removed outlier: 4.428A pdb=" N THR M 146 " --> pdb=" O PHE M 96 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ILE M 93 " --> pdb=" O VAL M 125 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N VAL M 127 " --> pdb=" O ILE M 93 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ASP M 95 " --> pdb=" O VAL M 127 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LYS M 73 " --> pdb=" O LYS M 126 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N ASP M 128 " --> pdb=" O LYS M 73 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 96 through 97 Processing sheet with id=AD8, first strand: chain 'J' and resid 112 through 113 removed outlier: 6.483A pdb=" N VAL J 141 " --> pdb=" O ILE J 331 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE J 331 " --> pdb=" O VAL J 141 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 151 through 154 removed outlier: 3.505A pdb=" N LEU J 287 " --> pdb=" O ALA J 298 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 309 through 310 removed outlier: 5.876A pdb=" N ASN J 309 " --> pdb=" O VAL J 345 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'J' and resid 380 through 381 removed outlier: 6.501A pdb=" N ILE J 380 " --> pdb=" O TRP J 426 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'J' and resid 391 through 392 Processing sheet with id=AE4, first strand: chain 'K' and resid 138 through 142 removed outlier: 3.545A pdb=" N ARG K 151 " --> pdb=" O GLU K 165 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N GLU K 165 " --> pdb=" O ARG K 151 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE K 190 " --> pdb=" O TYR K 161 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N ARG K 191 " --> pdb=" O HIS K 229 " (cutoff:3.500A) removed outlier: 11.300A pdb=" N SER K 222 " --> pdb=" O VAL K 249 " (cutoff:3.500A) removed outlier: 9.653A pdb=" N VAL K 249 " --> pdb=" O SER K 222 " (cutoff:3.500A) removed outlier: 10.331A pdb=" N VAL K 224 " --> pdb=" O ILE K 247 " (cutoff:3.500A) removed outlier: 9.311A pdb=" N ILE K 247 " --> pdb=" O VAL K 224 " (cutoff:3.500A) removed outlier: 10.880A pdb=" N LEU K 226 " --> pdb=" O GLU K 245 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N GLU K 245 " --> pdb=" O LEU K 226 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LYS K 228 " --> pdb=" O ASP K 243 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ARG K 180 " --> pdb=" O ILE K 257 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N ARG K 259 " --> pdb=" O ARG K 180 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 201 through 203 removed outlier: 3.642A pdb=" N LYS K 216 " --> pdb=" O THR K 203 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 201 through 207 removed outlier: 6.566A pdb=" N TYR L 179 " --> pdb=" O PRO L 219 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'N' and resid 347 through 349 Processing sheet with id=AE8, first strand: chain 'N' and resid 589 through 592 removed outlier: 6.059A pdb=" N GLY N 589 " --> pdb=" O VAL N 716 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N VAL N 718 " --> pdb=" O GLY N 589 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE N 591 " --> pdb=" O VAL N 718 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE N 617 " --> pdb=" O VAL N 717 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL N 616 " --> pdb=" O VAL N 644 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N ILE N 646 " --> pdb=" O VAL N 616 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N THR N 618 " --> pdb=" O ILE N 646 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N THR N 645 " --> pdb=" O PHE N 694 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'N' and resid 727 through 729 Processing sheet with id=AF1, first strand: chain 'P' and resid 51 through 54 removed outlier: 3.719A pdb=" N ARG P 51 " --> pdb=" O ARG P 116 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ASP P 113 " --> pdb=" O ILE P 91 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE P 91 " --> pdb=" O ASP P 113 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP P 86 " --> pdb=" O ARG P 138 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER P 70 " --> pdb=" O TYR P 135 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'P' and resid 78 through 83 removed outlier: 3.656A pdb=" N PHE P 121 " --> pdb=" O TRP P 83 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR P 126 " --> pdb=" O ARG P 97 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG P 97 " --> pdb=" O TYR P 126 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL P 96 " --> pdb=" O PHE P 109 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'a' and resid 15 through 24 removed outlier: 3.670A pdb=" N LYS a 16 " --> pdb=" O ILE a 33 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ARG a 31 " --> pdb=" O VAL a 18 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N SER a 20 " --> pdb=" O TYR a 29 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N TYR a 29 " --> pdb=" O SER a 20 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N THR a 22 " --> pdb=" O LEU a 27 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N LEU a 27 " --> pdb=" O THR a 22 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N TYR a 29 " --> pdb=" O THR a 205 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N THR a 205 " --> pdb=" O TYR a 29 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ARG a 31 " --> pdb=" O ILE a 203 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ILE a 203 " --> pdb=" O ARG a 31 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N ILE a 33 " --> pdb=" O LEU a 201 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N LEU a 201 " --> pdb=" O ILE a 33 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N SER a 35 " --> pdb=" O LEU a 199 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N LEU a 199 " --> pdb=" O SER a 35 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'a' and resid 121 through 122 removed outlier: 3.660A pdb=" N SER a 107 " --> pdb=" O ILE a 122 " (cutoff:3.500A) removed outlier: 8.831A pdb=" N CYS a 146 " --> pdb=" O SER a 67 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N SER a 67 " --> pdb=" O CYS a 146 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLY a 148 " --> pdb=" O VAL a 65 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL a 65 " --> pdb=" O GLY a 148 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLN a 150 " --> pdb=" O THR a 63 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'a' and resid 96 through 97 Processing sheet with id=AF6, first strand: chain 'a' and resid 114 through 117 Processing sheet with id=AF7, first strand: chain 'a' and resid 157 through 158 removed outlier: 3.686A pdb=" N ALA a 174 " --> pdb=" O LEU a 158 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'c' and resid 154 through 155 removed outlier: 3.519A pdb=" N GLN c 159 " --> pdb=" O ASP c 155 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'c' and resid 215 through 217 removed outlier: 3.533A pdb=" N ARG c 216 " --> pdb=" O ILE c 297 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'c' and resid 226 through 228 Processing sheet with id=AG2, first strand: chain 'c' and resid 253 through 255 removed outlier: 3.764A pdb=" N ALA c 261 " --> pdb=" O ILE c 253 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N MET c 255 " --> pdb=" O CYS c 259 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N CYS c 259 " --> pdb=" O MET c 255 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'c' and resid 351 through 353 Processing sheet with id=AG4, first strand: chain 'c' and resid 395 through 397 Processing sheet with id=AG5, first strand: chain 'c' and resid 438 through 441 removed outlier: 6.274A pdb=" N LYS c 438 " --> pdb=" O THR c1131 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N THR c1131 " --> pdb=" O LYS c 438 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE c 440 " --> pdb=" O LEU c1129 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N LEU c1129 " --> pdb=" O HIS c1116 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR c1114 " --> pdb=" O THR c1131 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'c' and resid 1104 through 1108 removed outlier: 3.512A pdb=" N LYS c1105 " --> pdb=" O ILE c 476 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'c' and resid 480 through 483 removed outlier: 3.749A pdb=" N LEU c 940 " --> pdb=" O CYS c 482 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'c' and resid 662 through 663 Processing sheet with id=AG9, first strand: chain 'c' and resid 669 through 674 removed outlier: 3.656A pdb=" N SER c 685 " --> pdb=" O VAL c 705 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'c' and resid 722 through 724 Processing sheet with id=AH2, first strand: chain 'c' and resid 1044 through 1045 Processing sheet with id=AH3, first strand: chain 'c' and resid 1248 through 1250 Processing sheet with id=AH4, first strand: chain 'i' and resid 341 through 343 removed outlier: 6.911A pdb=" N LEU i 279 " --> pdb=" O MET i 419 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N TYR i 421 " --> pdb=" O LEU i 279 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N CYS i 281 " --> pdb=" O TYR i 421 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N ASN i 423 " --> pdb=" O CYS i 281 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LYS i 418 " --> pdb=" O VAL i 449 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N PHE i 451 " --> pdb=" O LYS i 418 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N PHE i 420 " --> pdb=" O PHE i 451 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ASP i 453 " --> pdb=" O PHE i 420 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N PHE i 422 " --> pdb=" O ASP i 453 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'i' and resid 295 through 296 removed outlier: 3.507A pdb=" N ARG i 321 " --> pdb=" O ARG i 295 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'i' and resid 345 through 348 Processing sheet with id=AH7, first strand: chain 'i' and resid 393 through 397 removed outlier: 5.058A pdb=" N THR i 395 " --> pdb=" O HIS i 382 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N HIS i 382 " --> pdb=" O THR i 395 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N LYS i 397 " --> pdb=" O ILE i 380 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N ILE i 380 " --> pdb=" O LYS i 397 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N THR m 146 " --> pdb=" O PHE m 96 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE m 96 " --> pdb=" O THR m 146 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ILE m 93 " --> pdb=" O VAL m 125 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N VAL m 127 " --> pdb=" O ILE m 93 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ASP m 95 " --> pdb=" O VAL m 127 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N LYS m 73 " --> pdb=" O LYS m 126 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N ASP m 128 " --> pdb=" O LYS m 73 " (cutoff:3.500A) 2874 hydrogen bonds defined for protein. 8211 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: 33.06 Time building geometry restraints manager: 14.