Starting phenix.real_space_refine on Fri Dec 27 21:29:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t1i_40968/12_2024/8t1i_40968.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t1i_40968/12_2024/8t1i_40968.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t1i_40968/12_2024/8t1i_40968.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t1i_40968/12_2024/8t1i_40968.map" model { file = "/net/cci-nas-00/data/ceres_data/8t1i_40968/12_2024/8t1i_40968.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t1i_40968/12_2024/8t1i_40968.cif" } resolution = 4.68 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 156 5.16 5 C 31272 2.51 5 N 9130 2.21 5 O 9010 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 49568 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 2314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 2314 Classifications: {'peptide': 467} Incomplete info: {'truncation_to_alanine': 421} Link IDs: {'PTRANS': 32, 'TRANS': 434} Chain breaks: 5 Unresolved chain link angles: 32 Unresolved non-hydrogen bonds: 1447 Unresolved non-hydrogen angles: 1844 Unresolved non-hydrogen dihedrals: 1216 Unresolved non-hydrogen chiralities: 137 Planarities with less than four sites: {'GLN:plan1': 22, 'ASP:plan': 21, 'TYR:plan': 15, 'ASN:plan1': 19, 'TRP:plan': 3, 'HIS:plan': 16, 'PHE:plan': 18, 'GLU:plan': 22, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 696 Chain: "B" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 784 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 138} Link IDs: {'PTRANS': 5, 'TRANS': 152} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 495 Unresolved non-hydrogen angles: 620 Unresolved non-hydrogen dihedrals: 401 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 7, 'TYR:plan': 3, 'ASN:plan1': 5, 'TRP:plan': 1, 'HIS:plan': 4, 'PHE:plan': 1, 'GLU:plan': 19, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 267 Chain: "C" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 785 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 141} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 147} Chain breaks: 1 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 513 Unresolved non-hydrogen angles: 662 Unresolved non-hydrogen dihedrals: 426 Unresolved non-hydrogen chiralities: 46 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 4, 'TYR:plan': 8, 'ASN:plan1': 7, 'TRP:plan': 2, 'ASP:plan': 8, 'PHE:plan': 4, 'GLU:plan': 8, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 293 Chain: "D" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 801 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 153} Link IDs: {'PTRANS': 10, 'TRANS': 150} Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 574 Unresolved non-hydrogen angles: 721 Unresolved non-hydrogen dihedrals: 475 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 7, 'TYR:plan': 4, 'ASN:plan1': 6, 'ASP:plan': 10, 'PHE:plan': 6, 'GLU:plan': 16, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 315 Chain: "E" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 837 Classifications: {'peptide': 165} Incomplete info: {'truncation_to_alanine': 139} Link IDs: {'PTRANS': 8, 'TRANS': 156} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 460 Unresolved non-hydrogen angles: 582 Unresolved non-hydrogen dihedrals: 359 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 10, 'ASP:plan': 10, 'PHE:plan': 4, 'GLU:plan': 16, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 246 Chain: "F" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 363 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 250 Unresolved non-hydrogen angles: 312 Unresolved non-hydrogen dihedrals: 206 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 9, 'ARG:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 5, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 129 Chain: "G" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 605 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 113} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 410 Unresolved non-hydrogen angles: 515 Unresolved non-hydrogen dihedrals: 336 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 7, 'TYR:plan': 3, 'ASN:plan1': 4, 'HIS:plan': 3, 'PHE:plan': 6, 'GLU:plan': 11, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 223 Chain: "H" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 578 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 1, 'TRANS': 103} Chain breaks: 1 Unresolved non-hydrogen bonds: 250 Unresolved non-hydrogen angles: 315 Unresolved non-hydrogen dihedrals: 191 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 136 Chain: "I" Number of atoms: 6772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1086, 6772 Classifications: {'peptide': 1086} Incomplete info: {'truncation_to_alanine': 591} Link IDs: {'CIS': 1, 'PTRANS': 64, 'TRANS': 1020} Chain breaks: 17 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 1934 Unresolved non-hydrogen angles: 2444 Unresolved non-hydrogen dihedrals: 1522 Unresolved non-hydrogen chiralities: 231 Planarities with less than four sites: {'GLN:plan1': 38, 'HIS:plan': 8, 'TYR:plan': 6, 'ASN:plan1': 34, 'TRP:plan': 2, 'ASP:plan': 37, 'PHE:plan': 20, 'GLU:plan': 41, 'ARG:plan': 35} Unresolved non-hydrogen planarities: 924 Chain: "J" Number of atoms: 1171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1171 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 17, 'TRANS': 149} Unresolved non-hydrogen bonds: 156 Unresolved non-hydrogen angles: 196 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 6, 'ASN:plan1': 4, 'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 85 Chain: "K" Number of atoms: 5085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 738, 5085 Classifications: {'peptide': 738} Incomplete info: {'truncation_to_alanine': 228} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 36, 'TRANS': 699} Chain breaks: 9 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 656 Unresolved non-hydrogen angles: 801 Unresolved non-hydrogen dihedrals: 521 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'GLN:plan1': 16, 'ASP:plan': 22, 'ASN:plan1': 8, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 25, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 313 Chain: "L" Number of atoms: 3335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 3335 Classifications: {'peptide': 544} Incomplete info: {'truncation_to_alanine': 305} Link IDs: {'PTRANS': 20, 'TRANS': 523} Chain breaks: 9 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 985 Unresolved non-hydrogen angles: 1220 Unresolved non-hydrogen dihedrals: 781 Unresolved non-hydrogen chiralities: 90 Planarities with less than four sites: {'GLN:plan1': 36, 'HIS:plan': 5, 'TYR:plan': 2, 'ASN:plan1': 16, 'ASP:plan': 19, 'PHE:plan': 5, 'GLU:plan': 24, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 509 Chain: "M" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1140 Classifications: {'peptide': 180} Incomplete info: {'truncation_to_alanine': 98} Link IDs: {'PTRANS': 7, 'TRANS': 172} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 312 Unresolved non-hydrogen angles: 387 Unresolved non-hydrogen dihedrals: 244 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 10, 'ASN:plan1': 6, 'HIS:plan': 2, 'GLU:plan': 10, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 152 Chain: "N" Number of atoms: 475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 475 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 7, 'TRANS': 67} Chain breaks: 3 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 2, 'HIS:plan': 2, 'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 39 Chain: "O" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1013 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 104} Link IDs: {'PTRANS': 7, 'TRANS': 166} Chain breaks: 4 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 346 Unresolved non-hydrogen angles: 435 Unresolved non-hydrogen dihedrals: 281 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 7, 'ARG:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 3, 'PHE:plan': 5, 'GLU:plan': 10, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 169 Chain: "P" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 602 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 98} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 327 Unresolved non-hydrogen angles: 418 Unresolved non-hydrogen dihedrals: 257 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 9, 'PHE:plan': 3, 'GLU:plan': 10, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 183 Chain: "Q" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 754 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'PTRANS': 1, 'TRANS': 129} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 320 Unresolved non-hydrogen angles: 401 Unresolved non-hydrogen dihedrals: 250 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 11, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 173 Chain: "R" Number of atoms: 9744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1295, 9744 Classifications: {'peptide': 1295} Incomplete info: {'truncation_to_alanine': 219} Link IDs: {'CIS': 3, 'PTRANS': 68, 'TRANS': 1223} Chain breaks: 4 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 743 Unresolved non-hydrogen angles: 932 Unresolved non-hydrogen dihedrals: 606 Unresolved non-hydrogen chiralities: 67 Planarities with less than four sites: {'GLN:plan1': 18, 'HIS:plan': 5, 'TYR:plan': 4, 'ASN:plan1': 11, 'TRP:plan': 2, 'ASP:plan': 12, 'PHE:plan': 6, 'GLU:plan': 25, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 388 Chain: "S" Number of atoms: 5875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 901, 5875 Classifications: {'peptide': 901} Incomplete info: {'truncation_to_alanine': 397} Link IDs: {'PTRANS': 35, 'TRANS': 865} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1213 Unresolved non-hydrogen angles: 1510 Unresolved non-hydrogen dihedrals: 942 Unresolved non-hydrogen chiralities: 144 Planarities with less than four sites: {'GLN:plan1': 26, 'HIS:plan': 7, 'TYR:plan': 3, 'ASN:plan1': 19, 'ASP:plan': 28, 'PHE:plan': 1, 'GLU:plan': 42, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 535 Chain: "T" Number of atoms: 1299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1299 Classifications: {'peptide': 192} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 15, 'TRANS': 176} Chain breaks: 3 Unresolved non-hydrogen bonds: 193 Unresolved non-hydrogen angles: 244 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 6, 'ASN:plan1': 3, 'ARG:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 73 Chain: "U" Number of atoms: 481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 481 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 8, 'TRANS': 88} Chain breaks: 1 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 305 Unresolved non-hydrogen angles: 401 Unresolved non-hydrogen dihedrals: 250 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 10, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 3, 'HIS:plan': 2, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 178 Chain: "V" Number of atoms: 1657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 1657 Classifications: {'peptide': 266} Incomplete info: {'truncation_to_alanine': 146} Link IDs: {'PTRANS': 11, 'TRANS': 254} Chain breaks: 3 Unresolved non-hydrogen bonds: 477 Unresolved non-hydrogen angles: 592 Unresolved non-hydrogen dihedrals: 371 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'GLN:plan1': 13, 'ARG:plan': 13, 'TYR:plan': 1, 'ASN:plan1': 9, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 9, 'ASP:plan': 13} Unresolved non-hydrogen planarities: 242 Chain: "W" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 773 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 4, 'TRANS': 113} Unresolved non-hydrogen bonds: 177 Unresolved non-hydrogen angles: 223 Unresolved non-hydrogen dihedrals: 133 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 6, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 9, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 106 Chain: "X" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 839 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain breaks: 1 Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 157 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 48 Chain: "Y" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 843 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain breaks: 1 Unresolved non-hydrogen bonds: 257 Unresolved non-hydrogen angles: 326 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 9, 'ARG:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 7, 'HIS:plan': 1, 'GLU:plan': 8, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 144 Chain: "Z" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 543 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'PTRANS': 3, 'TRANS': 105} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 440 Unresolved non-hydrogen angles: 564 Unresolved non-hydrogen dihedrals: 385 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 4, 'TYR:plan': 10, 'ASN:plan1': 6, 'TRP:plan': 2, 'ASP:plan': 4, 'PHE:plan': 7, 'GLU:plan': 8, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 291 Chain: "a" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 100 Classifications: {'peptide': 20} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'TRANS': 19} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'UNK:plan-1': 20} Unresolved non-hydrogen planarities: 20 Time building chain proxies: 21.46, per 1000 atoms: 0.43 Number of scatterers: 49568 At special positions: 0 Unit cell: (164.28, 216.45, 391.83, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 156 16.00 O 9010 8.00 N 9130 7.00 C 31272 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS O 75 " - pdb=" SG CYS O 84 " distance=2.03 Simple disulfide: pdb=" SG CYS S 134 " - pdb=" SG CYS S 161 " distance=2.04 Simple disulfide: pdb=" SG CYS W 55 " - pdb=" SG CYS W 80 " 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: 10.31 Conformation dependent library (CDL) restraints added in 6.1 seconds 15310 Ramachandran restraints generated. 7655 Oldfield, 0 Emsley, 7655 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15072 Finding SS restraints... Secondary structure from input PDB file: 289 helices and 32 sheets defined 53.3% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.84 Creating SS restraints... Processing helix chain 'A' and resid 14 through 27 Processing helix chain 'A' and resid 34 through 46 removed outlier: 3.563A pdb=" N LYS A 38 " --> pdb=" O SER A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 70 removed outlier: 3.517A pdb=" N LEU A 69 " --> pdb=" O LEU A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 88 Processing helix chain 'A' and resid 135 through 144 Processing helix chain 'A' and resid 146 through 162 removed outlier: 4.096A pdb=" N PHE A 150 " --> pdb=" O ASN A 146 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A 160 " --> pdb=" O GLY A 156 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N TYR A 161 " --> pdb=" O LEU A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 195 Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 228 through 232 removed outlier: 3.835A pdb=" N LEU A 232 " --> pdb=" O SER A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 326 Processing helix chain 'A' and resid 338 through 350 Processing helix chain 'A' and resid 403 through 423 removed outlier: 3.818A pdb=" N ILE A 407 " --> pdb=" O ARG A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 501 removed outlier: 3.568A pdb=" N ARG A 500 " --> pdb=" O LYS A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 518 Processing helix chain 'B' and resid 27 through 52 Processing helix chain 'B' and resid 63 through 141 removed outlier: 3.559A pdb=" N GLY B 141 " --> pdb=" O LYS B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 156 Processing helix chain 'B' and resid 178 through 183 Processing helix chain 'C' and resid 26 through 35 removed outlier: 4.226A pdb=" N LEU C 30 " --> pdb=" O SER C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 135 removed outlier: 3.589A pdb=" N VAL C 114 " --> pdb=" O ASP C 110 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER C 135 " --> pdb=" O ASP C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 187 removed outlier: 4.552A pdb=" N VAL C 177 " --> pdb=" O GLN C 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 26 Processing helix chain 'D' and resid 73 through 99 Processing helix chain 'D' and resid 104 through 120 removed outlier: 3.514A pdb=" N LEU D 109 " --> pdb=" O ARG D 105 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU D 110 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N HIS D 118 " --> pdb=" O LEU D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 171 removed outlier: 3.736A pdb=" N ALA D 131 " --> pdb=" O ARG D 127 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N THR D 134 " --> pdb=" O GLN D 130 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL D 137 " --> pdb=" O GLU D 133 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU D 140 " --> pdb=" O ARG D 136 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG D 152 " --> pdb=" O GLU D 148 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE D 153 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU D 158 " --> pdb=" O GLN D 154 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG D 159 " --> pdb=" O LYS D 155 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE D 161 " --> pdb=" O LEU D 157 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU D 162 " --> pdb=" O GLU D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 175 removed outlier: 3.516A pdb=" N LEU D 175 " --> pdb=" O PRO D 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 172 through 175' Processing helix chain 'E' and resid 8 through 33 removed outlier: 3.660A pdb=" N LEU E 12 " --> pdb=" O LEU E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 64 Processing helix chain 'E' and resid 97 through 105 Processing helix chain 'E' and resid 114 through 127 removed outlier: 4.238A pdb=" N ASP E 127 " --> pdb=" O GLN E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 163 Processing helix chain 'E' and resid 174 through 181 removed outlier: 3.731A pdb=" N THR E 178 " --> pdb=" O ASN E 174 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA E 180 " --> pdb=" O GLY E 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 73 Processing helix chain 'F' and resid 82 through 100 Processing helix chain 'F' and resid 106 through 133 Processing helix chain 'G' and resid 8 through 29 removed outlier: 3.532A pdb=" N PHE G 29 " --> pdb=" O ILE G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 59 removed outlier: 4.385A pdb=" N GLN G 39 " --> pdb=" O ALA G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 72 Processing helix chain 'G' and resid 77 through 116 Processing helix chain 'G' and resid 117 through 127 removed outlier: 4.125A pdb=" N MET G 121 " --> pdb=" O PHE G 117 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE G 127 " --> pdb=" O LYS G 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 38 removed outlier: 4.030A pdb=" N GLU H 38 " --> pdb=" O GLU H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 68 removed outlier: 3.622A pdb=" N ALA H 49 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA H 50 " --> pdb=" O ASP H 46 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA H 51 " --> pdb=" O ARG H 47 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE H 52 " --> pdb=" O GLN H 48 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR H 53 " --> pdb=" O ALA H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 84 through 115 Processing helix chain 'I' and resid 57 through 78 removed outlier: 3.849A pdb=" N ILE I 61 " --> pdb=" O LEU I 57 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU I 78 " --> pdb=" O VAL I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 84 through 113 removed outlier: 3.628A pdb=" N ILE I 89 " --> pdb=" O VAL I 85 " (cutoff:3.500A) Processing helix chain 'I' and resid 114 through 149 Processing helix chain 'I' and resid 159 through 166 removed outlier: 3.579A pdb=" N ALA I 163 " --> pdb=" O ALA I 159 " (cutoff:3.500A) Processing helix chain 'I' and resid 177 through 184 Processing helix chain 'I' and resid 191 through 212 removed outlier: 3.812A pdb=" N VAL I 210 " --> pdb=" O ARG I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 277 through 291 Processing helix chain 'I' and resid 293 through 324 Processing helix chain 'I' and resid 402 through 430 Processing helix chain 'I' and resid 480 through 492 Processing helix chain 'I' and resid 495 through 517 removed outlier: 3.714A pdb=" N CYS I 511 " --> pdb=" O GLY I 507 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N HIS I 517 " --> pdb=" O GLN I 513 " (cutoff:3.500A) Processing helix chain 'I' and resid 601 through 609 removed outlier: 3.551A pdb=" N LYS I 609 " --> pdb=" O MET I 605 " (cutoff:3.500A) Processing helix chain 'I' and resid 643 through 668 removed outlier: 4.292A pdb=" N HIS I 649 " --> pdb=" O LYS I 645 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N CYS I 654 " --> pdb=" O PHE I 650 " (cutoff:3.500A) Proline residue: I 659 - end of helix Processing helix chain 'I' and resid 702 through 711 Processing helix chain 'I' and resid 768 through 788 Processing helix chain 'I' and resid 795 through 799 Processing helix chain 'I' and resid 854 through 868 removed outlier: 3.998A pdb=" N HIS I 859 " --> pdb=" O ASN I 855 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N GLN I 860 " --> pdb=" O THR I 856 " (cutoff:3.500A) Processing helix chain 'I' and resid 870 through 891 removed outlier: 3.643A pdb=" N LEU I 874 " --> pdb=" O ASN I 870 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N ALA I 883 " --> pdb=" O PHE I 879 " (cutoff:3.500A) Proline residue: I 884 - end of helix removed outlier: 3.985A pdb=" N LEU I 891 " --> pdb=" O ALA I 887 " (cutoff:3.500A) Processing helix chain 'I' and resid 965 through 975 removed outlier: 4.782A pdb=" N VAL I 973 " --> pdb=" O LEU I 969 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER I 975 " --> pdb=" O MET I 971 " (cutoff:3.500A) Processing helix chain 'I' and resid 1185 through 1191 Processing helix chain 'I' and resid 1210 through 1232 Processing helix chain 'I' and resid 1282 through 1296 Processing helix chain 'I' and resid 1301 through 1310 removed outlier: 3.876A pdb=" N ILE I1305 " --> pdb=" O ALA I1301 " (cutoff:3.500A) Processing helix chain 'I' and resid 1318 through 1328 Processing helix chain 'I' and resid 1412 through 1426 Proline residue: I1417 - end of helix Processing helix chain 'I' and resid 1439 through 1447 Processing helix chain 'J' and resid 621 through 631 removed outlier: 4.305A pdb=" N ALA J 625 " --> pdb=" O PRO J 621 " (cutoff:3.500A) Processing helix chain 'J' and resid 637 through 651 removed outlier: 3.557A pdb=" N ARG J 641 " --> pdb=" O HIS J 637 " (cutoff:3.500A) Proline residue: J 645 - end of helix Processing helix chain 'J' and resid 676 through 684 removed outlier: 3.842A pdb=" N GLN J 680 " --> pdb=" O PRO J 676 " (cutoff:3.500A) Processing helix chain 'J' and resid 739 through 746 removed outlier: 3.642A pdb=" N GLN J 743 " --> pdb=" O ASP J 739 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ASP J 745 " --> pdb=" O GLN J 741 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA J 746 " --> pdb=" O TRP J 742 " (cutoff:3.500A) Processing helix chain 'J' and resid 747 through 763 Processing helix chain 'J' and resid 770 through 784 Processing helix chain 'K' and resid 253 through 257 Processing helix chain 'K' and resid 453 through 472 Processing helix chain 'K' and resid 476 through 481 removed outlier: 3.645A pdb=" N LEU K 479 " --> pdb=" O TRP K 476 " (cutoff:3.500A) Processing helix chain 'K' and resid 483 through 485 No H-bonds generated for 'chain 'K' and resid 483 through 485' Processing helix chain 'K' and resid 486 through 500 Processing helix chain 