Starting phenix.real_space_refine on Wed Oct 28 14:07:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9toz_56103/10_2026/9toz_56103.cif Found real_map, /net/cci-nas-00/data/ceres_data/9toz_56103/10_2026/9toz_56103.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9toz_56103/10_2026/9toz_56103.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9toz_56103/10_2026/9toz_56103.map" model { file = "/net/cci-nas-00/data/ceres_data/9toz_56103/10_2026/9toz_56103.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9toz_56103/10_2026/9toz_56103.cif" } resolution = 3.1 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= 0.007 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 90 5.16 5 C 18306 2.51 5 N 4806 2.21 5 O 5220 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28422 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1579 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 10, 'TRANS': 212} Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 10, 'GLN:plan1': 1, 'ASN:plan1': 3, 'ASP:plan': 12, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 94 Chain: "B" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1579 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 10, 'TRANS': 212} Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 10, 'GLN:plan1': 1, 'ASN:plan1': 3, 'ASP:plan': 12, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 94 Chain: "C" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1579 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 10, 'TRANS': 212} Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 10, 'GLN:plan1': 1, 'ASN:plan1': 3, 'ASP:plan': 12, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 94 Chain: "D" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1579 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 10, 'TRANS': 212} Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 10, 'GLN:plan1': 1, 'ASN:plan1': 3, 'ASP:plan': 12, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 94 Chain: "E" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1579 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 10, 'TRANS': 212} Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 10, 'GLN:plan1': 1, 'ASN:plan1': 3, 'ASP:plan': 12, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 94 Chain: "F" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1579 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 10, 'TRANS': 212} Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 10, 'GLN:plan1': 1, 'ASN:plan1': 3, 'ASP:plan': 12, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 94 Chain: "G" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1579 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 10, 'TRANS': 212} Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 10, 'GLN:plan1': 1, 'ASN:plan1': 3, 'ASP:plan': 12, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 94 Chain: "H" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1579 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 10, 'TRANS': 212} Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 10, 'GLN:plan1': 1, 'ASN:plan1': 3, 'ASP:plan': 12, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 94 Chain: "I" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1579 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 10, 'TRANS': 212} Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 10, 'GLN:plan1': 1, 'ASN:plan1': 3, 'ASP:plan': 12, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 94 Chain: "J" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1579 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 10, 'TRANS': 212} Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 10, 'GLN:plan1': 1, 'ASN:plan1': 3, 'ASP:plan': 12, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 94 Chain: "K" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1579 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 10, 'TRANS': 212} Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 10, 'GLN:plan1': 1, 'ASN:plan1': 3, 'ASP:plan': 12, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 94 Chain: "L" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1579 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 10, 'TRANS': 212} Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 10, 'GLN:plan1': 1, 'ASN:plan1': 3, 'ASP:plan': 12, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 94 Chain: "M" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1579 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 10, 'TRANS': 212} Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 10, 'GLN:plan1': 1, 'ASN:plan1': 3, 'ASP:plan': 12, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 94 Chain: "N" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1579 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 10, 'TRANS': 212} Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 10, 'GLN:plan1': 1, 'ASN:plan1': 3, 'ASP:plan': 12, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 94 Chain: "O" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1579 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 10, 'TRANS': 212} Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 10, 'GLN:plan1': 1, 'ASN:plan1': 3, 'ASP:plan': 12, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 94 Chain: "P" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1579 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 10, 'TRANS': 212} Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 10, 'GLN:plan1': 1, 'ASN:plan1': 3, 'ASP:plan': 12, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 94 Chain: "Q" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1579 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 10, 'TRANS': 212} Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 10, 'GLN:plan1': 1, 'ASN:plan1': 3, 'ASP:plan': 12, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 94 Chain: "R" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1579 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 10, 'TRANS': 212} Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 10, 'GLN:plan1': 1, 'ASN:plan1': 3, 'ASP:plan': 12, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 94 Time building chain proxies: 6.64, per 1000 atoms: 0.23 Number of scatterers: 28422 At special positions: 0 Unit cell: (141.9, 141.9, 145.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 90 16.00 O 5220 8.00 N 4806 7.00 C 18306 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS H 126 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS R 108 " distance=2.04 Simple disulfide: pdb=" SG CYS B 108 " - pdb=" SG CYS I 126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS M 108 " distance=2.04 Simple disulfide: pdb=" SG CYS C 108 " - pdb=" SG CYS J 126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS N 108 " distance=2.04 Simple disulfide: pdb=" SG CYS D 108 " - pdb=" SG CYS K 126 " distance=2.04 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS O 108 " distance=2.04 Simple disulfide: pdb=" SG CYS E 108 " - pdb=" SG CYS L 126 " distance=2.04 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS P 108 " distance=2.04 Simple disulfide: pdb=" SG CYS F 108 " - pdb=" SG CYS G 126 " distance=2.04 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS Q 108 " distance=2.04 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: 2.77 Conformation dependent library (CDL) restraints added in 1.4 seconds 7956 Ramachandran restraints generated. 3978 Oldfield, 0 Emsley, 3978 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7524 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 36 sheets defined 8.5% alpha, 44.