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 10618 1.30 - 1.43: 16322 1.43 - 1.56: 36588 1.56 - 1.68: 52 1.68 - 1.81: 446 Bond restraints: 64026 Sorted by residual: bond pdb=" CA GLN C 110 " pdb=" C GLN C 110 " ideal model delta sigma weight residual 1.521 1.444 0.078 1.19e-02 7.06e+03 4.27e+01 bond pdb=" CA THR B 911 " pdb=" C THR B 911 " ideal model delta sigma weight residual 1.523 1.453 0.070 1.23e-02 6.61e+03 3.19e+01 bond pdb=" CA GLU B 668 " pdb=" C GLU B 668 " ideal model delta sigma weight residual 1.528 1.479 0.049 8.80e-03 1.29e+04 3.10e+01 bond pdb=" CA TRP L 74 " pdb=" C TRP L 74 " ideal model delta sigma weight residual 1.524 1.454 0.070 1.27e-02 6.20e+03 3.05e+01 bond pdb=" C HIS L 67 " pdb=" O HIS L 67 " ideal model delta sigma weight residual 1.236 1.169 0.068 1.26e-02 6.30e+03 2.88e+01 ... (remaining 64021 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.88: 86873 4.88 - 9.76: 210 9.76 - 14.64: 17 14.64 - 19.53: 1 19.53 - 24.41: 1 Bond angle restraints: 87102 Sorted by residual: angle pdb=" N GLY B 964 " pdb=" CA GLY B 964 " pdb=" C GLY B 964 " ideal model delta sigma weight residual 112.50 136.91 -24.41 1.16e+00 7.43e-01 4.43e+02 angle pdb=" N GLN c1002 " pdb=" CA GLN c1002 " pdb=" C GLN c1002 " ideal model delta sigma weight residual 111.40 98.77 12.63 1.22e+00 6.72e-01 1.07e+02 angle pdb=" N THR B 911 " pdb=" CA THR B 911 " pdb=" C THR B 911 " ideal model delta sigma weight residual 108.52 92.10 16.42 1.63e+00 3.76e-01 1.02e+02 angle pdb=" N TYR N 683 " pdb=" CA TYR N 683 " pdb=" C TYR N 683 " ideal model delta sigma weight residual 111.07 121.02 -9.95 1.07e+00 8.73e-01 8.65e+01 angle pdb=" C TRP i 276 " pdb=" N PRO i 277 " pdb=" CA PRO i 277 " ideal model delta sigma weight residual 120.38 110.93 9.45 1.03e+00 9.43e-01 8.43e+01 ... (remaining 87097 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.04: 37149 26.04 - 52.08: 988 52.08 - 78.12: 150 78.12 - 104.16: 24 104.16 - 130.20: 1 Dihedral angle restraints: 38312 sinusoidal: 14114 harmonic: 24198 Sorted by residual: dihedral pdb=" CB CYS m 101 " pdb=" SG CYS m 101 " pdb=" SG CYS m 104 " pdb=" CB CYS m 104 " ideal model delta sinusoidal sigma weight residual -86.00 -176.34 90.34 1 1.00e+01 1.00e-02 9.66e+01 dihedral pdb=" C LEU M 144 " pdb=" N LEU M 144 " pdb=" CA LEU M 144 " pdb=" CB LEU M 144 " ideal model delta harmonic sigma weight residual -122.60 -141.85 19.25 0 2.50e+00 1.60e-01 5.93e+01 dihedral pdb=" N LEU M 144 " pdb=" C LEU M 144 " pdb=" CA LEU M 144 " pdb=" CB LEU M 144 " ideal model delta harmonic sigma weight residual 122.80 141.40 -18.60 0 2.50e+00 1.60e-01 5.53e+01 ... (remaining 38309 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.192: 9673 0.192 - 0.384: 77 0.384 - 0.576: 14 0.576 - 0.767: 2 0.767 - 0.959: 1 Chirality restraints: 9767 Sorted by residual: chirality pdb=" CA LEU M 144 " pdb=" N LEU M 144 " pdb=" C LEU M 144 " pdb=" CB LEU M 144 " both_signs ideal model delta sigma weight residual False 2.51 1.55 0.96 2.00e-01 2.50e+01 2.30e+01 chirality pdb=" CA TYR B 133 " pdb=" N TYR B 133 " pdb=" C TYR B 133 " pdb=" CB TYR B 133 " both_signs ideal model delta sigma weight residual False 2.51 1.80 0.71 2.00e-01 2.50e+01 1.26e+01 chirality pdb=" CA LEU m 144 " pdb=" N LEU m 144 " pdb=" C LEU m 144 " pdb=" CB LEU m 144 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.38e+00 ... (remaining 9764 not shown) Planarity restraints: 11346 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR L 72 " -0.022 2.00e-02 2.50e+03 4.45e-02 1.98e+01 pdb=" C TYR L 72 " 0.077 2.00e-02 2.50e+03 pdb=" O TYR L 72 " -0.029 2.00e-02 2.50e+03 pdb=" N HIS L 73 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS L 73 " -0.022 2.00e-02 2.50e+03 4.37e-02 1.91e+01 pdb=" C HIS L 73 " 0.076 2.00e-02 2.50e+03 pdb=" O HIS L 73 " -0.028 2.00e-02 2.50e+03 pdb=" N TRP L 74 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY L 75 " 0.021 2.00e-02 2.50e+03 4.08e-02 1.66e+01 pdb=" C GLY L 75 " -0.070 2.00e-02 2.50e+03 pdb=" O GLY L 75 " 0.026 2.00e-02 2.50e+03 pdb=" N LYS L 76 " 0.023 2.00e-02 2.50e+03 ... (remaining 11343 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 110 2.41 - 3.04: 37143 3.04 - 3.66: 93198 3.66 - 4.28: 139466 4.28 - 4.90: 230784 Nonbonded interactions: 500701 Sorted by model distance: nonbonded pdb=" O3' A S -1 " pdb="MG MG C3001 " model vdw 1.793 2.170 nonbonded pdb=" OD2 ASP G 214 " pdb="FE FE G2001 " model vdw 1.844 2.260 nonbonded pdb=" OD2 ASP L 224 " pdb="FE FE L2001 " model vdw 1.881 2.260 nonbonded pdb=" CA SER J 402 " pdb=" OG SER J 405 " model vdw 1.915 3.470 nonbonded pdb=" NE2 HIS L 125 " pdb="FE FE L2001 " model vdw 1.938 2.340 ... (remaining 500696 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 11 through 67 or (resid 68 through 78 and (name N or name \ CA or name C or name O or name CB )) or resid 79 through 108 or (resid 109 and ( \ name N or name CA or name C or name O or name CB )) or resid 110 or (resid 111 a \ nd (name N or name CA or name C or name O or name CB )) or resid 112 through 192 \ or (resid 193 through 194 and (name N or name CA or name C or name O or name CB \ )) or resid 195 through 233 or (resid 234 through 235 and (name N or name CA or \ name C or name O or name CB )) or resid 236 through 309 or (resid 310 and (name \ N or name CA or name C or name O or name CB )) or resid 311 through 314 or (res \ id 315 and (name N or name CA or name C or name O or name CB )) or resid 316 thr \ ough 317 or (resid 318 and (name N or name CA or name C or name O or name CB )) \ or resid 319 through 326)) selection = (chain 'a' and (resid 11 through 23 or (resid 24 through 25 and (name N or name \ CA or name C or name O or name CB )) or resid 26 through 69 or (resid 70 through \ 78 and (name N or name CA or name C or name O or name CB )) or resid 79 through \ 81 or (resid 82 and (name N or name CA or name C or name O or name CB )) or res \ id 83 through 137 or (resid 138 through 141 and (name N or name CA or name C or \ name O or name CB )) or resid 142 through 158 or (resid 159 through 167 and (nam \ e N or name CA or name C or name O or name CB )) or resid 168 through 190 or (re \ sid 191 and (name N or name CA or name C or name O or name CB )) or (resid 192 t \ hrough 194 and (name N or name CA or name C or name O or name CB )) or resid 195 \ through 234 or (resid 255 and (name N or name CA or name C or name O or name CB \ )) or resid 263 or resid 267 through 304 or (resid 305 through 307 and (name N \ or name CA or name C or name O or name CB )) or resid 308 through 312 or (resid \ 313 and (name N or name CA or name C or name O or name CB )) or resid 314 throug \ h 326)) } ncs_group { reference = (chain 'M' and ((resid 69 through 70 and (name N or name CA or name C or name O \ or name CB )) or resid 71 through 87 or (resid 88 through 89 and (name N or name \ CA or name C or name O or name CB )) or resid 90 through 152 or (resid 153 and \ (name N or name CA or name C or name O or name CB )) or resid 154 or (resid 155 \ and (name N or name CA or name C or name O or name CB )) or resid 156 through 17 \ 7)) selection = (chain 'm' and (resid 69 through 88 or (resid 89 and (name N or name CA or name \ C or name O or name CB )) or resid 90 through 177)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.300 Construct map_model_manager: 0.090 Extract box with map and model: 2.150 Check model and map are aligned: 0.400 Set scattering table: 0.460 Process input model: 132.790 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.290 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: 0.030 Load rotamer database and sin/cos tables:12.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 158.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 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 : 0.005 0.078 64026 Z= 0.313 Angle : 0.717 24.408 87102 Z= 0.474 Chirality : 0.055 0.959 9767 Planarity : 0.005 0.086 11346 Dihedral : 11.746 130.196 22694 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.20 % Favored : 97.79 % Rotamer: Outliers : 5.25 % Allowed : 6.25 % Favored : 88.50 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.08), residues: 8281 helix: 0.24 (0.08), residues: 3458 sheet: -0.44 (0.16), residues: 1007 loop : -1.65 (0.09), residues: 3816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 762 HIS 0.008 0.001 HIS L 77 PHE 0.018 0.001 PHE L 245 TYR 0.021 0.001 TYR B1008 ARG 0.004 0.000 ARG B 443 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16562 Ramachandran restraints generated. 8281 Oldfield, 0 Emsley, 8281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16562 Ramachandran restraints generated. 8281 Oldfield, 0 Emsley, 8281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 882 residues out of total 7331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 306 poor density : 576 time to evaluate : 5.840 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: A 108 ILE cc_start: 0.9138 (OUTLIER) cc_final: 0.8933 (pp) REVERT: A 133 THR cc_start: 0.9166 (OUTLIER) cc_final: 0.8923 (p) REVERT: A 312 PHE cc_start: 0.8974 (t80) cc_final: 0.8469 (t80) REVERT: B 266 MET cc_start: 0.9379 (tpp) cc_final: 0.9159 (tpp) REVERT: B 366 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8265 (mp0) REVERT: B 411 ARG cc_start: 0.9325 (OUTLIER) cc_final: 0.8958 (mtt180) REVERT: B 826 ASN cc_start: 0.8902 (OUTLIER) cc_final: 0.8675 (p0) REVERT: B 911 THR cc_start: 0.8763 (OUTLIER) cc_final: 0.8402 (p) REVERT: B 1045 GLU cc_start: 0.8549 (tm-30) cc_final: 0.8275 (tm-30) REVERT: C 27 ILE cc_start: 0.8295 (OUTLIER) cc_final: 0.8093 (pt) REVERT: D 381 VAL cc_start: 0.9211 (OUTLIER) cc_final: 0.8834 (t) REVERT: E 595 CYS cc_start: 0.8355 (t) cc_final: 0.8045 (p) REVERT: E 597 MET cc_start: 0.3790 (ttm) cc_final: 0.2091 (mmm) REVERT: E 784 TRP cc_start: 0.8201 (p90) cc_final: 0.7471 (p90) REVERT: F 529 MET cc_start: 0.8996 (ttp) cc_final: 0.8480 (ttt) REVERT: G 73 MET cc_start: 0.8754 (mtp) cc_final: 0.8122 (mtt) REVERT: I 224 ILE cc_start: 0.9162 (OUTLIER) cc_final: 0.8805 (mm) REVERT: J 370 ASP cc_start: 0.9084 (OUTLIER) cc_final: 0.8795 (m-30) REVERT: L 70 PHE cc_start: 0.9053 (OUTLIER) cc_final: 0.8617 (m-80) REVERT: L 71 GLU cc_start: 0.9387 (OUTLIER) cc_final: 0.9116 (tm-30) REVERT: L 227 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8346 (mt-10) REVERT: P 52 VAL cc_start: 0.7943 (OUTLIER) cc_final: 0.7409 (p) REVERT: P 131 TYR cc_start: 0.8153 (t80) cc_final: 0.7701 (t80) REVERT: a 266 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7673 (tmmt) REVERT: c 1038 ASP cc_start: 0.6544 (OUTLIER) cc_final: 0.5672 (t0) REVERT: i 549 VAL cc_start: 0.9349 (OUTLIER) cc_final: 0.9133 (m) REVERT: m 101 CYS cc_start: 0.7388 (OUTLIER) cc_final: 0.6985 (p) outliers start: 306 outliers final: 42 residues processed: 834 average time/residue: 1.4657 time to fit residues: 1569.2773 Evaluate side-chains 367 residues out of total 7331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 307 time to evaluate : 5.