'K' and resid 505 through 523 removed outlier: 5.779A pdb=" N THR K 511 " --> pdb=" O GLN K 507 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N ARG K 512 " --> pdb=" O VAL K 508 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA K 515 " --> pdb=" O THR K 511 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEU K 523 " --> pdb=" O SER K 519 " (cutoff:3.500A) Processing helix chain 'K' and resid 531 through 552 Processing helix chain 'K' and resid 553 through 555 No H-bonds generated for 'chain 'K' and resid 553 through 555' Processing helix chain 'K' and resid 563 through 571 Processing helix chain 'K' and resid 578 through 587 removed outlier: 4.158A pdb=" N ILE K 584 " --> pdb=" O ASP K 580 " (cutoff:3.500A) Processing helix chain 'K' and resid 604 through 618 Processing helix chain 'K' and resid 636 through 656 Processing helix chain 'K' and resid 672 through 685 removed outlier: 4.039A pdb=" N LEU K 676 " --> pdb=" O SER K 672 " (cutoff:3.500A) Processing helix chain 'K' and resid 721 through 728 removed outlier: 4.157A pdb=" N ARG K 728 " --> pdb=" O GLY K 724 " (cutoff:3.500A) Processing helix chain 'K' and resid 803 through 810 removed outlier: 3.940A pdb=" N GLU K 807 " --> pdb=" O VAL K 803 " (cutoff:3.500A) Processing helix chain 'L' and resid 35 through 47 removed outlier: 3.605A pdb=" N ARG L 46 " --> pdb=" O ARG L 42 " (cutoff:3.500A) Processing helix chain 'L' and resid 95 through 118 Processing helix chain 'L' and resid 142 through 175 removed outlier: 4.286A pdb=" N SER L 146 " --> pdb=" O LEU L 142 " (cutoff:3.500A) Processing helix chain 'L' and resid 182 through 192 Processing helix chain 'L' and resid 287 through 316 removed outlier: 3.682A pdb=" N THR L 291 " --> pdb=" O PRO L 287 " (cutoff:3.500A) Processing helix chain 'L' and resid 366 through 384 Processing helix chain 'L' and resid 400 through 406 removed outlier: 3.835A pdb=" N ARG L 404 " --> pdb=" O HIS L 400 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER L 406 " --> pdb=" O ARG L 402 " (cutoff:3.500A) Processing helix chain 'L' and resid 413 through 418 Processing helix chain 'L' and resid 424 through 452 Processing helix chain 'L' and resid 482 through 486 removed outlier: 3.604A pdb=" N ILE L 485 " --> pdb=" O TYR L 482 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N CYS L 486 " --> pdb=" O GLU L 483 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 482 through 486' Processing helix chain 'L' and resid 517 through 539 removed outlier: 3.929A pdb=" N ASP L 521 " --> pdb=" O GLN L 517 " (cutoff:3.500A) Processing helix chain 'L' and resid 603 through 608 removed outlier: 4.439A pdb=" N LEU L 608 " --> pdb=" O LYS L 604 " (cutoff:3.500A) Processing helix chain 'L' and resid 635 through 641 Processing helix chain 'M' and resid 32 through 43 Processing helix chain 'M' and resid 112 through 121 Processing helix chain 'M' and resid 180 through 193 removed outlier: 4.351A pdb=" N ASP M 184 " --> pdb=" O ASP M 180 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ASP M 185 " --> pdb=" O MET M 181 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 87 removed outlier: 4.093A pdb=" N HIS N 86 " --> pdb=" O ASN N 82 " (cutoff:3.500A) Processing helix chain 'N' and resid 89 through 97 removed outlier: 3.580A pdb=" N CYS N 97 " --> pdb=" O TYR N 93 " (cutoff:3.500A) Processing helix chain 'N' and resid 112 through 116 Processing helix chain 'N' and resid 128 through 138 Proline residue: N 134 - end of helix Processing helix chain 'N' and resid 147 through 152 Processing helix chain 'O' and resid 16 through 32 Processing helix chain 'O' and resid 87 through 98 Processing helix chain 'O' and resid 154 through 165 removed outlier: 3.535A pdb=" N SER O 163 " --> pdb=" O GLU O 159 " (cutoff:3.500A) Processing helix chain 'O' and resid 185 through 195 removed outlier: 4.035A pdb=" N THR O 189 " --> pdb=" O GLY O 185 " (cutoff:3.500A) Processing helix chain 'O' and resid 196 through 200 Processing helix chain 'P' and resid 7 through 28 Processing helix chain 'P' and resid 49 through 75 Processing helix chain 'P' and resid 82 through 132 Processing helix chain 'Q' and resid 10 through 38 Processing helix chain 'Q' and resid 49 through 88 Processing helix chain 'Q' and resid 95 through 136 removed outlier: 3.680A pdb=" N ASP Q 99 " --> pdb=" O ASN Q 95 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 14 Processing helix chain 'R' and resid 32 through 50 removed outlier: 4.254A pdb=" N LEU R 37 " --> pdb=" O GLU R 33 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLY R 50 " --> pdb=" O GLN R 46 " (cutoff:3.500A) Processing helix chain 'R' and resid 51 through 54 removed outlier: 5.791A pdb=" N GLU R 54 " --> pdb=" O LEU R 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 51 through 54' Processing helix chain 'R' and resid 55 through 68 removed outlier: 3.660A pdb=" N PHE R 66 " --> pdb=" O TRP R 62 " (cutoff:3.500A) Processing helix chain 'R' and resid 72 through 89 Processing helix chain 'R' and resid 93 through 103 removed outlier: 3.790A pdb=" N ASN R 103 " --> pdb=" O GLU R 99 " (cutoff:3.500A) Processing helix chain 'R' and resid 111 through 125 Processing helix chain 'R' and resid 134 through 147 removed outlier: 4.237A pdb=" N LEU R 138 " --> pdb=" O VAL R 134 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS R 139 " --> pdb=" O ARG R 135 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA R 140 " --> pdb=" O ASP R 136 " (cutoff:3.500A) Processing helix chain 'R' and resid 161 through 174 Processing helix chain 'R' and resid 179 through 188 removed outlier: 3.564A pdb=" N ALA R 183 " --> pdb=" O PRO R 179 " (cutoff:3.500A) Processing helix chain 'R' and resid 203 through 218 Proline residue: R 214 - end of helix Processing helix chain 'R' and resid 266 through 275 Processing helix chain 'R' and resid 279 through 287 removed outlier: 3.625A pdb=" N VAL R 283 " --> pdb=" O SER R 279 " (cutoff:3.500A) Processing helix chain 'R' and resid 299 through 317 removed outlier: 3.683A pdb=" N GLN R 303 " --> pdb=" O VAL R 299 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU R 313 " --> pdb=" O VAL R 309 " (cutoff:3.500A) Processing helix chain 'R' and resid 317 through 324 removed outlier: 3.552A pdb=" N PHE R 321 " --> pdb=" O THR R 317 " (cutoff:3.500A) Processing helix chain 'R' and resid 326 through 342 removed outlier: 4.848A pdb=" N HIS R 333 " --> pdb=" O LEU R 329 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL R 342 " --> pdb=" O LEU R 338 " (cutoff:3.500A) Processing helix chain 'R' and resid 349 through 361 Processing helix chain 'R' and resid 368 through 383 Processing helix chain 'R' and resid 388 through 403 removed outlier: 3.785A pdb=" N PHE R 392 " --> pdb=" O ALA R 388 " (cutoff:3.500A) Proline residue: R 394 - end of helix Processing helix chain 'R' and resid 423 through 440 Processing helix chain 'R' and resid 441 through 445 Processing helix chain 'R' and resid 447 through 450 removed outlier: 4.302A pdb=" N SER R 450 " --> pdb=" O ILE R 447 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 447 through 450' Processing helix chain 'R' and resid 451 through 456 removed outlier: 3.834A pdb=" N GLU R 456 " --> pdb=" O LYS R 452 " (cutoff:3.500A) Processing helix chain 'R' and resid 488 through 495 Processing helix chain 'R' and resid 541 through 554 removed outlier: 3.622A pdb=" N THR R 553 " --> pdb=" O LYS R 549 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS R 554 " --> pdb=" O LEU R 550 " (cutoff:3.500A) Processing helix chain 'R' and resid 564 through 569 Processing helix chain 'R' and resid 570 through 577 Processing helix chain 'R' and resid 577 through 596 Proline residue: R 590 - end of helix removed outlier: 3.503A pdb=" N SER R 595 " --> pdb=" O THR R 591 " (cutoff:3.500A) Processing helix chain 'R' and resid 597 through 612 removed outlier: 4.013A pdb=" N HIS R 602 " --> pdb=" O TRP R 598 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N GLU R 606 " --> pdb=" O HIS R 602 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N MET R 607 " --> pdb=" O THR R 603 " (cutoff:3.500A) Processing helix chain 'R' and resid 616 through 633 Processing helix chain 'R' and resid 639 through 641 No H-bonds generated for 'chain 'R' and resid 639 through 641' Processing helix chain 'R' and resid 642 through 653 removed outlier: 3.804A pdb=" N GLU R 646 " --> pdb=" O HIS R 642 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG R 651 " --> pdb=" O SER R 647 " (cutoff:3.500A) Processing helix chain 'R' and resid 660 through 666 removed outlier: 4.190A pdb=" N THR R 666 " --> pdb=" O GLN R 662 " (cutoff:3.500A) Processing helix chain 'R' and resid 680 through 697 removed outlier: 3.842A pdb=" N VAL R 697 " --> pdb=" O ARG R 693 " (cutoff:3.500A) Processing helix chain 'R' and resid 709 through 720 removed outlier: 5.110A pdb=" N ILE R 715 " --> pdb=" O TRP R 711 " (cutoff:3.500A) Processing helix chain 'R' and resid 721 through 723 No H-bonds generated for 'chain 'R' and resid 721 through 723' Processing helix chain 'R' and resid 737 through 752 removed outlier: 4.301A pdb=" N GLN R 740 " --> pdb=" O ALA R 737 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS R 744 " --> pdb=" O ALA R 741 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N GLN R 745 " --> pdb=" O PHE R 742 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N ASN R 746 " --> pdb=" O PHE R 743 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN R 747 " --> pdb=" O LYS R 744 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL R 748 " --> pdb=" O GLN R 745 " (cutoff:3.500A) Proline residue: R 749 - end of helix removed outlier: 3.639A pdb=" N SER R 752 " --> pdb=" O PRO R 749 " (cutoff:3.500A) Processing helix chain 'R' and resid 754 through 770 Processing helix chain 'R' and resid 771 through 773 No H-bonds generated for 'chain 'R' and resid 771 through 773' Processing helix chain 'R' and resid 781 through 785 removed outlier: 3.557A pdb=" N PHE R 785 " --> pdb=" O VAL R 782 " (cutoff:3.500A) Processing helix chain 'R' and resid 788 through 790 No H-bonds generated for 'chain 'R' and resid 788 through 790' Processing helix chain 'R' and resid 791 through 796 removed outlier: 4.056A pdb=" N LYS R 795 " --> pdb=" O CYS R 791 " (cutoff:3.500A) Processing helix chain 'R' and resid 807 through 812 Processing helix chain 'R' and resid 814 through 838 removed outlier: 4.634A pdb=" N ALA R 821 " --> pdb=" O ARG R 817 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASP R 828 " --> pdb=" O ARG R 824 " (cutoff:3.500A) Processing helix chain 'R' and resid 843 through 856 removed outlier: 4.096A pdb=" N VAL R 854 " --> pdb=" O LEU R 850 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N TRP R 855 " --> pdb=" O ASN R 851 " (cutoff:3.500A) Processing helix chain 'R' and resid 864 through 873 removed outlier: 3.794A pdb=" N CYS R 868 " --> pdb=" O ARG R 864 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG R 872 " --> pdb=" O CYS R 868 " (cutoff:3.500A) Processing helix chain 'R' and resid 878 through 892 removed outlier: 3.572A pdb=" N CYS R 882 " --> pdb=" O GLU R 878 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N LEU R 890 " --> pdb=" O ILE R 886 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU R 891 " --> pdb=" O GLN R 887 " (cutoff:3.500A) Processing helix chain 'R' and resid 896 through 902 Processing helix chain 'R' and resid 903 through 908 removed outlier: 4.312A pdb=" N ASN R 907 " --> pdb=" O PHE R 903 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER R 908 " --> pdb=" O VAL R 904 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 903 through 908' Processing helix chain 'R' and resid 916 through 928 removed outlier: 3.555A pdb=" N TYR R 928 " --> pdb=" O TYR R 924 " (cutoff:3.500A) Processing helix chain 'R' and resid 956 through 973 removed outlier: 3.634A pdb=" N CYS R 960 " --> pdb=" O PHE R 956 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU R 964 " --> pdb=" O CYS R 960 " (cutoff:3.500A) Proline residue: R 965 - end of