Starting phenix.real_space_refine on Fri Dec 27 19:27:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t9d_41107/12_2024/8t9d_41107.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t9d_41107/12_2024/8t9d_41107.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t9d_41107/12_2024/8t9d_41107.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t9d_41107/12_2024/8t9d_41107.map" model { file = "/net/cci-nas-00/data/ceres_data/8t9d_41107/12_2024/8t9d_41107.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t9d_41107/12_2024/8t9d_41107.cif" } resolution = 4.66 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= 0.015 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 157 5.16 5 C 30973 2.51 5 N 9038 2.21 5 O 8968 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 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: 49136 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 2354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 2354 Classifications: {'peptide': 467} Incomplete info: {'truncation_to_alanine': 409} Link IDs: {'PTRANS': 30, 'TRANS': 436} Chain breaks: 5 Unresolved chain link angles: 30 Unresolved non-hydrogen bonds: 1407 Unresolved non-hydrogen angles: 1797 Unresolved non-hydrogen dihedrals: 1181 Unresolved non-hydrogen chiralities: 135 Planarities with less than four sites: {'GLN:plan1': 21, 'ASP:plan': 21, 'TYR:plan': 15, 'ASN:plan1': 18, 'TRP:plan': 3, 'HIS:plan': 16, 'PHE:plan': 18, 'GLU:plan': 21, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 685 Chain: "B" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 793 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 136} Link IDs: {'PTRANS': 5, 'TRANS': 152} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 490 Unresolved non-hydrogen angles: 613 Unresolved non-hydrogen dihedrals: 398 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 6, '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: 264 Chain: "C" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 931 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 148} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 165} Chain breaks: 1 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 561 Unresolved non-hydrogen angles: 728 Unresolved non-hydrogen dihedrals: 478 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 5, 'TYR:plan': 9, 'ASN:plan1': 7, 'TRP:plan': 4, 'ASP:plan': 8, 'PHE:plan': 5, 'GLU:plan': 6, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 325 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: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 902 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 158} Link IDs: {'PTRANS': 9, 'TRANS': 171} Chain breaks: 1 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 541 Unresolved non-hydrogen angles: 685 Unresolved non-hydrogen dihedrals: 434 Unresolved non-hydrogen chiralities: 52 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 10, 'TRP:plan': 1, 'ASP:plan': 11, 'PHE:plan': 6, 'GLU:plan': 16, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 283 Chain: "F" Number of atoms: 379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 379 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 235 Unresolved non-hydrogen angles: 291 Unresolved non-hydrogen dihedrals: 195 Unresolved non-hydrogen chiralities: 17 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': 2} Unresolved non-hydrogen planarities: 124 Chain: "G" Number of atoms: 608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 608 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 112} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 409 Unresolved non-hydrogen angles: 514 Unresolved non-hydrogen dihedrals: 335 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: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 583 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PTRANS': 1, 'TRANS': 103} Chain breaks: 1 Unresolved non-hydrogen bonds: 245 Unresolved non-hydrogen angles: 308 Unresolved non-hydrogen dihedrals: 188 Unresolved non-hydrogen chiralities: 27 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: 6855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1102, 6855 Classifications: {'peptide': 1102} Incomplete info: {'truncation_to_alanine': 590} Link IDs: {'CIS': 2, 'PTRANS': 64, 'TRANS': 1035} Chain breaks: 16 Unresolved chain link angles: 10 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1974 Unresolved non-hydrogen angles: 2496 Unresolved non-hydrogen dihedrals: 1561 Unresolved non-hydrogen chiralities: 232 Planarities with less than four sites: {'GLN:plan1': 39, 'HIS:plan': 8, 'TYR:plan': 7, 'ASN:plan1': 33, 'TRP:plan': 2, 'ASP:plan': 37, 'PHE:plan': 24, 'GLU:plan': 40, 'ARG:plan': 36} Unresolved non-hydrogen planarities: 957 Chain: "J" Number of atoms: 1176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1176 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 17, 'TRANS': 149} Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 79 Chain: "K" Number of atoms: 5037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 5037 Classifications: {'peptide': 732} Incomplete info: {'truncation_to_alanine': 220} Link IDs: {'CIS': 1, 'PTRANS': 34, 'TRANS': 696} Chain breaks: 10 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 643 Unresolved non-hydrogen angles: 789 Unresolved non-hydrogen dihedrals: 510 Unresolved non-hydrogen chiralities: 56 Planarities with less than four sites: {'GLN:plan1': 15, 'ASP:plan': 22, 'ASN:plan1': 8, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 24, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 316 Chain: "L" Number of atoms: 3393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 543, 3393 Classifications: {'peptide': 543} Incomplete info: {'truncation_to_alanine': 286} Link IDs: {'PTRANS': 23, 'TRANS': 519} Chain breaks: 7 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 933 Unresolved non-hydrogen angles: 1160 Unresolved non-hydrogen dihedrals: 744 Unresolved non-hydrogen chiralities: 84 Planarities with less than four sites: {'GLN:plan1': 33, 'HIS:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 16, 'TRP:plan': 2, 'ASP:plan': 17, 'PHE:plan': 2, 'GLU:plan': 24, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 486 Chain: "M" Number of atoms: 1146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1146 Classifications: {'peptide': 180} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 7, 'TRANS': 172} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 306 Unresolved non-hydrogen angles: 380 Unresolved non-hydrogen dihedrals: 239 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': 5} Unresolved non-hydrogen planarities: 147 Chain: "O" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1022 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 101} Link IDs: {'PTRANS': 7, 'TRANS': 166} Chain breaks: 4 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 337 Unresolved non-hydrogen angles: 424 Unresolved non-hydrogen dihedrals: 274 Unresolved non-hydrogen chiralities: 34 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: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 568 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'PTRANS': 2, 'TRANS': 111} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 312 Unresolved non-hydrogen angles: 399 Unresolved non-hydrogen dihedrals: 242 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': 2, 'GLU:plan': 10, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 177 Chain: "Q" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 759 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 98} Link IDs: {'PTRANS': 1, 'TRANS': 129} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 318 Unresolved non-hydrogen angles: 398 Unresolved non-hydrogen dihedrals: 249 Unresolved non-hydrogen chiralities: 29 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: 9758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1294, 9758 Classifications: {'peptide': 1294} Incomplete info: {'truncation_to_alanine': 211} Link IDs: {'CIS': 4, 'PTRANS': 67, 'TRANS': 1222} Chain breaks: 4 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 738 Unresolved non-hydrogen angles: 927 Unresolved non-hydrogen dihedrals: 608 Unresolved non-hydrogen chiralities: 64 Planarities with less than four sites: {'GLN:plan1': 18, 'HIS:plan': 6, 'TYR:plan': 5, 'ASN:plan1': 10, 'TRP:plan': 2, 'ASP:plan': 10, 'PHE:plan': 7, 'GLU:plan': 24, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 393 Chain: "S" Number of atoms: 5888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 901, 5888 Classifications: {'peptide': 901} Incomplete info: {'truncation_to_alanine': 386} Link IDs: {'PTRANS': 34, 'TRANS': 866} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 1208 Unresolved non-hydrogen angles: 1504 Unresolved non-hydrogen dihedrals: 945 Unresolved non-hydrogen chiralities: 139 Planarities with less than four sites: {'GLN:plan1': 24, 'HIS:plan': 7, 'TYR:plan': 5, 'ASN:plan1': 18, 'ASP:plan': 27, 'PHE:plan': 1, 'GLU:plan': 40, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 542 Chain: "T" Number of atoms: 1302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1302 Classifications: {'peptide': 192} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 16, 'TRANS': 175} Chain breaks: 3 Unresolved non-hydrogen bonds: 187 Unresolved non-hydrogen angles: 238 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 5, 'ASN:plan1': 3, 'ARG:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 69 Chain: "V" Number of atoms: 1683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1683 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 148} Link IDs: {'PTRANS': 11, 'TRANS': 258} Chain breaks: 2 Unresolved non-hydrogen bonds: 495 Unresolved non-hydrogen angles: 617 Unresolved non-hydrogen dihedrals: 388 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'GLN:plan1': 13, 'ARG:plan': 13, 'TYR:plan': 3, 'ASN:plan1': 10, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 9, 'ASP:plan': 13} Unresolved non-hydrogen planarities: 259 Chain: "W" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 781 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 4, 'TRANS': 113} Unresolved non-hydrogen bonds: 170 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 5, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 9, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 100 Chain: "X" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 842 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain breaks: 1 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 13 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: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 839 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain breaks: 1 Unresolved non-hydrogen bonds: 255 Unresolved non-hydrogen angles: 323 Unresolved non-hydrogen dihedrals: 195 Unresolved non-hydrogen chiralities: 26 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: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 516 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'PTRANS': 3, 'TRANS': 99} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 417 Unresolved non-hydrogen angles: 535 Unresolved non-hydrogen dihedrals: 368 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 4, 'TYR:plan': 10, 'ASN:plan1': 6, 'TRP:plan': 2, 'ASP:plan': 4, 'PHE:plan': 7, 'GLU:plan': 7, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 274 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 Chain: "9" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 120 Classifications: {'peptide': 24} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 4, 'TRANS': 19} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 2, 'PHE:plan': 3, 'GLU:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 49 Time building chain proxies: 22.47, per 1000 atoms: 0.46 Number of scatterers: 49136 At special positions: 0 Unit cell: (160.95, 223.11, 392.94, 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 157 16.00 O 8968 8.00 N 9038 7.00 C 30973 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=2.03 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: 10.58 Conformation dependent library (CDL) restraints added in 6.0 seconds 15130 Ramachandran restraints generated. 