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 411 ARG Chi-restraints excluded: chain B residue 535 GLU Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain B residue 826 ASN Chi-restraints excluded: chain B residue 911 THR Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 376 GLU Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 614 TRP Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 313 ASP Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 408 TYR Chi-restraints excluded: chain D residue 446 LYS Chi-restraints excluded: chain D residue 758 ASP Chi-restraints excluded: chain D residue 828 HIS Chi-restraints excluded: chain E residue 626 MET Chi-restraints excluded: chain E residue 632 GLN Chi-restraints excluded: chain E residue 650 VAL Chi-restraints excluded: chain E residue 679 LYS Chi-restraints excluded: chain F residue 515 ASP Chi-restraints excluded: chain G residue 90 ASN Chi-restraints excluded: chain I residue 224 ILE Chi-restraints excluded: chain J residue 370 ASP Chi-restraints excluded: chain J residue 404 LEU Chi-restraints excluded: chain J residue 405 SER Chi-restraints excluded: chain J residue 458 THR Chi-restraints excluded: chain L residue 70 PHE Chi-restraints excluded: chain L residue 71 GLU Chi-restraints excluded: chain L residue 72 TYR Chi-restraints excluded: chain L residue 225 VAL Chi-restraints excluded: chain L residue 227 GLU Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain O residue 148 ASP Chi-restraints excluded: chain P residue 52 VAL Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain a residue 227 ILE Chi-restraints excluded: chain a residue 266 LYS Chi-restraints excluded: chain a residue 312 PHE Chi-restraints excluded: chain c residue 312 VAL Chi-restraints excluded: chain c residue 320 ILE Chi-restraints excluded: chain c residue 569 LYS Chi-restraints excluded: chain c residue 1038 ASP Chi-restraints excluded: chain c residue 1153 LEU Chi-restraints excluded: chain c residue 1173 ASN Chi-restraints excluded: chain i residue 454 VAL Chi-restraints excluded: chain i residue 549 VAL Chi-restraints excluded: chain m residue 101 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 826 random chunks: chunk 697 optimal weight: 5.9990 chunk 626 optimal weight: 20.0000 chunk 347 optimal weight: 8.9990 chunk 213 optimal weight: 4.9990 chunk 422 optimal weight: 6.9990 chunk 334 optimal weight: 8.9990 chunk 647 optimal weight: 5.9990 chunk 250 optimal weight: 8.9990 chunk 393 optimal weight: 9.9990 chunk 481 optimal weight: 7.9990 chunk 750 optimal weight: 0.0980 overall best weight: 4.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN A 85 HIS A 196 GLN A 285 ASN B 6 ASN B 128 GLN B 267 ASN B 307 ASN B 334 ASN B 372 HIS B 386 GLN B 446 HIS B 495 GLN B 522 GLN B 549 GLN B 600 ASN B 622 GLN B 636 GLN B 696 HIS B 719 ASN ** B 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 881 HIS B 910 GLN B 934 ASN B 938 GLN B1064 GLN C 110 GLN C 336 GLN C 453 GLN C 460 ASN C 471 GLN C 513 GLN C 523 HIS C 553 ASN C 666 HIS D 109 HIS D 175 GLN D 194 ASN D 227 ASN D 269 ASN D 420 GLN D 778 GLN D 882 GLN E 526 ASN E 792 GLN ** F 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 ASN F 148 GLN F 238 ASN F 278 GLN F 288 HIS F 301 HIS F 317 HIS F 324 HIS F 402 ASN F 417 GLN F 484 GLN ** F 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 HIS G 92 GLN G 238 HIS G 253 GLN H 195 GLN H 247 GLN H 271 GLN H 300 GLN H 332 GLN H 353 GLN H 418 ASN I 139 GLN I 193 GLN I 263 ASN I 317 GLN I 346 GLN I 374 HIS I 440 GLN ** J 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 244 GLN J 254 ASN J 281 GLN J 313 GLN J 319 HIS ** J 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 446 GLN J 496 GLN K 139 HIS ** L 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 78 HIS L 84 ASN L 86 ASN ** L 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 109 GLN ** N 691 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 696 HIS O 99 GLN O 116 HIS O 120 ASN a 41 GLN a 72 HIS a 119 GLN a 134 GLN a 187 HIS a 196 GLN a 263 ASN a 285 ASN c 41 GLN c 73 GLN c 126 ASN c 211 GLN c 449 HIS c 464 ASN c 497 GLN c 924 GLN c 928 HIS ** c1001 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c1007 ASN c1046 ASN c1207 GLN c1212 GLN c1227 GLN c1315 ASN i 287 GLN i 303 HIS i 546 ASN ** i 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 607 GLN i 631 HIS Total number of N/Q/H flips: 117 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.110 64026 Z= 0.449 Angle : 0.642 12.109 87102 Z= 0.339 Chirality : 0.045 0.200 9767 Planarity : 0.005 0.078 11346 Dihedral : 7.344 132.782 9471 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.43 % Allowed : 11.07 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.09), residues: 8281 helix: 1.22 (0.09), residues: 3511 sheet: -0.26 (0.15), residues: 1043 loop : -1.14 (0.09), residues: 3727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP I 486 HIS 0.011 0.002 HIS E 495 PHE 0.025 0.002 PHE J 162 TYR 0.021 0.002 TYR B 891 ARG 0.020 0.001 ARG c 883 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16562 Ramachandran restraints generated. 8281 Oldfield, 0 Emsley, 8281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16562 Ramachandran restraints generated. 8281 Oldfield, 0 Emsley, 8281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 7331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 309 time to evaluate : 5.892 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: A 108 ILE cc_start: 0.9137 (OUTLIER) cc_final: 0.8814 (pp) REVERT: A 133 THR cc_start: 0.9221 (OUTLIER) cc_final: 0.8999 (p) REVERT: A 312 PHE cc_start: 0.8786 (t80) cc_final: 0.8557 (t80) REVERT: B 266 MET cc_start: 0.9409 (tpp) cc_final: 0.9201 (tpp) REVERT: B 411 ARG cc_start: 0.9376 (OUTLIER) cc_final: 0.9089 (mtt-85) REVERT: B 911 THR cc_start: 0.8411 (OUTLIER) cc_final: 0.8070 (p) REVERT: B 926 ARG cc_start: 0.9053 (OUTLIER) cc_final: 0.8635 (mtp180) REVERT: B 1017 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.8417 (mp10) REVERT: B 1045 GLU cc_start: 0.8534 (tm-30) cc_final: 0.8290 (tm-30) REVERT: C 614 TRP cc_start: 0.8462 (OUTLIER) cc_final: 0.8018 (t60) REVERT: D 125 MET cc_start: 0.8830 (tpt) cc_final: 0.8624 (mmm) REVERT: D 789 MET cc_start: 0.9229 (tpp) cc_final: 0.8890 (tmm) REVERT: E 597 MET cc_start: 0.3714 (ttm) cc_final: 0.2808 (tpt) REVERT: E 679 LYS cc_start: 0.5980 (OUTLIER) cc_final: 0.5681 (mmtp) REVERT: E 757 ILE cc_start: 0.7751 (OUTLIER) cc_final: 0.7510 (mt) REVERT: E 784 TRP cc_start: 0.8204 (p90) cc_final: 0.7530 (p90) REVERT: F 614 MET cc_start: 0.6002 (mmp) cc_final: 0.4993 (ppp) REVERT: G 103 THR cc_start: 0.9552 (OUTLIER) cc_final: 0.9276 (p) REVERT: G 137 MET cc_start: 0.7814 (mtm) cc_final: 0.7594 (mtm) REVERT: H 354 THR cc_start: 0.9174 (OUTLIER) cc_final: 0.8968 (p) REVERT: I 224 ILE cc_start: 0.9199 (OUTLIER) cc_final: 0.8792 (mm) REVERT: I 356 LYS cc_start: 0.9019 (OUTLIER) cc_final: 0.8746 (mmtm) REVERT: J 370 ASP cc_start: 0.9188 (OUTLIER) cc_final: 0.8963 (m-30) REVERT: L 70 PHE cc_start: 0.9156 (OUTLIER) cc_final: 0.8676 (m-80) REVERT: L 227 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7870 (mt-10) REVERT: N 634 MET cc_start: 0.8203 (mtt) cc_final: 0.8002 (mtt) REVERT: N 664 MET cc_start: 0.8550 (OUTLIER) cc_final: 0.8070 (tpp) REVERT: N 696 HIS cc_start: 0.8421 (OUTLIER) cc_final: 0.7720 (t-90) REVERT: P 53 GLU cc_start: 0.8017 (tm-30) cc_final: 0.7753 (tm-30) REVERT: a 119 GLN cc_start: 0.8917 (OUTLIER) cc_final: 0.8660 (tp40) REVERT: a 147 ILE cc_start: 0.9154 (OUTLIER) cc_final: 0.8839 (tp) REVERT: a 266 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.7800 (tmmt) REVERT: c 401 PRO cc_start: 0.7210 (Cg_endo) cc_final: 0.6940 (Cg_exo) REVERT: c 1038 ASP cc_start: 0.6221 (OUTLIER) cc_final: 0.5437 (t0) outliers start: 200 outliers final: 59 residues processed: 483 average time/residue: 1.3482 time to fit residues: 858.4391 Evaluate side-chains 365 residues out of total 7331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 284 time to evaluate : 7.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain B residue 38 PHE Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 411 ARG Chi-restraints excluded: chain B residue 535 GLU Chi-restraints excluded: chain B residue 911 THR Chi-restraints excluded: chain B residue 926 ARG Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 1017 GLN Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 614 TRP Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 313 ASP Chi-restraints excluded: chain D residue 314 HIS Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 408 TYR Chi-restraints excluded: chain D residue 446 LYS Chi-restraints excluded: chain D residue 758 ASP Chi-restraints excluded: chain D residue 821 LEU Chi-restraints excluded: chain D residue 828 HIS Chi-restraints excluded: chain E residue 632 GLN Chi-restraints excluded: chain E residue 650 VAL Chi-restraints excluded: chain E residue 679 LYS Chi-restraints excluded: chain E residue 708 VAL Chi-restraints excluded: chain E residue 757 ILE Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 495 GLU Chi-restraints excluded: chain F residue 515 ASP Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain H residue 354 THR Chi-restraints excluded: chain H residue 423 LEU Chi-restraints excluded: chain I residue 224 ILE Chi-restraints excluded: chain I residue 356 LYS Chi-restraints excluded: chain J residue 347 TYR Chi-restraints excluded: chain J residue 370 ASP Chi-restraints excluded: chain J residue 404 LEU Chi-restraints excluded: chain K residue 258 THR Chi-restraints excluded: chain K residue 266 VAL Chi-restraints excluded: chain L residue 70 PHE Chi-restraints excluded: chain L residue 222 THR Chi-restraints excluded: chain L residue 225 VAL Chi-restraints excluded: chain L residue 227 GLU Chi-restraints excluded: chain L residue 250 VAL Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain N residue 664 MET Chi-restraints excluded: chain N residue 696 HIS Chi-restraints excluded: chain N residue 718 VAL Chi-restraints excluded: chain N residue 744 GLU Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain a residue 119 GLN Chi-restraints excluded: chain a residue 147 ILE Chi-restraints excluded: chain a residue 217 GLU Chi-restraints excluded: chain a residue 227 ILE Chi-restraints excluded: chain a residue 232 MET Chi-restraints excluded: chain a residue 266 LYS Chi-restraints excluded: chain a residue 312 PHE Chi-restraints excluded: chain c residue 40 ASP Chi-restraints excluded: chain c residue 94 VAL Chi-restraints excluded: chain c residue 102 GLU Chi-restraints excluded: chain c residue 312 VAL Chi-restraints excluded: chain c residue 398 VAL Chi-restraints excluded: chain c residue 569 LYS Chi-restraints excluded: chain c residue 1038 ASP Chi-restraints excluded: chain c residue 1128 THR Chi-restraints excluded: chain c residue 1153 LEU Chi-restraints excluded: chain c residue 1194 ILE Chi-restraints excluded: chain i residue 454 VAL Chi-restraints excluded: chain i residue 558 THR Chi-restraints excluded: chain i residue 631 HIS Chi-restraints excluded: chain m residue 76 SER Chi-restraints excluded: chain m residue 101 CYS Chi-restraints excluded: chain m residue 127 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 826 random chunks: chunk 416 optimal weight: 3.9990 chunk 232 optimal weight: 5.9990 chunk 624 optimal weight: 20.0000 chunk 510 optimal weight: 6.9990 chunk 206 optimal weight: 3.9990 chunk 751 optimal weight: 0.9990 chunk 811 optimal weight: 0.9990 chunk 669 optimal weight: 0.9990 chunk 745 optimal weight: 9.9990 chunk 256 optimal weight: 7.9990 chunk 602 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 150 GLN B 549 GLN ** B 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 359 ASN F 494 GLN F 518 HIS J 180 ASN J 288 GLN ** J 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 691 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 696 HIS P 132 GLN a 134 GLN a 216 HIS a 221 ASN a 231 HIS a 276 GLN c 77 GLN ** c1001 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c1215 GLN i 361 ASN ** i 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 631 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 64026 Z= 0.195 Angle : 0.519 11.986 87102 Z= 0.272 Chirality : 0.042 0.193 9767 Planarity : 0.004 0.061 11346 Dihedral : 6.793 132.450 9438 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.52 % Allowed : 12.29 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.09), residues: 8281 helix: 1.62 (0.09), residues: 3488 sheet: -0.04 (0.16), residues: 1033 loop : -0.94 (0.10), residues: 3760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 762 HIS 0.008 0.001 HIS i 631 PHE 0.032 0.001 PHE B 207 TYR 0.016 0.001 TYR B 679 ARG 0.008 0.000 ARG N 615 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16562 Ramachandran restraints generated. 