Starting phenix.real_space_refine on Mon Aug 25 02:44:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fkj_29250/08_2025/8fkj_29250.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fkj_29250/08_2025/8fkj_29250.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8fkj_29250/08_2025/8fkj_29250.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fkj_29250/08_2025/8fkj_29250.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fkj_29250/08_2025/8fkj_29250.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fkj_29250/08_2025/8fkj_29250.map" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 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: 3 Type Number sf(0) Gaussians C 14825 2.51 5 N 5088 2.21 5 O 5088 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25001 Number of models: 1 Model: "" Number of chains: 27 Chain: "Y" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 817 Classifications: {'peptide': 166} Incomplete info: {'truncation_to_alanine': 139} Link IDs: {'PTRANS': 7, 'TRANS': 158} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 456 Unresolved non-hydrogen angles: 577 Unresolved non-hydrogen dihedrals: 368 Unresolved non-hydrogen chiralities: 52 Planarities with less than four sites: {'ARG:plan': 4, 'PHE:plan': 5, 'GLU:plan': 10, 'TYR:plan': 3, 'GLN:plan1': 4, 'ASN:plan1': 11, 'ASP:plan': 7, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 196 Chain: "A" Number of atoms: 2488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 2488 Classifications: {'peptide': 507} Incomplete info: {'truncation_to_alanine': 410} Link IDs: {'PTRANS': 20, 'TRANS': 486} Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1428 Unresolved non-hydrogen angles: 1826 Unresolved non-hydrogen dihedrals: 1148 Unresolved non-hydrogen chiralities: 154 Planarities with less than four sites: {'GLN:plan1': 26, 'GLU:plan': 37, 'ARG:plan': 29, 'ASP:plan': 21, 'ASN:plan1': 17, 'PHE:plan': 15, 'HIS:plan': 6, 'TRP:plan': 2, 'TYR:plan': 14} Unresolved non-hydrogen planarities: 747 Chain: "B" Number of atoms: 2483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 2483 Classifications: {'peptide': 506} Incomplete info: {'truncation_to_alanine': 409} Link IDs: {'PTRANS': 20, 'TRANS': 485} Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1421 Unresolved non-hydrogen angles: 1817 Unresolved non-hydrogen dihedrals: 1141 Unresolved non-hydrogen chiralities: 154 Planarities with less than four sites: {'GLN:plan1': 26, 'GLU:plan': 37, 'ARG:plan': 29, 'ASP:plan': 21, 'ASN:plan1': 17, 'PHE:plan': 14, 'HIS:plan': 6, 'TRP:plan': 2, 'TYR:plan': 14} Unresolved non-hydrogen planarities: 741 Chain: "C" Number of atoms: 2478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 2478 Classifications: {'peptide': 505} Incomplete info: {'truncation_to_alanine': 409} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 484} Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1424 Unresolved non-hydrogen angles: 1822 Unresolved non-hydrogen dihedrals: 1144 Unresolved non-hydrogen chiralities: 154 Planarities with less than four sites: {'GLN:plan1': 26, 'GLU:plan': 37, 'ARG:plan': 29, 'ASP:plan': 21, 'ASN:plan1': 17, 'PHE:plan': 15, 'HIS:plan': 6, 'TRP:plan': 2, 'TYR:plan': 14} Unresolved non-hydrogen planarities: 747 Chain: "D" Number of atoms: 2319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 2319 Classifications: {'peptide': 473} Incomplete info: {'truncation_to_alanine': 382} Link IDs: {'PTRANS': 23, 'TRANS': 449} Unresolved chain link angles: 23 Unresolved non-hydrogen bonds: 1309 Unresolved non-hydrogen angles: 1680 Unresolved non-hydrogen dihedrals: 1039 Unresolved non-hydrogen chiralities: 156 Planarities with less than four sites: {'ASP:plan': 25, 'HIS:plan': 7, 'PHE:plan': 17, 'GLU:plan': 38, 'GLN:plan1': 18, 'ASN:plan1': 11, 'ARG:plan': 22, 'TYR:plan': 10} Unresolved non-hydrogen planarities: 649 Chain: "E" Number of atoms: 2319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 2319 Classifications: {'peptide': 473} Incomplete info: {'truncation_to_alanine': 382} Link IDs: {'PTRANS': 23, 'TRANS': 449} Unresolved chain link angles: 23 Unresolved non-hydrogen bonds: 1309 Unresolved non-hydrogen angles: 1680 Unresolved non-hydrogen dihedrals: 1039 Unresolved non-hydrogen chiralities: 156 Planarities with less than four sites: {'ASP:plan': 25, 'HIS:plan': 7, 'PHE:plan': 17, 'GLU:plan': 38, 'GLN:plan1': 18, 'ASN:plan1': 11, 'ARG:plan': 22, 'TYR:plan': 10} Unresolved non-hydrogen planarities: 649 Chain: "F" Number of atoms: 2314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 2314 Classifications: {'peptide': 472} Incomplete info: {'truncation_to_alanine': 381} Link IDs: {'PTRANS': 23, 'TRANS': 448} Unresolved chain link angles: 23 Unresolved non-hydrogen bonds: 1308 Unresolved non-hydrogen angles: 1679 Unresolved non-hydrogen dihedrals: 1038 Unresolved non-hydrogen chiralities: 156 Planarities with less than four sites: {'ASP:plan': 25, 'HIS:plan': 7, 'PHE:plan': 17, 'GLU:plan': 38, 'GLN:plan1': 18, 'ASN:plan1': 11, 'ARG:plan': 22, 'TYR:plan': 10} Unresolved non-hydrogen planarities: 649 Chain: "R" Number of atoms: 356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 356 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 2, 'TRANS': 70} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 178 Unresolved non-hydrogen angles: 230 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'PHE:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 65 Chain: "S" Number of atoms: 356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 356 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 2, 'TRANS': 70} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 178 Unresolved non-hydrogen angles: 230 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'PHE:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 65 Chain: "T" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 360 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 178 Unresolved non-hydrogen angles: 230 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'PHE:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 65 Chain: "K" Number of atoms: 356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 356 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 2, 'TRANS': 70} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 178 Unresolved non-hydrogen angles: 230 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'PHE:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 65 Chain: "L" Number of atoms: 356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 356 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 2, 'TRANS': 70} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 178 Unresolved non-hydrogen angles: 230 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'PHE:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 65 Chain: "M" Number of atoms: 356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 356 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 2, 'TRANS': 70} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 178 Unresolved non-hydrogen angles: 230 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'PHE:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 65 Chain: "N" Number of atoms: 356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 356 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 2, 'TRANS': 70} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 178 Unresolved non-hydrogen angles: 230 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'PHE:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 65 Chain: "O" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 360 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 178 Unresolved non-hydrogen angles: 230 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'PHE:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 65 Chain: "P" Number of atoms: 356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 356 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 2, 'TRANS': 70} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 178 Unresolved non-hydrogen angles: 230 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'PHE:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 65 Chain: "Q" Number of atoms: 356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 356 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 2, 'TRANS': 70} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 178 Unresolved non-hydrogen angles: 230 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'PHE:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 65 Chain: "Z" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 772 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 138} Link IDs: {'PTRANS': 2, 'TRANS': 152} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 479 Unresolved non-hydrogen angles: 604 Unresolved non-hydrogen dihedrals: 388 Unresolved non-hydrogen chiralities: 46 Planarities with less than four sites: {'ASN:plan1': 5, 'ASP:plan': 8, 'GLU:plan': 16, 'PHE:plan': 6, 'TYR:plan': 3, 'ARG:plan': 7, 'HIS:plan': 2, 'GLN:plan1': 11, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 258 Chain: "7" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 851 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 156} Link IDs: {'PTRANS': 5, 'TRANS': 165} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 538 Unresolved non-hydrogen angles: 675 Unresolved non-hydrogen dihedrals: 446 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'ASN:plan1': 7, 'ASP:plan': 13, 'TRP:plan': 2, 'ARG:plan': 7, 'GLN:plan1': 9, 'PHE:plan': 5, 'GLU:plan': 13, 'HIS:plan': 2, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 269 Chain: "6" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 442 Classifications: {'peptide': 89} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 8, 'TRANS': 80} Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 284 Unresolved non-hydrogen angles: 366 Unresolved non-hydrogen dihedrals: 234 