7565 Oldfield, 0 Emsley, 7565 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14866 Finding SS restraints... Secondary structure from input PDB file: 288 helices and 27 sheets defined 51.7% alpha, 2.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.02 Creating SS restraints... Processing helix chain 'A' and resid 22 through 26 removed outlier: 4.015A pdb=" N LYS A 26 " --> pdb=" O LEU A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 65 removed outlier: 3.911A pdb=" N THR A 64 " --> pdb=" O SER A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 70 Processing helix chain 'A' and resid 73 through 89 Processing helix chain 'A' and resid 135 through 139 removed outlier: 3.741A pdb=" N LEU A 138 " --> pdb=" O CYS A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 161 Processing helix chain 'A' and resid 171 through 181 Processing helix chain 'A' and resid 182 through 195 Processing helix chain 'A' and resid 314 through 322 Processing helix chain 'A' and resid 338 through 349 removed outlier: 3.565A pdb=" N GLN A 345 " --> pdb=" O GLU A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 422 Processing helix chain 'A' and resid 423 through 425 No H-bonds generated for 'chain 'A' and resid 423 through 425' Processing helix chain 'A' and resid 491 through 502 Processing helix chain 'A' and resid 503 through 514 Processing helix chain 'B' and resid 27 through 52 Processing helix chain 'B' and resid 63 through 141 removed outlier: 3.566A pdb=" N GLY B 141 " --> pdb=" O LYS B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 157 removed outlier: 3.643A pdb=" N ILE B 148 " --> pdb=" O SER B 144 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA B 157 " --> pdb=" O HIS B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 184 Processing helix chain 'C' and resid 27 through 35 removed outlier: 3.554A pdb=" N GLU C 35 " --> pdb=" O ASP C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 52 Processing helix chain 'C' and resid 57 through 62 removed outlier: 4.280A pdb=" N ASN C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 104 removed outlier: 3.649A pdb=" N VAL C 104 " --> pdb=" O ILE C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 135 removed outlier: 4.306A pdb=" N VAL C 114 " --> pdb=" O ASP C 110 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER C 135 " --> pdb=" O ASP C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 182 Processing helix chain 'C' and resid 183 through 188 Processing helix chain 'D' and resid 19 through 25 Processing helix chain 'D' and resid 73 through 98 Processing helix chain 'D' and resid 103 through 175 removed outlier: 3.768A pdb=" N GLU D 107 " --> pdb=" O ILE D 103 " (cutoff:3.500A) Proline residue: D 128 - end of helix Proline residue: D 172 - end of helix Processing helix chain 'E' and resid 4 through 36 removed outlier: 3.658A pdb=" N LEU E 8 " --> pdb=" O GLU E 4 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N CYS E 31 " --> pdb=" O GLY E 27 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS E 32 " --> pdb=" O SER E 28 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASN E 35 " --> pdb=" O CYS E 31 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU E 36 " --> pdb=" O LYS E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 63 removed outlier: 3.601A pdb=" N SER E 48 " --> pdb=" O SER E 44 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLN E 55 " --> pdb=" O LEU E 51 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEU E 56 " --> pdb=" O LEU E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 124 Processing helix chain 'E' and resid 174 through 187 removed outlier: 3.784A pdb=" N ALA E 186 " --> pdb=" O VAL E 182 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N PHE E 187 " --> pdb=" O ALA E 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 78 Processing helix chain 'F' and resid 86 through 104 Processing helix chain 'F' and resid 110 through 138 removed outlier: 3.647A pdb=" N GLN F 114 " --> pdb=" O SER F 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 27 Processing helix chain 'G' and resid 36 through 60 Processing helix chain 'G' and resid 64 through 74 removed outlier: 4.164A pdb=" N PHE G 68 " --> pdb=" O PRO G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 117 Processing helix chain 'G' and resid 117 through 127 removed outlier: 3.705A pdb=" N MET G 121 " --> pdb=" O PHE G 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 20 Processing helix chain 'H' and resid 27 through 35 removed outlier: 3.905A pdb=" N THR H 30 " --> pdb=" O ASN H 27 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL H 31 " --> pdb=" O ALA H 28 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ILE H 32 " --> pdb=" O GLY H 29 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LEU H 33 " --> pdb=" O THR H 30 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU H 35 " --> pdb=" O ILE H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 51 removed outlier: 3.559A pdb=" N ALA H 50 " --> pdb=" O ASP H 46 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA H 51 " --> pdb=" O ARG H 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 46 through 51' Processing helix chain 'H' and resid 53 through 68 Processing helix chain 'H' and resid 86 through 114 Processing helix chain 'I' and resid 51 through 72 removed outlier: 4.332A pdb=" N LEU I 72 " --> pdb=" O VAL I 68 " (cutoff:3.500A) Processing helix chain 'I' and resid 73 through 76 Processing helix chain 'I' and resid 77 through 107 Processing helix chain 'I' and resid 108 through 142 Processing helix chain 'I' and resid 143 through 148 removed outlier: 4.225A pdb=" N HIS I 146 " --> pdb=" O ALA I 143 " (cutoff:3.500A) Processing helix chain 'I' and resid 153 through 163 removed outlier: 4.052A pdb=" N THR I 162 " --> pdb=" O ILE I 158 " (cutoff:3.500A) Processing helix chain 'I' and resid 172 through 177 removed outlier: 3.929A pdb=" N ILE I 177 " --> pdb=" O ILE I 173 " (cutoff:3.500A) Processing helix chain 'I' and resid 187 through 206 removed outlier: 4.766A pdb=" N HIS I 193 " --> pdb=" O GLN I 189 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLN I 194 " --> pdb=" O ALA I 190 " (cutoff:3.500A) Processing helix chain 'I' and resid 268 through 270 No H-bonds generated for 'chain 'I' and resid 268 through 270' Processing helix chain 'I' and resid 271 through 285 Processing helix chain 'I' and resid 287 through 319 removed outlier: 4.281A pdb=" N LEU I 296 " --> pdb=" O MET I 292 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N HIS I 297 " --> pdb=" O TYR I 293 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU I 318 " --> pdb=" O MET I 314 " (cutoff:3.500A) Processing helix chain 'I' and resid 382 through 386 removed outlier: 4.131A pdb=" N VAL I 386 " --> pdb=" O SER I 383 " (cutoff:3.500A) Processing helix chain 'I' and resid 396 through 424 Processing helix chain 'I' and resid 474 through 485 removed outlier: 3.946A pdb=" N MET I 478 " --> pdb=" O THR I 474 " (cutoff:3.500A) Processing helix chain 'I' and resid 489 through 509 Processing helix chain 'I' and resid 595 through 602 Processing helix chain 'I' and resid 638 through 662 Proline residue: I 653 - end of helix Processing helix chain 'I' and resid 696 through 705 Processing helix chain 'I' and resid 762 through 784 Processing helix chain 'I' and resid 789 through 793 Processing helix chain 'I' and resid 851 through 862 removed outlier: 3.561A pdb=" N THR I 862 " --> pdb=" O MET I 858 " (cutoff:3.500A) Processing helix chain 'I' and resid 864 through 883 removed outlier: 3.726A pdb=" N LEU I 868 " --> pdb=" O ASN I 864 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ALA I 877 " --> pdb=" O PHE I 873 " (cutoff:3.500A) Proline residue: I 878 - end of helix Processing helix chain 'I' and resid 959 through 967 removed outlier: 3.993A pdb=" N LEU I 963 " --> pdb=" O LEU I 959 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL I 967 " --> pdb=" O LEU I 963 " (cutoff:3.500A) Processing helix chain 'I' and resid 1181 through 1186 Processing helix chain 'I' and resid 1205 through 1227 removed outlier: 3.768A pdb=" N GLU I1227 " --> pdb=" O ILE I1223 " (cutoff:3.500A) Processing helix chain 'I' and resid 1277 through 1291 Processing helix chain 'I' and resid 1296 through 1305 removed outlier: 3.584A pdb=" N ILE I1300 " --> pdb=" O ALA I1296 " (cutoff:3.500A) Processing helix chain 'I' and resid 1310 through 1325 removed outlier: 3.624A pdb=" N ARG I1314 " --> pdb=" O THR I1310 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP I1315 " --> pdb=" O HIS I1311 " (cutoff:3.500A) Processing helix chain 'I' and resid 1406 through 1409 Processing helix chain 'I' and resid 1410 through 1421 removed outlier: 3.506A pdb=" N ARG I1421 " --> pdb=" O ASN I1417 " (cutoff:3.500A) Processing helix chain 'I' and resid 1434 through 1443 Processing helix chain 'J' and resid 621 through 630 removed outlier: 3.932A pdb=" N ARG J 630 " --> pdb=" O LEU J 626 " (cutoff:3.500A) Processing helix chain 'J' and resid 637 through 650 Proline residue: J 644 - end of helix Processing helix chain 'J' and resid 675 through 683 removed outlier: 3.787A pdb=" N GLN J 679 " --> pdb=" O PRO J 675 " (cutoff:3.500A) Processing helix chain 'J' and resid 738 through 745 Processing helix chain 'J' and resid 746 through 761 removed outlier: 3.607A pdb=" N LEU J 761 " --> pdb=" O THR J 757 " (cutoff:3.500A) Processing helix chain 'J' and resid 770 through 783 Processing helix chain 'K' and resid 144 through 149 Processing helix chain 'K' and resid 265 through 270 removed outlier: 3.676A pdb=" N THR K 268 " --> pdb=" O MET K 265 " (cutoff:3.500A) Processing helix chain 'K' and resid 466 through 485 Processing helix chain 'K' and resid 496 through 514 removed outlier: 4.032A pdb=" N VAL K 500 " --> pdb=" O GLN K 496 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN K 501 " --> pdb=" O PRO K 497 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N SER K 502 " --> pdb=" O SER K 498 " (cutoff:3.500A) Processing helix chain 'K' and resid 518 through 536 removed outlier: 6.439A pdb=" N THR K 524 " --> pdb=" O GLN K 520 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ARG K 525 " --> pdb=" O VAL K 521 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LEU K 536 " --> pdb=" O SER K 532 " (cutoff:3.500A) Processing helix chain 'K' and resid 544 through 565 Processing helix chain 'K' and resid 576 through 583 removed outlier: 3.771A pdb=" N ILE K 583 " --> pdb=" O ARG K 579 " (cutoff:3.500A) Processing helix chain 'K' and resid 584 through 586 No H-bonds generated for 'chain 'K' and resid 584 through 586' Processing helix chain 'K' and resid 591 through 600 removed outlier: 3.905A pdb=" N VAL K 595 " --> pdb=" O ASP K 591 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ILE K 597 " --> pdb=" O ASP K 593 " (cutoff:3.500A) Processing helix chain 'K' and resid 612 through 617 removed outlier: 3.526A pdb=" N GLN K 616 " --> pdb=" O GLN K 612 " (cutoff:3.500A) Processing helix chain 'K' and resid 617 through 632 removed outlier: 4.173A pdb=" N VAL K 621 " --> pdb=" O LEU K 617 " (cutoff:3.500A) Processing helix chain 'K' and resid 649 through 669 Processing helix chain 'K' and resid 685 through 699 Processing helix chain 'K' and resid 734 through 740 Processing helix chain 'K' and resid 816 through 823 removed outlier: 3.683A pdb=" N GLU K 820 " --> pdb=" O VAL K 816 " (cutoff:3.500A) Processing helix chain 'K' and resid 829 through 833 removed outlier: 4.289A pdb=" N GLY K 832 " --> pdb=" O ALA K 829 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG K 833 " --> pdb=" O VAL K 830 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 829 through 833' Processing helix chain 'L' and resid 35 through 40 Processing helix chain 'L' and resid 94 through 120 Processing helix chain 'L' and resid 143 through 171 Processing helix chain 'L' and resid 172 through 177 removed outlier: 3.555A pdb=" N GLU L 176 " --> pdb=" O THR L 172 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN L 177 " --> pdb=" O GLU L 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 172 through 177' Processing helix chain 'L' and resid 186 through 195 removed outlier: 3.685A pdb=" N LEU L 190 " --> pdb=" O GLU L 186 " (cutoff:3.500A) Processing helix chain 'L' and resid 289 through 313 Processing helix chain 'L' and resid 367 through 369 No H-bonds generated for 'chain 'L' and resid 367 through 369' Processing helix chain 'L' and resid 370 through 385 removed outlier: 4.361A pdb=" N ASN L 374 " --> pdb=" O VAL L 370 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU L 378 " --> pdb=" O ASN L 374 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ILE L 379 " --> pdb=" O LEU L 375 " (cutoff:3.500A) Processing helix chain 'L' and resid 402 through 407 Processing helix chain 'L' and resid 414 through 422 removed outlier: 4.418A pdb=" N GLN L 422 " --> pdb=" O ILE L 418 " (cutoff:3.500A) Processing helix chain 'L' and resid 426 through 454 removed outlier: 3.733A pdb=" N LEU L 451 " --> pdb=" O THR L 447 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA L 452 " --> pdb=" O ILE L 448 " (cutoff:3.500A) Processing helix chain 'L' and resid 520 through 541 Processing helix chain 'L' and resid 605 through 610 removed outlier: 4.318A pdb=" N LEU L 610 " --> pdb=" O LYS L 606 " (cutoff:3.500A) Processing helix chain 'L' and resid 637 through 643 Processing helix chain 'M' and resid 32 through 41 removed outlier: 3.555A pdb=" N GLY M 41 " --> pdb=" O HIS M 37 " (cutoff:3.500A) Processing helix chain 'M' and resid 112 through 121 Processing helix chain 'M' and resid 181 through 193 removed outlier: 3.789A pdb=" N ASP M 185 " --> pdb=" O MET M 181 " (cutoff:3.500A) Processing helix chain 'O' and resid 16 through 32 Processing helix chain 'O' and resid 87 through 98 removed outlier: 3.938A pdb=" N LEU O 94 " --> pdb=" O ASN O 90 " (cutoff:3.500A) Processing helix chain 'O' and resid 153 through 165 removed outlier: 3.692A pdb=" N LEU O 158 " --> pdb=" O TRP O 154 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU O 159 " --> pdb=" O SER O 155 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N PHE O 160 " --> pdb=" O LEU O 156 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU O 161 " --> pdb=" O LEU O 157 " (cutoff:3.500A) Processing helix chain 'O' and resid 189 through 199 Processing helix chain 'P' and resid 3 through 27 Processing helix chain 'P' and resid 49 through 75 Processing helix chain 'P' and resid 83 through 133 Processing helix chain 'Q' and resid 10 through 32 removed outlier: 3.995A pdb=" N LEU Q 14 " --> pdb=" O SER Q 10 " (cutoff:3.500A) Processing helix chain 'Q' and resid 53 through 60 removed outlier: 3.686A pdb=" N ASN Q 58 " --> pdb=" O GLY Q 54 " (cutoff:3.500A) Processing helix chain 'Q' and resid 65 through 73 removed outlier: 3.612A pdb=" N VAL Q 69 " --> pdb=" O ALA Q 65 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N ALA Q 71 " --> pdb=" O ASN Q 67 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 87 removed outlier: 3.657A pdb=" N LEU Q 78 " --> pdb=" O SER Q 74 " (cutoff:3.500A) Processing helix chain 'Q' and resid 98 through 137 removed outlier: 3.680A pdb=" N SER Q 137 " --> pdb=" O GLU Q 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 14 Processing helix chain 'R' and resid 34 through 51 removed outlier: 3.669A pdb=" N LEU R 51 " --> pdb=" O PHE R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 55 through 69 Processing helix chain 'R' and resid 72 through 89 Processing helix chain 'R' and resid 93 through 102 removed outlier: 4.114A pdb=" N VAL R 97 " --> pdb=" O PRO R 93 " (cutoff:3.500A) Processing helix chain 'R' and resid 111 through 125 Processing helix chain 'R' and resid 126 through 128 No H-bonds generated for 'chain 'R' and resid 126 through 128' Processing helix chain 'R' and resid 134 through 147 removed outlier: 3.542A pdb=" N LEU R 138 " --> pdb=" O VAL R 134 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR R 147 " --> pdb=" O GLU R 143 " (cutoff:3.500A) Processing helix chain 'R' and resid 157 through 174 removed outlier: 4.355A pdb=" N ALA R 163 " --> pdb=" O GLN R 159 " (cutoff:3.500A) Processing helix chain 'R' and resid 179 through 188 removed outlier: 3.569A pdb=" N ALA R 183 " --> pdb=" O PRO R 179 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG R 188 " --> pdb=" O VAL R 184 " (cutoff:3.500A) Processing helix chain 'R' and resid 203 through 219 Proline residue: R 214 - end of helix Processing helix chain 'R' and resid 259 through 263 Processing helix chain 'R' and resid 266 through 275 removed outlier: 3.675A pdb=" N LEU R 270 " --> pdb=" O GLN R 266 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU R 275 " --> pdb=" O ARG R 271 " (cutoff:3.500A) Processing helix chain 'R' and resid 278 through 287 removed outlier: 4.294A pdb=" N MET R 282 " --> pdb=" O TYR R 278 " (cutoff:3.500A) Processing helix chain 'R' and resid 299 through 317 removed outlier: 3.997A pdb=" N GLN R 303 " --> pdb=" O VAL R 299 " (cutoff:3.500A) Processing helix chain 'R' and resid 317 through 324 removed outlier: 4.436A pdb=" N PHE R 321 " --> pdb=" O THR R 317 " (cutoff:3.500A) Processing helix chain 'R' and resid 326 through 341 Processing helix chain 'R' and resid 349 through 360 removed outlier: 4.037A pdb=" N VAL R 353 " --> pdb=" O PHE R 349 " (cutoff:3.500A) Processing helix chain 'R' and resid 367 through 383 removed outlier: 4.593A pdb=" N HIS R 371 " --> pdb=" O LYS R 367 " (cutoff:3.500A) Processing helix chain 'R' and resid 388 through 403 removed outlier: 3.991A 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 419 through 440 removed outlier: 5.104A pdb=" N MET R 425 " --> pdb=" O HIS R 421 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N THR R 426 " --> pdb=" O ALA R 422 " (cutoff:3.500A) Processing helix chain 'R' and resid 441 through 445 Processing helix chain 'R' and resid 451 through 456 Processing helix chain 'R' and resid 490 through 495 Processing helix chain 'R' and resid 527 through 532 removed outlier: 4.104A pdb=" N LEU R 531 " --> pdb=" O LEU R 527 " (cutoff:3.500A) Processing helix chain 'R' and resid 541 through 554 removed outlier: 3.665A pdb=" N THR R 545 " --> pdb=" O HIS R 541 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG R 546 " --> pdb=" O SER R 542 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ALA R 553 " --> pdb=" O LYS R 549 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS R 554 " --> pdb=" O LEU R 550 " (cutoff:3.500A) Processing helix chain 'R' and resid 563 through 569 removed outlier: 3.586A pdb=" N TYR R 567 " --> pdb=" O LEU R 563 " (cutoff:3.500A) Processing helix chain 'R' and resid 571 through 577 Processing helix chain 'R' and resid 577 through 589 Processing helix chain 'R' and resid 590 through 595 Processing helix chain 'R' and resid 597 through 612 removed outlier: 4.292A pdb=" N LEU R 601 " --> pdb=" O ALA R 597 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N HIS R 602 " --> pdb=" O TRP R 598 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N THR R 603 " --> pdb=" O GLY R 599 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU R 604 " --> pdb=" O ILE R 600 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N GLU R 606 " --> pdb=" O HIS R 602 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N MET R 607 " --> pdb=" O THR R 603 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET R 612 " --> pdb=" O PHE R 608 " (cutoff:3.500A) Processing helix chain 'R' and resid 616 through 633 Processing helix chain 'R' and resid 642 through 655 removed outlier: 3.545A pdb=" N GLU R 646 " --> pdb=" O HIS R 642 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA R 655 " --> pdb=" O ARG R 651 " (cutoff:3.500A) Processing helix chain 'R' and resid 660 through 665 Processing helix chain 'R' and resid 666 through 669 removed outlier: 3.991A pdb=" N LEU R 669 " --> pdb=" O THR R 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 666 through 669' Processing helix chain 'R' and resid 670 through 675 Processing helix chain 'R' and resid 680 through 696 removed outlier: 4.032A pdb=" N HIS R 696 " --> pdb=" O ALA R 692 " (cutoff:3.500A) Processing helix chain 'R' and resid 709 through 721 removed outlier: 4.131A pdb=" N ASP R 714 " --> pdb=" O THR R 710 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ILE R 715 " --> pdb=" O TRP R 711 " (cutoff:3.500A) Processing helix chain 'R' and resid 739 through 743 removed outlier: 3.522A pdb=" N PHE R 742 " --> pdb=" O LEU R 739 " (cutoff:3.500A) Processing helix chain 'R' and resid 744 through 753 removed outlier: 3.792A pdb=" N ASN R 747 " --> pdb=" O LYS R 744 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL R 748 " --> pdb=" O GLN R 745 " (cutoff:3.500A) Proline residue: R 749 - end of helix Processing helix chain 'R' and resid 754 through 771 removed outlier: 3.824A pdb=" N LYS R 758 " --> pdb=" O PHE R 754 " (cutoff:3.500A) Processing helix chain 'R' and resid 773 through 781 removed outlier: 4.149A pdb=" N THR R 778 " --> pdb=" O ASN R 774 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N HIS R 779 " --> pdb=" O ASP R 775 " (cutoff:3.500A) Processing helix chain 'R' and resid 785 through 790 removed outlier: 3.689A pdb=" N LEU R 790 " --> pdb=" O PRO R 786 " (cutoff:3.500A) Processing helix chain 'R' and resid 791 through 795 removed outlier: 3.550A pdb=" N TRP R 794 " --> pdb=" O CYS R 791 " (cutoff:3.500A) Processing helix chain 'R' and resid 807 through 815 Processing helix chain 'R' and resid 818 through 835 Processing helix chain 'R' and resid 842 through 849 Processing helix chain 'R' and resid 849 through 854 Processing helix chain 'R' and resid 864 through 873 removed outlier: 3.521A pdb=" N CYS R 868 " --> pdb=" O ARG R 864 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG R 872 " --> pdb=" O CYS R 868 " (cutoff:3.500A) Processing helix chain 'R' and resid 878 through 892 removed outlier: 4.468A pdb=" N PHE R 884 " --> pdb=" O GLN R 880 " (cutoff:3.500A) Processing helix chain 'R' and resid 896 through 903 removed outlier: 3.671A pdb=" N VAL R 900 " --> pdb=" O PHE R 896 " (cutoff:3.500A) Processing helix chain 'R' and resid 903 through 908 removed outlier: 4.274A pdb=" N ASN R 907 " --> pdb=" O PHE R 903 " (cutoff:3.500A) removed outlier: 3.933A 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 Processing helix chain 'R' and resid 958 through 970 removed outlier: 4.167A pdb=" N ARG R 962 " --> pdb=" O ASN R 958 " (cutoff:3.500A) Proline residue: R 965 - end of helix Processing helix chain 'R' and resid 979 through 992 removed outlier: 3.605A pdb=" N SER R 983 " --> pdb=" O PRO R 979 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR R 986 " --> pdb=" O LYS R 982 " (cutoff:3.500A) Processing helix chain 'R' and resid 993 through 996 removed outlier: 3.521A pdb=" N LYS R 996 " --> pdb=" O GLY R 993 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 993 through 996' Processing helix chain 'R' and resid 1000 through 1007 removed outlier: 4.165A pdb=" N ASN R1007 " --> pdb=" O THR R1003 " (cutoff:3.500A) Processing helix chain 'R' and resid 1008 through 1010 No H-bonds generated for 'chain 'R' and resid 1008 through 1010' Processing helix chain 'R' and resid 