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 78 through 82 Processing helix chain 'A' and resid 154 through 167 removed outlier: 4.404A pdb=" N ASP A 158 " --> pdb=" O ASN A 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 82 Processing helix chain 'B' and resid 154 through 167 removed outlier: 4.405A pdb=" N ASP B 158 " --> pdb=" O ASN B 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 82 Processing helix chain 'C' and resid 154 through 167 removed outlier: 4.403A pdb=" N ASP C 158 " --> pdb=" O ASN C 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 82 Processing helix chain 'D' and resid 154 through 167 removed outlier: 4.404A pdb=" N ASP D 158 " --> pdb=" O ASN D 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 82 Processing helix chain 'E' and resid 154 through 167 removed outlier: 4.405A pdb=" N ASP E 158 " --> pdb=" O ASN E 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 82 Processing helix chain 'F' and resid 154 through 167 removed outlier: 4.404A pdb=" N ASP F 158 " --> pdb=" O ASN F 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 82 Processing helix chain 'G' and resid 154 through 167 removed outlier: 4.404A pdb=" N ASP G 158 " --> pdb=" O ASN G 154 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 82 Processing helix chain 'H' and resid 154 through 167 removed outlier: 4.404A pdb=" N ASP H 158 " --> pdb=" O ASN H 154 " (cutoff:3.500A) Processing helix chain 'I' and resid 78 through 82 Processing helix chain 'I' and resid 154 through 167 removed outlier: 4.405A pdb=" N ASP I 158 " --> pdb=" O ASN I 154 " (cutoff:3.500A) Processing helix chain 'J' and resid 78 through 82 Processing helix chain 'J' and resid 154 through 167 removed outlier: 4.405A pdb=" N ASP J 158 " --> pdb=" O ASN J 154 " (cutoff:3.500A) Processing helix chain 'K' and resid 78 through 82 Processing helix chain 'K' and resid 154 through 167 removed outlier: 4.404A pdb=" N ASP K 158 " --> pdb=" O ASN K 154 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 82 Processing helix chain 'L' and resid 154 through 167 removed outlier: 4.405A pdb=" N ASP L 158 " --> pdb=" O ASN L 154 " (cutoff:3.500A) Processing helix chain 'M' and resid 78 through 82 Processing helix chain 'M' and resid 154 through 167 removed outlier: 4.404A pdb=" N ASP M 158 " --> pdb=" O ASN M 154 " (cutoff:3.500A) Processing helix chain 'N' and resid 78 through 82 Processing helix chain 'N' and resid 154 through 167 removed outlier: 4.403A pdb=" N ASP N 158 " --> pdb=" O ASN N 154 " (cutoff:3.500A) Processing helix chain 'O' and resid 78 through 82 Processing helix chain 'O' and resid 154 through 167 removed outlier: 4.404A pdb=" N ASP O 158 " --> pdb=" O ASN O 154 " (cutoff:3.500A) Processing helix chain 'P' and resid 78 through 82 Processing helix chain 'P' and resid 154 through 167 removed outlier: 4.404A pdb=" N ASP P 158 " --> pdb=" O ASN P 154 " (cutoff:3.500A) Processing helix chain 'Q' and resid 78 through 82 Processing helix chain 'Q' and resid 154 through 167 removed outlier: 4.404A pdb=" N ASP Q 158 " --> pdb=" O ASN Q 154 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 82 Processing helix chain 'R' and resid 154 through 167 removed outlier: 4.404A pdb=" N ASP R 158 " --> pdb=" O ASN R 154 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 109 through 115 removed outlier: 7.215A pdb=" N VAL A 109 " --> pdb=" O ASP A 149 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ASP A 149 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP A 111 " --> pdb=" O THR A 147 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N SER A 187 " --> pdb=" O ASP A 213 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LYS A 215 " --> pdb=" O ALA A 185 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ALA A 185 " --> pdb=" O LYS A 215 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N VAL A 217 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ILE A 183 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ALA A 171 " --> pdb=" O GLU A 12 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N SER A 102 " --> pdb=" O ARG A 13 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ARG A 15 " --> pdb=" O ILE A 100 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE A 100 " --> pdb=" O ARG A 15 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU A 51 " --> pdb=" O THR A 96 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N VAL A 98 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N VAL A 49 " --> pdb=" O VAL A 98 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE A 100 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL A 47 " --> pdb=" O ILE A 100 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR A 74 " --> pdb=" O LYS A 65 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N VAL A 67 " --> pdb=" O SER A 72 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N SER A 72 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ALA A 24 " --> pdb=" O THR A 34 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 120 through 124 removed outlier: 4.386A pdb=" N GLN A 120 " --> pdb=" O THR A 137 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 109 through 115 removed outlier: 7.227A pdb=" N VAL B 109 " --> pdb=" O ASP B 149 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ASP B 149 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP B 111 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N SER B 187 " --> pdb=" O ASP B 213 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LYS B 215 " --> pdb=" O ALA B 185 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ALA B 185 " --> pdb=" O LYS B 215 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N VAL B 217 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE B 183 " --> pdb=" O VAL B 217 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ALA B 171 " --> pdb=" O GLU B 12 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N SER B 102 " --> pdb=" O ARG B 13 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ARG B 15 " --> pdb=" O ILE B 100 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE B 100 " --> pdb=" O ARG B 15 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU B 51 " --> pdb=" O THR B 96 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N VAL B 98 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N VAL B 49 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE B 100 " --> pdb=" O VAL B 47 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL B 47 " --> pdb=" O ILE B 100 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N THR B 74 " --> pdb=" O LYS B 65 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N VAL B 67 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N SER B 72 " --> pdb=" O VAL B 67 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ALA B 24 " --> pdb=" O THR B 34 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 120 through 124 removed outlier: 4.386A pdb=" N GLN B 120 " --> pdb=" O THR B 137 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 109 through 115 removed outlier: 7.223A pdb=" N VAL C 109 " --> pdb=" O ASP C 149 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ASP C 149 " --> pdb=" O VAL C 109 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP C 111 " --> pdb=" O THR C 147 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N SER C 187 " --> pdb=" O ASP C 213 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LYS C 215 " --> pdb=" O ALA C 185 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ALA C 185 " --> pdb=" O LYS C 215 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N VAL C 217 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ILE C 183 " --> pdb=" O VAL C 217 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ALA C 171 " --> pdb=" O GLU C 12 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N SER C 102 " --> pdb=" O ARG C 13 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ARG C 15 " --> pdb=" O ILE C 100 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE C 100 " --> pdb=" O ARG C 15 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU C 51 " --> pdb=" O THR C 96 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N VAL C 98 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N VAL C 49 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE C 100 " --> pdb=" O VAL C 47 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL C 47 " --> pdb=" O ILE C 100 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N THR C 74 " --> pdb=" O LYS C 65 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N VAL C 67 " --> pdb=" O SER C 72 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N SER C 72 " --> pdb=" O VAL C 67 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ALA C 24 " --> pdb=" O THR C 34 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 120 through 124 removed outlier: 4.386A pdb=" N GLN C 120 " --> pdb=" O THR C 137 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 109 through 115 removed outlier: 7.228A pdb=" N VAL D 109 " --> pdb=" O ASP D 149 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ASP D 149 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP D 111 " --> pdb=" O THR D 147 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N SER D 187 " --> pdb=" O ASP D 213 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LYS D 215 " --> pdb=" O ALA D 185 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ALA D 185 " --> pdb=" O