helix removed outlier: 3.553A pdb=" N ARG R 973 " --> pdb=" O ILE R 969 " (cutoff:3.500A) Processing helix chain 'R' and resid 980 through 990 removed outlier: 3.558A pdb=" N LEU R 984 " --> pdb=" O VAL R 980 " (cutoff:3.500A) Processing helix chain 'R' and resid 991 through 996 Processing helix chain 'R' and resid 1000 through 1007 removed outlier: 4.540A pdb=" N TYR R1004 " --> pdb=" O ARG R1000 " (cutoff:3.500A) Processing helix chain 'R' and resid 1012 through 1015 Processing helix chain 'R' and resid 1016 through 1035 removed outlier: 3.931A pdb=" N LYS R1025 " --> pdb=" O HIS R1021 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N HIS R1028 " --> pdb=" O ARG R1024 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA R1029 " --> pdb=" O LYS R1025 " (cutoff:3.500A) Processing helix chain 'R' and resid 1042 through 1051 removed outlier: 4.195A pdb=" N ASP R1046 " --> pdb=" O TRP R1042 " (cutoff:3.500A) Processing helix chain 'R' and resid 1058 through 1062 removed outlier: 3.917A pdb=" N TRP R1061 " --> pdb=" O ASP R1058 " (cutoff:3.500A) Processing helix chain 'R' and resid 1063 through 1077 Processing helix chain 'R' and resid 1099 through 1113 removed outlier: 4.090A pdb=" N HIS R1103 " --> pdb=" O ASN R1099 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N HIS R1106 " --> pdb=" O ALA R1102 " (cutoff:3.500A) Processing helix chain 'R' and resid 1119 through 1132 removed outlier: 4.472A pdb=" N GLY R1123 " --> pdb=" O GLY R1119 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ASN R1124 " --> pdb=" O LYS R1120 " (cutoff:3.500A) Processing helix chain 'R' and resid 1141 through 1156 removed outlier: 3.840A pdb=" N TRP R1145 " --> pdb=" O ASN R1141 " (cutoff:3.500A) Processing helix chain 'R' and resid 1157 through 1162 removed outlier: 3.544A pdb=" N TRP R1161 " --> pdb=" O PRO R1157 " (cutoff:3.500A) Processing helix chain 'R' and resid 1163 through 1170 Processing helix chain 'R' and resid 1182 through 1185 removed outlier: 3.666A pdb=" N GLY R1185 " --> pdb=" O GLU R1182 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 1182 through 1185' Processing helix chain 'R' and resid 1186 through 1192 removed outlier: 4.263A pdb=" N LEU R1190 " --> pdb=" O TYR R1186 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASP R1192 " --> pdb=" O PHE R1188 " (cutoff:3.500A) Processing helix chain 'R' and resid 1203 through 1219 Processing helix chain 'R' and resid 1222 through 1225 Processing helix chain 'R' and resid 1226 through 1234 Processing helix chain 'R' and resid 1235 through 1239 removed outlier: 4.050A pdb=" N VAL R1238 " --> pdb=" O LEU R1235 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL R1239 " --> pdb=" O LEU R1236 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 1235 through 1239' Processing helix chain 'R' and resid 1241 through 1253 removed outlier: 3.760A pdb=" N LEU R1245 " --> pdb=" O THR R1241 " (cutoff:3.500A) Processing helix chain 'R' and resid 1255 through 1263 removed outlier: 3.835A pdb=" N PHE R1259 " --> pdb=" O PHE R1255 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU R1262 " --> pdb=" O ARG R1258 " (cutoff:3.500A) Processing helix chain 'R' and resid 1266 through 1284 Processing helix chain 'R' and resid 1290 through 1305 removed outlier: 4.000A pdb=" N ILE R1294 " --> pdb=" O TYR R1290 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE R1305 " --> pdb=" O MET R1301 " (cutoff:3.500A) Processing helix chain 'R' and resid 1310 through 1319 removed outlier: 4.012A pdb=" N LYS R1316 " --> pdb=" O GLU R1312 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE R1317 " --> pdb=" O GLN R1313 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N CYS R1319 " --> pdb=" O GLU R1315 " (cutoff:3.500A) Processing helix chain 'R' and resid 1322 through 1330 Processing helix chain 'S' and resid 5 through 16 Processing helix chain 'S' and resid 21 through 30 removed outlier: 4.209A pdb=" N ILE S 25 " --> pdb=" O TYR S 21 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE S 30 " --> pdb=" O ASN S 26 " (cutoff:3.500A) Processing helix chain 'S' and resid 40 through 42 No H-bonds generated for 'chain 'S' and resid 40 through 42' Processing helix chain 'S' and resid 43 through 53 Processing helix chain 'S' and resid 60 through 69 Processing helix chain 'S' and resid 73 through 83 Processing helix chain 'S' and resid 84 through 89 removed outlier: 4.238A pdb=" N PHE S 88 " --> pdb=" O LYS S 84 " (cutoff:3.500A) Processing helix chain 'S' and resid 92 through 107 removed outlier: 4.726A pdb=" N MET S 103 " --> pdb=" O ASP S 99 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N PHE S 104 " --> pdb=" O ILE S 100 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N CYS S 105 " --> pdb=" O MET S 101 " (cutoff:3.500A) Processing helix chain 'S' and resid 115 through 134 removed outlier: 3.674A pdb=" N CYS S 134 " --> pdb=" O TRP S 130 " (cutoff:3.500A) Processing helix chain 'S' and resid 135 through 140 removed outlier: 3.917A pdb=" N GLU S 140 " --> pdb=" O ALA S 137 " (cutoff:3.500A) Processing helix chain 'S' and resid 156 through 169 removed outlier: 3.921A pdb=" N LEU S 160 " --> pdb=" O LYS S 156 " (cutoff:3.500A) Processing helix chain 'S' and resid 174 through 185 Processing helix chain 'S' and resid 186 through 204 Processing helix chain 'S' and resid 213 through 225 Processing helix chain 'S' and resid 226 through 228 No H-bonds generated for 'chain 'S' and resid 226 through 228' Processing helix chain 'S' and resid 242 through 255 Processing helix chain 'S' and resid 262 through 273 Processing helix chain 'S' and resid 277 through 292 removed outlier: 3.655A pdb=" N GLY S 292 " --> pdb=" O ALA S 288 " (cutoff:3.500A) Processing helix chain 'S' and resid 299 through 323 removed outlier: 3.874A pdb=" N LEU S 303 " --> pdb=" O GLY S 299 " (cutoff:3.500A) Proline residue: S 314 - end of helix Processing helix chain 'S' and resid 331 through 344 removed outlier: 3.612A pdb=" N LEU S 344 " --> pdb=" O PHE S 340 " (cutoff:3.500A) Processing helix chain 'S' and resid 344 through 356 removed outlier: 4.318A pdb=" N LEU S 348 " --> pdb=" O LEU S 344 " (cutoff:3.500A) Processing helix chain 'S' and resid 357 through 370 Processing helix chain 'S' and resid 378 through 387 Processing helix chain 'S' and resid 388 through 390 No H-bonds generated for 'chain 'S' and resid 388 through 390' Processing helix chain 'S' and resid 411 through 425 removed outlier: 4.454A pdb=" N THR S 421 " --> pdb=" O ASN S 417 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N MET S 422 " --> pdb=" O ILE S 418 " (cutoff:3.500A) Processing helix chain 'S' and resid 435 through 445 removed outlier: 3.676A pdb=" N HIS S 439 " --> pdb=" O GLY S 435 " (cutoff:3.500A) Processing helix chain 'S' and resid 447 through 455 removed outlier: 3.921A pdb=" N ALA S 451 " --> pdb=" O ASP S 447 " (cutoff:3.500A) Processing helix chain 'S' and resid 458 through 473 Processing helix chain 'S' and resid 480 through 505 Processing helix chain 'S' and resid 506 through 514 removed outlier: 3.649A pdb=" N SER S 514 " --> pdb=" O ILE S 510 " (cutoff:3.500A) Processing helix chain 'S' and resid 522 through 528 removed outlier: 3.682A pdb=" N TRP S 526 " --> pdb=" O PHE S 522 " (cutoff:3.500A) Processing helix chain 'S' and resid 550 through 562 removed outlier: 3.756A pdb=" N LEU S 555 " --> pdb=" O LYS S 551 " (cutoff:3.500A) Processing helix chain 'S' and resid 575 through 577 No H-bonds generated for 'chain 'S' and resid 575 through 577' Processing helix chain 'S' and resid 578 through 590 removed outlier: 3.767A pdb=" N LEU S 584 " --> pdb=" O SER S 580 " (cutoff:3.500A) Processing helix chain 'S' and resid 597 through 607 Processing helix chain 'S' and resid 612 through 627 removed outlier: 4.054A pdb=" N VAL S 616 " --> pdb=" O CYS S 612 " (cutoff:3.500A) Processing helix chain 'S' and resid 633 through 643 Processing helix chain 'S' and resid 659 through 672 Processing helix chain 'S' and resid 673 through 679 Processing helix chain 'S' and resid 707 through 712 Processing helix chain 'S' and resid 712 through 719 removed outlier: 3.967A pdb=" N GLU S 718 " --> pdb=" O ALA S 714 " (cutoff:3.500A) Processing helix chain 'S' and resid 723 through 737 removed outlier: 3.634A pdb=" N HIS S 735 " --> pdb=" O ASP S 731 " (cutoff:3.500A) Processing helix chain 'S' and resid 738 through 751 Processing helix chain 'S' and resid 755 through 770 Processing helix chain 'S' and resid 773 through 790 Proline residue: S 787 - end of helix Processing helix chain 'S' and resid 792 through 800 Processing helix chain 'S' and resid 801 through 803 No H-bonds generated for 'chain 'S' and resid 801 through 803' Processing helix chain 'S' and resid 804 through 820 removed outlier: 4.255A pdb=" N ALA S 808 " --> pdb=" O GLY S 804 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS S 809 " --> pdb=" O THR S 805 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER S 817 " --> pdb=" O TRP S 813 " (cutoff:3.500A) Processing helix chain 'S' and resid 826 through 831 removed outlier: 4.492A pdb=" N LYS S 831 " --> pdb=" O SER S 827 " (cutoff:3.500A) Processing helix chain 'S' and resid 893 through 910 Processing helix chain 'S' and resid 916 through 929 removed outlier: 3.776A pdb=" N GLN S 920 " --> pdb=" O GLY S 916 " (cutoff:3.500A) Processing helix chain 'S' and resid 945 through 954 removed outlier: 4.009A pdb=" N THR S 949 " --> pdb=" O MET S 945 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER S 951 " --> pdb=" O PHE S 947 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLU S 952 " --> pdb=" O THR S 948 " (cutoff:3.500A) Processing helix chain 'S' and resid 962 through 969 removed outlier: 3.518A pdb=" N THR S 969 " --> pdb=" O VAL S 965 " (cutoff:3.500A) Processing helix chain 'S' and resid 973 through 985 Processing helix chain 'T' and resid 30 through 40 removed outlier: 4.298A pdb=" N GLU T 34 " --> pdb=" O PRO T 30 " (cutoff:3.500A) Processing helix chain 'T' and resid 41 through 46 Processing helix chain 'T' and resid 88 through 91 removed outlier: 3.765A pdb=" N ALA T 91 " --> pdb=" O THR T 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 88 through 91' Processing helix chain 'T' and resid 92 through 97 Processing helix chain 'T' and resid 114 through 132 removed outlier: 3.750A pdb=" N THR T 120 " --> pdb=" O GLU T 116 " (cutoff:3.500A) Processing helix chain 'T' and resid 164 through 174 Processing helix chain 'T' and resid 190 through 195 Processing helix chain 'T' and resid 196 through 198 No H-bonds generated for 'chain 'T' and resid 196 through 198' Processing helix chain 'U' and resid 472 through 488 Processing helix chain 'U' and resid 536 through 545 Processing helix chain 'V' and resid 9 through 36 Processing helix chain 'V' and resid 48 through 61 removed outlier: 3.570A pdb=" N PHE V 52 " --> pdb=" O ARG V 48 " (cutoff:3.500A) Processing helix chain 'V' and resid 61 through 67 removed outlier: 3.542A pdb=" N ARG V 65 " --> pdb=" O HIS V 61 " (cutoff:3.500A) Processing helix chain 'V' and resid 67 through 72 Processing helix chain 'V' and resid 91 through 95 removed outlier: 3.629A pdb=" N ASP V 95 " --> pdb=" O LEU V 92 " (cutoff:3.500A) Processing helix chain 'V' and resid 105 through 128 Processing helix chain 'V' and resid 160 through 171 Processing helix chain 'V' and resid 238 through 253 Processing helix chain 'V' and resid 258 through 272 removed outlier: 3.658A pdb=" N VAL V 262 " --> pdb=" O MET V 258 " (cutoff:3.500A) Processing helix chain 'W' and resid 46 through 55 removed outlier: 4.046A pdb=" N CYS W 55 " --> pdb=" O SER W 51 " (cutoff:3.500A) Processing helix chain 'W' and resid 73 through 106 removed outlier: 3.972A pdb=" N GLN W 79 " --> pdb=" O THR W 75 " (cutoff:3.500A) Processing helix chain 'W' and resid 107 through 149 removed outlier: 3.734A pdb=" N GLN W 149 " --> pdb=" O ASP W 145 " (cutoff:3.500A) Processing helix chain 'X' and resid 54 through 89 Proline residue: X 64 - end of helix Processing helix chain 'X' and resid 101 through 136 