1012 through 1014 No H-bonds generated for 'chain 'R' and resid 1012 through 1014' Processing helix chain 'R' and resid 1015 through 1035 removed outlier: 4.182A pdb=" N ARG R1019 " --> pdb=" O HIS R1015 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LEU R1022 " --> pdb=" O ASP R1018 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N LYS R1025 " --> pdb=" O PHE R1021 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N HIS R1028 " --> pdb=" O ARG R1024 " (cutoff:3.500A) Processing helix chain 'R' and resid 1044 through 1051 Processing helix chain 'R' and resid 1063 through 1077 Processing helix chain 'R' and resid 1101 through 1109 removed outlier: 3.710A pdb=" N LEU R1105 " --> pdb=" O ALA R1101 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N VAL R1107 " --> pdb=" O HIS R1103 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N THR R1108 " --> pdb=" O ALA R1104 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N CYS R1109 " --> pdb=" O LEU R1105 " (cutoff:3.500A) Processing helix chain 'R' and resid 1120 through 1132 removed outlier: 4.144A pdb=" N VAL R1129 " --> pdb=" O ALA R1125 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N VAL R1130 " --> pdb=" O LEU R1126 " (cutoff:3.500A) Processing helix chain 'R' and resid 1141 through 1154 removed outlier: 3.512A pdb=" N TRP R1145 " --> pdb=" O ASN R1141 " (cutoff:3.500A) Processing helix chain 'R' and resid 1157 through 1172 removed outlier: 3.888A pdb=" N TRP R1161 " --> pdb=" O PRO R1157 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU R1164 " --> pdb=" O TYR R1160 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N HIS R1165 " --> pdb=" O TRP R1161 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASP R1166 " --> pdb=" O ILE R1162 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N VAL R1171 " --> pdb=" O ARG R1167 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE R1172 " --> pdb=" O ILE R1168 " (cutoff:3.500A) Processing helix chain 'R' and resid 1186 through 1192 Processing helix chain 'R' and resid 1194 through 1198 Processing helix chain 'R' and resid 1203 through 1219 removed outlier: 3.680A pdb=" N TYR R1207 " --> pdb=" O MET R1203 " (cutoff:3.500A) 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: 4.116A pdb=" N ILE R1238 " --> pdb=" O LEU R1235 " (cutoff:3.500A) removed outlier: 3.647A 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 1242 through 1253 Processing helix chain 'R' and resid 1255 through 1262 removed outlier: 3.715A pdb=" N PHE R1259 " --> pdb=" O PHE R1255 " (cutoff:3.500A) Processing helix chain 'R' and resid 1263 through 1284 removed outlier: 3.561A pdb=" N MET R1267 " --> pdb=" O ARG R1263 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ILE R1268 " --> pdb=" O THR R1264 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N GLU R1269 " --> pdb=" O ARG R1265 " (cutoff:3.500A) Processing helix chain 'R' and resid 1290 through 1305 removed outlier: 3.898A pdb=" N ILE R1294 " --> pdb=" O TYR R1290 " (cutoff:3.500A) Processing helix chain 'R' and resid 1310 through 1319 removed outlier: 4.000A pdb=" N LYS R1316 " --> pdb=" O GLU R1312 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE R1317 " --> pdb=" O GLN R1313 " (cutoff:3.500A) Processing helix chain 'R' and resid 1322 through 1330 Processing helix chain 'R' and resid 1331 through 1334 removed outlier: 3.646A pdb=" N HIS R1334 " --> pdb=" O PHE R1331 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 1331 through 1334' Processing helix chain 'S' and resid 5 through 16 removed outlier: 3.833A pdb=" N GLU S 16 " --> pdb=" O GLN S 12 " (cutoff:3.500A) Processing helix chain 'S' and resid 22 through 31 Processing helix chain 'S' and resid 36 through 39 removed outlier: 3.779A pdb=" N ILE S 39 " --> pdb=" O THR S 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 36 through 39' Processing helix chain 'S' and resid 40 through 53 removed outlier: 4.040A pdb=" N ASP S 44 " --> pdb=" O LEU S 40 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N LEU S 46 " --> pdb=" O LEU S 42 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N MET S 51 " --> pdb=" O LEU S 47 " (cutoff:3.500A) Processing helix chain 'S' and resid 60 through 69 Processing helix chain 'S' and resid 72 through 82 Processing helix chain 'S' and resid 92 through 107 removed outlier: 3.775A pdb=" N ALA S 96 " --> pdb=" O LEU S 92 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ARG S 107 " --> pdb=" O MET S 103 " (cutoff:3.500A) Processing helix chain 'S' and resid 115 through 132 Processing helix chain 'S' and resid 133 through 138 Processing helix chain 'S' and resid 156 through 168 Processing helix chain 'S' and resid 174 through 185 Processing helix chain 'S' and resid 186 through 203 Processing helix chain 'S' and resid 213 through 225 Processing helix chain 'S' and resid 241 through 255 removed outlier: 4.279A pdb=" N HIS S 245 " --> pdb=" O PHE S 241 " (cutoff:3.500A) Processing helix chain 'S' and resid 261 through 273 removed outlier: 4.408A pdb=" N GLU S 265 " --> pdb=" O GLN S 261 " (cutoff:3.500A) Processing helix chain 'S' and resid 277 through 292 removed outlier: 3.936A pdb=" N GLY S 292 " --> pdb=" O ALA S 288 " (cutoff:3.500A) Processing helix chain 'S' and resid 299 through 323 removed outlier: 4.053A pdb=" N LEU S 303 " --> pdb=" O GLY S 299 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE S 313 " --> pdb=" O THR S 309 " (cutoff:3.500A) Proline residue: S 314 - end of helix Processing helix chain 'S' and resid 332 through 342 Processing helix chain 'S' and resid 344 through 356 removed outlier: 3.823A pdb=" N LEU S 348 " --> pdb=" O LEU S 344 " (cutoff:3.500A) Processing helix chain 'S' and resid 357 through 373 Processing helix chain 'S' and resid 378 through 388 Processing helix chain 'S' and resid 413 through 427 removed outlier: 4.571A pdb=" N THR S 423 " --> pdb=" O ASN S 419 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N MET S 424 " --> pdb=" O ILE S 420 " (cutoff:3.500A) Processing helix chain 'S' and resid 438 through 447 removed outlier: 3.883A pdb=" N SER S 444 " --> pdb=" O GLY S 440 " (cutoff:3.500A) Processing helix chain 'S' and resid 449 through 456 Processing helix chain 'S' and resid 460 through 475 Processing helix chain 'S' and resid 482 through 508 Processing helix chain 'S' and resid 508 through 516 Processing helix chain 'S' and resid 525 through 530 Processing helix chain 'S' and resid 554 through 562 Processing helix chain 'S' and resid 575 through 578 Processing helix chain 'S' and resid 579 through 592 removed outlier: 4.299A pdb=" N ALA S 583 " --> pdb=" O LEU S 579 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N TRP S 592 " --> pdb=" O ILE S 588 " (cutoff:3.500A) Processing helix chain 'S' and resid 599 through 609 Processing helix chain 'S' and resid 614 through 629 removed outlier: 3.749A pdb=" N VAL S 618 " --> pdb=" O CYS S 614 " (cutoff:3.500A) Processing helix chain 'S' and resid 635 through 646 Processing helix chain 'S' and resid 659 through 674 removed outlier: 3.537A pdb=" N CYS S 674 " --> pdb=" O LEU S 670 " (cutoff:3.500A) Processing helix chain 'S' and resid 675 through 682 Processing helix chain 'S' and resid 709 through 714 Processing helix chain 'S' and resid 714 through 721 removed outlier: 3.586A pdb=" N GLU S 720 " --> pdb=" O ALA S 716 " (cutoff:3.500A) Processing helix chain 'S' and resid 725 through 739 removed outlier: 4.072A pdb=" N HIS S 730 " --> pdb=" O SER S 726 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ILE S 731 " --> pdb=" O ARG S 727 " (cutoff:3.500A) Processing helix chain 'S' and resid 740 through 753 Processing helix chain 'S' and resid 757 through 772 Processing helix chain 'S' and resid 775 through 788 Processing helix chain 'S' and resid 788 through 793 Processing helix chain 'S' and resid 797 through 802 removed outlier: 3.764A pdb=" N LEU S 801 " --> pdb=" O LYS S 797 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET S 802 " --> pdb=" O TRP S 798 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 797 through 802' Processing helix chain 'S' and resid 803 through 822 removed outlier: 3.847A pdb=" N THR S 807 " --> pdb=" O ASP S 803 " (cutoff:3.500A) Processing helix chain 'S' and resid 828 through 833 removed outlier: 3.978A pdb=" N LYS S 833 " --> pdb=" O SER S 829 " (cutoff:3.500A) Processing helix chain 'S' and resid 895 through 912 Processing helix chain 'S' and resid 919 through 932 removed outlier: 3.640A pdb=" N VAL S 932 " --> pdb=" O MET S 928 " (cutoff:3.500A) Processing helix chain 'S' and resid 947 through 957 Processing helix chain 'S' and resid 964 through 970 Processing helix chain 'S' and resid 975 through 987 removed outlier: 3.515A pdb=" N GLN S 980 " --> pdb=" O PRO S 976 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL S 981 " --> pdb=" O LEU S 977 " (cutoff:3.500A) Processing helix chain 'T' and resid 29 through 45 removed outlier: 3.567A pdb=" N GLU T 33 " --> pdb=" O GLY T 29 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY T 34 " --> pdb=" O PRO T 30 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N LEU T 41 " --> pdb=" O LYS T 37 " (cutoff:3.500A) Proline residue: T 42 - end of helix removed outlier: 3.541A pdb=" N GLU T 45 " --> pdb=" O LEU T 41 " (cutoff:3.500A) Processing helix chain 'T' and resid 88 through 91 removed outlier: 3.982A 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 100 removed outlier: 3.973A pdb=" N ASP T 99 " --> pdb=" O VAL T 95 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY T 100 " --> pdb=" O THR T 96 " (cutoff:3.500A) Processing helix chain 'T' and resid 113 through 132 removed outlier: 4.250A pdb=" N GLY T 117 " --> pdb=" O LEU T 113 " (cutoff:3.500A) Processing helix chain 'T' and resid 164 through 175 removed outlier: 3.505A pdb=" N GLU T 175 " --> pdb=" O GLN T 171 " (cutoff:3.500A) Processing helix chain 'T' and resid 193 through 197 removed outlier: 3.558A pdb=" N LYS T 197 " --> pdb=" O LEU T 194 " (cutoff:3.500A) Processing helix chain 'V' and resid 9 through 35 removed outlier: 4.349A pdb=" N ALA V 13 " --> pdb=" O VAL V 9 " (cutoff:3.500A) Processing helix chain 'V' and resid 47 through 72 removed outlier: 4.102A pdb=" N ALA V 51 " --> pdb=" O GLY V 47 " (cutoff:3.500A) Processing helix chain 'V' and resid 79 through 84 removed outlier: 4.036A pdb=" N ASN V 83 " --> pdb=" O PRO V 80 " (cutoff:3.500A) Processing helix chain 'V' and resid 85 through 90 Processing helix chain 'V' and resid 105 through 128 Processing helix chain 'V' and resid 161 through 171 removed outlier: 3.622A pdb=" N VAL V 165 " --> pdb=" O TYR V 161 " (cutoff:3.500A) Processing helix chain 'V' and resid 239 through 251 Processing helix chain 'V' and resid 258 through 272 Processing helix chain 'W' and resid 45 through 58 removed outlier: 4.152A pdb=" N GLU W 49 " --> pdb=" O VAL W 45 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N CYS W 55 " --> pdb=" O SER W 51 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N PHE W 56 " --> pdb=" O PHE W 52 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SER W 58 " --> pdb=" O ALA W 54 " (cutoff:3.500A) Processing helix chain 'W' and resid 72 through 106 removed outlier: 4.166A pdb=" N GLY W 76 " --> pdb=" O GLU W 72 " (cutoff:3.500A) Processing helix chain 'W' and resid 106 through 143 removed outlier: 3.963A pdb=" N VAL W 110 " --> pdb=" O LYS W 106 " (cutoff:3.500A) Processing helix chain 'X' and resid 55 through 90 Proline residue: X 65 - end of helix removed outlier: 4.022A pdb=" N ASN X 90 " --> pdb=" O THR X 86 " (cutoff:3.500A) Processing helix chain 'X' and resid 102 through 136 removed outlier: 3.534A pdb=" N LEU X 106 " --> pdb=" O PHE X 102 " (cutoff:3.500A) Processing helix chain 'X' and resid 156 through 186 Processing helix chain 'Y' and resid 29 through 57 removed outlier: 4.328A pdb=" N