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 6, 'TYR:plan': 2, 'ARG:plan': 1, 'GLU:plan': 17, 'ASN:plan1': 4, 'TRP:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 165 Chain: "U" Number of atoms: 419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 419 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 7, 'TRANS': 77} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 269 Unresolved non-hydrogen angles: 345 Unresolved non-hydrogen dihedrals: 241 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ASN:plan1': 5, 'ARG:plan': 3, 'HIS:plan': 3, 'PHE:plan': 5, 'TYR:plan': 6, 'GLN:plan1': 1, 'ASP:plan': 2, 'TRP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 140 Chain: "8" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 204 Classifications: {'peptide': 41} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 1, 'TRANS': 39} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 209 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'PHE:plan': 7, 'TYR:plan': 3, 'ASN:plan1': 1, 'GLN:plan1': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 84 Chain: "X" Number of atoms: 1104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1104 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 193} Link IDs: {'PTRANS': 7, 'TRANS': 216} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 717 Unresolved non-hydrogen angles: 943 Unresolved non-hydrogen dihedrals: 607 Unresolved non-hydrogen chiralities: 98 Planarities with less than four sites: {'PHE:plan': 18, 'TYR:plan': 10, 'ASN:plan1': 11, 'ARG:plan': 3, 'TRP:plan': 5, 'GLN:plan1': 3, 'GLU:plan': 3, 'ASP:plan': 2, 'HIS:plan': 4} Unresolved non-hydrogen planarities: 321 Chain: "J" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 183 Classifications: {'peptide': 37} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 3, 'TRANS': 33} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ARG:plan': 1, 'PHE:plan': 3, 'TYR:plan': 3, 'TRP:plan': 1, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 59 Chain: "G" Number of atoms: 1295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 1295 Classifications: {'peptide': 261} Incomplete info: {'truncation_to_alanine': 224} Link IDs: {'PTRANS': 9, 'TRANS': 251} Chain breaks: 1 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 764 Unresolved non-hydrogen angles: 957 Unresolved non-hydrogen dihedrals: 623 Unresolved non-hydrogen chiralities: 72 Planarities with less than four sites: {'GLU:plan': 16, 'ARG:plan': 11, 'ASN:plan1': 18, 'ASP:plan': 15, 'GLN:plan1': 9, 'PHE:plan': 8, 'TYR:plan': 7, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 366 Chain: "H" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 652 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'PTRANS': 6, 'TRANS': 125} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 352 Unresolved non-hydrogen angles: 448 Unresolved non-hydrogen dihedrals: 281 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 8, 'PHE:plan': 6, 'HIS:plan': 2, 'GLU:plan': 13, 'TYR:plan': 1, 'ASN:plan1': 7, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 174 Chain: "I" Number of atoms: 293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 293 Classifications: {'peptide': 59} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 2, 'TRANS': 56} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 215 Unresolved non-hydrogen dihedrals: 140 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'TRP:plan': 1, 'ARG:plan': 3, 'TYR:plan': 4, 'ASN:plan1': 3, 'GLN:plan1': 4, 'GLU:plan': 2, 'ASP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 94 Time building chain proxies: 7.13, per 1000 atoms: 0.29 Number of scatterers: 25001 At special positions: 0 Unit cell: (143, 147, 224, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 5088 8.00 N 5088 7.00 C 14825 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 2.45 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 953.7 nanoseconds 10064 Ramachandran restraints generated. 5032 Oldfield, 0 Emsley, 5032 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9298 Finding SS restraints... Secondary structure from input PDB file: 196 helices and 33 sheets defined 57.6% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'Y' and resid 16 through 30 removed outlier: 4.415A pdb=" N ALA Y 20 " --> pdb=" O GLU Y 16 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN Y 30 " --> pdb=" O ALA Y 26 " (cutoff:3.500A) Processing helix chain 'Y' and resid 33 through 50 removed outlier: 3.564A pdb=" N SER Y 39 " --> pdb=" O ALA Y 35 " (cutoff:3.500A) Processing helix chain 'Y' and resid 63 through 76 Processing helix chain 'Y' and resid 83 through 96 removed outlier: 4.369A pdb=" N ASN Y 87 " --> pdb=" O GLY Y 83 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU Y 94 " --> pdb=" O LYS Y 90 " (cutoff:3.500A) Processing helix chain 'Y' and resid 99 through 115 Processing helix chain 'Y' and resid 137 through 149 removed outlier: 4.252A pdb=" N LEU Y 141 " --> pdb=" O ILE Y 137 " (cutoff:3.500A) Processing helix chain 'Y' and resid 160 through 171 Processing helix chain 'A' and resid 5 through 16 Processing helix chain 'A' and resid 102 through 106 removed outlier: 3.625A pdb=" N LEU A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 158 Processing helix chain 'A' and resid 176 through 188 Processing helix chain 'A' and resid 188 through 193 Processing helix chain 'A' and resid 211 through 225 removed outlier: 3.521A pdb=" N VAL A 215 " --> pdb=" O LYS A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 261 Proline residue: A 249 - end of helix Processing helix chain 'A' and resid 272 through 287 removed outlier: 3.647A pdb=" N GLN A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 297 removed outlier: 3.679A pdb=" N TYR A 296 " --> pdb=" O ARG A 293 " (cutoff:3.500A) Proline residue: A 297 - end of helix Processing helix chain 'A' and resid 298 through 309 removed outlier: 3.983A pdb=" N TYR A 302 " --> pdb=" O GLY A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 348 removed outlier: 3.629A pdb=" N THR A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 361 removed outlier: 4.034A pdb=" N PHE A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 381 Processing helix chain 'A' and resid 382 through 403 removed outlier: 3.787A pdb=" N VAL A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N SER A 391 " --> pdb=" O GLN A 387 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 394 " --> pdb=" O GLY A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 409 removed outlier: 4.023A pdb=" N GLY A 409 " --> pdb=" O ALA A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 430 Processing helix chain 'A' and resid 442 through 452 removed outlier: 4.512A pdb=" N LEU A 446 " --> pdb=" O GLU A 442 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE A 447 " --> pdb=" O GLN A 443 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN A 452 " --> pdb=" O TYR A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 461 No H-bonds generated for 'chain 'A' and resid 459 through 461' Processing helix chain 'A' and resid 462 through 477 Processing helix chain 'A' and resid 478 through 489 Processing helix chain 'A' and resid 492 through 510 Processing helix chain 'B' and resid 5 through 24 Processing helix chain 'B' and resid 102 through 106 Processing helix chain 'B' and resid 176 through 187 Processing helix chain 'B' and resid 211 through 225 removed outlier: 3.584A pdb=" N HIS B 225 " --> pdb=" O THR B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 261 Proline residue: B 249 - end of helix Processing helix chain 'B' and resid 272 through 288 removed outlier: 4.017A pdb=" N GLN B 276 " --> pdb=" O ASP B 272 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG B 288 " --> pdb=" O SER B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 296 removed outlier: 3.502A pdb=" N ALA B 295 " --> pdb=" O GLY B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 298 No H-bonds generated for 'chain 'B' and resid 297 through 298' Processing helix chain 'B' and resid 299 through 309 Processing helix chain 'B' and resid 315 through 319 Processing helix chain 'B' and resid 338 through 348 Processing helix chain 'B' and resid 356 through 362 Processing helix chain 'B' and resid 382 through 387 Processing helix chain 'B' and resid 389 through 405 removed outlier: 3.614A pdb=" N PHE B 405 " --> pdb=" O GLU B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 431 removed outlier: 4.058A pdb=" N LYS B 431 " --> pdb=" O THR B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 452 Processing helix chain 'B' and resid 462 through 477 removed outlier: 4.799A pdb=" N SER B 468 " --> pdb=" O GLY B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 488 Processing helix chain 'B' and resid 492 through 509 Processing helix chain 'C' and resid 80 through 84 removed outlier: 3.840A pdb=" N LEU C 83 " --> pdb=" O SER C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 106 removed outlier: 4.130A pdb=" N LEU C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 158 Processing helix chain 'C' and resid 176 through 193 removed outlier: 3.705A pdb=" N LYS C 189 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ARG C 190 " --> pdb=" O LEU C 186 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N TRP C 191 " --> pdb=" O ASN C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 226 Processing helix chain 'C' and resid 227 through 229 No H-bonds generated for 'chain 'C' and resid 227 through 229' Processing helix chain 'C' and resid 241 through 262 Proline residue: C 249 - end of helix Processing helix chain 'C' and resid 272 through 287 Processing helix chain 'C' and resid 292 through 296 removed outlier: 3.552A pdb=" N TYR C 296 " --> pdb=" O ARG C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 310 Processing helix chain 'C' and resid 331 through 335 removed outlier: 3.687A pdb=" N GLY C 334 " --> pdb=" O THR C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 348 Processing helix chain 