LYS D 215 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N VAL D 217 " --> pdb=" O ILE D 183 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE D 183 " --> pdb=" O VAL D 217 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ALA D 171 " --> pdb=" O GLU D 12 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N SER D 102 " --> pdb=" O ARG D 13 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ARG D 15 " --> pdb=" O ILE D 100 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE D 100 " --> pdb=" O ARG D 15 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU D 51 " --> pdb=" O THR D 96 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N VAL D 98 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N VAL D 49 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE D 100 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL D 47 " --> pdb=" O ILE D 100 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR D 74 " --> pdb=" O LYS D 65 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N VAL D 67 " --> pdb=" O SER D 72 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N SER D 72 " --> pdb=" O VAL D 67 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ALA D 24 " --> pdb=" O THR D 34 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 120 through 124 removed outlier: 4.387A pdb=" N GLN D 120 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 109 through 115 removed outlier: 7.231A pdb=" N VAL E 109 " --> pdb=" O ASP E 149 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ASP E 149 " --> pdb=" O VAL E 109 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP E 111 " --> pdb=" O THR E 147 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N SER E 187 " --> pdb=" O ASP E 213 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LYS E 215 " --> pdb=" O ALA E 185 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ALA E 185 " --> pdb=" O LYS E 215 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N VAL E 217 " --> pdb=" O ILE E 183 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE E 183 " --> pdb=" O VAL E 217 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ALA E 171 " --> pdb=" O GLU E 12 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N SER E 102 " --> pdb=" O ARG E 13 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ARG E 15 " --> pdb=" O ILE E 100 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE E 100 " --> pdb=" O ARG E 15 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU E 51 " --> pdb=" O THR E 96 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N VAL E 98 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N VAL E 49 " --> pdb=" O VAL E 98 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE E 100 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL E 47 " --> pdb=" O ILE E 100 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR E 74 " --> pdb=" O LYS E 65 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N VAL E 67 " --> pdb=" O SER E 72 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N SER E 72 " --> pdb=" O VAL E 67 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ALA E 24 " --> pdb=" O THR E 34 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 120 through 124 removed outlier: 4.387A pdb=" N GLN E 120 " --> pdb=" O THR E 137 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 109 through 115 removed outlier: 7.226A pdb=" N VAL F 109 " --> pdb=" O ASP F 149 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ASP F 149 " --> pdb=" O VAL F 109 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP F 111 " --> pdb=" O THR F 147 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N SER F 187 " --> pdb=" O ASP F 213 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LYS F 215 " --> pdb=" O ALA F 185 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ALA F 185 " --> pdb=" O LYS F 215 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N VAL F 217 " --> pdb=" O ILE F 183 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ILE F 183 " --> pdb=" O VAL F 217 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ALA F 171 " --> pdb=" O GLU F 12 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N SER F 102 " --> pdb=" O ARG F 13 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ARG F 15 " --> pdb=" O ILE F 100 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE F 100 " --> pdb=" O ARG F 15 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU F 51 " --> pdb=" O THR F 96 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N VAL F 98 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N VAL F 49 " --> pdb=" O VAL F 98 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE F 100 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL F 47 " --> pdb=" O ILE F 100 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N THR F 74 " --> pdb=" O LYS F 65 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N VAL F 67 " --> pdb=" O SER F 72 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N SER F 72 " --> pdb=" O VAL F 67 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ALA F 24 " --> pdb=" O THR F 34 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 120 through 124 removed outlier: 4.387A pdb=" N GLN F 120 " --> pdb=" O THR F 137 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 109 through 115 removed outlier: 7.208A pdb=" N VAL G 109 " --> pdb=" O ASP G 149 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ASP G 149 " --> pdb=" O VAL G 109 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP G 111 " --> pdb=" O THR G 147 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N SER G 187 " --> pdb=" O ASP G 213 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LYS G 215 " --> pdb=" O ALA G 185 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ALA G 185 " --> pdb=" O LYS G 215 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N VAL G 217 " --> pdb=" O ILE G 183 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ILE G 183 " --> pdb=" O VAL G 217 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ALA G 171 " --> pdb=" O GLU G 12 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N SER G 102 " --> pdb=" O ARG G 13 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ARG G 15 " --> pdb=" O ILE G 100 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE G 100 " --> pdb=" O ARG G 15 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU G 51 " --> pdb=" O THR G 96 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N VAL G 98 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N VAL G 49 " --> pdb=" O VAL G 98 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE G 100 " --> pdb=" O VAL G 47 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL G 47 " --> pdb=" O ILE G 100 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR G 74 " --> pdb=" O LYS G 65 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N VAL G 67 " --> pdb=" O SER G 72 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N SER G 72 " --> pdb=" O VAL G 67 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ALA G 24 " --> pdb=" O THR G 34 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 120 through 124 removed outlier: 4.387A pdb=" N GLN G 120 " --> pdb=" O THR G 137 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 109 through 115 removed outlier: 7.208A pdb=" N VAL H 109 " --> pdb=" O ASP H 149 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ASP H 149 " --> pdb=" O VAL H 109 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP H 111 " --> pdb=" O THR H 147 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N SER H 187 " --> pdb=" O ASP H 213 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LYS H 215 " --> pdb=" O ALA H 185 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ALA H 185 " --> pdb=" O LYS H 215 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N VAL H 217 " --> pdb=" O ILE H 183 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ILE H 183 " --> pdb=" O VAL H 217 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ALA H 171 " --> pdb=" O GLU H 12 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N SER H 102 " --> pdb=" O ARG H 13 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ARG H 15 " --> pdb=" O ILE H 100 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE H 100 " --> pdb=" O ARG H 15 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU H 51 " --> pdb=" O THR H 96 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N VAL H 98 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N VAL H 49 " --> pdb=" O VAL H 98 