ASN Y 57 " --> pdb=" O GLN Y 53 " (cutoff:3.500A) Processing helix chain 'Y' and resid 69 through 102 removed outlier: 3.950A pdb=" N ASP Y 73 " --> pdb=" O GLY Y 69 " (cutoff:3.500A) Processing helix chain 'Y' and resid 139 through 169 removed outlier: 3.625A pdb=" N ASN Y 165 " --> pdb=" O ASP Y 161 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ASP Y 169 " --> pdb=" O ASN Y 165 " (cutoff:3.500A) Processing helix chain 'Z' and resid 11 through 15 Processing helix chain 'Z' and resid 21 through 30 Processing helix chain 'Z' and resid 45 through 54 removed outlier: 4.308A pdb=" N VAL Z 49 " --> pdb=" O ASP Z 45 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASN Z 50 " --> pdb=" O LYS Z 46 " (cutoff:3.500A) Processing helix chain 'Z' and resid 71 through 79 removed outlier: 4.118A pdb=" N MET Z 75 " --> pdb=" O GLN Z 71 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU Z 76 " --> pdb=" O CYS Z 72 " (cutoff:3.500A) Processing helix chain 'Z' and resid 80 through 82 No H-bonds generated for 'chain 'Z' and resid 80 through 82' Processing helix chain 'Z' and resid 90 through 103 removed outlier: 3.619A pdb=" N LEU Z 103 " --> pdb=" O GLU Z 99 " (cutoff:3.500A) Processing helix chain 'Z' and resid 104 through 107 removed outlier: 4.118A pdb=" N HIS Z 107 " --> pdb=" O HIS Z 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 104 through 107' Processing helix chain 'a' and resid 5 through 18 Processing sheet with id=AA1, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AA2, first strand: chain 'C' and resid 68 through 70 removed outlier: 3.997A pdb=" N ARG C 82 " --> pdb=" O ILE C 69 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 326 through 327 Processing sheet with id=AA4, first strand: chain 'I' and resid 432 through 433 Processing sheet with id=AA5, first strand: chain 'I' and resid 453 through 454 removed outlier: 3.557A pdb=" N HIS I 453 " --> pdb=" O MET I 466 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 514 through 517 removed outlier: 3.774A pdb=" N ASN I 536 " --> pdb=" O SER I 517 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 682 through 683 removed outlier: 3.576A pdb=" N THR I 709 " --> pdb=" O GLU I 723 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG I 711 " --> pdb=" O VAL I 721 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL I 721 " --> pdb=" O ARG I 711 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 913 through 918 removed outlier: 4.113A pdb=" N ILE I 914 " --> pdb=" O ILE I 926 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE I 926 " --> pdb=" O ILE I 914 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE I 918 " --> pdb=" O TYR I 922 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N TYR I 922 " --> pdb=" O PHE I 918 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 1365 through 1368 removed outlier: 7.320A pdb=" N VAL I1385 " --> pdb=" O LEU I1367 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 691 through 693 removed outlier: 3.621A pdb=" N ASN J 692 " --> pdb=" O ILE J 707 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE J 707 " --> pdb=" O ASN J 692 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'K' and resid 62 through 64 Processing sheet with id=AB3, first strand: chain 'K' and resid 142 through 143 Processing sheet with id=AB4, first strand: chain 'K' and resid 242 through 243 removed outlier: 3.562A pdb=" N GLU K 258 " --> pdb=" O LYS K 243 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 294 through 295 removed outlier: 3.682A pdb=" N ILE K 305 " --> pdb=" O LEU K 295 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 309 through 310 removed outlier: 3.600A pdb=" N ARG K 340 " --> pdb=" O SER K 310 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 352 through 354 removed outlier: 4.389A pdb=" N VAL K 354 " --> pdb=" O ALA K 383 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA K 383 " --> pdb=" O VAL K 354 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'L' and resid 324 through 326 Processing sheet with id=AB9, first strand: chain 'L' and resid 461 through 464 removed outlier: 3.603A pdb=" N GLN L 461 " --> pdb=" O LEU L 478 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU L 478 " --> pdb=" O GLN L 461 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL L 477 " --> pdb=" O GLN L 492 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN L 492 " --> pdb=" O VAL L 477 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU L 493 " --> pdb=" O VAL L 505 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG L 503 " --> pdb=" O LEU L 495 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 569 through 573 Processing sheet with id=AC2, first strand: chain 'M' and resid 19 through 20 removed outlier: 3.821A pdb=" N ALA M 175 " --> pdb=" O MET M 19 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'M' and resid 50 through 51 removed outlier: 3.572A pdb=" N LYS M 132 " --> pdb=" O LYS M 147 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE M 136 " --> pdb=" O ILE M 143 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE M 143 " --> pdb=" O PHE M 136 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'M' and resid 57 through 59 removed outlier: 6.968A pdb=" N VAL M 57 " --> pdb=" O ASP M 126 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'M' and resid 84 through 86 removed outlier: 3.876A pdb=" N LEU M 85 " --> pdb=" O ASP M 107 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP M 107 " --> pdb=" O LEU M 85 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'O' and resid 35 through 40 removed outlier: 3.614A pdb=" N GLY O 37 " --> pdb=" O ARG O 116 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N THR O 115 " --> pdb=" O VAL O 126 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N VAL O 126 " --> pdb=" O THR O 115 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU O 123 " --> pdb=" O GLU O 141 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU O 141 " --> pdb=" O LEU O 123 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'O' and resid 64 through 65 Processing sheet with id=AC8, first strand: chain 'T' and resid 68 through 69 removed outlier: 7.436A pdb=" N PHE T 20 " --> pdb=" O VAL T 69 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL T 21 " --> pdb=" O LEU T 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'V' and resid 178 through 180 2717 hydrogen bonds defined for protein. 7983 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: 16.66 Time building geometry restraints manager: 12.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 16726 1.34 - 1.46: 5157 1.46 - 1.57: 27849 1.57 - 1.69: 0 1.69 - 1.81: 233 Bond restraints: 49965 Sorted by residual: bond pdb=" N PRO C 189 " pdb=" CA PRO C 189 " ideal model delta sigma weight residual 1.465 1.694 -0.229 2.03e-02 2.43e+03 1.27e+02 bond pdb=" C PHE C 188 " pdb=" N PRO C 189 " ideal model delta sigma weight residual 1.329 1.452 -0.123 1.18e-02 7.18e+03 1.08e+02 bond pdb=" N PRO T 209 " pdb=" CD PRO T 209 " ideal model delta sigma weight residual 1.473 1.529 -0.056 1.40e-02 5.10e+03 1.59e+01 bond pdb=" N LEU 9 633 " pdb=" CA LEU 9 633 " ideal model delta sigma weight residual 1.453 1.488 -0.035 9.20e-03 1.18e+04 1.42e+01 bond pdb=" N PRO R1175 " pdb=" CD PRO R1175 " ideal model delta sigma weight residual 1.473 1.525 -0.052 1.40e-02 5.10e+03 1.39e+01 ... (remaining 49960 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.29: 68485 4.29 - 8.58: 239 8.58 - 12.87: 10 12.87 - 17.16: 1 17.16 - 21.45: 2 Bond angle restraints: 68737 Sorted by residual: angle pdb=" C PHE C 188 " pdb=" N PRO C 189 " pdb=" CA PRO C 189 " ideal model delta sigma weight residual 120.38 141.83 -21.45 1.03e+00 9.43e-01 4.34e+02 angle pdb=" C SER C 170 " pdb=" N ILE C 171 " pdb=" CA ILE C 171 " ideal model delta sigma weight residual 121.97 140.07 -18.10 1.80e+00 3.09e-01 1.01e+02 angle pdb=" CA PRO C 168 " pdb=" N PRO C 168 " pdb=" CD PRO C 168 " ideal model delta sigma weight residual 112.00 98.68 13.32 1.40e+00 5.10e-01 9.06e+01 angle pdb=" CA PRO T 209 " pdb=" N PRO T 209 " pdb=" CD PRO T 209 " ideal model delta sigma weight residual 112.00 99.24 12.76 1.40e+00 5.10e-01 8.31e+01 angle pdb=" CA PRO R1175 " pdb=" N PRO R1175 " pdb=" CD PRO R1175 " ideal model delta sigma weight residual 112.00 99.41 12.59 1.40e+00 5.10e-01 8.09e+01 ... (remaining 68732 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 27724 17.80 - 35.60: 1355 35.60 - 53.39: 250 53.39 - 71.19: 38 71.19 - 88.99: 18 Dihedral angle restraints: 29385 sinusoidal: 6719 harmonic: 22666 Sorted by residual: dihedral pdb=" CA SER H 85 " pdb=" C SER H 85 " pdb=" N SER H 86 " pdb=" CA SER H 86 " ideal model delta harmonic sigma weight residual -180.00 -138.45 -41.55 0 5.00e+00 4.00e-02 6.91e+01 dihedral pdb=" CA SER H 82 " pdb=" C SER H 82 " pdb=" N SER H 83 " pdb=" CA SER H 83 " ideal model delta harmonic sigma weight residual 180.00 148.17 31.83 0 5.00e+00 4.00e-02 4.05e+01 dihedral pdb=" CA ASP C 183 " pdb=" C ASP C 183 " pdb=" N LEU C 184 " pdb=" CA LEU C 184 " ideal model delta harmonic sigma weight residual -180.00 -150.53 -29.47 0 5.00e+00 4.00e-02 3.47e+01 ... (remaining 29382 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 7452 0.062 - 0.125: 989 0.125 - 0.187: 44 0.187 - 0.249: 4 0.249 - 0.312: 1 Chirality restraints: 8490 Sorted by residual: chirality pdb=" CA PRO C 189 " pdb=" N PRO C 189 " pdb=" C PRO C 189 " pdb=" CB PRO C 189 " both_signs ideal model delta sigma weight residual False 2.72 3.03 -0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" CA LEU C 184 " pdb=" N LEU C 184 " pdb=" C LEU C 184 " pdb=" CB LEU C 184 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA PRO 9 631 " pdb=" N PRO 9 631 " pdb=" C PRO 9 631 " pdb=" CB PRO 9 631 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 8487 not shown) Planarity restraints: 9157 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 196 " -0.117 5.00e-02 4.00e+02 1.67e-01 4.45e+01 pdb=" N PRO C 197 " 0.288 5.00e-02 4.00e+02 pdb=" CA PRO C 197 " -0.090 5.00e-02 4.00e+02 pdb=" CD PRO C 197 " -0.081 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN T 208 " 0.116 5.00e-02 4.00e+02 1.62e-01 4.19e+01 pdb=" N PRO T 209 " -0.279 5.00e-02 4.00e+02 pdb=" CA PRO T 209 " 0.089 5.00e-02 4.00e+02 pdb=" CD PRO T 209 " 0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER R1174 " 0.110 5.00e-02 4.00e+02 1.55e-01 3.83e+01 pdb=" N PRO R1175 " -0.267 5.00e-02 4.00e+02 pdb=" CA PRO R1175 " 0.081 5.00e-02 4.00e+02 pdb=" CD PRO R1175 " 0.076 5.00e-02 4.00e+02 ... (remaining 9154 not shown) Histogram of nonbonded interaction distances: 1.25 - 1.98: 10 1.98 - 2.71: 1859 2.71 - 3.44: 73373 3.44 - 4.17: 97503 4.17 - 4.90: 169021 Nonbonded interactions: 341766 Sorted by model distance: nonbonded pdb=" CB ARG K 350 " pdb=" CE1 HIS K 387 " model vdw 1.248 3.660 nonbonded pdb=" CB SER C 117 " pdb=" O THR E 111 " model vdw 1.561 3.440 nonbonded pdb=" OE1 GLU C 167 " pdb=" CB SER I 268 " model vdw 1.625 3.440 nonbonded pdb=" CB PRO C 141 " pdb=" O SER L 170 " model vdw 1.768 3.440 nonbonded pdb=" CB ARG K 350 " pdb=" NE2 HIS K 387 " model vdw 1.804 3.520 ... (remaining 341761 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: 8.560 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: 0.040 Extract box with map and model: 1.500 Check model and map are aligned: 0.290 Set scattering table: 0.340 Process input model: 90.200 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.190 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: 0.020 Load rotamer database and sin/cos tables:2.