'C' and resid 355 through 361 removed outlier: 3.642A pdb=" N PHE C 359 " --> pdb=" O GLU C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 381 removed outlier: 4.268A pdb=" N ALA C 379 " --> pdb=" O VAL C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 409 removed outlier: 4.322A pdb=" N VAL C 388 " --> pdb=" O ALA C 384 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N SER C 391 " --> pdb=" O GLN C 387 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU C 394 " --> pdb=" O GLY C 390 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ALA C 404 " --> pdb=" O ARG C 400 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N PHE C 405 " --> pdb=" O GLU C 401 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY C 409 " --> pdb=" O PHE C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 431 removed outlier: 3.583A pdb=" N LYS C 431 " --> pdb=" O THR C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 452 Proline residue: C 445 - end of helix removed outlier: 3.638A pdb=" N ASN C 452 " --> pdb=" O TYR C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 475 Processing helix chain 'C' and resid 478 through 489 Processing helix chain 'C' and resid 492 through 509 removed outlier: 4.176A pdb=" N THR C 509 " --> pdb=" O SER C 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 92 Processing helix chain 'D' and resid 138 through 144 Processing helix chain 'D' and resid 162 through 176 removed outlier: 3.732A pdb=" N PHE D 166 " --> pdb=" O GLY D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 204 Processing helix chain 'D' and resid 225 through 248 removed outlier: 4.113A pdb=" N ARG D 229 " --> pdb=" O PRO D 225 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ALA D 233 " --> pdb=" O ARG D 229 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU D 234 " --> pdb=" O ALA D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 272 Processing helix chain 'D' and resid 284 through 296 removed outlier: 3.715A pdb=" N ILE D 296 " --> pdb=" O LEU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 327 Processing helix chain 'D' and resid 359 through 364 removed outlier: 3.529A pdb=" N GLY D 364 " --> pdb=" O ALA D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 392 removed outlier: 3.934A pdb=" N ASP D 386 " --> pdb=" O LYS D 382 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ILE D 387 " --> pdb=" O SER D 383 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA D 389 " --> pdb=" O GLN D 385 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE D 390 " --> pdb=" O ASP D 386 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU D 391 " --> pdb=" O ILE D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 414 removed outlier: 4.546A pdb=" N LYS D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 426 removed outlier: 3.744A pdb=" N THR D 425 " --> pdb=" O ALA D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 447 removed outlier: 4.143A pdb=" N ALA D 439 " --> pdb=" O LYS D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 474 removed outlier: 4.105A pdb=" N LYS D 469 " --> pdb=" O ASP D 465 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA D 470 " --> pdb=" O VAL D 466 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 127 Processing helix chain 'E' and resid 138 through 144 removed outlier: 3.624A pdb=" N LEU E 144 " --> pdb=" O VAL E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 178 Processing helix chain 'E' and resid 190 through 205 Processing helix chain 'E' and resid 225 through 246 removed outlier: 4.321A pdb=" N ALA E 233 " --> pdb=" O ARG E 229 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N LEU E 234 " --> pdb=" O ALA E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 273 removed outlier: 3.713A pdb=" N GLY E 273 " --> pdb=" O SER E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 293 removed outlier: 4.306A pdb=" N LEU E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 296 No H-bonds generated for 'chain 'E' and resid 294 through 296' Processing helix chain 'E' and resid 312 through 316 removed outlier: 3.509A pdb=" N ASP E 316 " --> pdb=" O PRO E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 329 Processing helix chain 'E' and resid 336 through 343 removed outlier: 3.598A pdb=" N GLU E 341 " --> pdb=" O ARG E 337 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY E 343 " --> pdb=" O ILE E 339 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 353 removed outlier: 4.056A pdb=" N ASP E 352 " --> pdb=" O ASP E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 392 removed outlier: 3.617A pdb=" N ASP E 386 " --> pdb=" O LYS E 382 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE E 387 " --> pdb=" O SER E 383 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ILE E 390 " --> pdb=" O ASP E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 396 Processing helix chain 'E' and resid 397 through 415 removed outlier: 4.124A pdb=" N SER E 415 " --> pdb=" O GLN E 411 " (cutoff:3.500A) Processing helix chain 'E' and resid 433 through 446 removed outlier: 4.205A pdb=" N ALA E 439 " --> pdb=" O LYS E 435 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 457 Processing helix chain 'E' and resid 462 through 476 removed outlier: 3.989A pdb=" N VAL E 467 " --> pdb=" O ILE E 463 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ALA E 468 " --> pdb=" O GLU E 464 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 92 Processing helix chain 'F' and resid 138 through 143 Processing helix chain 'F' and resid 162 through 175 Processing helix chain 'F' and resid 190 through 204 Processing helix chain 'F' and resid 225 through 246 removed outlier: 4.295A pdb=" N ALA F 233 " --> pdb=" O ARG F 229 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU F 234 " --> pdb=" O ALA F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 272 removed outlier: 3.990A pdb=" N PHE F 261 " --> pdb=" O ASN F 257 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR F 262 " --> pdb=" O ILE F 258 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA F 270 " --> pdb=" O SER F 266 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU F 271 " --> pdb=" O GLU F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 277 through 281 Processing helix chain 'F' and resid 284 through 292 Processing helix chain 'F' and resid 312 through 316 Processing helix chain 'F' and resid 319 through 329 removed outlier: 4.061A pdb=" N ALA F 327 " --> pdb=" O ALA F 323 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N HIS F 328 " --> pdb=" O THR F 324 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU F 329 " --> pdb=" O THR F 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 336 through 342 removed outlier: 3.568A pdb=" N LEU F 342 " --> pdb=" O GLY F 338 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 364 removed outlier: 3.896A pdb=" N VAL F 363 " --> pdb=" O ASP F 359 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY F 364 " --> pdb=" O ALA F 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 359 through 364' Processing helix chain 'F' and resid 364 through 391 removed outlier: 4.373A pdb=" N ASP F 386 " --> pdb=" O LYS F 382 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ILE F 387 " --> pdb=" O SER F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 415 removed outlier: 4.197A pdb=" N SER F 415 " --> pdb=" O GLN F 411 " (cutoff:3.500A) Processing helix chain 'F' and resid 420 through 424 removed outlier: 3.748A pdb=" N VAL F 423 " --> pdb=" O VAL F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 433 through 447 Processing helix chain 'F' and resid 462 through 477 Processing helix chain 'R' and resid 3 through 16 removed outlier: 4.199A pdb=" N THR R 16 " --> pdb=" O ALA R 12 " (cutoff:3.500A) Processing helix chain 'R' and resid 17 through 40 removed outlier: 4.193A pdb=" N GLY R 21 " --> pdb=" O ILE R 17 " (cutoff:3.500A) Processing helix chain 'R' and resid 43 through 74 Proline residue: R 49 - end of helix removed outlier: 3.560A pdb=" N ALA R 56 " --> pdb=" O ILE R 52 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU R 57 " --> pdb=" O LEU R 53 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY R 62 " --> pdb=" O SER R 58 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER R 69 " --> pdb=" O CYS R 65 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU R 72 " --> pdb=" O VAL R 68 " (cutoff:3.500A) Processing helix chain 'S' and resid 3 through 15 Processing helix chain 'S' and resid 18 through 40 removed outlier: 4.477A pdb=" N ALA S 22 " --> pdb=" O GLY S 18 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA S 27 " --> pdb=" O GLY S 23 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 74 removed outlier: 4.343A pdb=" N THR S 46 " --> pdb=" O SER S 42 " (cutoff:3.500A) Proline residue: S 49 - end of helix removed outlier: 3.594A pdb=" N ALA S 60 " --> pdb=" O ALA S 56 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N THR S 61 " --> pdb=" O LEU S 57 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLY S 62 " --> pdb=" O SER S 58 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU S 73 " --> pdb=" O SER S 69 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 16 removed outlier: 3.880A pdb=" N THR T 16 " --> pdb=" O ALA T 12 " (cutoff:3.500A) Processing helix chain 'T' and resid 18 through 40 removed outlier: 3.744A pdb=" N ALA T 22 " --> pdb=" O GLY T 18 " (cutoff:3.500A) Processing helix chain 'T' and resid 43 through 75 Proline residue: T 49 - end of helix removed outlier: 3.648A pdb=" N ILE T 52 " --> pdb=" O PHE T 48 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU T 53 " --> pdb=" O PRO T 49 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL T 68 " --> pdb=" O PHE T 64 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N SER T 69 " --> pdb=" O CYS T 65 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 17 removed outlier: 4.091A pdb=" N ALA K 12 " --> pdb=" O LYS K 8 " (cutoff:3.500A) Processing helix chain 'K' and resid 18 