8281 Oldfield, 0 Emsley, 8281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16562 Ramachandran restraints generated. 8281 Oldfield, 0 Emsley, 8281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 7331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 303 time to evaluate : 5.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ILE cc_start: 0.9055 (OUTLIER) cc_final: 0.8776 (pp) REVERT: A 133 THR cc_start: 0.9209 (OUTLIER) cc_final: 0.8977 (p) REVERT: A 312 PHE cc_start: 0.8887 (t80) cc_final: 0.8673 (t80) REVERT: B 266 MET cc_start: 0.9381 (tpp) cc_final: 0.9152 (tpp) REVERT: B 366 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8296 (mm-30) REVERT: B 411 ARG cc_start: 0.9371 (OUTLIER) cc_final: 0.9096 (ptm160) REVERT: B 911 THR cc_start: 0.8408 (OUTLIER) cc_final: 0.8085 (p) REVERT: B 1045 GLU cc_start: 0.8412 (tm-30) cc_final: 0.8136 (tm-30) REVERT: C 614 TRP cc_start: 0.8387 (OUTLIER) cc_final: 0.8054 (t60) REVERT: D 125 MET cc_start: 0.8819 (tpt) cc_final: 0.8611 (mmm) REVERT: E 597 MET cc_start: 0.3668 (ttm) cc_final: 0.2682 (tpt) REVERT: E 679 LYS cc_start: 0.5959 (OUTLIER) cc_final: 0.5702 (mptp) REVERT: E 757 ILE cc_start: 0.7740 (OUTLIER) cc_final: 0.7506 (mt) REVERT: E 784 TRP cc_start: 0.8198 (p90) cc_final: 0.7504 (p90) REVERT: F 614 MET cc_start: 0.6177 (mmp) cc_final: 0.5426 (ppp) REVERT: G 103 THR cc_start: 0.9538 (OUTLIER) cc_final: 0.9283 (p) REVERT: H 354 THR cc_start: 0.9090 (OUTLIER) cc_final: 0.8858 (p) REVERT: I 224 ILE cc_start: 0.9197 (OUTLIER) cc_final: 0.8855 (mm) REVERT: I 356 LYS cc_start: 0.9019 (OUTLIER) cc_final: 0.8778 (mmtm) REVERT: J 370 ASP cc_start: 0.9162 (OUTLIER) cc_final: 0.8953 (m-30) REVERT: L 58 MET cc_start: 0.8344 (mtt) cc_final: 0.8051 (mmt) REVERT: L 70 PHE cc_start: 0.9019 (OUTLIER) cc_final: 0.8582 (m-80) REVERT: L 205 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8183 (mtpt) REVERT: L 227 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7721 (mt-10) REVERT: L 252 TRP cc_start: 0.7750 (OUTLIER) cc_final: 0.7529 (m100) REVERT: N 634 MET cc_start: 0.8205 (mtt) cc_final: 0.7998 (mtt) REVERT: N 664 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.7964 (tpp) REVERT: P 53 GLU cc_start: 0.8047 (tm-30) cc_final: 0.7804 (tm-30) REVERT: a 147 ILE cc_start: 0.9159 (OUTLIER) cc_final: 0.8867 (tp) REVERT: a 266 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.7819 (tmmt) REVERT: c 313 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7871 (mt-10) REVERT: c 384 ASP cc_start: 0.8558 (OUTLIER) cc_final: 0.8285 (m-30) REVERT: c 1038 ASP cc_start: 0.6667 (OUTLIER) cc_final: 0.5852 (t0) REVERT: i 557 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8567 (mt) outliers start: 147 outliers final: 50 residues processed: 436 average time/residue: 1.3256 time to fit residues: 766.4841 Evaluate side-chains 355 residues out of total 7331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 281 time to evaluate : 5.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain B residue 38 PHE Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 411 ARG Chi-restraints excluded: chain B residue 535 GLU Chi-restraints excluded: chain B residue 911 THR Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 1049 LEU Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 614 TRP Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 313 ASP Chi-restraints excluded: chain D residue 314 HIS Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 408 TYR Chi-restraints excluded: chain D residue 821 LEU Chi-restraints excluded: chain D residue 828 HIS Chi-restraints excluded: chain E residue 650 VAL Chi-restraints excluded: chain E residue 679 LYS Chi-restraints excluded: chain E residue 708 VAL Chi-restraints excluded: chain E residue 757 ILE Chi-restraints excluded: chain F residue 495 GLU Chi-restraints excluded: chain F residue 515 ASP Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 236 MET Chi-restraints excluded: chain H residue 354 THR Chi-restraints excluded: chain I residue 224 ILE Chi-restraints excluded: chain I residue 356 LYS Chi-restraints excluded: chain J residue 347 TYR Chi-restraints excluded: chain J residue 370 ASP Chi-restraints excluded: chain J residue 453 LEU Chi-restraints excluded: chain K residue 258 THR Chi-restraints excluded: chain K residue 266 VAL Chi-restraints excluded: chain L residue 70 PHE Chi-restraints excluded: chain L residue 72 TYR Chi-restraints excluded: chain L residue 205 LYS Chi-restraints excluded: chain L residue 222 THR Chi-restraints excluded: chain L residue 225 VAL Chi-restraints excluded: chain L residue 227 GLU Chi-restraints excluded: chain L residue 250 VAL Chi-restraints excluded: chain L residue 252 TRP Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain N residue 619 VAL Chi-restraints excluded: chain N residue 664 MET Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain a residue 12 THR Chi-restraints excluded: chain a residue 147 ILE Chi-restraints excluded: chain a residue 227 ILE Chi-restraints excluded: chain a residue 266 LYS Chi-restraints excluded: chain a residue 312 PHE Chi-restraints excluded: chain c residue 94 VAL Chi-restraints excluded: chain c residue 102 GLU Chi-restraints excluded: chain c residue 312 VAL Chi-restraints excluded: chain c residue 313 GLU Chi-restraints excluded: chain c residue 384 ASP Chi-restraints excluded: chain c residue 386 TYR Chi-restraints excluded: chain c residue 398 VAL Chi-restraints excluded: chain c residue 984 THR Chi-restraints excluded: chain c residue 1038 ASP Chi-restraints excluded: chain c residue 1153 LEU Chi-restraints excluded: chain c residue 1194 ILE Chi-restraints excluded: chain c residue 1274 ILE Chi-restraints excluded: chain i residue 341 VAL Chi-restraints excluded: chain i residue 454 VAL Chi-restraints excluded: chain i residue 557 LEU Chi-restraints excluded: chain m residue 116 VAL Chi-restraints excluded: chain m residue 127 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 826 random chunks: chunk 742 optimal weight: 9.9990 chunk 564 optimal weight: 6.9990 chunk 389 optimal weight: 30.0000 chunk 83 optimal weight: 7.9990 chunk 358 optimal weight: 0.0030 chunk 504 optimal weight: 6.9990 chunk 754 optimal weight: 10.0000 chunk 798 optimal weight: 0.3980 chunk 394 optimal weight: 8.9990 chunk 714 optimal weight: 7.9990 chunk 215 optimal weight: 8.9990 overall best weight: 4.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 HIS B 322 GLN B 540 ASN B 621 HIS B 711 HIS ** B 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 209 GLN D 118 ASN D 218 GLN D 359 ASN F 81 ASN F 196 HIS F 402 ASN ** J 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 88 GLN ** L 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 691 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c1001 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c1095 GLN c1196 GLN i 288 HIS i 303 HIS i 539 HIS ** i 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 631 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 64026 Z= 0.416 Angle : 0.600 13.355 87102 Z= 0.313 Chirality : 0.044 0.208 9767 Planarity : 0.004 0.066 11346 Dihedral : 6.823 133.938 9421 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.69 % Allowed : 12.73 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.09), residues: 8281 helix: 1.68 (0.09), residues: 3494 sheet: -0.12 (0.16), residues: 1033 loop : -0.82 (0.10), residues: 3754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 762 HIS 0.008 0.001 HIS E 433 PHE 0.027 0.002 PHE J 162 TYR 0.024 0.002 TYR i 641 ARG 0.007 0.001 ARG D 316 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16562 Ramachandran restraints generated. 8281 Oldfield, 0 Emsley, 8281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16562 Ramachandran restraints generated. 8281 Oldfield, 0 Emsley, 8281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 7331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 290 time to evaluate : 5.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ILE cc_start: 0.9091 (OUTLIER) cc_final: 0.8825 (pp) REVERT: A 312 PHE cc_start: 0.8936 (t80) cc_final: 0.8718 (t80) REVERT: B 266 MET cc_start: 0.9439 (tpp) cc_final: 0.9217 (tpp) REVERT: B 366 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8364 (mm-30) REVERT: B 911 THR cc_start: 0.8400 (OUTLIER) cc_final: 0.8005 (p) REVERT: B 1045 GLU cc_start: 0.8483 (tm-30) cc_final: 0.8232 (tm-30) REVERT: C 614 TRP cc_start: 0.8534 (OUTLIER) cc_final: 0.8061 (t60) REVERT: E 597 MET cc_start: 0.3550 (ttm) cc_final: 0.2485 (tpt) REVERT: E 679 LYS cc_start: 0.6015 (OUTLIER) cc_final: 0.5746 (mptp) REVERT: E 757 ILE cc_start: 0.7751 (OUTLIER) cc_final: 0.7531 (mt) REVERT: E 784 TRP cc_start: 0.8276 (p90) cc_final: 0.7622 (p90) REVERT: F 614 MET cc_start: 0.6441 (mmp) cc_final: 0.5816 (ppp) REVERT: G 69 MET cc_start: 0.8456 (tpp) cc_final: 0.8194 (tpp) REVERT: G 103 THR cc_start: 0.9543 (OUTLIER) cc_final: 0.9330 (p) REVERT: G 137 MET cc_start: 0.8272 (mtm) cc_final: 0.7857 (mtm) REVERT: H 354 THR cc_start: 0.9158 (OUTLIER) cc_final: 0.8930 (p) REVERT: I 224 ILE cc_start: 0.9209 (OUTLIER) cc_final: 0.8962 (mm) REVERT: L 58 MET cc_start: 0.8474 (mtt) cc_final: 0.8142 (mmt) REVERT: L 70 PHE cc_start: 0.9073 (OUTLIER) cc_final: 0.8648 (m-80) REVERT: L 205 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8055 (mtpt) REVERT: L 227 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7777 (mt-10) REVERT: L 252 TRP cc_start: 0.7915 (OUTLIER) cc_final: 0.7597 (m100) REVERT: N 696 HIS cc_start: 0.8479 (OUTLIER) cc_final: 0.7953 (t-90) REVERT: P 53 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7873 (tm-30) REVERT: a 147 ILE cc_start: 0.9194 (OUTLIER) cc_final: 0.8934 (tp) REVERT: a 266 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.7845 (tmmt) REVERT: c 102 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8168 (mp0) REVERT: c 313 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7876 (mt-10) REVERT: c 401 PRO cc_start: 0.7530 (Cg_exo) cc_final: 0.7303 (Cg_endo) REVERT: c 1038 ASP cc_start: 0.6353 (OUTLIER) cc_final: 0.5871 (t0) outliers start: 157 outliers final: 64 residues processed: 428 average time/residue: 1.2593 time to fit residues: 728.1265 Evaluate side-chains 361 residues out of total 7331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 278 time to evaluate : 5.