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 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 : 0.003 0.229 49965 Z= 0.227 Angle : 0.817 21.454 68737 Z= 0.531 Chirality : 0.040 0.312 8490 Planarity : 0.006 0.167 9157 Dihedral : 11.889 88.991 14510 Min Nonbonded Distance : 1.248 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.33 % Allowed : 10.19 % Favored : 89.48 % Rotamer: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -3.52 (0.09), residues: 7565 helix: -0.19 (0.08), residues: 3527 sheet: -4.19 (0.22), residues: 315 loop : -4.59 (0.08), residues: 3723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP T 97 HIS 0.008 0.001 HIS K 548 PHE 0.036 0.001 PHE C 130 TYR 0.013 0.001 TYR R 955 ARG 0.003 0.000 ARG R1019 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15130 Ramachandran restraints generated. 7565 Oldfield, 0 Emsley, 7565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15130 Ramachandran restraints generated. 7565 Oldfield, 0 Emsley, 7565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 6920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 540 time to evaluate : 5.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 661 LEU cc_start: 0.8737 (pp) cc_final: 0.8523 (pp) REVERT: I 699 LYS cc_start: 0.9600 (mtmt) cc_final: 0.9121 (mmtt) REVERT: I 776 LEU cc_start: 0.9153 (tp) cc_final: 0.8885 (tt) REVERT: I 1216 MET cc_start: 0.9357 (mtt) cc_final: 0.9085 (mtt) REVERT: K 486 TYR cc_start: 0.8416 (m-10) cc_final: 0.8174 (m-10) REVERT: K 526 ILE cc_start: 0.9482 (tp) cc_final: 0.9261 (tt) REVERT: K 658 LEU cc_start: 0.9354 (mt) cc_final: 0.9092 (mt) REVERT: L 378 LEU cc_start: 0.9415 (tp) cc_final: 0.9096 (tp) REVERT: Q 135 TYR cc_start: 0.7191 (t80) cc_final: 0.6970 (t80) REVERT: R 85 MET cc_start: 0.9167 (ptp) cc_final: 0.8777 (ppp) REVERT: R 213 ARG cc_start: 0.8825 (ptm160) cc_final: 0.8539 (tmm160) REVERT: R 379 PHE cc_start: 0.9138 (t80) cc_final: 0.8915 (t80) REVERT: R 1146 MET cc_start: 0.9330 (mmm) cc_final: 0.8979 (tpp) REVERT: R 1277 MET cc_start: 0.9458 (mmm) cc_final: 0.9168 (mmm) REVERT: S 767 LEU cc_start: 0.9190 (tp) cc_final: 0.8943 (tt) REVERT: T 143 LEU cc_start: 0.7924 (mm) cc_final: 0.7648 (tt) REVERT: V 190 LEU cc_start: 0.9427 (pp) cc_final: 0.9221 (mp) outliers start: 0 outliers final: 0 residues processed: 540 average time/residue: 0.4632 time to fit residues: 421.8326 Evaluate side-chains 366 residues out of total 6920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 366 time to evaluate : 4.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 768 random chunks: chunk 648 optimal weight: 8.9990 chunk 582 optimal weight: 0.9990 chunk 322 optimal weight: 0.7980 chunk 198 optimal weight: 4.9990 chunk 392 optimal weight: 0.0060 chunk 310 optimal weight: 2.9990 chunk 601 optimal weight: 0.0030 chunk 232 optimal weight: 7.9990 chunk 366 optimal weight: 0.3980 chunk 448 optimal weight: 10.0000 chunk 697 optimal weight: 5.9990 overall best weight: 0.4408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 638 ASN I 680 HIS I 860 ASN J 628 ASN ** K 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 225 ASN K 240 GLN K 282 HIS K 449 HIS K 473 HIS L 367 HIS L 466 ASN M 84 HIS M 134 HIS Q 102 ASN R 276 GLN R 333 HIS R 534 HIS R 552 HIS R 664 GLN R 684 ASN R 726 ASN ** R 874 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 998 HIS R1015 HIS R1028 HIS R1054 ASN ** R1128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R1197 HIS R1223 GLN R1300 HIS ** S 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 747 ASN S 760 HIS S 836 HIS S 920 HIS V 252 HIS W 79 GLN ** W 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 84 GLN X 85 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 49965 Z= 0.161 Angle : 0.595 9.188 68737 Z= 0.302 Chirality : 0.041 0.287 8490 Planarity : 0.004 0.085 9157 Dihedral : 4.015 38.655 7979 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.61 % Favored : 90.22 % Rotamer: Outliers : 0.20 % Allowed : 5.29 % Favored : 94.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % 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: -2.41 (0.10), residues: 7565 helix: 0.89 (0.09), residues: 3620 sheet: -3.62 (0.23), residues: 343 loop : -4.31 (0.09), residues: 3602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP T 97 HIS 0.010 0.001 HIS R 333 PHE 0.026 0.001 PHE C 130 TYR 0.026 0.001 TYR H 84 ARG 0.011 0.000 ARG Y 83 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15130 Ramachandran restraints generated. 7565 Oldfield, 0 Emsley, 7565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15130 Ramachandran restraints generated. 7565 Oldfield, 0 Emsley, 7565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 6920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 443 time to evaluate : 4.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 661 LEU cc_start: 0.8712 (pp) cc_final: 0.8449 (pp) REVERT: I 776 LEU cc_start: 0.9198 (tp) cc_final: 0.8908 (tt) REVERT: I 916 LEU cc_start: 0.8897 (tp) cc_final: 0.8622 (tp) REVERT: I 1216 MET cc_start: 0.9365 (mtt) cc_final: 0.8913 (mmt) REVERT: J 709 LYS cc_start: 0.8051 (mmpt) cc_final: 0.7379 (mmmt) REVERT: K 43 ASN cc_start: 0.7998 (t0) cc_final: 0.7789 (t0) REVERT: K 168 LEU cc_start: 0.7713 (tp) cc_final: 0.7463 (tp) REVERT: K 434 MET cc_start: 0.8133 (mpp) cc_final: 0.7711 (mpp) REVERT: K 486 TYR cc_start: 0.8332 (m-10) cc_final: 0.8068 (m-10) REVERT: Q 131 GLU cc_start: 0.8356 (mm-30) cc_final: 0.7846 (mm-30) REVERT: R 1017 ARG cc_start: 0.8206 (mmp-170) cc_final: 0.7811 (mmp80) REVERT: R 1146 MET cc_start: 0.9316 (mmm) cc_final: 0.8673 (tpp) REVERT: R 1275 TYR cc_start: 0.9287 (m-80) cc_final: 0.8970 (m-80) REVERT: R 1277 MET cc_start: 0.9435 (mmm) cc_final: 0.9164 (mmm) REVERT: R 1304 MET cc_start: 0.8999 (tpt) cc_final: 0.8179 (tpp) REVERT: S 248 ILE cc_start: 0.9555 (mm) cc_final: 0.9346 (tt) REVERT: S 767 LEU cc_start: 0.9173 (tp) cc_final: 0.8763 (tt) REVERT: T 143 LEU cc_start: 0.7855 (mm) cc_final: 0.7492 (tt) outliers start: 6 outliers final: 1 residues processed: 449 average time/residue: 0.4435 time to fit residues: 349.3063 Evaluate side-chains 356 residues out of total 6920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 355 time to evaluate : 4.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 768 random chunks: chunk 387 optimal weight: 4.9990 chunk 216 optimal weight: 0.5980 chunk 580 optimal weight: 6.9990 chunk 474 optimal weight: 0.9980 chunk 192 optimal weight: 4.9990 chunk 698 optimal weight: 0.9980 chunk 754 optimal weight: 30.0000 chunk 622 optimal weight: 0.0050 chunk 692 optimal weight: 2.9990 chunk 238 optimal weight: 10.0000 chunk 560 optimal weight: 0.7980 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 138 HIS K 282 HIS ** K 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 333 HIS ** R 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 972 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R1128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 679 GLN ** S 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 82 GLN ** X 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 79 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 49965 Z= 0.150 Angle : 0.570 8.880 68737 Z= 0.288 Chirality : 0.040 0.223 8490 Planarity : 0.004 0.071 9157 Dihedral : 3.896 39.975 7979 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.74 % Favored : 90.10 % Rotamer: Outliers : 0.10 % Allowed : 4.79 % Favored : 95.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.92 (0.10), residues: 7565 helix: 1.35 (0.09), residues: 3620 sheet: -3.31 (0.24), residues: 355 loop : -4.15 (0.09), residues: 3590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP T 97 HIS 0.010 0.001 HIS R 921 PHE 0.022 0.001 PHE L 308 TYR 0.019 0.001 TYR Q 135 ARG 0.006 0.000 ARG O 26 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15130 Ramachandran restraints generated. 7565 Oldfield, 0 Emsley, 7565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15130 Ramachandran restraints generated. 7565 Oldfield, 0 Emsley, 7565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 6920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 412 time to evaluate : 4.473 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 776 LEU cc_start: 0.9275 (tp) cc_final: 0.8995 (tt) REVERT: I 855 LEU cc_start: 0.9520 (mt) cc_final: 0.9302 (mt) REVERT: I 916 LEU cc_start: 0.8869 (tp) cc_final: 0.8636 (tp) REVERT: I 1216 MET cc_start: 0.9379 (mtt) cc_final: 0.8941 (mmt) REVERT: K 43 ASN cc_start: 0.8108 (t0) cc_final: 0.7899 (t0) REVERT: K 65 LEU cc_start: 0.9152 (pp) cc_final: 0.8919 (pp) REVERT: K 168 LEU cc_start: 0.7827 (tp) cc_final: 0.7571 (tp) REVERT: K 486 TYR cc_start: 0.8351 (m-10) cc_final: 0.8064 (m-10) REVERT: L 439 PHE cc_start: 0.8357 (t80) cc_final: 0.7975 (t80) REVERT: R 687 LEU cc_start: 0.9787 (tp) cc_final: 0.9542 (mp) REVERT: R 770 MET cc_start: 0.2070 (mtp) cc_final: 0.1801 (mtp) REVERT: R 1017 ARG cc_start: 0.8255 (mmp-170) cc_final: 0.7933 (mmp80) REVERT: R 1146 MET cc_start: 0.9311 (mmm) cc_final: 0.8884 (tpt) REVERT: R 1197 HIS cc_start: 0.8697 (m170) cc_final: 0.8428 (t-170) REVERT: R 1275 TYR cc_start: 0.9300 (m-80) cc_final: 0.8978 (m-80) REVERT: R 1277 MET cc_start: 0.9449 (mmm) cc_final: 0.9174 (mmm) REVERT: R 1291 MET cc_start: 0.7899 (mtp) cc_final: 0.7255 (mmm) REVERT: R 1304 MET cc_start: 0.9011 (tpt) cc_final: 0.8176 (tpp) REVERT: S 767 LEU cc_start: 0.9302 (tp) cc_final: 0.9033 (tt) REVERT: T 98 LEU cc_start: 0.9464 (mt) cc_final: 0.9120 (mt) outliers start: 3 outliers final: 0 residues processed: 415 average time/residue: 0.4848 time to fit residues: 359.2601 Evaluate side-chains 341 residues out of total 6920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 341 time to evaluate : 4.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 768 random chunks: chunk 690 optimal weight: 30.0000 chunk 525 optimal weight: 0.7980 chunk 362 optimal weight: 0.9990 chunk 77 optimal weight: 0.0770 chunk 333 optimal weight: 4.9990 chunk 469 optimal weight: 0.8980 chunk 701 optimal weight: 0.9990 chunk 742 optimal weight: 3.9990 chunk 366 optimal weight: 0.0060 chunk 664 optimal weight: 0.6980 chunk 200 optimal weight: 1.9990 overall best weight: 0.4954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 679 GLN K 282 HIS L 385 GLN R 333 HIS R 841 GLN R 874 HIS ** R 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 972 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 679 GLN ** S 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 81 ASN ** X 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 49965 Z= 0.144 Angle : 0.564 8.992 68737 Z= 0.283 Chirality : 0.040 0.157 8490 Planarity : 0.004 0.072 9157 Dihedral : 3.816 39.595 7979 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.60 % Favored : 90.26 % Rotamer: Outliers : 0.13 % Allowed : 3.96 % Favored : 95.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % 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: -1.64 (0.10), residues: 7565 helix: 1.57 (0.09), residues: 3622 sheet: -3.10 (0.25), residues: 348 loop : -3.99 (0.09), residues: 3595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.001 TRP T 97 HIS 0.009 0.001 HIS R 921 PHE 0.020 0.001 PHE L 308 TYR 0.026 0.001 TYR H 84 ARG 0.007 0.000 ARG R 685 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15130 Ramachandran restraints generated. 7565 Oldfield, 0 Emsley, 7565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15130 Ramachandran restraints generated. 