through 40 removed outlier: 4.024A pdb=" N ALA K 22 " --> pdb=" O GLY K 18 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA K 27 " --> pdb=" O GLY K 23 " (cutoff:3.500A) Processing helix chain 'K' and resid 42 through 74 removed outlier: 4.006A pdb=" N THR K 46 " --> pdb=" O SER K 42 " (cutoff:3.500A) Proline residue: K 49 - end of helix removed outlier: 5.308A pdb=" N THR K 61 " --> pdb=" O LEU K 57 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLY K 62 " --> pdb=" O SER K 58 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER K 69 " --> pdb=" O CYS K 65 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE K 74 " --> pdb=" O PHE K 70 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 16 Processing helix chain 'L' and resid 19 through 40 removed outlier: 4.117A pdb=" N ALA L 27 " --> pdb=" O GLY L 23 " (cutoff:3.500A) Processing helix chain 'L' and resid 43 through 72 Proline residue: L 49 - end of helix removed outlier: 4.481A pdb=" N LEU L 53 " --> pdb=" O PRO L 49 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N THR L 61 " --> pdb=" O LEU L 57 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLY L 62 " --> pdb=" O SER L 58 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU L 72 " --> pdb=" O VAL L 68 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 18 removed outlier: 3.851A pdb=" N ILE M 17 " --> pdb=" O GLY M 13 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLY M 18 " --> pdb=" O ILE M 14 " (cutoff:3.500A) Processing helix chain 'M' and resid 20 through 40 removed outlier: 3.741A pdb=" N ILE M 24 " --> pdb=" O LEU M 20 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL M 29 " --> pdb=" O GLY M 25 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 74 removed outlier: 3.849A pdb=" N PHE M 48 " --> pdb=" O LYS M 44 " (cutoff:3.500A) Proline residue: M 49 - end of helix removed outlier: 4.842A pdb=" N LEU M 53 " --> pdb=" O PRO M 49 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY M 54 " --> pdb=" O MET M 50 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR M 61 " --> pdb=" O LEU M 57 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLY M 62 " --> pdb=" O SER M 58 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 16 Processing helix chain 'N' and resid 18 through 40 removed outlier: 3.854A pdb=" N ALA N 22 " --> pdb=" O GLY N 18 " (cutoff:3.500A) Processing helix chain 'N' and resid 43 through 74 Proline residue: N 49 - end of helix removed outlier: 3.503A pdb=" N ALA N 60 " --> pdb=" O ALA N 56 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N THR N 61 " --> pdb=" O LEU N 57 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLY N 62 " --> pdb=" O SER N 58 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 16 Processing helix chain 'O' and resid 19 through 40 Processing helix chain 'O' and resid 43 through 72 Proline residue: O 49 - end of helix removed outlier: 4.467A pdb=" N LEU O 53 " --> pdb=" O PRO O 49 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N THR O 61 " --> pdb=" O LEU O 57 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLY O 62 " --> pdb=" O SER O 58 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 17 Processing helix chain 'P' and resid 18 through 40 removed outlier: 4.393A pdb=" N ALA P 22 " --> pdb=" O GLY P 18 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA P 27 " --> pdb=" O GLY P 23 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N PHE P 30 " --> pdb=" O ILE P 26 " (cutoff:3.500A) Processing helix chain 'P' and resid 43 through 59 Proline residue: P 49 - end of helix removed outlier: 3.990A pdb=" N LEU P 53 " --> pdb=" O PRO P 49 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N GLY P 54 " --> pdb=" O MET P 50 " (cutoff:3.500A) Processing helix chain 'P' and resid 59 through 74 Processing helix chain 'Q' and resid 3 through 16 removed outlier: 3.752A pdb=" N LYS Q 8 " --> pdb=" O VAL Q 4 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR Q 9 " --> pdb=" O LEU Q 5 " (cutoff:3.500A) Processing helix chain 'Q' and resid 18 through 40 removed outlier: 3.709A pdb=" N ALA Q 22 " --> pdb=" O GLY Q 18 " (cutoff:3.500A) Processing helix chain 'Q' and resid 43 through 74 removed outlier: 3.713A pdb=" N VAL Q 47 " --> pdb=" O ILE Q 43 " (cutoff:3.500A) Proline residue: Q 49 - end of helix removed outlier: 4.583A pdb=" N THR Q 61 " --> pdb=" O LEU Q 57 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU Q 72 " --> pdb=" O VAL Q 68 " (cutoff:3.500A) Processing helix chain 'Z' and resid 56 through 112 removed outlier: 4.086A pdb=" N LEU Z 63 " --> pdb=" O LEU Z 59 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY Z 64 " --> pdb=" O LEU Z 60 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR Z 72 " --> pdb=" O LEU Z 68 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ALA Z 74 " --> pdb=" O ALA Z 70 " (cutoff:3.500A) Proline residue: Z 75 - end of helix removed outlier: 3.612A pdb=" N GLN Z 112 " --> pdb=" O ASP Z 108 " (cutoff:3.500A) Processing helix chain 'Z' and resid 113 through 117 removed outlier: 3.536A pdb=" N VAL Z 116 " --> pdb=" O LEU Z 113 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA Z 117 " --> pdb=" O GLN Z 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 113 through 117' Processing helix chain 'Z' and resid 119 through 133 removed outlier: 3.546A pdb=" N LYS Z 128 " --> pdb=" O PHE Z 124 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR Z 130 " --> pdb=" O VAL Z 126 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL Z 131 " --> pdb=" O SER Z 127 " (cutoff:3.500A) Processing helix chain 'Z' and resid 133 through 186 removed outlier: 4.434A pdb=" N ALA Z 137 " --> pdb=" O LEU Z 133 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER Z 178 " --> pdb=" O LYS Z 174 " (cutoff:3.500A) Processing helix chain 'Z' and resid 187 through 207 removed outlier: 3.748A pdb=" N GLU Z 191 " --> pdb=" O PRO Z 187 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU Z 194 " --> pdb=" O GLN Z 190 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLN Z 195 " --> pdb=" O GLU Z 191 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LYS Z 207 " --> pdb=" O GLN Z 203 " (cutoff:3.500A) Processing helix chain '7' and resid 4 through 17 removed outlier: 3.702A pdb=" N ASN 7 8 " --> pdb=" O LYS 7 4 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ASP 7 11 " --> pdb=" O ALA 7 7 " (cutoff:3.500A) Processing helix chain '7' and resid 27 through 47 Processing helix chain '7' and resid 57 through 62 Processing helix chain '7' and resid 67 through 78 Processing helix chain '7' and resid 90 through 123 Processing helix chain '7' and resid 136 through 142 removed outlier: 3.505A pdb=" N LYS 7 140 " --> pdb=" O ASP 7 136 " (cutoff:3.500A) Processing helix chain '7' and resid 142 through 155 removed outlier: 4.057A pdb=" N ASP 7 146 " --> pdb=" O LYS 7 142 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ALA 7 147 " --> pdb=" O PRO 7 143 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS 7 155 " --> pdb=" O GLU 7 151 " (cutoff:3.500A) Processing helix chain '6' and resid 5 through 22 removed outlier: 3.885A pdb=" N ALA 6 17 " --> pdb=" O ASP 6 13 " (cutoff:3.500A) Proline residue: 6 18 - end of helix Processing helix chain '6' and resid 42 through 44 No H-bonds generated for 'chain '6' and resid 42 through 44' Processing helix chain '6' and resid 45 through 51 Processing helix chain '6' and resid 76 through 89 removed outlier: 3.722A pdb=" N LEU 6 80 " --> pdb=" O GLU 6 76 " (cutoff:3.500A) Processing helix chain '6' and resid 90 through 92 No H-bonds generated for 'chain '6' and resid 90 through 92' Processing helix chain 'U' and resid 6 through 12 removed outlier: 3.938A pdb=" N VAL U 9 " --> pdb=" O PRO U 6 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER U 11 " --> pdb=" O LYS U 8 " (cutoff:3.500A) Processing helix chain 'U' and resid 16 through 32 Processing helix chain 'U' and resid 48 through 56 removed outlier: 4.048A pdb=" N LYS U 54 " --> pdb=" O ARG U 50 " (cutoff:3.500A) Processing helix chain 'U' and resid 63 through 85 removed outlier: 4.683A pdb=" N PHE U 69 " --> pdb=" O PRO U 65 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA U 70 " --> pdb=" O LEU U 66 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER U 79 " --> pdb=" O ALA U 75 " (cutoff:3.500A) Processing helix chain '8' and resid 12 through 47 removed outlier: 5.261A pdb=" N LEU 8 19 " --> pdb=" O TYR 8 15 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N MET 8 20 " --> pdb=" O GLY 8 16 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LEU 8 24 " --> pdb=" O MET 8 20 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ILE 8 25 " --> pdb=" O ILE 8 21 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER 8 28 " --> pdb=" O LEU 8 24 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN 8 29 " --> pdb=" O ILE 8 25 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N LEU 8 32 " --> pdb=" O SER 8 28 " (cutoff:3.500A) Proline residue: 8 33 - end of helix Processing helix chain 'X' and resid 27 through 46 removed outlier: 3.660A pdb=" N LEU X 31 " --> pdb=" O THR X 27 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE X 35 " --> pdb=" O LEU X 31 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N VAL X 36 " --> pdb=" O TYR X 32 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N THR X 41 " --> pdb=" O LEU X 37 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N SER X 42 " --> pdb=" O LEU X 38 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N TYR X 44 " --> pdb=" O ILE X 40 " (cutoff:3.500A) Processing helix chain 'X' and resid 59 through 77 removed outlier: 4.700A pdb=" N ASP X 67 " --> pdb=" O GLU X 63 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR X 68 " --> pdb=" O ALA X 64 " (cutoff:3.500A) Processing helix chain 'X' and resid 81 through 100 removed outlier: 4.275A pdb=" N TYR X 85 " --> pdb=" O ASN X 81 " (cutoff:3.500A) Proline residue: X 87 - end of helix removed outlier: 4.409A pdb=" N MET X 94 " --> pdb=" O PHE X 90 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE X 95 " --> pdb=" O THR X 91 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ILE X 96 " --> pdb=" O LEU X 92 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N PHE X 97 " --> pdb=" O PHE X 93 " (cutoff:3.500A) Processing helix chain 'X' and resid 116 through 133 removed outlier: 3.712A pdb=" N SER X 120 " --> pdb=" O VAL X 116 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE X 123 " --> pdb=" O ILE X 119 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL X 124 " --> pdb=" O SER X 120 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE X 125 " --> pdb=" O LEU X 121 " (cutoff:3.500A) Processing helix chain 'X' and resid 137 through 144 removed outlier: 3.942A pdb=" N PHE X 142 " --> pdb=" O TRP X 139 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU X 144 " --> pdb=" O PHE X 141 " (cutoff:3.500A) Processing helix chain 'X' and resid 154 through 174 removed outlier: 3.759A pdb=" N LEU X 158 " --> pdb=" O LEU X 154 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE X 161 " --> pdb=" O LEU X 157 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU X 164 " --> pdb=" O ILE X 160 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ALA X 170 " --> pdb=" O TYR X 166 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ILE X 171 " --> pdb=" O PHE X 167 " (cutoff:3.500A) Processing helix chain 'X' and resid 175 through 195 removed outlier: 4.980A pdb=" N MET X 188 " --> pdb=" O GLY X 184 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N VAL X 189 " --> pdb=" O HIS X 185 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE X 190 " --> pdb=" O LEU X 186 " (cutoff:3.500A) Processing helix chain 'X' and resid 196 through 198 No H-bonds generated for 'chain 'X' and resid 196 through 198' Processing helix chain 'X' and resid 211 through 213 No H-bonds generated for 'chain 'X' and resid 211 through 213' Processing helix chain 'X' and resid 214 through 247 removed outlier: 3.812A pdb=" N ALA X 218 " --> pdb=" O ALA X 214 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE X 228 " --> pdb=" O PHE X 224 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 31 Processing helix chain 'G' and resid 6 through 55 removed outlier: 3.862A pdb=" N LYS G 33 " --> pdb=" O THR G 29 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER G 40 " --> pdb=" O LYS G 36 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS G 43 " --> pdb=" O ILE G 39 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU G 48 " --> pdb=" O MET G 44 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE G 51 " --> pdb=" O ALA G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 102 Processing helix chain 'G' and resid 112 through 122 removed outlier: 3.718A pdb=" N THR G 121 " --> pdb=" O GLN G 117 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N HIS G 122 " --> pdb=" O LEU G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 136 removed outlier: 3.668A pdb=" N LYS G 135 " --> pdb=" O GLY G 132 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ASP G 136 " --> pdb=" O ILE G 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 132 through 136' Processing helix chain 'G' and resid 139 through 151 Processing helix chain 'G' and resid 184 through 190 removed outlier: 3.926A pdb=" N GLU G 189 " --> pdb=" O ALA G 185 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN G 190 " --> pdb=" O LYS G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 236 removed outlier: 3.851A pdb=" N ASP G 208 " --> pdb=" O ASN G 204 " (cutoff:3.500A) Processing helix chain 'G' and resid 236 through 274 Processing helix chain 'H' and resid 99 through 102 Processing helix chain 'H' and resid 103 through 110 removed outlier: 3.897A pdb=" N GLU H 107 " --> pdb=" O ASN H 103 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 115 Processing helix chain 'H' and resid 116 through 128 removed outlier: 4.646A pdb=" N ILE H 125 " --> pdb=" O ALA H 121 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLN H 126 " --> pdb=" O GLU H 122 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU H 128 " --> pdb=" O ALA H 124 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 137 removed outlier: 3.855A pdb=" N ASN H 132 " --> pdb=" O GLU H 128 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU H 133 " --> pdb=" O VAL H 129 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 7 removed outlier: 4.200A pdb=" N ALA I 6 " --> pdb=" O ALA I 2 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLY I 7 " --> pdb=" O TRP I 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 2 through 7' Processing helix chain 'I' and resid 9 through 24 Processing helix chain 'I' and resid 32 through 39 removed outlier: 3.664A pdb=" N ASN I 36 " --> pdb=" O ALA I 32 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 35 removed outlier: 6.776A pdb=" N ARG A 42 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N GLY A 74 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A 66 " --> pdb=" O GLY A 74 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N LEU A 54 " --> pdb=" O THR A 93 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR A 93 " --> pdb=" O LEU A 54 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 100 Processing sheet with id=AA3, first strand: chain 'A' and resid 110 through 111 removed outlier: 6.313A pdb=" N VAL A 110 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N TYR A 205 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ASP A 271 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N VAL A 206 " --> pdb=" O ASP A 271 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 267 through 268 Processing sheet with id=AA5, first strand: chain 'B' and resid 35 through 37 removed outlier: 3.581A pdb=" N VAL B 43 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN B 67 " --> pdb=" O GLY B 74 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL B 76 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ALA B 65 " --> pdb=" O VAL B 76 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 53 through 57 removed outlier: 6.950A pdb=" N LEU B 54 " --> pdb=" O THR B 93 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 98 through 101 removed outlier: 3.841A pdb=" N SER B 129 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 167 through 170 removed outlier: 3.628A pdb=" N ILE B 170 " --> pdb=" O ILE B 352 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 206 through 210 Processing sheet with id=AB1, first strand: chain 'B' and resid 266 through 268 Processing sheet with id=AB2, first strand: chain 'C' and resid 40 through 45 removed outlier: 3.585A pdb=" N VAL C 90 " --> pdb=" O GLY C 31 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU C 54 " --> pdb=" O THR C 93 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU C 66 " --> pdb=" O GLY C 74 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLY C 74 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N VAL F 50 " --> pdb=" O ILE F 62 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE F 62 " --> pdb=" O VAL F 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 98 through 100 removed outlier: 3.570A pdb=" N VAL C 99 " --> pdb=" O SER C 129 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 231 through 233 removed outlier: 7.155A pdb=" N CYS C 203 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N TYR C 202 " --> pdb=" O HIS C 265 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ALA C 266 " --> pdb=" O THR C 324 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N LEU C 326 " --> pdb=" O ALA C 266 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE C 268 " --> pdb=" O LEU C 326 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 350 through 351 Processing sheet with id=AB6, first strand: chain 'D' and resid 48 through 53 removed outlier: 3.797A pdb=" N GLU D 49 " --> pdb=" O ILE D 62 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ARG D 60 " --> pdb=" O ALA D 51 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N HIS D 53 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N THR D 58 " --> pdb=" O HIS D 53 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N HIS D 24 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N VAL D 13 " --> pdb=" O HIS D 24 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 39 through 41 Processing sheet with id=AB8, first strand: chain 'D' and resid 133 through 134 removed outlier: 4.137A pdb=" N TYR D 147 " --> pdb=" O LEU D 134 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 153 through 156 Processing sheet with id=AC1, first strand: chain 'D' and resid 254 through 255 Processing sheet with id=AC2, first strand: chain 'E' and resid 13 through 17 removed outlier: 5.603A pdb=" N VAL E 13 " --> pdb=" O HIS E 24 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N HIS E 24 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ILE E 62 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N VAL E 50 " --> pdb=" O ILE E 62 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU E 77 " --> pdb=" O GLU E 38 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 85 through 86 Processing sheet with id=AC4, first strand: chain 'E' and resid 182 through 185 removed outlier: 5.670A pdb=" N VAL E 183 " --> pdb=" O PHE E 254 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU E 253 " --> pdb=" O VAL E 307 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'F' and resid 84 through 87 removed outlier: 3.971A pdb=" N LEU F 113 " --> pdb=" O VAL F 87 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 95 through 96 removed outlier: 7.197A pdb=" N SER F 182 " --> pdb=" O ALA F 216 " (cutoff:3.500A) removed outlier: 8.656A pdb=" N VAL F 218 " --> pdb=" O SER F 182 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N PHE F 184 " --> pdb=" O VAL F 218 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 133 through 134 removed outlier: 3.982A pdb=" N TYR F 147 " --> pdb=" O LEU F 134 