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE H 100 " --> pdb=" O VAL H 47 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL H 47 " --> pdb=" O ILE H 100 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR H 74 " --> pdb=" O LYS H 65 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N VAL H 67 " --> pdb=" O SER H 72 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N SER H 72 " --> pdb=" O VAL H 67 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ALA H 24 " --> pdb=" O THR H 34 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 120 through 124 removed outlier: 4.386A pdb=" N GLN H 120 " --> pdb=" O THR H 137 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 109 through 115 removed outlier: 7.208A pdb=" N VAL I 109 " --> pdb=" O ASP I 149 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ASP I 149 " --> pdb=" O VAL I 109 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP I 111 " --> pdb=" O THR I 147 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N SER I 187 " --> pdb=" O ASP I 213 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LYS I 215 " --> pdb=" O ALA I 185 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ALA I 185 " --> pdb=" O LYS I 215 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N VAL I 217 " --> pdb=" O ILE I 183 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE I 183 " --> pdb=" O VAL I 217 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ALA I 171 " --> pdb=" O GLU I 12 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N SER I 102 " --> pdb=" O ARG I 13 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ARG I 15 " --> pdb=" O ILE I 100 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE I 100 " --> pdb=" O ARG I 15 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU I 51 " --> pdb=" O THR I 96 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N VAL I 98 " --> pdb=" O VAL I 49 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N VAL I 49 " --> pdb=" O VAL I 98 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE I 100 " --> pdb=" O VAL I 47 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL I 47 " --> pdb=" O ILE I 100 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR I 74 " --> pdb=" O LYS I 65 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N VAL I 67 " --> pdb=" O SER I 72 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N SER I 72 " --> pdb=" O VAL I 67 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ALA I 24 " --> pdb=" O THR I 34 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 120 through 124 removed outlier: 4.385A pdb=" N GLN I 120 " --> pdb=" O THR I 137 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 109 through 115 removed outlier: 7.207A pdb=" N VAL J 109 " --> pdb=" O ASP J 149 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ASP J 149 " --> pdb=" O VAL J 109 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP J 111 " --> pdb=" O THR J 147 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N SER J 187 " --> pdb=" O ASP J 213 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LYS J 215 " --> pdb=" O ALA J 185 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ALA J 185 " --> pdb=" O LYS J 215 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N VAL J 217 " --> pdb=" O ILE J 183 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ILE J 183 " --> pdb=" O VAL J 217 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ALA J 171 " --> pdb=" O GLU J 12 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N SER J 102 " --> pdb=" O ARG J 13 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ARG J 15 " --> pdb=" O ILE J 100 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE J 100 " --> pdb=" O ARG J 15 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU J 51 " --> pdb=" O THR J 96 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N VAL J 98 " --> pdb=" O VAL J 49 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N VAL J 49 " --> pdb=" O VAL J 98 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE J 100 " --> pdb=" O VAL J 47 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL J 47 " --> pdb=" O ILE J 100 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR J 74 " --> pdb=" O LYS J 65 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N VAL J 67 " --> pdb=" O SER J 72 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N SER J 72 " --> pdb=" O VAL J 67 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ALA J 24 " --> pdb=" O THR J 34 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 120 through 124 removed outlier: 4.386A pdb=" N GLN J 120 " --> pdb=" O THR J 137 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 109 through 115 removed outlier: 7.208A pdb=" N VAL K 109 " --> pdb=" O ASP K 149 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ASP K 149 " --> pdb=" O VAL K 109 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP K 111 " --> pdb=" O THR K 147 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N SER K 187 " --> pdb=" O ASP K 213 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LYS K 215 " --> pdb=" O ALA K 185 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ALA K 185 " --> pdb=" O LYS K 215 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N VAL K 217 " --> pdb=" O ILE K 183 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE K 183 " --> pdb=" O VAL K 217 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ALA K 171 " --> pdb=" O GLU K 12 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N SER K 102 " --> pdb=" O ARG K 13 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ARG K 15 " --> pdb=" O ILE K 100 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE K 100 " --> pdb=" O ARG K 15 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU K 51 " --> pdb=" O THR K 96 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N VAL K 98 " --> pdb=" O VAL K 49 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N VAL K 49 " --> pdb=" O VAL K 98 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE K 100 " --> pdb=" O VAL K 47 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL K 47 " --> pdb=" O ILE K 100 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR K 74 " --> pdb=" O LYS K 65 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N VAL K 67 " --> pdb=" O SER K 72 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N SER K 72 " --> pdb=" O VAL K 67 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ALA K 24 " --> pdb=" O THR K 34 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 120 through 124 removed outlier: 4.386A pdb=" N GLN K 120 " --> pdb=" O THR K 137 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 109 through 115 removed outlier: 7.208A pdb=" N VAL L 109 " --> pdb=" O ASP L 149 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ASP L 149 " --> pdb=" O VAL L 109 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP L 111 " --> pdb=" O THR L 147 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N SER L 187 " --> pdb=" O ASP L 213 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LYS L 215 " --> pdb=" O ALA L 185 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ALA L 185 " --> pdb=" O LYS L 215 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N VAL L 217 " --> pdb=" O ILE L 183 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE L 183 " --> pdb=" O VAL L 217 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ALA L 171 " --> pdb=" O GLU L 12 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N SER L 102 " --> pdb=" O ARG L 13 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ARG L 15 " --> pdb=" O ILE L 100 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE L 100 " --> pdb=" O ARG L 15 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU L 51 " --> pdb=" O THR L 96 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N VAL L 98 " --> pdb=" O VAL L 49 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N VAL L 49 " --> pdb=" O VAL L 98 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE L 100 " --> pdb=" O VAL L 47 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL L 47 " --> pdb=" O ILE L 100 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N THR L 74 " --> pdb=" O LYS L 65 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N VAL L 67 " --> pdb=" O SER L 72 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N SER L 72 " --> pdb=" O VAL L 67 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ALA L 24 " --> pdb=" O THR L 34 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 120 