7565 Oldfield, 0 Emsley, 7565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 6920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 406 time to evaluate : 4.528 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 776 LEU cc_start: 0.9313 (tp) cc_final: 0.9031 (tt) REVERT: I 855 LEU cc_start: 0.9519 (mt) cc_final: 0.9310 (mt) REVERT: I 916 LEU cc_start: 0.8929 (tp) cc_final: 0.8706 (tp) REVERT: I 1216 MET cc_start: 0.9403 (mtt) cc_final: 0.8954 (mmt) REVERT: K 43 ASN cc_start: 0.8168 (t0) cc_final: 0.7936 (t0) REVERT: K 65 LEU cc_start: 0.9087 (pp) cc_final: 0.8882 (pp) REVERT: K 168 LEU cc_start: 0.7870 (tp) cc_final: 0.7646 (tp) REVERT: K 282 HIS cc_start: 0.7058 (t70) cc_final: 0.6782 (t-170) REVERT: K 478 LEU cc_start: 0.9725 (tt) cc_final: 0.9517 (tt) REVERT: K 486 TYR cc_start: 0.8304 (m-10) cc_final: 0.8038 (m-10) REVERT: K 659 MET cc_start: 0.8328 (ppp) cc_final: 0.8124 (ppp) REVERT: L 439 PHE cc_start: 0.8388 (t80) cc_final: 0.8045 (t80) REVERT: R 141 ILE cc_start: 0.9634 (mt) cc_final: 0.9347 (tp) REVERT: R 286 MET cc_start: 0.9201 (ptt) cc_final: 0.8824 (ptm) REVERT: R 841 GLN cc_start: 0.6934 (OUTLIER) cc_final: 0.6671 (pp30) REVERT: R 922 MET cc_start: 0.8127 (mmp) cc_final: 0.7899 (mmm) REVERT: R 1017 ARG cc_start: 0.8226 (mmp-170) cc_final: 0.7807 (mmp80) REVERT: R 1146 MET cc_start: 0.9328 (mmm) cc_final: 0.8890 (tpt) REVERT: R 1197 HIS cc_start: 0.8668 (m170) cc_final: 0.8437 (t-170) REVERT: R 1275 TYR cc_start: 0.9303 (m-80) cc_final: 0.8943 (m-80) REVERT: R 1277 MET cc_start: 0.9465 (mmm) cc_final: 0.9161 (mmm) REVERT: R 1291 MET cc_start: 0.7701 (mtp) cc_final: 0.7263 (ttt) REVERT: R 1304 MET cc_start: 0.8988 (tpt) cc_final: 0.8137 (tpp) REVERT: S 768 LEU cc_start: 0.9383 (tt) cc_final: 0.9112 (pp) REVERT: T 169 LEU cc_start: 0.7943 (pp) cc_final: 0.7640 (pp) outliers start: 4 outliers final: 0 residues processed: 410 average time/residue: 0.4264 time to fit residues: 311.6532 Evaluate side-chains 344 residues out of total 6920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 343 time to evaluate : 4.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 768 random chunks: chunk 618 optimal weight: 5.9990 chunk 421 optimal weight: 3.9990 chunk 10 optimal weight: 0.0070 chunk 552 optimal weight: 3.9990 chunk 306 optimal weight: 0.0050 chunk 633 optimal weight: 0.0870 chunk 513 optimal weight: 5.9990 chunk 0 optimal weight: 40.0000 chunk 379 optimal weight: 7.9990 chunk 666 optimal weight: 2.9990 chunk 187 optimal weight: 7.9990 overall best weight: 1.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 311 GLN K 496 GLN ** L 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 70 GLN R 103 ASN R 333 HIS ** R 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 874 HIS ** R 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 679 GLN ** S 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 49965 Z= 0.165 Angle : 0.571 8.921 68737 Z= 0.292 Chirality : 0.041 0.187 8490 Planarity : 0.004 0.072 9157 Dihedral : 3.864 39.746 7979 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.06 % Favored : 89.77 % Rotamer: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % 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: -1.43 (0.10), residues: 7565 helix: 1.73 (0.09), residues: 3632 sheet: -2.92 (0.24), residues: 372 loop : -3.90 (0.09), residues: 3561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP T 97 HIS 0.009 0.001 HIS R 921 PHE 0.025 0.001 PHE L 308 TYR 0.012 0.001 TYR L 471 ARG 0.006 0.000 ARG K 210 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15130 Ramachandran restraints generated. 7565 Oldfield, 0 Emsley, 7565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15130 Ramachandran restraints generated. 7565 Oldfield, 0 Emsley, 7565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 6920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 401 time to evaluate : 4.395 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: I 652 MET cc_start: 0.9343 (mmt) cc_final: 0.9039 (mmt) REVERT: I 776 LEU cc_start: 0.9430 (tp) cc_final: 0.9111 (pp) REVERT: I 782 GLU cc_start: 0.8317 (pt0) cc_final: 0.7963 (pp20) REVERT: I 855 LEU cc_start: 0.9527 (mt) cc_final: 0.9322 (mt) REVERT: I 1216 MET cc_start: 0.9431 (mtt) cc_final: 0.9007 (mmt) REVERT: K 478 LEU cc_start: 0.9749 (tt) cc_final: 0.9542 (tt) REVERT: K 486 TYR cc_start: 0.8378 (m-10) cc_final: 0.8091 (m-10) REVERT: K 659 MET cc_start: 0.8438 (ppp) cc_final: 0.8204 (ppp) REVERT: R 922 MET cc_start: 0.8202 (mmp) cc_final: 0.7965 (mmm) REVERT: R 1017 ARG cc_start: 0.8200 (mmp-170) cc_final: 0.7831 (mmp80) REVERT: R 1275 TYR cc_start: 0.9328 (m-80) cc_final: 0.8980 (m-80) REVERT: R 1277 MET cc_start: 0.9485 (mmm) cc_final: 0.9181 (mmm) REVERT: R 1291 MET cc_start: 0.7894 (mtp) cc_final: 0.7513 (ttt) REVERT: R 1304 MET cc_start: 0.9019 (tpt) cc_final: 0.8151 (tpp) REVERT: S 623 TRP cc_start: 0.8762 (m100) cc_final: 0.8327 (m100) outliers start: 0 outliers final: 0 residues processed: 401 average time/residue: 0.4167 time to fit residues: 299.9839 Evaluate side-chains 329 residues out of total 6920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 329 time to evaluate : 4.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 768 random chunks: chunk 249 optimal weight: 0.0770 chunk 668 optimal weight: 9.9990 chunk 146 optimal weight: 40.0000 chunk 435 optimal weight: 30.0000 chunk 183 optimal weight: 0.8980 chunk 743 optimal weight: 2.9990 chunk 616 optimal weight: 0.8980 chunk 344 optimal weight: 0.0050 chunk 61 optimal weight: 0.3980 chunk 245 optimal weight: 50.0000 chunk 390 optimal weight: 4.9990 overall best weight: 0.4552 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 828 HIS K 74 HIS ** L 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 71 HIS R 333 HIS R 371 HIS ** R 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 679 GLN ** S 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 49965 Z= 0.138 Angle : 0.571 9.454 68737 Z= 0.284 Chirality : 0.040 0.224 8490 Planarity : 0.004 0.071 9157 Dihedral : 3.768 40.548 7979 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.58 % Favored : 90.26 % Rotamer: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % 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: -1.28 (0.10), residues: 7565 helix: 1.83 (0.09), residues: 3635 sheet: -2.81 (0.25), residues: 368 loop : -3.80 (0.09), residues: 3562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP T 97 HIS 0.009 0.001 HIS R 921 PHE 0.033 0.001 PHE I 644 TYR 0.013 0.001 TYR R1247 ARG 0.006 0.000 ARG S 705 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15130 Ramachandran restraints generated. 7565 Oldfield, 0 Emsley, 7565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15130 Ramachandran restraints generated. 7565 Oldfield, 0 Emsley, 7565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 6920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 402 time to evaluate : 4.383 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: I 916 LEU cc_start: 0.8839 (tp) cc_final: 0.8568 (tp) REVERT: I 1216 MET cc_start: 0.9394 (mtt) cc_final: 0.8958 (mmt) REVERT: K 43 ASN cc_start: 0.8477 (t0) cc_final: 0.8248 (t0) REVERT: K 65 LEU cc_start: 0.9128 (pp) cc_final: 0.8913 (pp) REVERT: K 168 LEU cc_start: 0.7951 (tp) cc_final: 0.7723 (tp) REVERT: K 434 MET cc_start: 0.6975 (mmt) cc_final: 0.6623 (mmp) REVERT: K 486 TYR cc_start: 0.8381 (m-10) cc_final: 0.8120 (m-10) REVERT: K 659 MET cc_start: 0.8414 (ppp) cc_final: 0.8209 (ppp) REVERT: R 922 MET cc_start: 0.8134 (mmp) cc_final: 0.7899 (mmm) REVERT: R 1017 ARG cc_start: 0.8177 (mmp-170) cc_final: 0.7768 (mmp80) REVERT: R 1146 MET cc_start: 0.9408 (mmm) cc_final: 0.9133 (tpp) REVERT: R 1275 TYR cc_start: 0.9297 (m-80) cc_final: 0.8929 (m-80) REVERT: R 1277 MET cc_start: 0.9485 (mmm) cc_final: 0.9165 (mmm) REVERT: R 1291 MET cc_start: 0.7790 (mtp) cc_final: 0.7385 (ttt) REVERT: R 1304 MET cc_start: 0.8975 (tpt) cc_final: 0.8107 (tpp) REVERT: S 623 TRP cc_start: 0.8737 (m100) cc_final: 0.8347 (m100) outliers start: 0 outliers final: 0 residues processed: 402 average time/residue: 0.4331 time to fit residues: 306.8248 Evaluate side-chains 336 residues out of total 6920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 336 time to evaluate : 4.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 768 random chunks: chunk 716 optimal weight: 0.0570 chunk 83 optimal weight: 0.0060 chunk 423 optimal weight: 7.9990 chunk 542 optimal weight: 4.9990 chunk 420 optimal weight: 9.9990 chunk 625 optimal weight: 2.9990 chunk 414 optimal weight: 0.6980 chunk 740 optimal weight: 2.9990 chunk 463 optimal weight: 3.9990 chunk 451 optimal weight: 0.9990 chunk 341 optimal weight: 9.9990 overall best weight: 0.9518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 385 GLN R 333 HIS R 613 HIS R 874 HIS ** R 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R1165 HIS S 679 GLN ** S 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 49965 Z= 0.148 Angle : 0.563 9.926 68737 Z= 0.282 Chirality : 0.040 0.176 8490 Planarity : 0.004 0.072 9157 Dihedral : 3.757 41.353 7979 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.65 % Favored : 90.18 % Rotamer: Outliers : 0.03 % Allowed : 1.72 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % 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: -1.15 (0.10), residues: 7565 helix: 1.93 (0.09), residues: 3639 sheet: -2.71 (0.25), residues: 368 loop : -3.74 (0.09), residues: 3558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.001 TRP T 97 HIS 0.008 0.001 HIS R 921 PHE 0.016 0.001 PHE R1243 TYR 0.011 0.001 TYR V 217 ARG 0.004 0.000 ARG I 775 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15130 Ramachandran restraints generated. 7565 Oldfield, 0 Emsley, 7565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15130 Ramachandran restraints generated. 7565 Oldfield, 0 Emsley, 7565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 6920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 390 time to evaluate : 4.554 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: I 652 MET cc_start: 0.9383 (mmt) cc_final: 0.9095 (mmt) REVERT: I 776 LEU cc_start: 0.9191 (tp) cc_final: 0.8915 (tt) REVERT: I 916 LEU cc_start: 0.8846 (tp) cc_final: 0.8604 (tp) REVERT: I 1216 MET cc_start: 0.9409 (mtt) cc_final: 0.8986 (mmt) REVERT: K 43 ASN cc_start: 0.8480 (t0) cc_final: 0.8258 (t0) REVERT: K 65 LEU cc_start: 0.9114 (pp) cc_final: 0.8894 (pp) REVERT: K 168 LEU cc_start: 0.8044 (tp) cc_final: 0.7819 (tp) REVERT: K 486 TYR cc_start: 0.8397 (m-10) cc_final: 0.8139 (m-10) REVERT: K 659 MET cc_start: 0.8462 (ppp) cc_final: 0.8246 (ppp) REVERT: R 922 MET cc_start: 0.8166 (mmp) cc_final: 0.7920 (mmm) REVERT: R 1017 ARG cc_start: 0.8130 (mmp-170) cc_final: 0.7733 (mmp80) REVERT: R 1146 MET cc_start: 0.9368 (mmm) cc_final: 0.9090 (tpp) REVERT: R 1275 TYR cc_start: 0.9311 (m-80) cc_final: 0.8967 (m-80) REVERT: R 1277 MET cc_start: 0.9484 (mmm) cc_final: 0.9181 (mmm) REVERT: R 1304 MET cc_start: 0.9021 (tpt) cc_final: 0.8145 (tpp) REVERT: S 623 TRP cc_start: 0.8852 (m100) cc_final: 0.8455 (m100) REVERT: W 79 GLN cc_start: 0.9514 (mp10) cc_final: 0.9162 (mp10) outliers start: 1 outliers final: 0 residues processed: 391 average time/residue: 0.4043 time to fit residues: 282.2853 Evaluate side-chains 326 residues out of total 6920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 326 time to evaluate : 4.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 768 random chunks: chunk 457 optimal weight: 4.9990 chunk 295 optimal weight: 0.7980 chunk 442 optimal weight: 40.0000 chunk 222 optimal weight: 3.9990 chunk 145 optimal weight: 50.0000 chunk 143 optimal weight: 0.9990 chunk 470 optimal weight: 5.9990 chunk 504 optimal weight: 7.9990 chunk 365 optimal weight: 5.9990 chunk 68 optimal weight: 50.0000 chunk 581 optimal weight: 0.7980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 680 HIS J 762 GLN L 329 ASN L 347 HIS ** L 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 373 HIS L 383 HIS ** L 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 333 HIS ** R 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 745 GLN ** R 921 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R1128 ASN R1198 GLN S 679 GLN ** S 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 49965 Z= 0.224 Angle : 0.633 9.032 68737 Z= 0.330 Chirality : 0.042 0.343 8490 Planarity : 0.004 0.071 9157 Dihedral : 4.247 47.413 7979 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.39 % Favored : 88.46 % Rotamer: Outliers : 0.03 % Allowed : 1.82 % Favored : 98.