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 331 through 332 Processing sheet with id=AC9, first strand: chain 'G' and resid 73 through 74 removed outlier: 6.913A pdb=" N LEU G 73 " --> pdb=" O SER G 163 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'G' and resid 107 through 110 removed outlier: 7.874A pdb=" N ILE G 107 " --> pdb=" O LYS G 127 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N SER G 129 " --> pdb=" O ILE G 107 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N THR G 109 " --> pdb=" O SER G 129 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'G' and resid 166 through 167 Processing sheet with id=AD3, first strand: chain 'H' and resid 25 through 26 removed outlier: 3.547A pdb=" N SER H 25 " --> pdb=" O LEU H 12 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LYS H 11 " --> pdb=" O LEU H 83 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL H 85 " --> pdb=" O LYS H 11 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLY H 73 " --> pdb=" O LEU H 52 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA H 75 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLU H 50 " --> pdb=" O ALA H 75 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL H 77 " --> pdb=" O THR H 48 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR H 48 " --> pdb=" O VAL H 77 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 38 through 39 removed outlier: 4.064A pdb=" N ASN H 31 " --> pdb=" O GLU H 58 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 55 through 56 Processing sheet with id=AD6, first strand: chain 'I' and resid 43 through 44 2050 hydrogen bonds defined for protein. 5946 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: 5.14 Time building geometry restraints manager: 3.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 5089 1.29 - 1.35: 5057 1.35 - 1.42: 2 1.42 - 1.48: 5076 1.48 - 1.55: 9749 Bond restraints: 24973 Sorted by residual: bond pdb=" N ILE D 339 " pdb=" CA ILE D 339 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.93e+00 bond pdb=" C ALA E 119 " pdb=" N ASP E 120 " ideal model delta sigma weight residual 1.329 1.284 0.045 1.60e-02 3.91e+03 7.93e+00 bond pdb=" N ILE D 344 " pdb=" CA ILE D 344 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.50e+00 bond pdb=" N SER D 336 " pdb=" CA SER D 336 " ideal model delta sigma weight residual 1.454 1.487 -0.032 1.27e-02 6.20e+03 6.54e+00 bond pdb=" N VAL D 348 " pdb=" CA VAL D 348 " ideal model delta sigma weight residual 1.449 1.493 -0.044 1.80e-02 3.09e+03 5.96e+00 ... (remaining 24968 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 34146 2.08 - 4.15: 477 4.15 - 6.23: 27 6.23 - 8.30: 3 8.30 - 10.38: 1 Bond angle restraints: 34654 Sorted by residual: angle pdb=" C HIS Y 78 " pdb=" CA HIS Y 78 " pdb=" CB HIS Y 78 " ideal model delta sigma weight residual 116.54 110.42 6.12 1.15e+00 7.56e-01 2.83e+01 angle pdb=" N PRO D 346 " pdb=" CA PRO D 346 " pdb=" C PRO D 346 " ideal model delta sigma weight residual 113.57 107.52 6.05 1.31e+00 5.83e-01 2.13e+01 angle pdb=" CA VAL D 348 " pdb=" C VAL D 348 " pdb=" O VAL D 348 " ideal model delta sigma weight residual 121.68 118.25 3.43 7.90e-01 1.60e+00 1.88e+01 angle pdb=" C LEU H 32 " pdb=" N PRO H 33 " pdb=" CA PRO H 33 " ideal model delta sigma weight residual 119.84 125.17 -5.33 1.25e+00 6.40e-01 1.82e+01 angle pdb=" N ILE H 88 " pdb=" CA ILE H 88 " pdb=" C ILE H 88 " ideal model delta sigma weight residual 113.42 108.58 4.84 1.17e+00 7.31e-01 1.71e+01 ... (remaining 34649 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 5.07: 12915 5.07 - 10.14: 1168 10.14 - 15.20: 242 15.20 - 20.27: 29 20.27 - 25.34: 4 Dihedral angle restraints: 14358 sinusoidal: 0 harmonic: 14358 Sorted by residual: dihedral pdb=" CA LYS B 153 " pdb=" C LYS B 153 " pdb=" N ALA B 154 " pdb=" CA ALA B 154 " ideal model delta harmonic sigma weight residual 180.00 154.66 25.34 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" CA ALA B 439 " pdb=" C ALA B 439 " pdb=" N THR B 440 " pdb=" CA THR B 440 " ideal model delta harmonic sigma weight residual 180.00 -155.81 -24.19 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA LEU B 429 " pdb=" C LEU B 429 " pdb=" N LEU B 430 " pdb=" CA LEU B 430 " ideal model delta harmonic sigma weight residual -180.00 -158.65 -21.35 0 5.00e+00 4.00e-02 1.82e+01 ... (remaining 14355 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 2792 0.032 - 0.064: 1238 0.064 - 0.096: 399 0.096 - 0.128: 211 0.128 - 0.160: 9 Chirality restraints: 4649 Sorted by residual: chirality pdb=" CA LEU D 342 " pdb=" N LEU D 342 " pdb=" C LEU D 342 " pdb=" CB LEU D 342 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.36e-01 chirality pdb=" CA ILE C 352 " pdb=" N ILE C 352 " pdb=" C ILE C 352 " pdb=" CB ILE C 352 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.95e-01 chirality pdb=" CA ILE D 275 " pdb=" N ILE D 275 " pdb=" C ILE D 275 " pdb=" CB ILE D 275 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 ... (remaining 4646 not shown) Planarity restraints: 5060 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN E 385 " -0.007 2.00e-02 2.50e+03 1.46e-02 2.13e+00 pdb=" C GLN E 385 " 0.025 2.00e-02 2.50e+03 pdb=" O GLN E 385 " -0.009 2.00e-02 2.50e+03 pdb=" N ASP E 386 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 172 " 0.006 2.00e-02 2.50e+03 1.10e-02 1.22e+00 pdb=" C ASP A 172 " -0.019 2.00e-02 2.50e+03 pdb=" O ASP A 172 " 0.007 2.00e-02 2.50e+03 pdb=" N ARG A 173 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN D 221 " 0.005 2.00e-02 2.50e+03 1.09e-02 1.18e+00 pdb=" C GLN D 221 " -0.019 2.00e-02 2.50e+03 pdb=" O GLN D 221 " 0.007 2.00e-02 2.50e+03 pdb=" N MET D 222 " 0.006 2.00e-02 2.50e+03 ... (remaining 5057 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 1727 2.73 - 3.27: 28123 3.27 - 3.81: 40346 3.81 - 4.36: 39345 4.36 - 4.90: 66302 Nonbonded interactions: 175843 Sorted by model distance: nonbonded pdb=" N ALA D 36 " pdb=" O GLY D 81 " model vdw 2.185 3.120 nonbonded pdb=" O LEU E 253 " pdb=" N VAL E 307 " model vdw 2.186 3.120 nonbonded pdb=" O GLY B 39 " pdb=" N LEU B 77 " model vdw 2.194 3.120 nonbonded pdb=" O ILE X 131 " pdb=" N TYR X 135 " model vdw 2.203 3.120 nonbonded pdb=" O ARG A 166 " pdb=" N ASP A 349 " model vdw 2.208 3.120 ... (remaining 175838 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 509) selection = (chain 'B' and resid 6 through 509) selection = (chain 'C' and resid 6 through 509) } ncs_group { reference = (chain 'D' and resid 7 through 478) selection = (chain 'E' and resid 7 through 478) selection = chain 'F' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = (chain 'O' and resid 2 through 74) selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = (chain 'T' and resid 2 through 74) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 25.680 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6534 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 0.045 24973 Z= 0.225 Angle : 0.661 10.377 34654 Z= 0.455 Chirality : 0.043 0.160 4649 Planarity : 0.002 0.015 5060 Dihedral : 5.087 25.342 5060 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.94 % Favored : 89.94 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.12), residues: 5032 helix: 1.08 (0.10), residues: 2510 sheet: -2.05 (0.26), residues: 370 loop : -1.75 (0.14), residues: 2152 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR Y 19 PHE 0.000 0.000 PHE Y 13 TRP 0.000 0.000 TRP A 191 Details of bonding type rmsd covalent geometry : bond 0.00301 (24973) covalent geometry : angle 0.66070 (34654) hydrogen bonds : bond 0.17986 ( 2050) hydrogen bonds : angle 6.71915 ( 5946) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10064 Ramachandran restraints generated. 5032 Oldfield, 0 Emsley, 5032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10064 Ramachandran restraints generated. 5032 Oldfield, 0 Emsley, 5032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 4137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.830 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1051 time to fit residues: 15.6426 Evaluate side-chains 74 residues out of total 4137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 432 optimal weight: 50.0000 chunk 197 optimal weight: 30.0000 chunk 388 optimal weight: 8.9990 chunk 455 optimal weight: 10.0000 chunk 215 optimal weight: 40.0000 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 30.0000 chunk 494 optimal weight: 30.0000 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 9.9990 overall best weight: 5.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.107481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.092467 restraints weight = 158054.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.091061 restraints weight = 181560.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.091384 restraints weight = 158538.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.091562 restraints weight = 131054.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.091608 restraints weight = 127104.122| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6660 moved from start: 0.0851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 24973 Z= 0.171 Angle : 0.473 7.782 34654 Z= 0.298 Chirality : 0.043 0.141 4649 Planarity : 0.003 0.018 5060 Dihedral : 4.935 26.855 5060 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.37 % Favored : 91.61 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.12), residues: 5032 helix: 1.09 (0.10), residues: 2570 sheet: -2.34 (0.25), residues: 376 loop : -1.81 (0.14), residues: 2086 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR Y 19 PHE 0.000 0.000 PHE Y 13 TRP 0.000 0.000 TRP A 191 Details of bonding type rmsd covalent geometry : bond 0.00237 (24973) covalent geometry : angle 0.47324 (34654) hydrogen bonds : bond 0.04465 ( 2050) hydrogen bonds : angle 5.37943 ( 5946) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10064 Ramachandran restraints generated. 5032 Oldfield, 0 Emsley, 5032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10064 Ramachandran restraints generated. 