through 124 removed outlier: 4.385A pdb=" N GLN L 120 " --> pdb=" O THR L 137 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 109 through 115 removed outlier: 7.227A pdb=" N VAL M 109 " --> pdb=" O ASP M 149 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ASP M 149 " --> pdb=" O VAL M 109 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP M 111 " --> pdb=" O THR M 147 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N SER M 187 " --> pdb=" O ASP M 213 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LYS M 215 " --> pdb=" O ALA M 185 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ALA M 185 " --> pdb=" O LYS M 215 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N VAL M 217 " --> pdb=" O ILE M 183 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ILE M 183 " --> pdb=" O VAL M 217 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ALA M 171 " --> pdb=" O GLU M 12 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N SER M 102 " --> pdb=" O ARG M 13 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ARG M 15 " --> pdb=" O ILE M 100 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE M 100 " --> pdb=" O ARG M 15 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU M 51 " --> pdb=" O THR M 96 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N VAL M 98 " --> pdb=" O VAL M 49 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N VAL M 49 " --> pdb=" O VAL M 98 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE M 100 " --> pdb=" O VAL M 47 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL M 47 " --> pdb=" O ILE M 100 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR M 74 " --> pdb=" O LYS M 65 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N VAL M 67 " --> pdb=" O SER M 72 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N SER M 72 " --> pdb=" O VAL M 67 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ALA M 24 " --> pdb=" O THR M 34 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 120 through 124 removed outlier: 4.386A pdb=" N GLN M 120 " --> pdb=" O THR M 137 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 109 through 115 removed outlier: 7.228A pdb=" N VAL N 109 " --> pdb=" O ASP N 149 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ASP N 149 " --> pdb=" O VAL N 109 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP N 111 " --> pdb=" O THR N 147 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N SER N 187 " --> pdb=" O ASP N 213 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LYS N 215 " --> pdb=" O ALA N 185 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ALA N 185 " --> pdb=" O LYS N 215 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N VAL N 217 " --> pdb=" O ILE N 183 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE N 183 " --> pdb=" O VAL N 217 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ALA N 171 " --> pdb=" O GLU N 12 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N SER N 102 " --> pdb=" O ARG N 13 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ARG N 15 " --> pdb=" O ILE N 100 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE N 100 " --> pdb=" O ARG N 15 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU N 51 " --> pdb=" O THR N 96 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N VAL N 98 " --> pdb=" O VAL N 49 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N VAL N 49 " --> pdb=" O VAL N 98 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE N 100 " --> pdb=" O VAL N 47 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL N 47 " --> pdb=" O ILE N 100 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N THR N 74 " --> pdb=" O LYS N 65 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N VAL N 67 " --> pdb=" O SER N 72 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N SER N 72 " --> pdb=" O VAL N 67 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ALA N 24 " --> pdb=" O THR N 34 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 120 through 124 removed outlier: 4.386A pdb=" N GLN N 120 " --> pdb=" O THR N 137 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'O' and resid 109 through 115 removed outlier: 7.225A pdb=" N VAL O 109 " --> pdb=" O ASP O 149 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ASP O 149 " --> pdb=" O VAL O 109 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP O 111 " --> pdb=" O THR O 147 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N SER O 187 " --> pdb=" O ASP O 213 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LYS O 215 " --> pdb=" O ALA O 185 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ALA O 185 " --> pdb=" O LYS O 215 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N VAL O 217 " --> pdb=" O ILE O 183 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE O 183 " --> pdb=" O VAL O 217 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ALA O 171 " --> pdb=" O GLU O 12 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N SER O 102 " --> pdb=" O ARG O 13 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ARG O 15 " --> pdb=" O ILE O 100 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE O 100 " --> pdb=" O ARG O 15 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU O 51 " --> pdb=" O THR O 96 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N VAL O 98 " --> pdb=" O VAL O 49 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N VAL O 49 " --> pdb=" O VAL O 98 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE O 100 " --> pdb=" O VAL O 47 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL O 47 " --> pdb=" O ILE O 100 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR O 74 " --> pdb=" O LYS O 65 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N VAL O 67 " --> pdb=" O SER O 72 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N SER O 72 " --> pdb=" O VAL O 67 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ALA O 24 " --> pdb=" O THR O 34 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'O' and resid 120 through 124 removed outlier: 4.387A pdb=" N GLN O 120 " --> pdb=" O THR O 137 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'P' and resid 109 through 115 removed outlier: 7.226A pdb=" N VAL P 109 " --> pdb=" O ASP P 149 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ASP P 149 " --> pdb=" O VAL P 109 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP P 111 " --> pdb=" O THR P 147 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N SER P 187 " --> pdb=" O ASP P 213 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LYS P 215 " --> pdb=" O ALA P 185 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ALA P 185 " --> pdb=" O LYS P 215 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N VAL P 217 " --> pdb=" O ILE P 183 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ILE P 183 " --> pdb=" O VAL P 217 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ALA P 171 " --> pdb=" O GLU P 12 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N SER P 102 " --> pdb=" O ARG P 13 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ARG P 15 " --> pdb=" O ILE P 100 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE P 100 " --> pdb=" O ARG P 15 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU P 51 " --> pdb=" O THR P 96 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N VAL P 98 " --> pdb=" O VAL P 49 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N VAL P 49 " --> pdb=" O VAL P 98 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE P 100 " --> pdb=" O VAL P 47 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL P 47 " --> pdb=" O ILE P 100 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR P 74 " --> pdb=" O LYS P 65 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N VAL P 67 " --> pdb=" O SER P 72 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N SER P 72 " --> pdb=" O VAL P 67 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ALA P 24 " --> pdb=" O THR P 34 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'P' and resid 120 through 124 removed outlier: 4.386A pdb=" N GLN P 120 " --> pdb=" O THR P 137 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Q' and resid 109 through 115 removed outlier: 7.229A pdb=" N VAL Q 109 " --> pdb=" O ASP Q 149 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ASP Q 149 " --> pdb=" O VAL Q 109 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP Q 111 " --> pdb=" O THR Q 147 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N SER Q 187 " --> pdb=" O ASP Q 213 