removed outlier: 4.228A pdb=" N LEU X 105 " --> pdb=" O PHE X 101 " (cutoff:3.500A) Processing helix chain 'X' and resid 155 through 185 Processing helix chain 'Y' and resid 29 through 57 removed outlier: 4.019A pdb=" N ASN Y 57 " --> pdb=" O GLN Y 53 " (cutoff:3.500A) Processing helix chain 'Y' and resid 68 through 102 Processing helix chain 'Y' and resid 139 through 176 Processing helix chain 'Z' and resid 11 through 17 removed outlier: 3.965A pdb=" N ARG Z 15 " --> pdb=" O ASP Z 11 " (cutoff:3.500A) Processing helix chain 'Z' and resid 18 through 21 removed outlier: 3.551A pdb=" N GLU Z 21 " --> pdb=" O PHE Z 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 18 through 21' Processing helix chain 'Z' and resid 34 through 40 removed outlier: 3.517A pdb=" N GLN Z 39 " --> pdb=" O ASN Z 35 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG Z 40 " --> pdb=" O PHE Z 36 " (cutoff:3.500A) Processing helix chain 'Z' and resid 45 through 55 Processing helix chain 'Z' and resid 60 through 64 removed outlier: 3.806A pdb=" N TYR Z 63 " --> pdb=" O GLU Z 60 " (cutoff:3.500A) Processing helix chain 'Z' and resid 71 through 81 Processing helix chain 'Z' and resid 90 through 103 removed outlier: 3.658A pdb=" N ALA Z 94 " --> pdb=" O ASN Z 90 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU Z 103 " --> pdb=" O GLU Z 99 " (cutoff:3.500A) Processing helix chain 'Z' and resid 106 through 118 removed outlier: 3.888A pdb=" N ARG Z 110 " --> pdb=" O GLN Z 106 " (cutoff:3.500A) Processing helix chain 'a' and resid 5 through 18 Processing sheet with id=AA1, first strand: chain 'A' and resid 103 through 104 Processing sheet with id=AA2, first strand: chain 'A' and resid 211 through 215 removed outlier: 4.508A pdb=" N MET A 220 " --> pdb=" O PRO A 213 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER A 215 " --> pdb=" O HIS A 218 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N HIS A 218 " --> pdb=" O SER A 215 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 258 through 260 Processing sheet with id=AA4, first strand: chain 'A' and resid 266 through 269 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AA6, first strand: chain 'A' and resid 362 through 366 removed outlier: 8.224A pdb=" N GLN A 371 " --> pdb=" O LEU A 438 " (cutoff:3.500A) removed outlier: 8.491A pdb=" N PHE A 440 " --> pdb=" O GLN A 371 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N CYS A 373 " --> pdb=" O PHE A 440 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N VAL A 442 " --> pdb=" O CYS A 373 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N PHE A 375 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N GLN A 439 " --> pdb=" O GLN A 455 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N GLN A 455 " --> pdb=" O GLN A 439 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ARG A 449 " --> pdb=" O LEU A 445 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 340 through 344 Processing sheet with id=AA8, first strand: chain 'I' and resid 438 through 439 removed outlier: 3.512A pdb=" N GLU I 438 " --> pdb=" O ILE I 445 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 459 through 460 removed outlier: 3.504A pdb=" N HIS I 459 " --> pdb=" O MET I 472 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET I 472 " --> pdb=" O HIS I 459 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'I' and resid 521 through 523 removed outlier: 3.716A pdb=" N ILE I 521 " --> pdb=" O LEU I 544 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE I 556 " --> pdb=" O TYR I 575 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 688 through 689 Processing sheet with id=AB3, first strand: chain 'I' and resid 813 through 815 removed outlier: 3.534A pdb=" N ALA I 840 " --> pdb=" O SER I 827 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N HIS I 838 " --> pdb=" O GLN I 829 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 911 through 913 removed outlier: 4.230A pdb=" N PHE I 924 " --> pdb=" O TYR I 928 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N TYR I 928 " --> pdb=" O PHE I 924 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 1367 through 1369 Processing sheet with id=AB6, first strand: chain 'I' and resid 1375 through 1376 removed outlier: 3.605A pdb=" N THR I1375 " --> pdb=" O ILE I1388 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 691 through 693 removed outlier: 4.512A pdb=" N ILE J 708 " --> pdb=" O ASN J 693 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 50 through 52 Processing sheet with id=AB9, first strand: chain 'K' and resid 157 through 158 removed outlier: 3.547A pdb=" N LEU K 158 " --> pdb=" O LYS K 162 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 227 through 231 removed outlier: 5.953A pdb=" N VAL K 227 " --> pdb=" O SER K 250 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N SER K 250 " --> pdb=" O VAL K 227 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N PHE K 229 " --> pdb=" O LEU K 248 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 292 through 297 removed outlier: 6.910A pdb=" N SER K 292 " --> pdb=" O ASN K 334 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ASN K 334 " --> pdb=" O SER K 292 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL K 294 " --> pdb=" O ALA K 332 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ALA K 332 " --> pdb=" O VAL K 294 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N CYS K 296 " --> pdb=" O LEU K 330 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 302 through 303 Processing sheet with id=AC4, first strand: chain 'K' and resid 369 through 373 Processing sheet with id=AC5, first strand: chain 'L' and resid 322 through 324 Processing sheet with id=AC6, first strand: chain 'L' and resid 459 through 462 removed outlier: 3.828A pdb=" N ARG L 501 " --> pdb=" O LEU L 493 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 569 through 571 Processing sheet with id=AC8, first strand: chain 'M' and resid 18 through 20 Processing sheet with id=AC9, first strand: chain 'M' and resid 23 through 24 removed outlier: 4.225A pdb=" N VAL M 145 " --> pdb=" O HIS M 134 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL M 130 " --> pdb=" O PHE M 149 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N VAL M 57 " --> pdb=" O ASP M 126 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N GLU M 128 " --> pdb=" O GLU M 55 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N GLU M 55 " --> pdb=" O GLU M 128 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N VAL M 130 " --> pdb=" O ASP M 53 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ASP M 53 " --> pdb=" O VAL M 130 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 83 through 91 Processing sheet with id=AD2, first strand: chain 'O' and resid 7 through 8 Processing sheet with id=AD3, first strand: chain 'T' and resid 19 through 22 removed outlier: 5.666A pdb=" N PHE T 20 " --> pdb=" O VAL T 69 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'T' and resid 144 through 145 removed outlier: 6.828A pdb=" N LEU T 144 " --> pdb=" O VAL T 183 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'V' and resid 177 through 180 removed outlier: 3.637A pdb=" N SER V 177 " --> pdb=" O THR V 193 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL V 203 " --> pdb=" O ARG V 211 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ARG V 211 " --> pdb=" O VAL V 203 " (cutoff:3.500A) 2974 hydrogen bonds defined for protein. 8733 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: 16.43 Time building geometry restraints manager: 12.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.46: 23415 1.46 - 1.70: 26763 1.70 - 1.94: 234 1.94 - 2.17: 2 2.17 - 2.41: 1 Bond restraints: 50415 Sorted by residual: bond pdb=" C SER O 104 " pdb=" N ALA O 105 " ideal model delta sigma weight residual 1.332 2.413 -1.081 1.40e-02 5.10e+03 5.96e+03 bond pdb=" CD2 TYR O 46 " pdb=" CE2 TYR O 46 " ideal model delta sigma weight residual 1.382 2.130 -0.748 3.00e-02 1.11e+03 6.22e+02 bond pdb=" CD1 TYR O 46 " pdb=" CE1 TYR O 46 " ideal model delta sigma weight residual 1.382 2.100 -0.718 3.00e-02 1.11e+03 5.72e+02 bond pdb=" CE1 TYR O 46 " pdb=" CZ TYR O 46 " ideal model delta sigma weight residual 1.378 1.786 -0.408 2.40e-02 1.74e+03 2.89e+02 bond pdb=" CE2 TYR O 46 " pdb=" CZ TYR O 46 " ideal model delta sigma weight residual 1.378 1.786 -0.408 2.40e-02 1.74e+03 2.89e+02 ... (remaining 50410 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.77: 69374 7.77 - 15.55: 6 15.55 - 23.32: 1 23.32 - 31.09: 0 31.09 - 38.87: 1 Bond angle restraints: 69382 Sorted by residual: angle pdb=" C SER O 104 " pdb=" N ALA O 105 " pdb=" CA ALA O 105 " ideal model delta sigma weight residual 121.54 160.41 -38.87 1.91e+00 2.74e-01 4.14e+02 angle pdb=" C ALA K 286 " pdb=" N THR K 290 " pdb=" CA THR K 290 " ideal model delta sigma weight residual 121.70 137.26 -15.56 1.80e+00 3.09e-01 7.47e+01 angle pdb=" CA SER O 104 " pdb=" C SER O 104 " pdb=" N ALA O 105 " ideal model delta sigma weight residual 115.75 123.84 -8.09 1.08e+00 8.57e-01 5.61e+01 angle pdb=" CA SER O 104 " pdb=" C SER O 104 " pdb=" O SER O 104 " ideal model delta sigma weight residual 120.89 111.42 9.47 1.27e+00 6.20e-01 5.56e+01 angle pdb=" C GLU I 795 " pdb=" N ILE I 796 " pdb=" CA ILE I 796 " ideal model delta sigma weight residual 120.24 123.01 -2.77 6.30e-01 2.52e+00 1.94e+01 ... (remaining 69377 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 28038 17.99 - 35.99: 1317 35.99 - 53.98: 196 53.98 - 71.98: 21 71.98 - 89.97: 10 Dihedral angle restraints: 29582 sinusoidal: 6600 harmonic: 22982 Sorted by residual: dihedral pdb=" CB CYS O 75 " pdb=" SG CYS O 75 " pdb=" SG CYS O 84 " pdb=" CB CYS O 84 " ideal model delta sinusoidal sigma weight residual -86.00 -6.71 -79.29 1 1.00e+01 1.00e-02 7.82e+01 dihedral pdb=" CA GLU C 58 " pdb=" C GLU C 58 " pdb=" N HIS C 59 " pdb=" CA HIS C 59 " ideal model delta harmonic sigma weight residual 180.00 142.55 37.45 0 5.00e+00 4.00e-02 5.61e+01 dihedral pdb=" CA THR A 104 " pdb=" C THR A 104 " pdb=" N SER A 105 " pdb=" CA SER A 105 " ideal model delta harmonic sigma weight residual 180.00 146.94 33.06 0 5.00e+00 4.00e-02 4.37e+01 ... (remaining 29579 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 6193 0.039 - 0.079: 1801 0.079 - 0.118: 529 0.118 - 0.158: 37 0.158 - 0.197: 1 Chirality restraints: 8561 Sorted by residual: chirality pdb=" CB VAL R1310 " pdb=" CA VAL R1310 " pdb=" CG1 VAL R1310 " pdb=" CG2 VAL R1310 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.72e-01 chirality pdb=" CA THR K 290 " pdb=" N THR K 290 " pdb=" C THR K 290 " pdb=" CB THR K 290 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.16 2.00e-01 2.50e+01 6.03e-01 chirality pdb=" CA LEU U 531 " pdb=" N LEU U 531 " pdb=" C LEU U 531 " pdb=" CB LEU U 531 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.81e-01 ... (remaining 8558 not shown) Planarity restraints: 9251 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR O 46 " 0.024 2.00e-02 2.50e+03 2.34e-02 1.09e+01 pdb=" CG TYR O 46 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TYR O 46 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR O 46 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR O 46 " 0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR O 46 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR O 46 " -0.020 2.00e-02 2.50e+03 pdb=" OH TYR O 46 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU V 292 " 0.043 5.00e-02 4.00e+02 6.48e-02 6.72e+00 pdb=" N PRO V 293 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO V 293 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO V 293 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 104 " 0.012 2.00e-02 2.50e+03 2.54e-02 6.44e+00 pdb=" C THR A 104 " -0.044 2.00e-02 2.50e+03 pdb=" O THR A 104 " 0.017 2.00e-02 2.50e+03 pdb=" N SER A 105 " 0.015 2.00e-02 2.50e+03 ... (remaining 9248 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 306 2.55 - 3.13: 42199 3.13 - 3.72: 79673 3.72 - 4.31: 92469 4.31 - 4.90: 147993 Nonbonded interactions: 362640 Sorted by model distance: nonbonded pdb=" CE1 TYR O 46 " pdb=" N ALA O 105 " model vdw 1.958 3.420 nonbonded pdb=" CD1 TYR O 46 " pdb=" N ALA O 105 " model vdw 1.965 3.420 nonbonded pdb=" CZ TYR O 46 " pdb=" N ALA O 105 " model vdw 2.070 3.340 nonbonded pdb=" CD2 TYR O 46 " pdb=" N ALA O 105 " model vdw 2.091 3.420 nonbonded pdb=" O THR R 532 " pdb=" OH TYR R 573 " model vdw 2.095 3.040 ... (remaining 362635 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 1.690 Check model and map are aligned: 0.300 Set scattering table: 0.370 Process input model: 87.950 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 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 : 0.008 1.081 50415 Z= 0.466 Angle : 0.632 38.866 69382 Z= 0.356 Chirality : 0.039 0.197 8561 Planarity : 0.003 0.065 9251 Dihedral : 11.369 89.973 14501 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 12.20 % Favored : 87.75 % Rotamer: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.26 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.42 (0.09), residues: 7655 helix: -0.36 (0.08), residues: 3764 sheet: -3.63 (0.20), residues: 398 loop : -4.49 (0.09), residues: 3493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP K 810 HIS 0.009 0.001 HIS R 921 PHE 0.017 0.001 PHE I 469 TYR 0.052 0.001 TYR O 46 ARG 0.003 0.000 ARG K 198 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15310 Ramachandran restraints generated. 