5032 Oldfield, 0 Emsley, 5032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 4137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.958 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1119 time to fit residues: 16.8271 Evaluate side-chains 74 residues out of total 4137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 225 optimal weight: 9.9990 chunk 370 optimal weight: 20.0000 chunk 97 optimal weight: 20.0000 chunk 216 optimal weight: 20.0000 chunk 271 optimal weight: 30.0000 chunk 414 optimal weight: 40.0000 chunk 159 optimal weight: 20.0000 chunk 468 optimal weight: 0.1980 chunk 221 optimal weight: 50.0000 chunk 47 optimal weight: 50.0000 chunk 426 optimal weight: 50.0000 overall best weight: 14.0394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.103892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.088886 restraints weight = 159962.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.087796 restraints weight = 147909.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.087619 restraints weight = 161536.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.087693 restraints weight = 155366.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.087829 restraints weight = 136337.955| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 24973 Z= 0.357 Angle : 0.684 8.845 34654 Z= 0.442 Chirality : 0.047 0.211 4649 Planarity : 0.004 0.018 5060 Dihedral : 6.543 29.047 5060 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 13.28 % Favored : 86.65 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.23 (0.11), residues: 5032 helix: -0.42 (0.10), residues: 2555 sheet: -2.84 (0.25), residues: 319 loop : -2.56 (0.13), residues: 2158 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR Y 19 PHE 0.000 0.000 PHE Y 13 TRP 0.000 0.000 TRP A 191 Details of bonding type rmsd covalent geometry : bond 0.00503 (24973) covalent geometry : angle 0.68439 (34654) hydrogen bonds : bond 0.05886 ( 2050) hydrogen bonds : angle 6.72337 ( 5946) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10064 Ramachandran restraints generated. 5032 Oldfield, 0 Emsley, 5032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10064 Ramachandran restraints generated. 5032 Oldfield, 0 Emsley, 5032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 4137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.948 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1103 time to fit residues: 16.6505 Evaluate side-chains 74 residues out of total 4137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 293 optimal weight: 30.0000 chunk 210 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 chunk 286 optimal weight: 9.9990 chunk 296 optimal weight: 5.9990 chunk 376 optimal weight: 30.0000 chunk 259 optimal weight: 20.0000 chunk 418 optimal weight: 50.0000 chunk 470 optimal weight: 50.0000 chunk 148 optimal weight: 30.0000 chunk 126 optimal weight: 20.0000 overall best weight: 9.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.104896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.089510 restraints weight = 157262.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.088878 restraints weight = 152088.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.088744 restraints weight = 146569.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.088785 restraints weight = 137898.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.088890 restraints weight = 125944.416| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 24973 Z= 0.240 Angle : 0.553 7.436 34654 Z= 0.351 Chirality : 0.044 0.137 4649 Planarity : 0.003 0.017 5060 Dihedral : 5.842 25.226 5060 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.41 % Favored : 88.55 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.92 (0.12), residues: 5032 helix: -0.09 (0.10), residues: 2560 sheet: -3.16 (0.26), residues: 302 loop : -2.45 (0.13), residues: 2170 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR Y 19 PHE 0.000 0.000 PHE Y 13 TRP 0.000 0.000 TRP A 191 Details of bonding type rmsd covalent geometry : bond 0.00334 (24973) covalent geometry : angle 0.55267 (34654) hydrogen bonds : bond 0.04710 ( 2050) hydrogen bonds : angle 5.97720 ( 5946) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10064 Ramachandran restraints generated. 5032 Oldfield, 0 Emsley, 5032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10064 Ramachandran restraints generated. 5032 Oldfield, 0 Emsley, 5032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 4137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.928 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1137 time to fit residues: 17.0131 Evaluate side-chains 74 residues out of total 4137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 70 optimal weight: 40.0000 chunk 284 optimal weight: 6.9990 chunk 441 optimal weight: 0.0770 chunk 257 optimal weight: 50.0000 chunk 104 optimal weight: 4.9990 chunk 410 optimal weight: 9.9990 chunk 230 optimal weight: 6.9990 chunk 76 optimal weight: 7.9990 chunk 229 optimal weight: 7.9990 chunk 301 optimal weight: 6.9990 chunk 27 optimal weight: 20.0000 overall best weight: 5.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.106464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.091607 restraints weight = 156281.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.090324 restraints weight = 174729.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.090705 restraints weight = 148471.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.090736 restraints weight = 127637.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.090767 restraints weight = 128030.384| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 24973 Z= 0.147 Angle : 0.449 7.510 34654 Z= 0.280 Chirality : 0.043 0.140 4649 Planarity : 0.002 0.016 5060 Dihedral : 4.987 24.890 5060 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.23 % Favored : 89.73 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.08 (0.12), residues: 5032 helix: 0.77 (0.10), residues: 2599 sheet: -3.31 (0.26), residues: 303 loop : -2.27 (0.14), residues: 2130 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR Y 19 PHE 0.000 0.000 PHE Y 13 TRP 0.000 0.000 TRP A 191 Details of bonding type rmsd covalent geometry : bond 0.00204 (24973) covalent geometry : angle 0.44884 (34654) hydrogen bonds : bond 0.03802 ( 2050) hydrogen bonds : angle 5.10809 ( 5946) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10064 Ramachandran restraints generated. 5032 Oldfield, 0 Emsley, 5032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10064 Ramachandran restraints generated. 5032 Oldfield, 0 Emsley, 5032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 4137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.944 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1122 time to fit residues: 16.8874 Evaluate side-chains 74 residues out of total 4137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 461 optimal weight: 20.0000 chunk 453 optimal weight: 6.9990 chunk 262 optimal weight: 0.0570 chunk 494 optimal weight: 7.9990 chunk 74 optimal weight: 6.9990 chunk 468 optimal weight: 50.0000 chunk 68 optimal weight: 40.0000 chunk 144 optimal weight: 8.9990 chunk 130 optimal weight: 5.9990 chunk 310 optimal weight: 5.9990 chunk 135 optimal weight: 30.0000 overall best weight: 5.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.106140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.091619 restraints weight = 158174.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.090628 restraints weight = 169411.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.091330 restraints weight = 144660.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.091143 restraints weight = 112327.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.091230 restraints weight = 117869.604| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6667 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 24973 Z= 0.157 Angle : 0.453 6.453 34654 Z= 0.284 Chirality : 0.043 0.137 4649 Planarity : 0.002 0.016 5060 Dihedral : 4.878 25.488 5060 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.00 % Favored : 89.96 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.12), residues: 5032 helix: 1.05 (0.10), residues: 2604 sheet: -3.25 (0.26), residues: 311 loop : -2.21 (0.14), residues: 2117 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR Y 19 PHE 0.000 0.000 PHE Y 13 TRP 0.000 0.000 TRP A 191 Details of bonding type rmsd covalent geometry : bond 0.00219 (24973) covalent geometry : angle 0.45294 (34654) hydrogen bonds : bond 0.03718 ( 2050) hydrogen bonds : angle 5.01447 ( 5946) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10064 Ramachandran restraints generated. 5032 Oldfield, 0 Emsley, 5032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10064 Ramachandran restraints generated. 5032 Oldfield, 0 Emsley, 5032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 4137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.951 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1117 time to fit residues: 16.7527 Evaluate side-chains 74 residues out of total 4137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 442 optimal weight: 8.9990 chunk 308 optimal weight: 9.9990 chunk 417 optimal weight: 0.1980 chunk 19 optimal weight: 20.0000 chunk 44 optimal weight: 0.9990 chunk 132 optimal weight: 30.0000 chunk 293 optimal weight: 40.0000 chunk 474 optimal weight: 5.9990 chunk 171 optimal weight: 30.0000 chunk 284 optimal weight: 20.0000 chunk 57 optimal weight: 20.0000 overall best weight: 5.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.106229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.090151 restraints weight = 157418.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.089772 restraints weight = 137359.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.089642 restraints weight = 127449.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.089767 restraints weight = 125561.