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LYS Q 215 " --> pdb=" O ALA Q 185 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ALA Q 185 " --> pdb=" O LYS Q 215 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N VAL Q 217 " --> pdb=" O ILE Q 183 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE Q 183 " --> pdb=" O VAL Q 217 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ALA Q 171 " --> pdb=" O GLU Q 12 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N SER Q 102 " --> pdb=" O ARG Q 13 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ARG Q 15 " --> pdb=" O ILE Q 100 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE Q 100 " --> pdb=" O ARG Q 15 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU Q 51 " --> pdb=" O THR Q 96 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N VAL Q 98 " --> pdb=" O VAL Q 49 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N VAL Q 49 " --> pdb=" O VAL Q 98 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE Q 100 " --> pdb=" O VAL Q 47 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL Q 47 " --> pdb=" O ILE Q 100 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N THR Q 74 " --> pdb=" O LYS Q 65 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N VAL Q 67 " --> pdb=" O SER Q 72 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N SER Q 72 " --> pdb=" O VAL Q 67 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ALA Q 24 " --> pdb=" O THR Q 34 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Q' and resid 120 through 124 removed outlier: 4.387A pdb=" N GLN Q 120 " --> pdb=" O THR Q 137 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'R' and resid 109 through 115 removed outlier: 7.221A pdb=" N VAL R 109 " --> pdb=" O ASP R 149 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ASP R 149 " --> pdb=" O VAL R 109 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP R 111 " --> pdb=" O THR R 147 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N SER R 187 " --> pdb=" O ASP R 213 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LYS R 215 " --> pdb=" O ALA R 185 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ALA R 185 " --> pdb=" O LYS R 215 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N VAL R 217 " --> pdb=" O ILE R 183 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ILE R 183 " --> pdb=" O VAL R 217 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ALA R 171 " --> pdb=" O GLU R 12 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N SER R 102 " --> pdb=" O ARG R 13 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ARG R 15 " --> pdb=" O ILE R 100 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE R 100 " --> pdb=" O ARG R 15 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU R 51 " --> pdb=" O THR R 96 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N VAL R 98 " --> pdb=" O VAL R 49 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N VAL R 49 " --> pdb=" O VAL R 98 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE R 100 " --> pdb=" O VAL R 47 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL R 47 " --> pdb=" O ILE R 100 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N THR R 74 " --> pdb=" O LYS R 65 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N VAL R 67 " --> pdb=" O SER R 72 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N SER R 72 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ALA R 24 " --> pdb=" O THR R 34 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'R' and resid 120 through 124 removed outlier: 4.386A pdb=" N GLN R 120 " --> pdb=" O THR R 137 " (cutoff:3.500A) 1062 hydrogen bonds defined for protein. 2754 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: 5.92 Time building geometry restraints manager: 3.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 9072 1.35 - 1.47: 7330 1.47 - 1.60: 12434 1.60 - 1.72: 0 1.72 - 1.84: 144 Bond restraints: 28980 Sorted by residual: bond pdb=" CB CYS M 108 " pdb=" SG CYS M 108 " ideal model delta sigma weight residual 1.808 1.844 -0.036 3.30e-02 9.18e+02 1.22e+00 bond pdb=" CB CYS D 108 " pdb=" SG CYS D 108 " ideal model delta sigma weight residual 1.808 1.844 -0.036 3.30e-02 9.18e+02 1.18e+00 bond pdb=" CB CYS P 108 " pdb=" SG CYS P 108 " ideal model delta sigma weight residual 1.808 1.844 -0.036 3.30e-02 9.18e+02 1.17e+00 bond pdb=" CB CYS C 108 " pdb=" SG CYS C 108 " ideal model delta sigma weight residual 1.808 1.844 -0.036 3.30e-02 9.18e+02 1.16e+00 bond pdb=" CB CYS E 108 " pdb=" SG CYS E 108 " ideal model delta sigma weight residual 1.808 1.843 -0.035 3.30e-02 9.18e+02 1.16e+00 ... (remaining 28975 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 38600 1.42 - 2.85: 875 2.85 - 4.27: 215 4.27 - 5.70: 36 5.70 - 7.12: 18 Bond angle restraints: 39744 Sorted by residual: angle pdb=" CB MET O 200 " pdb=" CG MET O 200 " pdb=" SD MET O 200 " ideal model delta sigma weight residual 112.70 105.58 7.12 3.00e+00 1.11e-01 5.64e+00 angle pdb=" CB MET P 200 " pdb=" CG MET P 200 " pdb=" SD MET P 200 " ideal model delta sigma weight residual 112.70 105.58 7.12 3.00e+00 1.11e-01 5.63e+00 angle pdb=" CB MET J 200 " pdb=" CG MET J 200 " pdb=" SD MET J 200 " ideal model delta sigma weight residual 112.70 105.58 7.12 3.00e+00 1.11e-01 5.63e+00 angle pdb=" CB MET G 200 " pdb=" CG MET G 200 " pdb=" SD MET G 200 " ideal model delta sigma weight residual 112.70 105.59 7.11 3.00e+00 1.11e-01 5.61e+00 angle pdb=" CB MET Q 200 " pdb=" CG MET Q 200 " pdb=" SD MET Q 200 " ideal model delta sigma weight residual 112.70 105.59 7.11 3.00e+00 1.11e-01 5.61e+00 ... (remaining 39739 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.10: 15342 14.10 - 28.20: 1235 28.20 - 42.29: 361 42.29 - 56.39: 162 56.39 - 70.49: 18 Dihedral angle restraints: 17118 sinusoidal: 5454 harmonic: 11664 Sorted by residual: dihedral pdb=" CA VAL A 35 " pdb=" C VAL A 35 " pdb=" N ASN A 36 " pdb=" CA ASN A 36 " ideal model delta harmonic sigma weight residual 180.00 164.59 15.41 0 5.00e+00 4.00e-02 9.50e+00 dihedral pdb=" CA VAL I 35 " pdb=" C VAL I 35 " pdb=" N ASN I 36 " pdb=" CA ASN I 36 " ideal model delta harmonic sigma weight residual 180.00 164.61 15.39 0 5.00e+00 4.00e-02 9.47e+00 dihedral pdb=" CA VAL P 35 " pdb=" C VAL P 35 " pdb=" N ASN P 36 " pdb=" CA ASN P 36 " ideal model delta harmonic sigma weight residual 180.00 164.62 15.38 0 5.00e+00 4.00e-02 9.46e+00 ... (remaining 17115 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 2852 0.027 - 0.055: 1218 0.055 - 0.082: 327 0.082 - 0.110: 381 0.110 - 0.137: 226 Chirality restraints: 5004 Sorted by residual: chirality pdb=" CA ILE J 210 " pdb=" N ILE J 210 " pdb=" C ILE J 210 " pdb=" CB ILE J 210 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.69e-01 chirality pdb=" CA ILE I 210 " pdb=" N ILE I 210 " pdb=" C ILE I 210 " pdb=" CB ILE I 210 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.57e-01 chirality pdb=" CA ILE M 210 " pdb=" N ILE M 210 " pdb=" C ILE M 210 " pdb=" CB ILE M 210 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.56e-01 ... (remaining 5001 not shown) Planarity restraints: 4986 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL R 189 " 0.028 5.00e-02 4.00e+02 4.26e-02 2.91e+00 pdb=" N PRO R 190 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO R 190 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO R 190 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 189 " 0.028 5.00e-02 4.00e+02 4.26e-02 2.91e+00 pdb=" N PRO A 190 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 190 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 190 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 189 " 0.028 5.00e-02 4.00e+02 4.25e-02 2.89e+00 pdb=" N PRO G 190 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO G 190 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO G 190 " 0.024 5.00e-02 4.00e+02 ... (remaining 4983 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 10806 2.88 - 3.39: 25228 3.39 - 3.89: 46630 3.89 - 4.40: 49812 4.40 - 4.90: 90713 Nonbonded interactions: 223189 Sorted by model distance: nonbonded pdb=" O PRO I 4 " pdb=" OG SER I 7 " model vdw 2.376 3.040 nonbonded pdb=" O PRO B 4 " pdb=" OG SER B 7 " model vdw 2.376 3.040 nonbonded pdb=" O PRO F 4 " pdb=" OG SER F 7 " model vdw 2.376 3.040 nonbonded pdb=" O PRO L 4 " pdb=" OG SER L 7 " model vdw 2.376 3.040 nonbonded pdb=" O PRO C 4 " pdb=" OG SER C 7 " model vdw 2.377 3.040 ... (remaining 223184 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: 0.13 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 27.670 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.090 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 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 0.036 28992 Z= 0.151 Angle : 0.586 7.124 39768 Z= 0.320 Chirality : 0.047 0.137 5004 Planarity : 0.005 0.043 4986 Dihedral : 13.002 70.489 9558 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.33 % Allowed : 14.00 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.12), residues: 3978 helix: 1.43 (0.36), residues: 234 sheet: 0.20 (0.11), residues: 1854 loop : -0.43 (0.13), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 133 TYR 0.016 0.002 TYR P 173 PHE 0.006 0.001 PHE A 10 TRP 0.005 0.001 TRP B 103 HIS 0.001 0.001 HIS N 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.15 (28980) covalent geometry : angle 0.57896 / 0.32 (39744) SS BOND : bond 0.00828 / 0.55 ( 12) SS BOND : angle 3.70179 / 2.43 ( 24) hydrogen bonds : bond 0.15095 / 10.20 ( 1062) hydrogen bonds : angle 6.67634 / 4.77 ( 2754) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7956 Ramachandran restraints generated. 