7655 Oldfield, 0 Emsley, 7655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15310 Ramachandran restraints generated. 7655 Oldfield, 0 Emsley, 7655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 7017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 368 time to evaluate : 4.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 312 GLU cc_start: 0.8945 (tp30) cc_final: 0.8717 (mt-10) REVERT: I 705 LYS cc_start: 0.9494 (ttpt) cc_final: 0.9293 (ttpp) REVERT: M 85 LEU cc_start: 0.9442 (tt) cc_final: 0.9168 (mm) REVERT: M 146 TYR cc_start: 0.9213 (p90) cc_final: 0.8739 (p90) REVERT: N 68 MET cc_start: 0.4262 (mmt) cc_final: 0.3862 (mmm) REVERT: N 77 LEU cc_start: 0.9333 (mt) cc_final: 0.9059 (pp) REVERT: R 525 MET cc_start: 0.3621 (ppp) cc_final: 0.3178 (ppp) REVERT: R 607 MET cc_start: 0.7903 (tpp) cc_final: 0.7294 (mmm) REVERT: R 742 PHE cc_start: 0.9266 (t80) cc_final: 0.8794 (t80) REVERT: R 743 PHE cc_start: 0.9129 (m-80) cc_final: 0.8692 (m-80) REVERT: R 770 MET cc_start: 0.6376 (mtt) cc_final: 0.5826 (mtt) REVERT: S 166 GLU cc_start: 0.9179 (tm-30) cc_final: 0.8856 (tt0) REVERT: T 36 ARG cc_start: 0.9743 (ttt180) cc_final: 0.9256 (mmp80) REVERT: Y 173 MET cc_start: 0.7325 (mmm) cc_final: 0.7099 (mmm) outliers start: 0 outliers final: 0 residues processed: 368 average time/residue: 0.4282 time to fit residues: 276.2976 Evaluate side-chains 304 residues out of total 7017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 304 time to evaluate : 4.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 776 random chunks: chunk 655 optimal weight: 0.6980 chunk 588 optimal weight: 3.9990 chunk 326 optimal weight: 0.5980 chunk 200 optimal weight: 3.9990 chunk 396 optimal weight: 9.9990 chunk 314 optimal weight: 0.1980 chunk 608 optimal weight: 1.9990 chunk 235 optimal weight: 9.9990 chunk 369 optimal weight: 8.9990 chunk 452 optimal weight: 0.9980 chunk 704 optimal weight: 7.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 380 HIS ** I 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 866 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 876 GLN I 889 ASN I1226 GLN K 92 GLN ** K 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 459 GLN K 488 GLN ** K 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 554 HIS K 773 HIS L 216 HIS L 308 GLN L 327 ASN L 332 GLN L 435 HIS L 461 HIS L 533 HIS R 378 GLN R 455 HIS R 459 GLN R 596 HIS R 639 ASN R 642 HIS R 684 ASN R 726 ASN ** R 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 851 ASN R 921 HIS R 972 HIS R1051 HIS R1165 HIS R1334 HIS S 8 GLN S 111 HIS ** S 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 426 HIS S 625 HIS ** S 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 758 HIS S 920 GLN T 72 ASN ** V 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 109 GLN Y 79 GLN Y 146 ASN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.0995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.951 50415 Z= 0.404 Angle : 0.604 35.400 69382 Z= 0.311 Chirality : 0.041 0.268 8561 Planarity : 0.004 0.058 9251 Dihedral : 4.228 37.521 8086 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.13 % Favored : 88.87 % Rotamer: Outliers : 0.07 % Allowed : 5.24 % Favored : 94.69 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.26 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.10), residues: 7657 helix: 0.74 (0.08), residues: 3850 sheet: -3.23 (0.21), residues: 405 loop : -4.25 (0.09), residues: 3402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP R 855 HIS 0.009 0.001 HIS L 435 PHE 0.024 0.001 PHE Q 85 TYR 0.053 0.001 TYR O 46 ARG 0.011 0.000 ARG W 74 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15314 Ramachandran restraints generated. 7657 Oldfield, 0 Emsley, 7657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15314 Ramachandran restraints generated. 7657 Oldfield, 0 Emsley, 7657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 7017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 339 time to evaluate : 4.504 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: I 312 GLU cc_start: 0.8945 (tp30) cc_final: 0.8687 (mt-10) REVERT: I 322 ILE cc_start: 0.9219 (mt) cc_final: 0.8926 (mt) REVERT: K 421 MET cc_start: 0.6380 (mpp) cc_final: 0.6178 (mpp) REVERT: L 375 LEU cc_start: 0.9316 (pp) cc_final: 0.9097 (mt) REVERT: M 71 ARG cc_start: 0.8977 (mmp80) cc_final: 0.8774 (mmm160) REVERT: M 85 LEU cc_start: 0.9421 (tt) cc_final: 0.9145 (mm) REVERT: M 146 TYR cc_start: 0.9164 (p90) cc_final: 0.8746 (p90) REVERT: N 68 MET cc_start: 0.4216 (mmt) cc_final: 0.3823 (mmm) REVERT: N 77 LEU cc_start: 0.9333 (mt) cc_final: 0.9061 (pp) REVERT: Q 85 PHE cc_start: 0.8492 (m-80) cc_final: 0.8244 (m-80) REVERT: R 425 MET cc_start: 0.9100 (tpt) cc_final: 0.8170 (mtt) REVERT: R 525 MET cc_start: 0.4273 (ppp) cc_final: 0.3475 (ppp) REVERT: R 574 MET cc_start: 0.7305 (mtm) cc_final: 0.6918 (mtt) REVERT: R 607 MET cc_start: 0.7752 (tpp) cc_final: 0.7179 (mmm) REVERT: R 742 PHE cc_start: 0.9303 (t80) cc_final: 0.8820 (t80) REVERT: R 743 PHE cc_start: 0.9094 (m-80) cc_final: 0.8643 (m-80) REVERT: R 770 MET cc_start: 0.6229 (mtt) cc_final: 0.5592 (mtt) REVERT: R 853 MET cc_start: 0.8335 (mpp) cc_final: 0.8060 (mpp) REVERT: R 922 MET cc_start: 0.8927 (mmp) cc_final: 0.8472 (mmm) REVERT: S 166 GLU cc_start: 0.9147 (tm-30) cc_final: 0.8829 (tt0) REVERT: S 268 MET cc_start: 0.8657 (mtt) cc_final: 0.8444 (mmt) REVERT: T 36 ARG cc_start: 0.9742 (ttt180) cc_final: 0.9215 (mmp80) REVERT: Y 173 MET cc_start: 0.7447 (mmm) cc_final: 0.7180 (mmm) outliers start: 2 outliers final: 0 residues processed: 341 average time/residue: 0.4389 time to fit residues: 266.6537 Evaluate side-chains 289 residues out of total 7017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 4.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 776 random chunks: chunk 391 optimal weight: 9.9990 chunk 218 optimal weight: 8.9990 chunk 586 optimal weight: 0.4980 chunk 479 optimal weight: 9.9990 chunk 194 optimal weight: 0.7980 chunk 705 optimal weight: 0.1980 chunk 762 optimal weight: 3.9990 chunk 628 optimal weight: 9.9990 chunk 700 optimal weight: 1.9990 chunk 240 optimal weight: 8.9990 chunk 566 optimal weight: 6.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 754 HIS ** K 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 290 GLN R 602 HIS ** R 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R1334 HIS ** S 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 38 HIS ** V 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.961 50415 Z= 0.406 Angle : 0.591 35.614 69382 Z= 0.305 Chirality : 0.040 0.202 8561 Planarity : 0.004 0.064 9251 Dihedral : 4.191 37.754 8086 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.98 % Favored : 89.02 % Rotamer: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.26 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.78 (0.10), residues: 7657 helix: 1.22 (0.09), residues: 3853 sheet: -3.05 (0.22), residues: 416 loop : -4.06 (0.09), residues: 3388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP T 97 HIS 0.010 0.001 HIS R1334 PHE 0.021 0.001 PHE T 128 TYR 0.033 0.001 TYR O 46 ARG 0.005 0.000 ARG L 505 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15314 Ramachandran restraints generated. 7657 Oldfield, 0 Emsley, 7657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15314 Ramachandran restraints generated. 7657 Oldfield, 0 Emsley, 7657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 7017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 327 time to evaluate : 4.380 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: J 710 LYS cc_start: 0.9106 (mppt) cc_final: 0.8677 (mmtm) REVERT: K 421 MET cc_start: 0.6648 (mpp) cc_final: 0.6413 (mpp) REVERT: L 375 LEU cc_start: 0.9318 (pp) cc_final: 0.9041 (mt) REVERT: M 85 LEU cc_start: 0.9408 (tt) cc_final: 0.9172 (mm) REVERT: M 146 TYR cc_start: 0.9203 (p90) cc_final: 0.8773 (p90) REVERT: N 68 MET cc_start: 0.4615 (mmt) cc_final: 0.4255 (mmm) REVERT: N 77 LEU cc_start: 0.9336 (mt) cc_final: 0.9065 (pp) REVERT: Q 85 PHE cc_start: 0.8444 (m-80) cc_final: 0.8209 (m-80) REVERT: R 207 ASP cc_start: 0.8869 (m-30) cc_final: 0.8462 (p0) REVERT: R 525 MET cc_start: 0.4322 (ppp) cc_final: 0.3367 (ppp) REVERT: R 574 MET cc_start: 0.7574 (mtm) cc_final: 0.7116 (mtt) REVERT: R 607 MET cc_start: 0.7746 (tpp) cc_final: 0.7195 (mmm) REVERT: R 729 SER cc_start: 0.8382 (t) cc_final: 0.8109 (p) REVERT: R 770 MET cc_start: 0.6327 (mtt) cc_final: 0.5700 (mtt) REVERT: R 853 MET cc_start: 0.8278 (mpp) cc_final: 0.7793 (mpp) REVERT: R 922 MET cc_start: 0.9080 (mmp) cc_final: 0.8586 (mmm) REVERT: R 1017 ARG cc_start: 0.9517 (tmt170) cc_final: 0.9316 (tpt90) REVERT: S 51 MET cc_start: 0.5975 (tpp) cc_final: 0.5689 (tpt) REVERT: S 268 MET cc_start: 0.8784 (mtt) cc_final: 0.8494 (mmt) REVERT: T 36 ARG cc_start: 0.9742 (ttt180) cc_final: 0.9210 (mmp80) outliers start: 0 outliers final: 0 residues processed: 327 average time/residue: 0.4206 time to fit residues: 247.1413 Evaluate side-chains 286 residues out of total 7017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 286 time to evaluate : 4.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 776 random chunks: chunk 697 optimal weight: 50.0000 chunk 530 optimal weight: 8.9990 chunk 366 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 336 optimal weight: 40.0000 chunk 474 optimal weight: 0.5980 chunk 708 optimal weight: 5.9990 chunk 750 optimal weight: 8.9990 chunk 370 optimal weight: 6.9990 chunk 671 optimal weight: 0.8980 chunk 202 optimal weight: 1.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1188 ASN ** J 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 768 HIS ** K 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 371 HIS L 526 GLN ** R 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 459 GLN ** R 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 858 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R1261 GLN ** S 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 101 GLN X 86 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.951 50415 Z= 0.427 Angle : 0.622 35.994 69382 Z= 0.328 Chirality : 0.041 0.179 8561 Planarity : 0.004 0.065 9251 Dihedral : 4.378 37.688 8086 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.26 % Favored : 87.74 % Rotamer: Outliers : 0.07 % Allowed : 4.97 % Favored : 94.96 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.26 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.53 (0.10), residues: 7657 helix: 1.41 (0.09), residues: 3855 sheet: -2.96 (0.22), residues: 414 loop : -3.93 (0.10), residues: 3388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP T 97 HIS 0.007 0.001 HIS S 728 PHE 0.018 0.002 PHE K 143 TYR 0.065 0.002 TYR O 46 ARG 0.006 0.001 ARG K 198 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15314 Ramachandran restraints generated. 