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain B residue 38 PHE Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 535 GLU Chi-restraints excluded: chain B residue 911 THR Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 1049 LEU Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 614 TRP Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 313 ASP Chi-restraints excluded: chain D residue 314 HIS Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 408 TYR Chi-restraints excluded: chain D residue 476 GLN Chi-restraints excluded: chain D residue 758 ASP Chi-restraints excluded: chain D residue 821 LEU Chi-restraints excluded: chain D residue 871 ASP Chi-restraints excluded: chain E residue 679 LYS Chi-restraints excluded: chain E residue 708 VAL Chi-restraints excluded: chain E residue 757 ILE Chi-restraints excluded: chain F residue 280 CYS Chi-restraints excluded: chain F residue 495 GLU Chi-restraints excluded: chain F residue 515 ASP Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain H residue 354 THR Chi-restraints excluded: chain I residue 224 ILE Chi-restraints excluded: chain J residue 300 LEU Chi-restraints excluded: chain J residue 347 TYR Chi-restraints excluded: chain J residue 453 LEU Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 258 THR Chi-restraints excluded: chain K residue 266 VAL Chi-restraints excluded: chain L residue 70 PHE Chi-restraints excluded: chain L residue 72 TYR Chi-restraints excluded: chain L residue 205 LYS Chi-restraints excluded: chain L residue 222 THR Chi-restraints excluded: chain L residue 225 VAL Chi-restraints excluded: chain L residue 227 GLU Chi-restraints excluded: chain L residue 250 VAL Chi-restraints excluded: chain L residue 252 TRP Chi-restraints excluded: chain M residue 64 LYS Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain N residue 696 HIS Chi-restraints excluded: chain N residue 718 VAL Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain a residue 12 THR Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain a residue 147 ILE Chi-restraints excluded: chain a residue 227 ILE Chi-restraints excluded: chain a residue 232 MET Chi-restraints excluded: chain a residue 266 LYS Chi-restraints excluded: chain a residue 312 PHE Chi-restraints excluded: chain c residue 94 VAL Chi-restraints excluded: chain c residue 102 GLU Chi-restraints excluded: chain c residue 312 VAL Chi-restraints excluded: chain c residue 313 GLU Chi-restraints excluded: chain c residue 386 TYR Chi-restraints excluded: chain c residue 984 THR Chi-restraints excluded: chain c residue 1038 ASP Chi-restraints excluded: chain c residue 1128 THR Chi-restraints excluded: chain c residue 1153 LEU Chi-restraints excluded: chain c residue 1194 ILE Chi-restraints excluded: chain c residue 1274 ILE Chi-restraints excluded: chain i residue 454 VAL Chi-restraints excluded: chain i residue 631 HIS Chi-restraints excluded: chain m residue 101 CYS Chi-restraints excluded: chain m residue 116 VAL Chi-restraints excluded: chain m residue 127 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 826 random chunks: chunk 664 optimal weight: 5.9990 chunk 453 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 594 optimal weight: 40.0000 chunk 329 optimal weight: 0.3980 chunk 681 optimal weight: 1.9990 chunk 551 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 407 optimal weight: 0.7980 chunk 716 optimal weight: 10.0000 chunk 201 optimal weight: 2.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 ASN C 135 ASN ** F 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 559 GLN I 200 ASN ** J 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 390 ASN L 77 HIS ** L 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 691 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c1001 ASN i 631 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 64026 Z= 0.194 Angle : 0.516 13.398 87102 Z= 0.268 Chirality : 0.042 0.182 9767 Planarity : 0.004 0.059 11346 Dihedral : 6.589 133.110 9411 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.26 % Allowed : 13.37 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.09), residues: 8281 helix: 1.84 (0.09), residues: 3489 sheet: -0.01 (0.16), residues: 1023 loop : -0.75 (0.10), residues: 3769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 762 HIS 0.017 0.001 HIS i 631 PHE 0.024 0.001 PHE B 207 TYR 0.017 0.001 TYR J 347 ARG 0.008 0.000 ARG L 278 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16562 Ramachandran restraints generated. 8281 Oldfield, 0 Emsley, 8281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16562 Ramachandran restraints generated. 8281 Oldfield, 0 Emsley, 8281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 7331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 291 time to evaluate : 5.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ILE cc_start: 0.9027 (OUTLIER) cc_final: 0.8794 (pp) REVERT: A 133 THR cc_start: 0.9204 (OUTLIER) cc_final: 0.8947 (p) REVERT: A 312 PHE cc_start: 0.8910 (t80) cc_final: 0.8698 (t80) REVERT: B 21 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8244 (mt-10) REVERT: B 266 MET cc_start: 0.9404 (tpp) cc_final: 0.9188 (tpp) REVERT: B 366 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8352 (mm-30) REVERT: B 411 ARG cc_start: 0.9308 (OUTLIER) cc_final: 0.9091 (ptm160) REVERT: B 911 THR cc_start: 0.8454 (OUTLIER) cc_final: 0.8141 (p) REVERT: B 1045 GLU cc_start: 0.8419 (tm-30) cc_final: 0.8159 (tm-30) REVERT: C 614 TRP cc_start: 0.8478 (OUTLIER) cc_final: 0.8096 (t60) REVERT: E 548 MET cc_start: 0.6255 (tmt) cc_final: 0.5643 (ppp) REVERT: E 597 MET cc_start: 0.3631 (ttm) cc_final: 0.2549 (tpt) REVERT: E 619 MET cc_start: 0.6093 (ptm) cc_final: 0.5809 (ptp) REVERT: E 679 LYS cc_start: 0.5939 (OUTLIER) cc_final: 0.5628 (mptp) REVERT: E 757 ILE cc_start: 0.7730 (OUTLIER) cc_final: 0.7525 (mt) REVERT: E 784 TRP cc_start: 0.8276 (p90) cc_final: 0.7636 (p90) REVERT: F 268 MET cc_start: 0.8753 (mtt) cc_final: 0.8517 (mtt) REVERT: F 614 MET cc_start: 0.6326 (mmp) cc_final: 0.5754 (ppp) REVERT: G 103 THR cc_start: 0.9550 (OUTLIER) cc_final: 0.9345 (p) REVERT: G 137 MET cc_start: 0.8267 (mtm) cc_final: 0.7925 (mtm) REVERT: H 354 THR cc_start: 0.9066 (OUTLIER) cc_final: 0.8824 (p) REVERT: I 142 GLN cc_start: 0.9112 (OUTLIER) cc_final: 0.8819 (pt0) REVERT: L 58 MET cc_start: 0.8508 (mtt) cc_final: 0.8196 (mmt) REVERT: L 70 PHE cc_start: 0.9016 (OUTLIER) cc_final: 0.8663 (m-80) REVERT: L 132 MET cc_start: 0.8237 (pmm) cc_final: 0.8024 (pmm) REVERT: L 227 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7649 (mt-10) REVERT: L 252 TRP cc_start: 0.7864 (OUTLIER) cc_final: 0.7628 (m100) REVERT: P 53 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7859 (tm-30) REVERT: P 71 MET cc_start: 0.8937 (OUTLIER) cc_final: 0.8517 (tpp) REVERT: P 122 GLU cc_start: 0.8778 (mp0) cc_final: 0.8500 (mp0) REVERT: a 266 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.7819 (tmmt) REVERT: c 102 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8125 (mp0) REVERT: c 195 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.8121 (ttp80) REVERT: c 313 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7833 (mt-10) REVERT: i 542 THR cc_start: 0.9098 (OUTLIER) cc_final: 0.8878 (p) outliers start: 132 outliers final: 57 residues processed: 413 average time/residue: 1.3322 time to fit residues: 729.1105 Evaluate side-chains 353 residues out of total 7331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 275 time to evaluate : 5.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain B residue 38 PHE Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 411 ARG Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 535 GLU Chi-restraints excluded: chain B residue 911 THR Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain B residue 1049 LEU Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 614 TRP Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 313 ASP Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 408 TYR Chi-restraints excluded: chain D residue 476 GLN Chi-restraints excluded: chain D residue 758 ASP Chi-restraints excluded: chain D residue 821 LEU Chi-restraints excluded: chain E residue 622 LYS Chi-restraints excluded: chain E residue 626 MET Chi-restraints excluded: chain E residue 679 LYS Chi-restraints excluded: chain E residue 708 VAL Chi-restraints excluded: chain E residue 757 ILE Chi-restraints excluded: chain E residue 763 VAL Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 495 GLU Chi-restraints excluded: chain F residue 515 ASP Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain H residue 354 THR Chi-restraints excluded: chain I residue 142 GLN Chi-restraints excluded: chain J residue 300 LEU Chi-restraints excluded: chain J residue 347 TYR Chi-restraints excluded: chain J residue 404 LEU Chi-restraints excluded: chain J residue 453 LEU Chi-restraints excluded: chain K residue 258 THR Chi-restraints excluded: chain K residue 266 VAL Chi-restraints excluded: chain L residue 70 PHE Chi-restraints excluded: chain L residue 72 TYR Chi-restraints excluded: chain L residue 225 VAL Chi-restraints excluded: chain L residue 227 GLU Chi-restraints excluded: chain L residue 250 VAL Chi-restraints excluded: chain L residue 252 TRP Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain N residue 619 VAL Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain P residue 71 MET Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain a residue 12 THR Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain a residue 227 ILE Chi-restraints excluded: chain a residue 232 MET Chi-restraints excluded: chain a residue 266 LYS Chi-restraints excluded: chain a residue 312 PHE Chi-restraints excluded: chain c residue 94 VAL Chi-restraints excluded: chain c residue 102 GLU Chi-restraints excluded: chain c residue 195 ARG Chi-restraints excluded: chain c residue 312 VAL Chi-restraints excluded: chain c residue 313 GLU Chi-restraints excluded: chain c residue 984 THR Chi-restraints excluded: chain c residue 1153 LEU Chi-restraints excluded: chain c residue 1194 ILE Chi-restraints excluded: chain i residue 454 VAL Chi-restraints excluded: chain i residue 542 THR Chi-restraints excluded: chain i residue 558 THR Chi-restraints excluded: chain i residue 581 VAL Chi-restraints excluded: chain m residue 116 VAL Chi-restraints excluded: chain m residue 127 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 826 random chunks: chunk 268 optimal weight: 40.0000 chunk 719 optimal weight: 40.0000 chunk 157 optimal weight: 5.9990 chunk 468 optimal weight: 7.9990 chunk 197 optimal weight: 9.9990 chunk 799 optimal weight: 10.0000 chunk 663 optimal weight: 1.9990 chunk 370 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 264 optimal weight: 50.0000 chunk 419 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 862 ASN ** F 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 399 GLN I 115 ASN ** J 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 691 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c1001 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 546 ASN i 631 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 64026 Z= 0.396 Angle : 0.592 14.486 87102 Z= 0.308 Chirality : 0.044 0.209 9767 Planarity : 0.004 0.059 11346 Dihedral : 6.658 134.074 9407 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.61 % Allowed : 13.66 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.09), residues: 8281 helix: 1.82 (0.09), residues: 3488 sheet: -0.12 (0.16), residues: 1032 loop : -0.73 (0.10), residues: 3761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 762 HIS 0.007 0.001 HIS c 85 PHE 0.027 0.002 PHE J 162 TYR 0.023 0.001 TYR J 347 ARG 0.012 0.001 ARG D 876 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16562 Ramachandran restraints generated. 