3978 Oldfield, 0 Emsley, 3978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7956 Ramachandran restraints generated. 3978 Oldfield, 0 Emsley, 3978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 302 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 GLN cc_start: 0.6315 (OUTLIER) cc_final: 0.5810 (mm-40) REVERT: B 134 GLN cc_start: 0.6534 (OUTLIER) cc_final: 0.6097 (mm-40) REVERT: C 193 ASP cc_start: 0.8530 (t0) cc_final: 0.8025 (p0) REVERT: D 134 GLN cc_start: 0.6124 (OUTLIER) cc_final: 0.5674 (mm-40) REVERT: E 134 GLN cc_start: 0.6556 (OUTLIER) cc_final: 0.6341 (mm-40) REVERT: F 193 ASP cc_start: 0.8539 (t0) cc_final: 0.8029 (p0) REVERT: G 119 GLN cc_start: 0.8685 (tp-100) cc_final: 0.8128 (tp40) REVERT: H 119 GLN cc_start: 0.8669 (tp-100) cc_final: 0.8271 (tp40) REVERT: I 119 GLN cc_start: 0.8636 (tp-100) cc_final: 0.8137 (tp-100) REVERT: J 119 GLN cc_start: 0.8693 (tp-100) cc_final: 0.8186 (tp40) REVERT: K 119 GLN cc_start: 0.8686 (tp-100) cc_final: 0.8242 (tp40) REVERT: L 119 GLN cc_start: 0.8624 (tp-100) cc_final: 0.8348 (tp-100) REVERT: M 134 GLN cc_start: 0.3756 (OUTLIER) cc_final: 0.3489 (mm-40) REVERT: O 89 TYR cc_start: 0.8728 (m-80) cc_final: 0.8437 (m-10) REVERT: O 134 GLN cc_start: 0.3583 (OUTLIER) cc_final: 0.3291 (mm-40) REVERT: R 89 TYR cc_start: 0.8723 (m-80) cc_final: 0.8412 (m-10) REVERT: R 134 GLN cc_start: 0.3732 (OUTLIER) cc_final: 0.3442 (mm-40) outliers start: 36 outliers final: 4 residues processed: 338 average time/residue: 0.2271 time to fit residues: 114.7262 Evaluate side-chains 219 residues out of total 3438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 208 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain D residue 134 GLN Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 134 GLN Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain M residue 134 GLN Chi-restraints excluded: chain O residue 134 GLN Chi-restraints excluded: chain R residue 134 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: [197, 388, 215, 20, 132, 261, 248, 207, 155, 244, 183] chunk 197 optimal weight: 9.9990 chunk 388 optimal weight: 9.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 30.0000 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 40.0000 overall best weight: 8.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 134 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.039577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.032541 restraints weight = 190929.636| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 4.08 r_work: 0.2853 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 28992 Z= 0.319 Angle : 0.604 12.768 39768 Z= 0.320 Chirality : 0.045 0.192 5004 Planarity : 0.005 0.046 4986 Dihedral : 4.997 37.721 4295 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.85 % Allowed : 14.15 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.21 (0.13), residues: 3978 helix: 2.38 (0.38), residues: 234 sheet: 0.47 (0.12), residues: 1512 loop : -0.29 (0.12), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 133 TYR 0.019 0.002 TYR L 173 PHE 0.013 0.002 PHE I 148 TRP 0.006 0.001 TRP I 54 HIS 0.004 0.001 HIS N 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00654 / 0.32 (28980) covalent geometry : angle 0.60357 / 0.32 (39744) SS BOND : bond 0.00079 / 0.05 ( 12) SS BOND : angle 1.16397 / 0.75 ( 24) hydrogen bonds : bond 0.03698 / 2.53 ( 1062) hydrogen bonds : angle 5.58940 / 4.00 ( 2754) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7956 Ramachandran restraints generated. 3978 Oldfield, 0 Emsley, 3978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7956 Ramachandran restraints generated. 3978 Oldfield, 0 Emsley, 3978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 3438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 265 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 200 MET cc_start: 0.8327 (mmp) cc_final: 0.8044 (mmp) REVERT: C 193 ASP cc_start: 0.9074 (t0) cc_final: 0.7974 (p0) REVERT: E 200 MET cc_start: 0.8315 (mmp) cc_final: 0.8010 (mmp) REVERT: F 193 ASP cc_start: 0.9060 (t0) cc_final: 0.7968 (p0) REVERT: G 68 THR cc_start: 0.8591 (OUTLIER) cc_final: 0.8312 (m) REVERT: H 164 ASP cc_start: 0.9195 (t0) cc_final: 0.8982 (t0) REVERT: I 204 GLU cc_start: 0.8827 (pm20) cc_final: 0.8626 (pm20) REVERT: I 219 MET cc_start: 0.7890 (mpp) cc_final: 0.7681 (mpp) REVERT: J 68 THR cc_start: 0.8586 (OUTLIER) cc_final: 0.8317 (m) REVERT: J 124 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.8096 (ptpt) REVERT: J 219 MET cc_start: 0.7826 (mpp) cc_final: 0.7600 (mpp) REVERT: K 164 ASP cc_start: 0.9093 (t0) cc_final: 0.8869 (t0) REVERT: K 204 GLU cc_start: 0.8457 (pt0) cc_final: 0.8206 (pt0) REVERT: K 219 MET cc_start: 0.8503 (mtt) cc_final: 0.7765 (mpp) REVERT: L 173 TYR cc_start: 0.8984 (OUTLIER) cc_final: 0.7499 (p90) REVERT: L 204 GLU cc_start: 0.8785 (pm20) cc_final: 0.8582 (pm20) REVERT: M 89 TYR cc_start: 0.9486 (m-80) cc_final: 0.8913 (m-80) REVERT: N 88 LYS cc_start: 0.9217 (tppt) cc_final: 0.8819 (tppt) REVERT: N 120 GLN cc_start: 0.8829 (mm110) cc_final: 0.8612 (mp10) REVERT: N 193 ASP cc_start: 0.8288 (t0) cc_final: 0.8076 (t0) REVERT: O 88 LYS cc_start: 0.9168 (tppt) cc_final: 0.8867 (tppt) REVERT: O 99 LYS cc_start: 0.9302 (tttt) cc_final: 0.9061 (ttpp) REVERT: O 193 ASP cc_start: 0.8339 (t0) cc_final: 0.8003 (t0) REVERT: P 89 TYR cc_start: 0.9454 (m-80) cc_final: 0.8833 (m-80) REVERT: Q 88 LYS cc_start: 0.9195 (tppt) cc_final: 0.8782 (tppt) REVERT: Q 193 ASP cc_start: 0.8280 (t0) cc_final: 0.8066 (t0) REVERT: R 88 LYS cc_start: 0.9158 (tppt) cc_final: 0.8855 (tppt) REVERT: R 193 ASP cc_start: 0.8245 (t0) cc_final: 0.7953 (t0) outliers start: 50 outliers final: 20 residues processed: 305 average time/residue: 0.1975 time to fit residues: 93.3110 Evaluate side-chains 245 residues out of total 3438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 221 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 TYR Chi-restraints excluded: chain B residue 122 TYR Chi-restraints excluded: chain C residue 122 TYR Chi-restraints excluded: chain C residue 138 PHE Chi-restraints excluded: chain D residue 122 TYR Chi-restraints excluded: chain E residue 122 TYR Chi-restraints excluded: chain F residue 122 TYR Chi-restraints excluded: chain F residue 138 PHE Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain H residue 88 LYS Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain I residue 137 THR Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 124 LYS Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain K residue 88 LYS Chi-restraints excluded: chain K residue 137 THR Chi-restraints excluded: chain L residue 137 THR Chi-restraints excluded: chain L residue 173 TYR Chi-restraints excluded: chain M residue 122 TYR Chi-restraints excluded: chain O residue 122 TYR Chi-restraints excluded: chain P residue 122 TYR Chi-restraints excluded: chain R residue 122 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: [383, 166, 377, 15, 61, 382, 53, 27, 280, 100, 118] chunk 383 optimal weight: 20.0000 chunk 166 optimal weight: 10.0000 chunk 377 optimal weight: 20.0000 chunk 15 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 382 optimal weight: 5.9990 chunk 53 optimal weight: 20.0000 chunk 27 optimal weight: 8.9990 chunk 280 optimal weight: 9.9990 chunk 100 optimal weight: 7.9990 chunk 118 optimal weight: 5.