7657 Oldfield, 0 Emsley, 7657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15314 Ramachandran restraints generated. 7657 Oldfield, 0 Emsley, 7657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 7017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 318 time to evaluate : 4.488 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: J 648 MET cc_start: 0.8908 (tpt) cc_final: 0.8642 (tpp) REVERT: L 375 LEU cc_start: 0.9319 (pp) cc_final: 0.9087 (mt) REVERT: L 637 MET cc_start: 0.8403 (pmm) cc_final: 0.7939 (mmp) REVERT: M 85 LEU cc_start: 0.9414 (tt) cc_final: 0.9166 (mm) REVERT: M 146 TYR cc_start: 0.9257 (p90) cc_final: 0.8860 (p90) REVERT: N 68 MET cc_start: 0.4748 (mmt) cc_final: 0.4412 (mmm) REVERT: N 77 LEU cc_start: 0.9346 (mt) cc_final: 0.9077 (pp) REVERT: R 207 ASP cc_start: 0.8977 (m-30) cc_final: 0.8561 (p0) REVERT: R 425 MET cc_start: 0.9085 (tpt) cc_final: 0.8135 (mtt) REVERT: R 525 MET cc_start: 0.4831 (ppp) cc_final: 0.3931 (ppp) REVERT: R 574 MET cc_start: 0.7976 (mtm) cc_final: 0.7502 (mtt) REVERT: R 770 MET cc_start: 0.6726 (mtt) cc_final: 0.6297 (mtt) REVERT: R 796 MET cc_start: 0.8422 (tpp) cc_final: 0.8141 (tpp) REVERT: R 853 MET cc_start: 0.8044 (mpp) cc_final: 0.7783 (mpp) REVERT: R 922 MET cc_start: 0.9109 (mmp) cc_final: 0.8605 (mmm) REVERT: S 268 MET cc_start: 0.8771 (mtt) cc_final: 0.8500 (mmt) REVERT: T 36 ARG cc_start: 0.9745 (ttt180) cc_final: 0.9202 (mmp80) REVERT: X 74 MET cc_start: 0.8924 (ptt) cc_final: 0.8636 (ptm) outliers start: 2 outliers final: 0 residues processed: 320 average time/residue: 0.4251 time to fit residues: 245.2457 Evaluate side-chains 275 residues out of total 7017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 4.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 776 random chunks: chunk 624 optimal weight: 0.0870 chunk 425 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 558 optimal weight: 0.0970 chunk 309 optimal weight: 0.9990 chunk 640 optimal weight: 9.9990 chunk 518 optimal weight: 0.9980 chunk 0 optimal weight: 40.0000 chunk 383 optimal weight: 10.0000 chunk 673 optimal weight: 5.9990 chunk 189 optimal weight: 0.9980 overall best weight: 0.6356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 310 GLN ** I 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 509 GLN ** J 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 768 HIS ** K 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 464 ASN L 526 GLN R 378 GLN R 618 HIS ** R 696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 858 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 49 GLN ** S 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.975 50415 Z= 0.400 Angle : 0.598 35.117 69382 Z= 0.303 Chirality : 0.040 0.184 8561 Planarity : 0.004 0.061 9251 Dihedral : 4.254 38.088 8086 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.01 % Allowed : 10.60 % Favored : 89.38 % Rotamer: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.26 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.27 (0.10), residues: 7657 helix: 1.66 (0.09), residues: 3856 sheet: -2.87 (0.23), residues: 419 loop : -3.85 (0.10), residues: 3382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP T 97 HIS 0.006 0.001 HIS R 921 PHE 0.023 0.001 PHE V 208 TYR 0.044 0.001 TYR O 46 ARG 0.010 0.000 ARG R1000 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15314 Ramachandran restraints generated. 7657 Oldfield, 0 Emsley, 7657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15314 Ramachandran restraints generated. 7657 Oldfield, 0 Emsley, 7657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 7017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 327 time to evaluate : 4.460 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: K 421 MET cc_start: 0.6341 (mpp) cc_final: 0.5947 (mpp) REVERT: L 375 LEU cc_start: 0.9293 (pp) cc_final: 0.9048 (mt) REVERT: M 85 LEU cc_start: 0.9403 (tt) cc_final: 0.9167 (mm) REVERT: M 146 TYR cc_start: 0.9187 (p90) cc_final: 0.8808 (p90) REVERT: N 68 MET cc_start: 0.4707 (mmt) cc_final: 0.4377 (mmm) REVERT: N 77 LEU cc_start: 0.9352 (mt) cc_final: 0.9084 (pp) REVERT: Q 85 PHE cc_start: 0.8384 (m-80) cc_final: 0.8115 (m-80) REVERT: R 425 MET cc_start: 0.9030 (tpt) cc_final: 0.8359 (mmt) REVERT: R 525 MET cc_start: 0.4532 (ppp) cc_final: 0.3467 (ppp) REVERT: R 574 MET cc_start: 0.7574 (mtm) cc_final: 0.7291 (mtt) REVERT: R 607 MET cc_start: 0.7509 (tpp) cc_final: 0.6854 (mmp) REVERT: R 770 MET cc_start: 0.6577 (mtt) cc_final: 0.5976 (mtt) REVERT: R 853 MET cc_start: 0.8237 (mpp) cc_final: 0.7783 (mpp) REVERT: R 922 MET cc_start: 0.9096 (mmp) cc_final: 0.8691 (mmm) REVERT: R 1017 ARG cc_start: 0.9299 (tpt90) cc_final: 0.9081 (tpt90) REVERT: R 1151 LEU cc_start: 0.9347 (mt) cc_final: 0.9120 (mt) REVERT: S 268 MET cc_start: 0.8766 (mtt) cc_final: 0.8459 (mmt) REVERT: X 74 MET cc_start: 0.8790 (ptt) cc_final: 0.8564 (ptm) outliers start: 0 outliers final: 0 residues processed: 327 average time/residue: 0.4193 time to fit residues: 247.3651 Evaluate side-chains 280 residues out of total 7017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 280 time to evaluate : 4.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 776 random chunks: chunk 252 optimal weight: 0.6980 chunk 675 optimal weight: 0.0170 chunk 148 optimal weight: 20.0000 chunk 440 optimal weight: 40.0000 chunk 185 optimal weight: 0.6980 chunk 750 optimal weight: 7.9990 chunk 623 optimal weight: 20.0000 chunk 347 optimal weight: 1.9990 chunk 62 optimal weight: 40.0000 chunk 248 optimal weight: 0.7980 chunk 394 optimal weight: 5.9990 overall best weight: 0.8420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 680 GLN J 768 HIS ** K 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 459 GLN R 618 HIS ** R 696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 858 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.956 50415 Z= 0.397 Angle : 0.590 34.840 69382 Z= 0.299 Chirality : 0.040 0.196 8561 Planarity : 0.004 0.101 9251 Dihedral : 4.186 37.793 8086 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.01 % Allowed : 11.06 % Favored : 88.93 % Rotamer: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.26 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.15 (0.10), residues: 7657 helix: 1.77 (0.09), residues: 3860 sheet: -2.79 (0.23), residues: 415 loop : -3.81 (0.10), residues: 3382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.001 TRP T 97 HIS 0.006 0.001 HIS I 315 PHE 0.018 0.001 PHE V 208 TYR 0.068 0.001 TYR O 46 ARG 0.010 0.000 ARG W 74 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15314 Ramachandran restraints generated. 7657 Oldfield, 0 Emsley, 7657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15314 Ramachandran restraints generated. 7657 Oldfield, 0 Emsley, 7657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 7017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 325 time to evaluate : 4.548 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: I 896 MET cc_start: 0.8588 (mmt) cc_final: 0.8201 (mmm) REVERT: K 421 MET cc_start: 0.6169 (mpp) cc_final: 0.5920 (mpp) REVERT: K 644 GLU cc_start: 0.8550 (tp30) cc_final: 0.8342 (mm-30) REVERT: L 375 LEU cc_start: 0.9304 (pp) cc_final: 0.9032 (mt) REVERT: M 85 LEU cc_start: 0.9405 (tt) cc_final: 0.9185 (mm) REVERT: M 146 TYR cc_start: 0.9102 (p90) cc_final: 0.8779 (p90) REVERT: N 68 MET cc_start: 0.4865 (mmt) cc_final: 0.4546 (mmm) REVERT: N 77 LEU cc_start: 0.9351 (mt) cc_final: 0.9084 (pp) REVERT: Q 85 PHE cc_start: 0.8368 (m-80) cc_final: 0.8082 (m-80) REVERT: R 425 MET cc_start: 0.8995 (tpt) cc_final: 0.8351 (mmt) REVERT: R 525 MET cc_start: 0.4582 (ppp) cc_final: 0.3504 (ppp) REVERT: R 607 MET cc_start: 0.7501 (tpp) cc_final: 0.6866 (mmp) REVERT: R 742 PHE cc_start: 0.9326 (t80) cc_final: 0.9110 (t80) REVERT: R 770 MET cc_start: 0.6506 (mtt) cc_final: 0.6098 (mtt) REVERT: R 853 MET cc_start: 0.8330 (mpp) cc_final: 0.7980 (mpp) REVERT: R 922 MET cc_start: 0.9005 (mmp) cc_final: 0.8654 (mmm) REVERT: R 1017 ARG cc_start: 0.9277 (tpt90) cc_final: 0.9041 (tpt90) REVERT: R 1151 LEU cc_start: 0.9370 (mt) cc_final: 0.9168 (mt) REVERT: S 51 MET cc_start: 0.4629 (tpp) cc_final: 0.4128 (tpp) REVERT: S 268 MET cc_start: 0.8725 (mtt) cc_final: 0.8420 (mmt) REVERT: W 44 LEU cc_start: 0.8241 (tp) cc_final: 0.7817 (pp) REVERT: X 74 MET cc_start: 0.8785 (ptt) cc_final: 0.8580 (ptm) outliers start: 0 outliers final: 0 residues processed: 325 average time/residue: 0.4171 time to fit residues: 245.9111 Evaluate side-chains 284 residues out of total 7017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 4.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 776 random chunks: chunk 723 optimal weight: 10.0000 chunk 84 optimal weight: 50.0000 chunk 427 optimal weight: 0.3980 chunk 548 optimal weight: 0.7980 chunk 424 optimal weight: 10.0000 chunk 632 optimal weight: 8.9990 chunk 419 optimal weight: 0.9990 chunk 747 optimal weight: 5.9990 chunk 468 optimal weight: 0.7980 chunk 455 optimal weight: 20.0000 chunk 345 optimal weight: 40.0000 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 768 HIS ** K 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 526 GLN ** R 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 622 GLN ** R 696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 858 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 49 GLN ** S 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.958 50415 Z= 0.409 Angle : 0.596 35.400 69382 Z= 0.307 Chirality : 0.040 0.169 8561 Planarity : 0.004 0.089 9251 Dihedral : 4.221 38.283 8086 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.68 % Favored : 88.32 % Rotamer: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.26 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.08 (0.10), residues: 7657 helix: 1.81 (0.09), residues: 3864 sheet: -2.75 (0.23), residues: 411 loop : -3.76 (0.10), residues: 3382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP T 97 HIS 0.008 0.001 HIS R 333 PHE 0.016 0.001 PHE R1243 TYR 0.045 0.001 TYR O 46 ARG 0.008 0.000 ARG R1093 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15314 Ramachandran restraints generated. 7657 Oldfield, 0 Emsley, 7657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15314 Ramachandran restraints generated. 7657 Oldfield, 0 Emsley, 7657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 7017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 321 time to evaluate : 4.490 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: I 896 MET cc_start: 0.8688 (mmt) cc_final: 0.8287 (mmm) REVERT: K 421 MET cc_start: 0.6242 (mpp) cc_final: 0.6004 (mpp) REVERT: K 644 GLU cc_start: 0.8539 (tp30) cc_final: 0.8292 (mm-30) REVERT: L 375 LEU cc_start: 0.9309 (pp) cc_final: 0.9042 (mt) REVERT: L 637 MET cc_start: 0.8266 (pmm) cc_final: 0.7872 (mmp) REVERT: M 146 TYR cc_start: 0.9135 (p90) cc_final: 0.8752 (p90) REVERT: N 77 LEU cc_start: 0.9337 (mt) cc_final: 0.9059 (pp) REVERT: Q 85 PHE cc_start: 0.8451 (m-80) cc_final: 0.8169 (m-80) REVERT: R 425 MET cc_start: 0.8973 (tpt) cc_final: 0.7958 (mtt) REVERT: R 525 MET cc_start: 0.5004 (ppp) cc_final: 0.4660 (ppp) REVERT: R 729 SER cc_start: 0.8406 (t) cc_final: 0.8131 (p) REVERT: R 770 MET cc_start: 0.6576 (mtt) cc_final: 0.6174 (mtt) REVERT: R 853 MET cc_start: 0.8337 (mpp) cc_final: 0.7935 (mpp) REVERT: R 922 MET cc_start: 0.9064 (mmp) cc_final: 0.8778 (mmm) REVERT: R 1017 ARG cc_start: 0.9286 (tpt90) cc_final: 0.9043 (tpt90) REVERT: S 268 MET cc_start: 0.8756 (mtt) cc_final: 0.8460 (mmt) REVERT: W 44 LEU cc_start: 0.8308 (tp) cc_final: 0.8026 (pp) outliers start: 0 outliers final: 0 residues processed: 321 average time/residue: 0.4286 time to fit residues: 247.6372 Evaluate side-chains 281 residues out of total 7017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 4.