8281 Oldfield, 0 Emsley, 8281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16562 Ramachandran restraints generated. 8281 Oldfield, 0 Emsley, 8281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 7331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 284 time to evaluate : 6.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ILE cc_start: 0.9034 (OUTLIER) cc_final: 0.8763 (pp) REVERT: A 133 THR cc_start: 0.9221 (OUTLIER) cc_final: 0.8956 (p) REVERT: B 21 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8272 (mt-10) REVERT: B 911 THR cc_start: 0.8489 (OUTLIER) cc_final: 0.8122 (p) REVERT: B 1045 GLU cc_start: 0.8499 (tm-30) cc_final: 0.8274 (tm-30) REVERT: C 331 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.8350 (tt0) REVERT: C 614 TRP cc_start: 0.8580 (OUTLIER) cc_final: 0.8099 (t60) REVERT: D 476 GLN cc_start: 0.9449 (OUTLIER) cc_final: 0.9138 (mm-40) REVERT: E 548 MET cc_start: 0.6359 (tmt) cc_final: 0.5512 (ppp) REVERT: E 597 MET cc_start: 0.3682 (ttm) cc_final: 0.2510 (tpt) REVERT: E 679 LYS cc_start: 0.5960 (OUTLIER) cc_final: 0.5673 (mptp) REVERT: E 784 TRP cc_start: 0.8346 (p90) cc_final: 0.7744 (p90) REVERT: F 268 MET cc_start: 0.8907 (mtt) cc_final: 0.8393 (mtt) REVERT: F 614 MET cc_start: 0.6304 (mmp) cc_final: 0.5772 (ptp) REVERT: G 69 MET cc_start: 0.8363 (tpp) cc_final: 0.8036 (tpp) REVERT: G 137 MET cc_start: 0.8343 (mtm) cc_final: 0.7904 (mtm) REVERT: H 354 THR cc_start: 0.9130 (OUTLIER) cc_final: 0.8877 (p) REVERT: I 142 GLN cc_start: 0.9149 (OUTLIER) cc_final: 0.8860 (pt0) REVERT: J 370 ASP cc_start: 0.9115 (OUTLIER) cc_final: 0.8714 (m-30) REVERT: L 58 MET cc_start: 0.8579 (mtt) cc_final: 0.8256 (mmt) REVERT: L 227 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.7711 (mt-10) REVERT: L 252 TRP cc_start: 0.7878 (OUTLIER) cc_final: 0.7578 (m100) REVERT: N 634 MET cc_start: 0.8252 (mtt) cc_final: 0.7986 (mpt) REVERT: N 696 HIS cc_start: 0.8580 (OUTLIER) cc_final: 0.7808 (t70) REVERT: P 53 GLU cc_start: 0.8236 (tm-30) cc_final: 0.7877 (tm-30) REVERT: P 122 GLU cc_start: 0.8902 (mp0) cc_final: 0.8618 (mp0) REVERT: a 266 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.7847 (tmmt) REVERT: c 195 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.8196 (ttp80) REVERT: c 313 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7857 (mt-10) outliers start: 152 outliers final: 66 residues processed: 417 average time/residue: 1.2899 time to fit residues: 718.1170 Evaluate side-chains 359 residues out of total 7331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 276 time to evaluate : 5.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain B residue 38 PHE Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 535 GLU Chi-restraints excluded: chain B residue 829 ILE Chi-restraints excluded: chain B residue 911 THR Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 1049 LEU Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 331 GLN Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 614 TRP Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 313 ASP Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 408 TYR Chi-restraints excluded: chain D residue 476 GLN Chi-restraints excluded: chain D residue 758 ASP Chi-restraints excluded: chain D residue 821 LEU Chi-restraints excluded: chain D residue 871 ASP Chi-restraints excluded: chain E residue 595 CYS Chi-restraints excluded: chain E residue 619 MET Chi-restraints excluded: chain E residue 622 LYS Chi-restraints excluded: chain E residue 626 MET Chi-restraints excluded: chain E residue 679 LYS Chi-restraints excluded: chain E residue 708 VAL Chi-restraints excluded: chain E residue 763 VAL Chi-restraints excluded: chain F residue 495 GLU Chi-restraints excluded: chain F residue 515 ASP Chi-restraints excluded: chain F residue 566 LEU Chi-restraints excluded: chain H residue 354 THR Chi-restraints excluded: chain I residue 142 GLN Chi-restraints excluded: chain I residue 413 CYS Chi-restraints excluded: chain J residue 300 LEU Chi-restraints excluded: chain J residue 347 TYR Chi-restraints excluded: chain J residue 370 ASP Chi-restraints excluded: chain J residue 453 LEU Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 258 THR Chi-restraints excluded: chain K residue 266 VAL Chi-restraints excluded: chain L residue 72 TYR Chi-restraints excluded: chain L residue 225 VAL Chi-restraints excluded: chain L residue 227 GLU Chi-restraints excluded: chain L residue 250 VAL Chi-restraints excluded: chain L residue 252 TRP Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain N residue 696 HIS Chi-restraints excluded: chain O residue 150 LEU Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain a residue 12 THR Chi-restraints excluded: chain a residue 227 ILE Chi-restraints excluded: chain a residue 232 MET Chi-restraints excluded: chain a residue 266 LYS Chi-restraints excluded: chain a residue 312 PHE Chi-restraints excluded: chain c residue 94 VAL Chi-restraints excluded: chain c residue 102 GLU Chi-restraints excluded: chain c residue 195 ARG Chi-restraints excluded: chain c residue 255 MET Chi-restraints excluded: chain c residue 312 VAL Chi-restraints excluded: chain c residue 313 GLU Chi-restraints excluded: chain c residue 984 THR Chi-restraints excluded: chain c residue 1153 LEU Chi-restraints excluded: chain c residue 1194 ILE Chi-restraints excluded: chain i residue 454 VAL Chi-restraints excluded: chain i residue 558 THR Chi-restraints excluded: chain i residue 631 HIS Chi-restraints excluded: chain m residue 101 CYS Chi-restraints excluded: chain m residue 116 VAL Chi-restraints excluded: chain m residue 127 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 826 random chunks: chunk 770 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 455 optimal weight: 0.8980 chunk 583 optimal weight: 50.0000 chunk 452 optimal weight: 0.1980 chunk 672 optimal weight: 1.9990 chunk 446 optimal weight: 0.5980 chunk 796 optimal weight: 6.9990 chunk 498 optimal weight: 1.9990 chunk 485 optimal weight: 5.9990 chunk 367 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 ASN B 666 ASN ** F 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 691 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c1001 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 546 ASN i 631 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 64026 Z= 0.166 Angle : 0.522 14.391 87102 Z= 0.267 Chirality : 0.041 0.181 9767 Planarity : 0.004 0.055 11346 Dihedral : 6.407 132.835 9402 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.72 % Allowed : 14.62 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.09), residues: 8281 helix: 1.94 (0.09), residues: 3489 sheet: 0.05 (0.16), residues: 995 loop : -0.66 (0.10), residues: 3797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 251 HIS 0.019 0.001 HIS i 631 PHE 0.024 0.001 PHE B 207 TYR 0.017 0.001 TYR J 347 ARG 0.013 0.000 ARG G 190 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16562 Ramachandran restraints generated. 8281 Oldfield, 0 Emsley, 8281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16562 Ramachandran restraints generated. 8281 Oldfield, 0 Emsley, 8281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 7331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 283 time to evaluate : 6.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ILE cc_start: 0.8992 (OUTLIER) cc_final: 0.8764 (pp) REVERT: A 133 THR cc_start: 0.9180 (OUTLIER) cc_final: 0.8914 (p) REVERT: B 266 MET cc_start: 0.9401 (tpp) cc_final: 0.9154 (mmp) REVERT: B 911 THR cc_start: 0.8457 (OUTLIER) cc_final: 0.8173 (p) REVERT: B 1045 GLU cc_start: 0.8432 (tm-30) cc_final: 0.8202 (tm-30) REVERT: C 382 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.8547 (ptp-110) REVERT: C 614 TRP cc_start: 0.8429 (OUTLIER) cc_final: 0.8104 (t60) REVERT: E 597 MET cc_start: 0.3822 (ttm) cc_final: 0.2608 (tpt) REVERT: E 619 MET cc_start: 0.6191 (OUTLIER) cc_final: 0.5939 (ptp) REVERT: E 679 LYS cc_start: 0.5840 (OUTLIER) cc_final: 0.5530 (mptp) REVERT: E 784 TRP cc_start: 0.8333 (p90) cc_final: 0.7695 (p90) REVERT: F 268 MET cc_start: 0.9026 (mtt) cc_final: 0.8490 (mtt) REVERT: F 511 MET cc_start: 0.6952 (mmm) cc_final: 0.6456 (mmt) REVERT: F 614 MET cc_start: 0.6242 (mmp) cc_final: 0.5744 (ptp) REVERT: G 69 MET cc_start: 0.8426 (tpp) cc_final: 0.8189 (tpp) REVERT: H 354 THR cc_start: 0.9028 (OUTLIER) cc_final: 0.8781 (p) REVERT: I 142 GLN cc_start: 0.9088 (OUTLIER) cc_final: 0.8788 (pt0) REVERT: L 58 MET cc_start: 0.8522 (mtt) cc_final: 0.8193 (mmt) REVERT: L 252 TRP cc_start: 0.7848 (OUTLIER) cc_final: 0.7601 (m100) REVERT: N 634 MET cc_start: 0.8166 (mtt) cc_final: 0.7943 (mpt) REVERT: N 696 HIS cc_start: 0.8597 (OUTLIER) cc_final: 0.7783 (t70) REVERT: P 53 GLU cc_start: 0.8225 (tm-30) cc_final: 0.7851 (tm-30) REVERT: P 122 GLU cc_start: 0.8906 (mp0) cc_final: 0.8659 (mp0) REVERT: a 266 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.7820 (tmmt) REVERT: c 102 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.8109 (mp0) REVERT: c 195 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.8155 (ttp80) REVERT: c 313 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7827 (mt-10) REVERT: c 1153 LEU cc_start: 0.9655 (OUTLIER) cc_final: 0.9383 (mm) REVERT: m 132 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7932 (mt-10) outliers start: 100 outliers final: 51 residues processed: 375 average time/residue: 1.3357 time to fit residues: 663.6949 Evaluate side-chains 342 residues out of total 7331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 274 time to evaluate : 5.