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % 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: -1.26 (0.10), residues: 7565 helix: 1.73 (0.09), residues: 3658 sheet: -2.51 (0.25), residues: 373 loop : -3.72 (0.09), residues: 3534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.003 TRP R 727 HIS 0.023 0.002 HIS R 725 PHE 0.023 0.002 PHE M 117 TYR 0.022 0.002 TYR Q 134 ARG 0.009 0.001 ARG H 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15130 Ramachandran restraints generated. 7565 Oldfield, 0 Emsley, 7565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15130 Ramachandran restraints generated. 7565 Oldfield, 0 Emsley, 7565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 6920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 369 time to evaluate : 4.560 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: I 652 MET cc_start: 0.9483 (mmt) cc_final: 0.9216 (mmt) REVERT: I 962 PHE cc_start: 0.9037 (m-80) cc_final: 0.8831 (m-80) REVERT: I 1216 MET cc_start: 0.9484 (mtt) cc_final: 0.9062 (mmt) REVERT: J 646 MET cc_start: 0.9049 (tpt) cc_final: 0.8837 (tpp) REVERT: K 43 ASN cc_start: 0.8451 (t0) cc_final: 0.8181 (t0) REVERT: K 65 LEU cc_start: 0.9183 (pp) cc_final: 0.8905 (pp) REVERT: K 168 LEU cc_start: 0.8518 (tp) cc_final: 0.8032 (tt) REVERT: K 486 TYR cc_start: 0.8264 (m-10) cc_final: 0.8032 (m-10) REVERT: K 659 MET cc_start: 0.8552 (ppp) cc_final: 0.8232 (ppp) REVERT: R 574 MET cc_start: 0.0629 (tpp) cc_final: 0.0337 (tpp) REVERT: R 871 MET cc_start: 0.8969 (mmp) cc_final: 0.8767 (mmm) REVERT: R 922 MET cc_start: 0.8454 (mmp) cc_final: 0.8209 (mmm) REVERT: R 1277 MET cc_start: 0.9494 (mmm) cc_final: 0.9232 (mmm) REVERT: R 1304 MET cc_start: 0.9061 (tpt) cc_final: 0.8103 (tpp) REVERT: S 72 MET cc_start: 0.7163 (mtm) cc_final: 0.6567 (ptp) REVERT: S 623 TRP cc_start: 0.8918 (m100) cc_final: 0.8585 (m100) REVERT: S 768 LEU cc_start: 0.9585 (tt) cc_final: 0.9258 (pp) outliers start: 1 outliers final: 0 residues processed: 370 average time/residue: 0.4118 time to fit residues: 274.3221 Evaluate side-chains 316 residues out of total 6920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 316 time to evaluate : 4.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 768 random chunks: chunk 673 optimal weight: 9.9990 chunk 709 optimal weight: 10.0000 chunk 647 optimal weight: 5.9990 chunk 689 optimal weight: 0.0170 chunk 708 optimal weight: 6.9990 chunk 415 optimal weight: 30.0000 chunk 300 optimal weight: 1.9990 chunk 541 optimal weight: 0.7980 chunk 211 optimal weight: 20.0000 chunk 623 optimal weight: 9.9990 chunk 652 optimal weight: 3.9990 overall best weight: 2.5624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 874 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 921 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 49965 Z= 0.215 Angle : 0.616 9.202 68737 Z= 0.319 Chirality : 0.042 0.338 8490 Planarity : 0.004 0.070 9157 Dihedral : 4.305 48.817 7979 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.63 % Favored : 89.19 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % 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: -1.22 (0.10), residues: 7565 helix: 1.74 (0.09), residues: 3672 sheet: -2.42 (0.24), residues: 398 loop : -3.70 (0.10), residues: 3495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.078 0.002 TRP S 23 HIS 0.010 0.001 HIS S 737 PHE 0.030 0.002 PHE Y 52 TYR 0.035 0.002 TYR R 951 ARG 0.006 0.000 ARG I 317 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15130 Ramachandran restraints generated. 7565 Oldfield, 0 Emsley, 7565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15130 Ramachandran restraints generated. 7565 Oldfield, 0 Emsley, 7565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 6920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 371 time to evaluate : 4.360 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: I 652 MET cc_start: 0.9495 (mmt) cc_final: 0.9257 (mmt) REVERT: I 916 LEU cc_start: 0.8828 (tp) cc_final: 0.8578 (tp) REVERT: I 1216 MET cc_start: 0.9485 (mtt) cc_final: 0.9035 (mmt) REVERT: K 43 ASN cc_start: 0.8458 (t0) cc_final: 0.8095 (t0) REVERT: K 65 LEU cc_start: 0.9204 (pp) cc_final: 0.8998 (pp) REVERT: K 168 LEU cc_start: 0.8500 (tp) cc_final: 0.7998 (tt) REVERT: K 282 HIS cc_start: 0.7441 (t70) cc_final: 0.7210 (t-170) REVERT: K 434 MET cc_start: 0.7228 (mmt) cc_final: 0.6611 (mmp) REVERT: K 486 TYR cc_start: 0.8376 (m-10) cc_final: 0.8154 (m-10) REVERT: K 659 MET cc_start: 0.8610 (ppp) cc_final: 0.8266 (ppp) REVERT: R 141 ILE cc_start: 0.9656 (mt) cc_final: 0.9374 (tp) REVERT: R 922 MET cc_start: 0.8529 (mmp) cc_final: 0.8286 (mmm) REVERT: R 1277 MET cc_start: 0.9499 (mmm) cc_final: 0.9213 (mmm) REVERT: R 1304 MET cc_start: 0.9036 (tpt) cc_final: 0.8089 (tpp) REVERT: S 72 MET cc_start: 0.7468 (mtm) cc_final: 0.6018 (ptp) REVERT: S 623 TRP cc_start: 0.8905 (m100) cc_final: 0.8581 (m100) REVERT: S 768 LEU cc_start: 0.9516 (tt) cc_final: 0.9287 (pp) REVERT: T 116 GLU cc_start: 0.7514 (mm-30) cc_final: 0.7291 (mm-30) REVERT: W 92 GLU cc_start: 0.9336 (mm-30) cc_final: 0.8891 (tp30) REVERT: W 96 LEU cc_start: 0.9556 (mm) cc_final: 0.8906 (mm) outliers start: 0 outliers final: 0 residues processed: 371 average time/residue: 0.4131 time to fit residues: 275.9199 Evaluate side-chains 317 residues out of total 6920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 317 time to evaluate : 4.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 768 random chunks: chunk 687 optimal weight: 7.9990 chunk 452 optimal weight: 4.9990 chunk 729 optimal weight: 0.9990 chunk 445 optimal weight: 20.0000 chunk 346 optimal weight: 50.0000 chunk 507 optimal weight: 2.9990 chunk 765 optimal weight: 20.0000 chunk 704 optimal weight: 9.9990 chunk 609 optimal weight: 5.9990 chunk 63 optimal weight: 30.0000 chunk 470 optimal weight: 0.2980 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 964 ASN ** K 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 395 HIS K 567 HIS ** K 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 373 HIS ** L 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 333 HIS R 613 HIS ** R 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 874 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 921 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R1010 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R1218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 157 GLN ** S 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 730 HIS ** V 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.4886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 49965 Z= 0.272 Angle : 0.683 12.254 68737 Z= 0.359 Chirality : 0.043 0.491 8490 Planarity : 0.005 0.070 9157 Dihedral : 4.763 54.679 7979 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.19 % Allowed : 12.56 % Favored : 87.26 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.27 % 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: -1.40 (0.10), residues: 7565 helix: 1.49 (0.09), residues: 3674 sheet: -2.37 (0.25), residues: 391 loop : -3.69 (0.10), residues: 3500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP S 23 HIS 0.014 0.002 HIS K 81 PHE 0.042 0.002 PHE Y 52 TYR 0.078 0.002 TYR S 742 ARG 0.025 0.001 ARG K 210 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15130 Ramachandran restraints generated. 7565 Oldfield, 0 Emsley, 7565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15130 Ramachandran restraints generated. 7565 Oldfield, 0 Emsley, 7565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 6920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 348 time to evaluate : 4.534 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: I 652 MET cc_start: 0.9547 (mmt) cc_final: 0.9323 (mmt) REVERT: I 776 LEU cc_start: 0.9332 (tt) cc_final: 0.9115 (pp) REVERT: I 916 LEU cc_start: 0.8833 (tp) cc_final: 0.8594 (tp) REVERT: I 1216 MET cc_start: 0.9516 (mtt) cc_final: 0.9043 (mmt) REVERT: J 646 MET cc_start: 0.9037 (tpt) cc_final: 0.8688 (tpp) REVERT: K 168 LEU cc_start: 0.8633 (tp) cc_final: 0.8131 (tt) REVERT: K 382 LEU cc_start: 0.9522 (tp) cc_final: 0.9081 (mp) REVERT: K 486 TYR cc_start: 0.8570 (m-10) cc_final: 0.8283 (m-10) REVERT: K 659 MET cc_start: 0.8624 (ppp) cc_final: 0.8262 (ppp) REVERT: R 191 TYR cc_start: 0.7629 (t80) cc_final: 0.7417 (t80) REVERT: R 282 MET cc_start: 0.9490 (tmm) cc_final: 0.9215 (tmm) REVERT: R 286 MET cc_start: 0.9205 (ttp) cc_final: 0.8966 (ptm) REVERT: R 612 MET cc_start: 0.8491 (tpp) cc_final: 0.8175 (tpp) REVERT: R 922 MET cc_start: 0.8543 (mmp) cc_final: 0.8275 (mmm) REVERT: R 1146 MET cc_start: 0.9458 (mmp) cc_final: 0.9214 (mmm) REVERT: R 1267 MET cc_start: 0.9143 (ptm) cc_final: 0.8892 (ptm) REVERT: R 1277 MET cc_start: 0.9504 (mmm) cc_final: 0.9247 (mmm) REVERT: R 1291 MET cc_start: 0.8410 (mtp) cc_final: 0.7017 (mpp) REVERT: R 1304 MET cc_start: 0.9042 (tpt) cc_final: 0.8060 (tpp) REVERT: S 72 MET cc_start: 0.7192 (mtm) cc_final: 0.5522 (mtt) REVERT: S 768 LEU cc_start: 0.9587 (tt) cc_final: 0.9333 (pp) REVERT: T 116 GLU cc_start: 0.7511 (mm-30) cc_final: 0.7264 (mm-30) REVERT: W 92 GLU cc_start: 0.9301 (mm-30) cc_final: 0.8977 (tp30) REVERT: W 96 LEU cc_start: 0.9568 (mm) cc_final: 0.8869 (mm) outliers start: 0 outliers final: 0 residues processed: 348 average time/residue: 0.4188 time to fit residues: 264.6590 Evaluate side-chains 299 residues out of total 6920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 4.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 768 random chunks: chunk 373 optimal weight: 0.9990 chunk 483 optimal weight: 8.9990 chunk 649 optimal weight: 0.0570 chunk 186 optimal weight: 7.9990 chunk 561 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 169 optimal weight: 0.0170 chunk 610 optimal weight: 0.0980 chunk 255 optimal weight: 0.0570 chunk 626 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 overall best weight: 0.2454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 680 HIS K 282 HIS ** K 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 218 HIS ** L 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 535 HIS R 613 HIS ** R 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R1218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 428 HIS ** V 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 100 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.057396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.039683 restraints weight = 566756.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.040282 restraints weight = 447183.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.040460 restraints weight = 333091.620| |-----------------------------------------------------------------------------| r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2977 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2977 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.4752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 49965 Z= 0.154 Angle : 0.611 9.969 68737 Z= 0.306 Chirality : 0.042 0.323 8490 Planarity : 0.004 0.071 9157 Dihedral : 4.327 49.979 7979 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.05 % Favored : 89.80 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % 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: -1.13 (0.10), residues: 7565 helix: 1.74 (0.09), residues: 3699 sheet: -2.24 (0.26), residues: 375 loop : -3.63 (0.10), residues: 3491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP S 23 HIS 0.010 0.001 HIS R 921 PHE 0.021 0.001 PHE I 962 TYR 0.014 0.001 TYR V 217 ARG 0.006 0.000 ARG Q 101 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7692.80 seconds wall clock time: 135 minutes 51.06 seconds (8151.06 seconds total)