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 776 random chunks: chunk 462 optimal weight: 0.9980 chunk 298 optimal weight: 9.9990 chunk 446 optimal weight: 50.0000 chunk 225 optimal weight: 0.9990 chunk 146 optimal weight: 0.7980 chunk 144 optimal weight: 50.0000 chunk 475 optimal weight: 5.9990 chunk 509 optimal weight: 4.9990 chunk 369 optimal weight: 4.9990 chunk 69 optimal weight: 7.9990 chunk 587 optimal weight: 4.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 768 HIS ** L 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 526 GLN ** R 696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 726 ASN ** R 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 858 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 252 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 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 : 0.008 0.955 50415 Z= 0.424 Angle : 0.624 35.420 69382 Z= 0.322 Chirality : 0.041 0.189 8561 Planarity : 0.004 0.083 9251 Dihedral : 4.377 37.813 8086 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.62 % Favored : 87.38 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.26 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.09 (0.10), residues: 7657 helix: 1.75 (0.09), residues: 3873 sheet: -2.62 (0.24), residues: 405 loop : -3.72 (0.10), residues: 3379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP T 97 HIS 0.010 0.001 HIS K 535 PHE 0.031 0.002 PHE K 539 TYR 0.042 0.002 TYR O 46 ARG 0.009 0.001 ARG K 384 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15314 Ramachandran restraints generated. 7657 Oldfield, 0 Emsley, 7657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15314 Ramachandran restraints generated. 7657 Oldfield, 0 Emsley, 7657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 7017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 318 time to evaluate : 4.502 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: I 653 MET cc_start: 0.6886 (ppp) cc_final: 0.6664 (ppp) REVERT: I 896 MET cc_start: 0.8768 (mmt) cc_final: 0.8347 (mmm) REVERT: J 648 MET cc_start: 0.8933 (tpt) cc_final: 0.8696 (tpp) REVERT: J 710 LYS cc_start: 0.9181 (mppt) cc_final: 0.8395 (mmtm) REVERT: K 421 MET cc_start: 0.6371 (mpp) cc_final: 0.6151 (mpp) REVERT: K 644 GLU cc_start: 0.8542 (tp30) cc_final: 0.8103 (tp30) REVERT: L 375 LEU cc_start: 0.9326 (pp) cc_final: 0.9050 (mt) REVERT: L 637 MET cc_start: 0.8358 (pmm) cc_final: 0.7785 (mmp) REVERT: M 146 TYR cc_start: 0.9161 (p90) cc_final: 0.8769 (p90) REVERT: N 77 LEU cc_start: 0.9300 (mt) cc_final: 0.9016 (pp) REVERT: R 286 MET cc_start: 0.8504 (mtm) cc_final: 0.8302 (mtm) REVERT: R 425 MET cc_start: 0.9004 (tpt) cc_final: 0.7988 (mtt) REVERT: R 729 SER cc_start: 0.8505 (t) cc_final: 0.8284 (p) REVERT: R 770 MET cc_start: 0.6639 (mtt) cc_final: 0.6233 (mtt) REVERT: R 853 MET cc_start: 0.8434 (mpp) cc_final: 0.8006 (mpp) REVERT: R 922 MET cc_start: 0.9170 (mmp) cc_final: 0.8795 (mmm) REVERT: S 268 MET cc_start: 0.8800 (mtt) cc_final: 0.8475 (mmt) REVERT: W 44 LEU cc_start: 0.8480 (tp) cc_final: 0.8241 (pp) outliers start: 0 outliers final: 0 residues processed: 318 average time/residue: 0.4101 time to fit residues: 234.9536 Evaluate side-chains 275 residues out of total 7017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 4.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 776 random chunks: chunk 680 optimal weight: 10.0000 chunk 716 optimal weight: 0.6980 chunk 653 optimal weight: 6.9990 chunk 696 optimal weight: 20.0000 chunk 419 optimal weight: 5.9990 chunk 303 optimal weight: 10.0000 chunk 547 optimal weight: 0.6980 chunk 213 optimal weight: 2.9990 chunk 629 optimal weight: 3.9990 chunk 659 optimal weight: 6.9990 chunk 694 optimal weight: 50.0000 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1230 GLN I1231 GLN J 768 HIS ** L 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 526 GLN ** R 696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 858 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R1198 GLN ** S 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.951 50415 Z= 0.430 Angle : 0.632 35.438 69382 Z= 0.330 Chirality : 0.041 0.201 8561 Planarity : 0.004 0.081 9251 Dihedral : 4.521 38.492 8086 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.81 % Favored : 87.19 % Rotamer: Outliers : 0.03 % Allowed : 0.84 % Favored : 99.12 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.26 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.13 (0.10), residues: 7657 helix: 1.70 (0.09), residues: 3879 sheet: -2.69 (0.23), residues: 398 loop : -3.73 (0.10), residues: 3380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP T 97 HIS 0.012 0.001 HIS R 730 PHE 0.021 0.002 PHE R1259 TYR 0.041 0.002 TYR O 46 ARG 0.006 0.001 ARG I1227 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15314 Ramachandran restraints generated. 7657 Oldfield, 0 Emsley, 7657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15314 Ramachandran restraints generated. 7657 Oldfield, 0 Emsley, 7657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 7017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 313 time to evaluate : 4.480 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: I 653 MET cc_start: 0.6983 (ppp) cc_final: 0.6757 (ppp) REVERT: I 896 MET cc_start: 0.8820 (mmt) cc_final: 0.8458 (mmm) REVERT: J 648 MET cc_start: 0.8908 (tpt) cc_final: 0.8686 (tpp) REVERT: K 390 MET cc_start: 0.8175 (ptt) cc_final: 0.7812 (ptt) REVERT: K 421 MET cc_start: 0.6593 (mpp) cc_final: 0.6352 (mpp) REVERT: K 644 GLU cc_start: 0.8577 (tp30) cc_final: 0.8240 (tp30) REVERT: L 375 LEU cc_start: 0.9333 (pp) cc_final: 0.9061 (mt) REVERT: M 146 TYR cc_start: 0.9169 (p90) cc_final: 0.8735 (p90) REVERT: N 77 LEU cc_start: 0.9292 (mt) cc_final: 0.9005 (pp) REVERT: R 286 MET cc_start: 0.8519 (mtm) cc_final: 0.8272 (mtm) REVERT: R 425 MET cc_start: 0.9025 (tpt) cc_final: 0.8023 (mtt) REVERT: R 770 MET cc_start: 0.6772 (mtt) cc_final: 0.6363 (mtt) REVERT: R 853 MET cc_start: 0.8644 (mpp) cc_final: 0.8249 (mpp) REVERT: R 922 MET cc_start: 0.9181 (mmp) cc_final: 0.8787 (mmm) REVERT: R 1017 ARG cc_start: 0.9343 (tpt90) cc_final: 0.9119 (tpt90) REVERT: S 268 MET cc_start: 0.8817 (mtt) cc_final: 0.8486 (mmt) REVERT: W 44 LEU cc_start: 0.8526 (tp) cc_final: 0.8297 (pp) outliers start: 1 outliers final: 1 residues processed: 314 average time/residue: 0.4343 time to fit residues: 247.3797 Evaluate side-chains 273 residues out of total 7017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 272 time to evaluate : 4.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 776 random chunks: chunk 457 optimal weight: 8.9990 chunk 737 optimal weight: 20.0000 chunk 449 optimal weight: 0.4980 chunk 349 optimal weight: 6.9990 chunk 512 optimal weight: 2.9990 chunk 773 optimal weight: 20.0000 chunk 711 optimal weight: 0.9980 chunk 615 optimal weight: 2.9990 chunk 63 optimal weight: 50.0000 chunk 475 optimal weight: 1.9990 chunk 377 optimal weight: 5.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 768 HIS L 526 GLN R 640 GLN ** R 696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 745 GLN ** R 858 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 874 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.952 50415 Z= 0.411 Angle : 0.621 35.364 69382 Z= 0.318 Chirality : 0.041 0.205 8561 Planarity : 0.004 0.081 9251 Dihedral : 4.470 37.955 8086 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.49 % Favored : 87.51 % Rotamer: Outliers : 0.03 % Allowed : 0.57 % Favored : 99.39 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.26 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.10), residues: 7657 helix: 1.77 (0.09), residues: 3880 sheet: -2.65 (0.23), residues: 407 loop : -3.68 (0.10), residues: 3370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP T 97 HIS 0.009 0.001 HIS R1300 PHE 0.024 0.001 PHE L 220 TYR 0.039 0.001 TYR O 46 ARG 0.005 0.000 ARG R1093 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15314 Ramachandran restraints generated. 7657 Oldfield, 0 Emsley, 7657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15314 Ramachandran restraints generated. 7657 Oldfield, 0 Emsley, 7657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 7017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 316 time to evaluate : 4.457 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: I 653 MET cc_start: 0.6925 (ppp) cc_final: 0.6697 (ppp) REVERT: I 896 MET cc_start: 0.8768 (mmt) cc_final: 0.8440 (mmm) REVERT: J 648 MET cc_start: 0.8921 (tpt) cc_final: 0.8706 (tpp) REVERT: K 390 MET cc_start: 0.8266 (ptt) cc_final: 0.7435 (ppp) REVERT: K 421 MET cc_start: 0.6590 (mpp) cc_final: 0.6332 (mpp) REVERT: K 644 GLU cc_start: 0.8559 (tp30) cc_final: 0.8169 (tp30) REVERT: L 375 LEU cc_start: 0.9323 (pp) cc_final: 0.9038 (mt) REVERT: L 637 MET cc_start: 0.8354 (pmm) cc_final: 0.7825 (mmp) REVERT: M 146 TYR cc_start: 0.9141 (p90) cc_final: 0.8751 (p90) REVERT: N 77 LEU cc_start: 0.9285 (mt) cc_final: 0.8998 (pp) REVERT: Q 85 PHE cc_start: 0.8427 (m-10) cc_final: 0.8145 (m-80) REVERT: R 196 LEU cc_start: 0.7842 (mp) cc_final: 0.7596 (tp) REVERT: R 286 MET cc_start: 0.8490 (mtm) cc_final: 0.8210 (mtm) REVERT: R 425 MET cc_start: 0.9002 (tpt) cc_final: 0.7986 (mtt) REVERT: R 770 MET cc_start: 0.6692 (mtt) cc_final: 0.6288 (mtt) REVERT: R 922 MET cc_start: 0.9160 (mmp) cc_final: 0.8772 (mmm) REVERT: R 1017 ARG cc_start: 0.9324 (tpt90) cc_final: 0.9094 (tpt90) REVERT: S 268 MET cc_start: 0.8793 (mtt) cc_final: 0.8460 (mmt) outliers start: 1 outliers final: 0 residues processed: 317 average time/residue: 0.4346 time to fit residues: 248.9408 Evaluate side-chains 275 residues out of total 7017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 4.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 776 random chunks: chunk 488 optimal weight: 2.9990 chunk 655 optimal weight: 0.1980 chunk 188 optimal weight: 5.9990 chunk 567 optimal weight: 0.9980 chunk 90 optimal weight: 50.0000 chunk 171 optimal weight: 0.0030 chunk 616 optimal weight: 0.0050 chunk 258 optimal weight: 3.9990 chunk 633 optimal weight: 5.9990 chunk 78 optimal weight: 0.9980 chunk 113 optimal weight: 30.0000 overall best weight: 0.4404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 768 HIS ** K 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 526 GLN ** R 696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 726 ASN ** R 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 874 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 106 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 = 0.3214 r_free = 0.3214 target = 0.039205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.027572 restraints weight = 783320.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.028182 restraints weight = 640572.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.028619 restraints weight = 453308.483| |-----------------------------------------------------------------------------| r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2820 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2820 r_free = 0.2820 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2820 r_free = 0.2820 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2820 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.948 50415 Z= 0.400 Angle : 0.616 35.460 69382 Z= 0.309 Chirality : 0.041 0.208 8561 Planarity : 0.004 0.080 9251 Dihedral : 4.273 38.640 8086 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.74 % Favored : 89.26 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.26 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.87 (0.10), residues: 7657 helix: 1.94 (0.09), residues: 3873 sheet: -2.60 (0.23), residues: 421 loop : -3.62 (0.10), residues: 3363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP T 97 HIS 0.010 0.001 HIS J 706 PHE 0.020 0.001 PHE L 220 TYR 0.038 0.001 TYR O 46 ARG 0.005 0.000 ARG R1093 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7624.31 seconds wall clock time: 134 minutes 49.59 seconds (8089.59 seconds total)