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain B residue 38 PHE Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 911 THR Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain B residue 1049 LEU Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 382 ARG Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 614 TRP Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain D residue 313 ASP Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 408 TYR Chi-restraints excluded: chain D residue 476 GLN Chi-restraints excluded: chain D residue 867 ILE Chi-restraints excluded: chain E residue 595 CYS Chi-restraints excluded: chain E residue 619 MET Chi-restraints excluded: chain E residue 622 LYS Chi-restraints excluded: chain E residue 644 TRP Chi-restraints excluded: chain E residue 679 LYS Chi-restraints excluded: chain E residue 708 VAL Chi-restraints excluded: chain F residue 566 LEU Chi-restraints excluded: chain H residue 354 THR Chi-restraints excluded: chain I residue 142 GLN Chi-restraints excluded: chain I residue 272 MET Chi-restraints excluded: chain J residue 300 LEU Chi-restraints excluded: chain J residue 347 TYR Chi-restraints excluded: chain J residue 453 LEU Chi-restraints excluded: chain K residue 266 VAL Chi-restraints excluded: chain L residue 72 TYR Chi-restraints excluded: chain L residue 225 VAL Chi-restraints excluded: chain L residue 250 VAL Chi-restraints excluded: chain L residue 252 TRP Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain N residue 696 HIS Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain a residue 12 THR Chi-restraints excluded: chain a residue 227 ILE Chi-restraints excluded: chain a residue 266 LYS Chi-restraints excluded: chain a residue 312 PHE Chi-restraints excluded: chain c residue 94 VAL Chi-restraints excluded: chain c residue 102 GLU Chi-restraints excluded: chain c residue 195 ARG Chi-restraints excluded: chain c residue 312 VAL Chi-restraints excluded: chain c residue 313 GLU Chi-restraints excluded: chain c residue 984 THR Chi-restraints excluded: chain c residue 1153 LEU Chi-restraints excluded: chain c residue 1194 ILE Chi-restraints excluded: chain i residue 454 VAL Chi-restraints excluded: chain i residue 581 VAL Chi-restraints excluded: chain m residue 101 CYS Chi-restraints excluded: chain m residue 116 VAL Chi-restraints excluded: chain m residue 127 VAL Chi-restraints excluded: chain m residue 131 ASP Chi-restraints excluded: chain m residue 132 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 826 random chunks: chunk 492 optimal weight: 0.8980 chunk 317 optimal weight: 50.0000 chunk 475 optimal weight: 3.9990 chunk 239 optimal weight: 10.0000 chunk 156 optimal weight: 6.9990 chunk 154 optimal weight: 1.9990 chunk 506 optimal weight: 9.9990 chunk 542 optimal weight: 8.9990 chunk 393 optimal weight: 10.0000 chunk 74 optimal weight: 0.8980 chunk 625 optimal weight: 10.0000 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 HIS B 666 ASN F 318 HIS ** F 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 226 ASN I 115 ASN ** J 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 691 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c1001 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 546 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.3839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 64026 Z= 0.293 Angle : 0.559 15.409 87102 Z= 0.285 Chirality : 0.042 0.201 9767 Planarity : 0.004 0.055 11346 Dihedral : 6.332 133.439 9393 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.78 % Allowed : 14.74 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.09), residues: 8281 helix: 1.96 (0.09), residues: 3484 sheet: -0.00 (0.16), residues: 1012 loop : -0.63 (0.10), residues: 3785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 762 HIS 0.007 0.001 HIS c 85 PHE 0.021 0.001 PHE B 207 TYR 0.025 0.001 TYR N 683 ARG 0.014 0.000 ARG N 614 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16562 Ramachandran restraints generated. 8281 Oldfield, 0 Emsley, 8281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16562 Ramachandran restraints generated. 8281 Oldfield, 0 Emsley, 8281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 7331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 278 time to evaluate : 5.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ILE cc_start: 0.9021 (OUTLIER) cc_final: 0.8769 (pp) REVERT: A 133 THR cc_start: 0.9204 (OUTLIER) cc_final: 0.8935 (p) REVERT: B 640 ASP cc_start: 0.7865 (OUTLIER) cc_final: 0.7617 (m-30) REVERT: B 911 THR cc_start: 0.8483 (OUTLIER) cc_final: 0.8136 (p) REVERT: B 1045 GLU cc_start: 0.8448 (tm-30) cc_final: 0.8236 (tm-30) REVERT: C 382 ARG cc_start: 0.8827 (OUTLIER) cc_final: 0.8600 (ptp-110) REVERT: C 614 TRP cc_start: 0.8479 (OUTLIER) cc_final: 0.8070 (t60) REVERT: D 476 GLN cc_start: 0.9426 (OUTLIER) cc_final: 0.9109 (mm-40) REVERT: E 548 MET cc_start: 0.6520 (tmt) cc_final: 0.5677 (ppp) REVERT: E 597 MET cc_start: 0.3810 (ttm) cc_final: 0.2649 (tpt) REVERT: E 679 LYS cc_start: 0.5857 (OUTLIER) cc_final: 0.5566 (mptp) REVERT: E 784 TRP cc_start: 0.8358 (p90) cc_final: 0.7740 (p90) REVERT: F 268 MET cc_start: 0.9036 (mtt) cc_final: 0.8488 (mtt) REVERT: F 614 MET cc_start: 0.6218 (mmp) cc_final: 0.5738 (ptp) REVERT: G 69 MET cc_start: 0.8490 (tpp) cc_final: 0.8093 (tpp) REVERT: H 354 THR cc_start: 0.9081 (OUTLIER) cc_final: 0.8846 (p) REVERT: I 142 GLN cc_start: 0.9133 (OUTLIER) cc_final: 0.8833 (pt0) REVERT: J 362 PHE cc_start: 0.6806 (OUTLIER) cc_final: 0.5562 (t80) REVERT: L 227 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.7856 (mt-10) REVERT: L 252 TRP cc_start: 0.7894 (OUTLIER) cc_final: 0.7642 (m100) REVERT: N 696 HIS cc_start: 0.8549 (OUTLIER) cc_final: 0.7775 (t70) REVERT: P 53 GLU cc_start: 0.8254 (tm-30) cc_final: 0.7884 (tm-30) REVERT: P 122 GLU cc_start: 0.8923 (mp0) cc_final: 0.8670 (mp0) REVERT: a 266 LYS cc_start: 0.8399 (OUTLIER) cc_final: 0.7820 (tmmt) REVERT: c 102 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8148 (mp0) REVERT: c 195 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.8159 (ttp80) REVERT: c 313 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7826 (mt-10) REVERT: c 384 ASP cc_start: 0.8753 (OUTLIER) cc_final: 0.8539 (m-30) REVERT: c 1153 LEU cc_start: 0.9667 (OUTLIER) cc_final: 0.9401 (mm) outliers start: 104 outliers final: 60 residues processed: 374 average time/residue: 1.3137 time to fit residues: 655.2270 Evaluate side-chains 352 residues out of total 7331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 272 time to evaluate : 5.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain B residue 38 PHE Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain B residue 911 THR Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain B residue 1049 LEU Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 382 ARG Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 614 TRP Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 621 ILE Chi-restraints excluded: chain D residue 313 ASP Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 408 TYR Chi-restraints excluded: chain D residue 476 GLN Chi-restraints excluded: chain D residue 821 LEU Chi-restraints excluded: chain D residue 867 ILE Chi-restraints excluded: chain E residue 595 CYS Chi-restraints excluded: chain E residue 622 LYS Chi-restraints excluded: chain E residue 644 TRP Chi-restraints excluded: chain E residue 679 LYS Chi-restraints excluded: chain E residue 708 VAL Chi-restraints excluded: chain F residue 566 LEU Chi-restraints excluded: chain H residue 354 THR Chi-restraints excluded: chain I residue 142 GLN Chi-restraints excluded: chain I residue 272 MET Chi-restraints excluded: chain J residue 300 LEU Chi-restraints excluded: chain J residue 347 TYR Chi-restraints excluded: chain J residue 362 PHE Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 266 VAL Chi-restraints excluded: chain L residue 72 TYR Chi-restraints excluded: chain L residue 225 VAL Chi-restraints excluded: chain L residue 227 GLU Chi-restraints excluded: chain L residue 250 VAL Chi-restraints excluded: chain L residue 252 TRP Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain N residue 696 HIS Chi-restraints excluded: chain N residue 718 VAL Chi-restraints excluded: chain O residue 148 ASP Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain a residue 12 THR Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain a residue 110 VAL Chi-restraints excluded: chain a residue 227 ILE Chi-restraints excluded: chain a residue 266 LYS Chi-restraints excluded: chain a residue 312 PHE Chi-restraints excluded: chain c residue 94 VAL Chi-restraints excluded: chain c residue 102 GLU Chi-restraints excluded: chain c residue 195 ARG Chi-restraints excluded: chain c residue 255 MET Chi-restraints excluded: chain c residue 312 VAL Chi-restraints excluded: chain c residue 313 GLU Chi-restraints excluded: chain c residue 384 ASP Chi-restraints excluded: chain c residue 984 THR Chi-restraints excluded: chain c residue 1153 LEU Chi-restraints excluded: chain c residue 1194 ILE Chi-restraints excluded: chain i residue 454 VAL Chi-restraints excluded: chain i residue 558 THR Chi-restraints excluded: chain i residue 581 VAL Chi-restraints excluded: chain m residue 101 CYS Chi-restraints excluded: chain m residue 116 VAL Chi-restraints excluded: chain m residue 127 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 826 random chunks: chunk 724 optimal weight: 50.0000 chunk 762 optimal weight: 9.9990 chunk 695 optimal weight: 0.8980 chunk 741 optimal weight: 0.0050 chunk 446 optimal weight: 0.6980 chunk 323 optimal weight: 0.3980 chunk 582 optimal weight: 50.0000 chunk 227 optimal weight: 0.5980 chunk 670 optimal weight: 2.9990 chunk 701 optimal weight: 0.9990 chunk 739 optimal weight: 40.0000 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 666 ASN F 403 HIS ** J 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 691 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 363 ASN i 546 ASN i 631 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 64026 Z= 0.143 Angle : 0.526 15.765 87102 Z= 0.266 Chirality : 0.041 0.168 9767 Planarity : 0.004 0.054 11346 Dihedral : 6.185 132.576 9393 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.58 % Allowed : 15.00 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.09), residues: 8281 helix: 2.01 (0.09), residues: 3490 sheet: 0.11 (0.16), residues: 1006 loop : -0.62 (0.10), residues: 3785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 251 HIS 0.006 0.001 HIS c 85 PHE 0.024 0.001 PHE B 207 TYR 0.016 0.001 TYR B1008 ARG 0.013 0.000 ARG N 614 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16562 Ramachandran restraints generated. 8281 Oldfield, 0 Emsley, 8281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16562 Ramachandran restraints generated. 8281 Oldfield, 0 Emsley, 8281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 7331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 287 time to evaluate : 5.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ILE cc_start: 0.8940 (OUTLIER) cc_final: 0.8723 (pp) REVERT: A 133 THR cc_start: 0.9156 (OUTLIER) cc_final: 0.8885 (p) REVERT: B 911 THR cc_start: 0.8462 (OUTLIER) cc_final: 0.8220 (p) REVERT: B 1045 GLU cc_start: 0.8416 (tm-30) cc_final: 0.8179 (tm-30) REVERT: C 382 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.8566 (ptp-110) REVERT: C 614 TRP cc_start: 0.8368 (OUTLIER) cc_final: 0.8069 (t60) REVERT: D 816 MET cc_start: 0.8358 (ppp) cc_final: 0.8025 (pmm) REVERT: E 548 MET cc_start: 0.6616 (tmt) cc_final: 0.5776 (ppp) REVERT: E 597 MET cc_start: 0.3746 (ttm) cc_final: 0.2656 (tpt) REVERT: E 679 LYS cc_start: 0.5746 (OUTLIER) cc_final: 0.5477 (mptp) REVERT: E 784 TRP cc_start: 0.8354 (p90) cc_final: 0.7766 (p90) REVERT: F 268 MET cc_start: 0.9065 (mtt) cc_final: 0.8613 (mtt) REVERT: F 614 MET cc_start: 0.6206 (mmp) cc_final: 0.5765 (ptp) REVERT: G 69 MET cc_start: 0.8417 (tpp) cc_final: 0.8053 (tpp) REVERT: H 354 THR cc_start: 0.9005 (OUTLIER) cc_final: 0.8783 (p) REVERT: J 362 PHE cc_start: 0.6801 (OUTLIER) cc_final: 0.5563 (t80) REVERT: L 227 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.7854 (mt-10) REVERT: L 250 VAL cc_start: 0.9343 (OUTLIER) cc_final: 0.9084 (m) REVERT: N 634 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.7934 (mpt) REVERT: N 696 HIS cc_start: 0.8546 (OUTLIER) cc_final: 0.7827 (t-90) REVERT: P 53 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7859 (tm-30) REVERT: P 122 GLU cc_start: 0.8873 (mp0) cc_final: 0.8641 (mp0) REVERT: a 266 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.7776 (tmmt) REVERT: c 102 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8117 (mp0) REVERT: c 195 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.8149 (ttp80) REVERT: c 313 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7819 (mt-10) REVERT: c 1153 LEU cc_start: 0.9607 (OUTLIER) cc_final: 0.9403 (mm) REVERT: i 272 PHE cc_start: 0.8006 (OUTLIER) cc_final: 0.7596 (t80) REVERT: m 132 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.8011 (mt-10) outliers start: 92 outliers final: 50 residues processed: 369 average time/residue: 1.3584 time to fit residues: 667.1291 Evaluate side-chains 342 residues out of total 7331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 273 time to evaluate : 5.