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.089789 restraints weight = 115376.843| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6809 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 24973 Z= 0.150 Angle : 0.435 6.162 34654 Z= 0.273 Chirality : 0.043 0.137 4649 Planarity : 0.002 0.016 5060 Dihedral : 4.751 24.286 5060 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.17 % Favored : 89.73 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.12), residues: 5032 helix: 1.20 (0.10), residues: 2602 sheet: -3.12 (0.25), residues: 344 loop : -2.18 (0.14), residues: 2086 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR Y 19 PHE 0.000 0.000 PHE Y 13 TRP 0.000 0.000 TRP A 191 Details of bonding type rmsd covalent geometry : bond 0.00207 (24973) covalent geometry : angle 0.43526 (34654) hydrogen bonds : bond 0.03559 ( 2050) hydrogen bonds : angle 4.88003 ( 5946) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10064 Ramachandran restraints generated. 5032 Oldfield, 0 Emsley, 5032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10064 Ramachandran restraints generated. 5032 Oldfield, 0 Emsley, 5032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 4137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.923 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1113 time to fit residues: 16.7026 Evaluate side-chains 74 residues out of total 4137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 39 optimal weight: 30.0000 chunk 2 optimal weight: 30.0000 chunk 65 optimal weight: 7.9990 chunk 274 optimal weight: 30.0000 chunk 165 optimal weight: 6.9990 chunk 459 optimal weight: 50.0000 chunk 434 optimal weight: 10.0000 chunk 68 optimal weight: 50.0000 chunk 81 optimal weight: 0.0870 chunk 322 optimal weight: 50.0000 chunk 248 optimal weight: 40.0000 overall best weight: 11.0170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.103424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.089823 restraints weight = 159760.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.089183 restraints weight = 174705.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.089444 restraints weight = 146498.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.089506 restraints weight = 127530.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.089555 restraints weight = 117904.958| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6751 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 24973 Z= 0.285 Angle : 0.603 8.059 34654 Z= 0.385 Chirality : 0.045 0.172 4649 Planarity : 0.003 0.017 5060 Dihedral : 6.055 24.062 5060 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 14.13 % Favored : 85.81 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.85 (0.12), residues: 5032 helix: 0.09 (0.10), residues: 2575 sheet: -3.36 (0.27), residues: 303 loop : -2.58 (0.13), residues: 2154 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR Y 19 PHE 0.000 0.000 PHE Y 13 TRP 0.000 0.000 TRP A 191 Details of bonding type rmsd covalent geometry : bond 0.00403 (24973) covalent geometry : angle 0.60329 (34654) hydrogen bonds : bond 0.04949 ( 2050) hydrogen bonds : angle 6.16250 ( 5946) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10064 Ramachandran restraints generated. 5032 Oldfield, 0 Emsley, 5032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10064 Ramachandran restraints generated. 5032 Oldfield, 0 Emsley, 5032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 4137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.811 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1057 time to fit residues: 15.7670 Evaluate side-chains 74 residues out of total 4137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 411 optimal weight: 0.9990 chunk 224 optimal weight: 8.9990 chunk 340 optimal weight: 6.9990 chunk 181 optimal weight: 30.0000 chunk 311 optimal weight: 6.9990 chunk 76 optimal weight: 9.9990 chunk 21 optimal weight: 40.0000 chunk 454 optimal weight: 9.9990 chunk 369 optimal weight: 5.9990 chunk 327 optimal weight: 30.0000 chunk 85 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.105114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.089640 restraints weight = 158698.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.089060 restraints weight = 135587.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.088906 restraints weight = 130289.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.089007 restraints weight = 128449.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.089157 restraints weight = 117263.752| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6831 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 24973 Z= 0.167 Angle : 0.471 7.401 34654 Z= 0.296 Chirality : 0.043 0.141 4649 Planarity : 0.002 0.018 5060 Dihedral : 5.245 22.661 5060 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.57 % Favored : 89.37 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.24 (0.12), residues: 5032 helix: 0.66 (0.10), residues: 2596 sheet: -3.31 (0.27), residues: 305 loop : -2.38 (0.14), residues: 2131 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR Y 19 PHE 0.000 0.000 PHE Y 13 TRP 0.000 0.000 TRP A 191 Details of bonding type rmsd covalent geometry : bond 0.00232 (24973) covalent geometry : angle 0.47100 (34654) hydrogen bonds : bond 0.03926 ( 2050) hydrogen bonds : angle 5.36545 ( 5946) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10064 Ramachandran restraints generated. 5032 Oldfield, 0 Emsley, 5032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10064 Ramachandran restraints generated. 5032 Oldfield, 0 Emsley, 5032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 4137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.841 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.0930 time to fit residues: 13.7140 Evaluate side-chains 74 residues out of total 4137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 459 optimal weight: 40.0000 chunk 496 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 82 optimal weight: 40.0000 chunk 51 optimal weight: 5.9990 chunk 70 optimal weight: 40.0000 chunk 320 optimal weight: 5.9990 chunk 234 optimal weight: 0.0000 chunk 419 optimal weight: 5.9990 chunk 266 optimal weight: 30.0000 chunk 497 optimal weight: 8.9990 overall best weight: 4.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.105759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.091525 restraints weight = 159200.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.090595 restraints weight = 165230.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.090945 restraints weight = 146734.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.090946 restraints weight = 127532.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.091065 restraints weight = 121227.177| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6686 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 24973 Z= 0.141 Angle : 0.433 5.962 34654 Z= 0.271 Chirality : 0.043 0.138 4649 Planarity : 0.002 0.016 5060 Dihedral : 4.780 21.268 5060 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.89 % Favored : 89.05 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.12), residues: 5032 helix: 1.10 (0.10), residues: 2612 sheet: -3.29 (0.25), residues: 324 loop : -2.26 (0.14), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR Y 19 PHE 0.000 0.000 PHE Y 13 TRP 0.000 0.000 TRP A 191 Details of bonding type rmsd covalent geometry : bond 0.00196 (24973) covalent geometry : angle 0.43337 (34654) hydrogen bonds : bond 0.03538 ( 2050) hydrogen bonds : angle 4.94572 ( 5946) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10064 Ramachandran restraints generated. 5032 Oldfield, 0 Emsley, 5032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10064 Ramachandran restraints generated. 5032 Oldfield, 0 Emsley, 5032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 4137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.988 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1114 time to fit residues: 16.7538 Evaluate side-chains 74 residues out of total 4137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 130 optimal weight: 7.9990 chunk 309 optimal weight: 9.9990 chunk 69 optimal weight: 10.0000 chunk 427 optimal weight: 20.0000 chunk 346 optimal weight: 40.0000 chunk 318 optimal weight: 20.0000 chunk 247 optimal weight: 40.0000 chunk 193 optimal weight: 1.9990 chunk 326 optimal weight: 50.0000 chunk 299 optimal weight: 0.7980 chunk 477 optimal weight: 9.9990 overall best weight: 6.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.104939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.089645 restraints weight = 159207.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.089080 restraints weight = 155834.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.089107 restraints weight = 145738.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.089192 restraints weight = 129150.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.089284 restraints weight = 120772.398| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6785 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 24973 Z= 0.169 Angle : 0.462 7.389 34654 Z= 0.291 Chirality : 0.043 0.139 4649 Planarity : 0.002 0.017 5060 Dihedral : 5.020 21.716 5060 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.98 % Favored : 87.96 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.12), residues: 5032 helix: 0.97 (0.10), residues: 2605 sheet: -3.25 (0.25), residues: 333 loop : -2.30 (0.14), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR Y 19 PHE 0.000 0.000 PHE Y 13 TRP 0.000 0.000 TRP A 191 Details of bonding type rmsd covalent geometry : bond 0.00237 (24973) covalent geometry : angle 0.46227 (34654) hydrogen bonds : bond 0.03765 ( 2050) hydrogen bonds : angle 5.17210 ( 5946) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3406.58 seconds wall clock time: 59 minutes 1.83 seconds (3541.83 seconds total)