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain B residue 38 PHE Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 911 THR Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain B residue 1049 LEU Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 382 ARG Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 614 TRP Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain D residue 313 ASP Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 408 TYR Chi-restraints excluded: chain D residue 476 GLN Chi-restraints excluded: chain D residue 867 ILE Chi-restraints excluded: chain E residue 442 HIS Chi-restraints excluded: chain E residue 595 CYS Chi-restraints excluded: chain E residue 622 LYS Chi-restraints excluded: chain E residue 644 TRP Chi-restraints excluded: chain E residue 679 LYS Chi-restraints excluded: chain E residue 708 VAL Chi-restraints excluded: chain H residue 354 THR Chi-restraints excluded: chain I residue 272 MET Chi-restraints excluded: chain J residue 300 LEU Chi-restraints excluded: chain J residue 347 TYR Chi-restraints excluded: chain J residue 362 PHE Chi-restraints excluded: chain K residue 266 VAL Chi-restraints excluded: chain L residue 72 TYR Chi-restraints excluded: chain L residue 225 VAL Chi-restraints excluded: chain L residue 227 GLU Chi-restraints excluded: chain L residue 250 VAL Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain N residue 634 MET Chi-restraints excluded: chain N residue 683 TYR Chi-restraints excluded: chain N residue 696 HIS Chi-restraints excluded: chain N residue 718 VAL Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain a residue 12 THR Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain a residue 110 VAL Chi-restraints excluded: chain a residue 227 ILE Chi-restraints excluded: chain a residue 266 LYS Chi-restraints excluded: chain a residue 312 PHE Chi-restraints excluded: chain c residue 102 GLU Chi-restraints excluded: chain c residue 195 ARG Chi-restraints excluded: chain c residue 312 VAL Chi-restraints excluded: chain c residue 313 GLU Chi-restraints excluded: chain c residue 984 THR Chi-restraints excluded: chain c residue 1153 LEU Chi-restraints excluded: chain c residue 1194 ILE Chi-restraints excluded: chain i residue 272 PHE Chi-restraints excluded: chain i residue 454 VAL Chi-restraints excluded: chain i residue 581 VAL Chi-restraints excluded: chain i residue 631 HIS Chi-restraints excluded: chain m residue 101 CYS Chi-restraints excluded: chain m residue 116 VAL Chi-restraints excluded: chain m residue 127 VAL Chi-restraints excluded: chain m residue 132 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 826 random chunks: chunk 487 optimal weight: 5.9990 chunk 784 optimal weight: 20.0000 chunk 478 optimal weight: 9.9990 chunk 372 optimal weight: 9.9990 chunk 545 optimal weight: 10.0000 chunk 822 optimal weight: 6.9990 chunk 757 optimal weight: 10.0000 chunk 655 optimal weight: 10.0000 chunk 68 optimal weight: 7.9990 chunk 506 optimal weight: 9.9990 chunk 401 optimal weight: 8.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 666 ASN B 913 ASN ** C 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 189 HIS D 476 GLN E 667 ASN I 115 ASN ** J 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 691 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 145 GLN ** c1001 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c1002 GLN c1227 GLN i 546 ASN ** i 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.4323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.160 64026 Z= 0.730 Angle : 0.781 16.610 87102 Z= 0.403 Chirality : 0.049 0.299 9767 Planarity : 0.005 0.084 11346 Dihedral : 6.704 135.052 9393 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.19 % Favored : 95.80 % Rotamer: Outliers : 1.65 % Allowed : 15.05 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.09), residues: 8281 helix: 1.60 (0.09), residues: 3514 sheet: -0.15 (0.16), residues: 1031 loop : -0.75 (0.10), residues: 3736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP L 252 HIS 0.020 0.002 HIS i 631 PHE 0.039 0.002 PHE J 162 TYR 0.089 0.002 TYR N 683 ARG 0.017 0.001 ARG D 876 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16562 Ramachandran restraints generated. 8281 Oldfield, 0 Emsley, 8281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16562 Ramachandran restraints generated. 8281 Oldfield, 0 Emsley, 8281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 7331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 275 time to evaluate : 5.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ILE cc_start: 0.9047 (OUTLIER) cc_final: 0.8729 (pp) REVERT: B 911 THR cc_start: 0.8559 (OUTLIER) cc_final: 0.8127 (p) REVERT: C 382 ARG cc_start: 0.8897 (OUTLIER) cc_final: 0.8237 (ptp-110) REVERT: C 614 TRP cc_start: 0.8690 (OUTLIER) cc_final: 0.7979 (t60) REVERT: E 548 MET cc_start: 0.6537 (tmt) cc_final: 0.5665 (ppp) REVERT: E 679 LYS cc_start: 0.5941 (OUTLIER) cc_final: 0.5649 (mptp) REVERT: F 268 MET cc_start: 0.9078 (mtt) cc_final: 0.8663 (mtt) REVERT: F 614 MET cc_start: 0.6350 (mmp) cc_final: 0.5959 (ptp) REVERT: G 69 MET cc_start: 0.8420 (tpp) cc_final: 0.8130 (tpp) REVERT: H 354 THR cc_start: 0.9168 (OUTLIER) cc_final: 0.8950 (p) REVERT: J 370 ASP cc_start: 0.9153 (OUTLIER) cc_final: 0.8800 (m-30) REVERT: N 614 ARG cc_start: 0.8099 (mmp80) cc_final: 0.7871 (mmp80) REVERT: N 634 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.8067 (mpt) REVERT: N 696 HIS cc_start: 0.8520 (OUTLIER) cc_final: 0.7881 (t-90) REVERT: P 53 GLU cc_start: 0.8307 (tm-30) cc_final: 0.7949 (tm-30) REVERT: P 122 GLU cc_start: 0.8933 (mp0) cc_final: 0.8711 (mp0) REVERT: a 266 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.7821 (tmmt) REVERT: c 102 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8188 (mp0) REVERT: c 195 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.8266 (ttp80) REVERT: c 313 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7678 (mt-10) REVERT: c 951 MET cc_start: 0.8074 (mmp) cc_final: 0.7832 (mmm) REVERT: i 272 PHE cc_start: 0.8066 (OUTLIER) cc_final: 0.7534 (t80) outliers start: 96 outliers final: 48 residues processed: 362 average time/residue: 1.3256 time to fit residues: 640.9688 Evaluate side-chains 333 residues out of total 7331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 271 time to evaluate : 5.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain B residue 38 PHE Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 911 THR Chi-restraints excluded: chain B residue 921 TYR Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 1049 LEU Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 382 ARG Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 614 TRP Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain D residue 313 ASP Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 408 TYR Chi-restraints excluded: chain D residue 821 LEU Chi-restraints excluded: chain E residue 595 CYS Chi-restraints excluded: chain E residue 622 LYS Chi-restraints excluded: chain E residue 644 TRP Chi-restraints excluded: chain E residue 679 LYS Chi-restraints excluded: chain E residue 708 VAL Chi-restraints excluded: chain H residue 354 THR Chi-restraints excluded: chain J residue 300 LEU Chi-restraints excluded: chain J residue 347 TYR Chi-restraints excluded: chain J residue 370 ASP Chi-restraints excluded: chain K residue 148 PHE Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 266 VAL Chi-restraints excluded: chain L residue 72 TYR Chi-restraints excluded: chain L residue 225 VAL Chi-restraints excluded: chain L residue 250 VAL Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain N residue 634 MET Chi-restraints excluded: chain N residue 696 HIS Chi-restraints excluded: chain N residue 718 VAL Chi-restraints excluded: chain O residue 148 ASP Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain a residue 12 THR Chi-restraints excluded: chain a residue 110 VAL Chi-restraints excluded: chain a residue 227 ILE Chi-restraints excluded: chain a residue 266 LYS Chi-restraints excluded: chain a residue 312 PHE Chi-restraints excluded: chain c residue 94 VAL Chi-restraints excluded: chain c residue 102 GLU Chi-restraints excluded: chain c residue 195 ARG Chi-restraints excluded: chain c residue 312 VAL Chi-restraints excluded: chain c residue 313 GLU Chi-restraints excluded: chain c residue 984 THR Chi-restraints excluded: chain c residue 1153 LEU Chi-restraints excluded: chain c residue 1194 ILE Chi-restraints excluded: chain i residue 272 PHE Chi-restraints excluded: chain i residue 454 VAL Chi-restraints excluded: chain i residue 558 THR Chi-restraints excluded: chain m residue 101 CYS Chi-restraints excluded: chain m residue 116 VAL Chi-restraints excluded: chain m residue 127 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 826 random chunks: chunk 520 optimal weight: 5.9990 chunk 698 optimal weight: 5.9990 chunk 200 optimal weight: 0.9990 chunk 604 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 182 optimal weight: 1.9990 chunk 656 optimal weight: 1.9990 chunk 274 optimal weight: 30.0000 chunk 673 optimal weight: 0.8980 chunk 83 optimal weight: 5.9990 chunk 120 optimal weight: 0.7980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 666 ASN ** C 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 173 HIS ** J 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 691 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c1001 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 546 ASN ** i 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.081193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.059019 restraints weight = 325630.335| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 3.83 r_work: 0.2818 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.4336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.203 64026 Z= 0.570 Angle : 0.827 61.598 87102 Z= 0.421 Chirality : 0.049 1.750 9767 Planarity : 0.005 0.084 11346 Dihedral : 6.710 135.098 9393 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.24 % Favored : 95.75 % Rotamer: Outliers : 1.53 % Allowed : 15.22 % Favored : 83.25 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.09), residues: 8281 helix: 1.58 (0.09), residues: 3514 sheet: -0.18 (0.16), residues: 1014 loop : -0.75 (0.10), residues: 3753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP L 252 HIS 0.018 0.002 HIS i 631 PHE 0.037 0.002 PHE J 162 TYR 0.053 0.002 TYR N 683 ARG 0.016 0.001 ARG D 876 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16073.63 seconds wall clock time: 280 minutes 55.28 seconds (16855.28 seconds total)