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 120 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.039860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.032850 restraints weight = 188766.381| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 4.05 r_work: 0.2869 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 28992 Z= 0.188 Angle : 0.510 9.464 39768 Z= 0.275 Chirality : 0.044 0.144 5004 Planarity : 0.004 0.045 4986 Dihedral : 4.278 18.660 4266 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.30 % Allowed : 13.74 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.31 (0.13), residues: 3978 helix: 2.47 (0.38), residues: 234 sheet: 0.55 (0.12), residues: 1620 loop : -0.28 (0.13), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 133 TYR 0.018 0.001 TYR J 173 PHE 0.010 0.001 PHE C 10 TRP 0.003 0.001 TRP I 54 HIS 0.002 0.001 HIS O 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.19 (28980) covalent geometry : angle 0.51026 / 0.27 (39744) SS BOND : bond 0.00046 / 0.03 ( 12) SS BOND : angle 0.79366 / 0.51 ( 24) hydrogen bonds : bond 0.02998 / 2.05 ( 1062) hydrogen bonds : angle 5.25613 / 3.75 ( 2754) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7956 Ramachandran restraints generated. 3978 Oldfield, 0 Emsley, 3978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7956 Ramachandran restraints generated. 3978 Oldfield, 0 Emsley, 3978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 3438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 237 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 200 MET cc_start: 0.8274 (mmp) cc_final: 0.8044 (mmp) REVERT: C 193 ASP cc_start: 0.9077 (t0) cc_final: 0.8019 (p0) REVERT: F 193 ASP cc_start: 0.9074 (t0) cc_final: 0.8013 (p0) REVERT: G 173 TYR cc_start: 0.9003 (OUTLIER) cc_final: 0.8293 (p90) REVERT: H 164 ASP cc_start: 0.9175 (t0) cc_final: 0.8892 (t0) REVERT: H 174 MET cc_start: 0.8397 (tpp) cc_final: 0.8042 (tpp) REVERT: H 204 GLU cc_start: 0.8731 (pm20) cc_final: 0.8485 (pm20) REVERT: I 146 TYR cc_start: 0.9050 (m-80) cc_final: 0.8370 (m-80) REVERT: I 174 MET cc_start: 0.8375 (tpp) cc_final: 0.8036 (tpp) REVERT: I 219 MET cc_start: 0.7979 (mpp) cc_final: 0.7773 (mpp) REVERT: J 173 TYR cc_start: 0.8987 (OUTLIER) cc_final: 0.8262 (p90) REVERT: J 219 MET cc_start: 0.7889 (mpp) cc_final: 0.7603 (mpp) REVERT: K 164 ASP cc_start: 0.9044 (t0) cc_final: 0.8773 (t0) REVERT: K 174 MET cc_start: 0.8460 (tpp) cc_final: 0.8075 (tpp) REVERT: K 204 GLU cc_start: 0.8389 (pt0) cc_final: 0.8120 (pt0) REVERT: K 219 MET cc_start: 0.8595 (mtt) cc_final: 0.7912 (mpp) REVERT: L 174 MET cc_start: 0.8386 (tpp) cc_final: 0.8074 (tpp) REVERT: L 204 GLU cc_start: 0.8730 (pm20) cc_final: 0.8424 (pm20) REVERT: M 99 LYS cc_start: 0.9373 (tttt) cc_final: 0.9097 (ttpp) REVERT: M 193 ASP cc_start: 0.8451 (t0) cc_final: 0.8121 (t0) REVERT: N 68 THR cc_start: 0.9529 (OUTLIER) cc_final: 0.9301 (m) REVERT: N 88 LYS cc_start: 0.9228 (tppt) cc_final: 0.8867 (tppt) REVERT: N 193 ASP cc_start: 0.8308 (t0) cc_final: 0.8000 (t0) REVERT: O 88 LYS cc_start: 0.9161 (tppt) cc_final: 0.8755 (tppt) REVERT: O 89 TYR cc_start: 0.9534 (m-80) cc_final: 0.9331 (m-10) REVERT: O 99 LYS cc_start: 0.9404 (tttt) cc_final: 0.9183 (ttpp) REVERT: O 193 ASP cc_start: 0.8380 (t0) cc_final: 0.7965 (t0) REVERT: P 193 ASP cc_start: 0.8423 (t0) cc_final: 0.8101 (t0) REVERT: Q 68 THR cc_start: 0.9519 (OUTLIER) cc_final: 0.9294 (m) REVERT: Q 88 LYS cc_start: 0.9227 (tppt) cc_final: 0.8847 (tppt) REVERT: Q 193 ASP cc_start: 0.8320 (t0) cc_final: 0.8013 (t0) REVERT: R 88 LYS cc_start: 0.9135 (tppt) cc_final: 0.8781 (tppt) REVERT: R 193 ASP cc_start: 0.8311 (t0) cc_final: 0.7980 (t0) outliers start: 62 outliers final: 26 residues processed: 291 average time/residue: 0.1909 time to fit residues: 87.9532 Evaluate side-chains 242 residues out of total 3438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 212 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 TYR Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain D residue 122 TYR Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain G residue 120 GLN Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 173 TYR Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain I residue 137 THR Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 173 TYR Chi-restraints excluded: chain K residue 137 THR Chi-restraints excluded: chain L residue 137 THR Chi-restraints excluded: chain M residue 122 TYR Chi-restraints excluded: chain M residue 137 THR Chi-restraints excluded: chain N residue 68 THR Chi-restraints excluded: chain N residue 137 THR Chi-restraints excluded: chain O residue 122 TYR Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain P residue 122 TYR Chi-restraints excluded: chain P residue 137 THR Chi-restraints excluded: chain P residue 219 MET Chi-restraints excluded: chain Q residue 68 THR Chi-restraints excluded: chain Q residue 137 THR Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 122 TYR Chi-restraints excluded: chain R residue 137 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: [80, 329, 66, 275, 100, 115, 222, 205, 227, 363, 327] chunk 80 optimal weight: 6.9990 chunk 329 optimal weight: 8.9990 chunk 66 optimal weight: 6.9990 chunk 275 optimal weight: 10.0000 chunk 100 optimal weight: 7.9990 chunk 115 optimal weight: 0.9990 chunk 222 optimal weight: 5.9990 chunk 205 optimal weight: 40.0000 chunk 227 optimal weight: 40.0000 chunk 363 optimal weight: 8.9990 chunk 327 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 120 GLN ** G 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.039277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.032275 restraints weight = 189827.019| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 4.05 r_work: 0.2844 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 28992 Z= 0.228 Angle : 0.499 8.153 39768 Z= 0.270 Chirality : 0.044 0.155 5004 Planarity : 0.004 0.045 4986 Dihedral : 4.280 17.564 4266 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.93 % Allowed : 13.63 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.16 (0.13), residues: 3978 helix: 2.62 (0.38), residues: 234 sheet: 0.17 (0.11), residues: 1872 loop : -0.17 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 133 TYR 0.020 0.001 TYR G 173 PHE 0.010 0.001 PHE E 10 TRP 0.006 0.001 TRP M 54 HIS 0.003 0.001 HIS E 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.23 (28980) covalent geometry : angle 0.49802 / 0.27 (39744) SS BOND : bond 0.00132 / 0.08 ( 12) SS BOND : angle 1.05517 / 0.71 ( 24) hydrogen bonds : bond 0.03018 / 2.06 ( 1062) hydrogen bonds : angle 5.19584 / 3.69 ( 2754) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7956 Ramachandran restraints generated. 3978 Oldfield, 0 Emsley, 3978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7956 Ramachandran restraints generated. 3978 Oldfield, 0 Emsley, 3978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 3438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 239 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 137 THR cc_start: 0.6673 (OUTLIER) cc_final: 0.6339 (p) REVERT: B 193 ASP cc_start: 0.8255 (t0) cc_final: 0.7688 (p0) REVERT: C 193 ASP cc_start: 0.9055 (t0) cc_final: 0.8075 (p0) REVERT: D 137 THR cc_start: 0.6768 (OUTLIER) cc_final: 0.6427 (p) REVERT: E 137 THR cc_start: 0.6620 (OUTLIER) cc_final: 0.6323 (p) REVERT: E 193 ASP cc_start: 0.8197 (t0) cc_final: 0.7639 (p0) REVERT: F 193 ASP cc_start: 0.9067 (t0) cc_final: 0.8081 (p0) REVERT: G 173 TYR cc_start: 0.8992 (OUTLIER) cc_final: 0.8534 (p90) REVERT: G 193 ASP cc_start: 0.8812 (t0) cc_final: 0.8347 (p0) REVERT: G 219 MET cc_start: 0.8402 (mpp) cc_final: 0.8015 (pmm) REVERT: H 174 MET cc_start: 0.8565 (tpp) cc_final: 0.8280 (tpp) REVERT: H 193 ASP cc_start: 0.8857 (t0) cc_final: 0.8385 (p0) REVERT: H 204 GLU cc_start: 0.8627 (pm20) cc_final: 0.8244 (pm20) REVERT: I 146 TYR cc_start: 0.9075 (m-80) cc_final: 0.8422 (m-80) REVERT: I 174 MET cc_start: 0.8535 (tpp) cc_final: 0.8237 (tpp) REVERT: I 193 ASP cc_start: 0.8768 (t0) cc_final: 0.8394 (p0) REVERT: I 219 MET cc_start: 0.8031 (mpp) cc_final: 0.7712 (mpp) REVERT: J 173 TYR cc_start: 0.8979 (OUTLIER) cc_final: 0.8547 (p90) REVERT: J 193 ASP cc_start: 0.8788 (t0) cc_final: 0.8328 (p0) REVERT: J 219 MET cc_start: 0.7964 (mpp) cc_final: 0.7583 (mpp) REVERT: K 65 LYS cc_start: 0.9017 (ptpp) cc_final: 0.8770 (ptpp) REVERT: K 164 ASP cc_start: 0.9087 (t0) cc_final: 0.8764 (t0) REVERT: K 174 MET cc_start: 0.8612 (tpp) cc_final: 0.8321 (tpp) REVERT: K 193 ASP cc_start: 0.8907 (t0) cc_final: 0.8419 (p0) REVERT: K 204 GLU cc_start: 0.8409 (pt0) cc_final: 0.8187 (pt0) REVERT: K 219 MET cc_start: 0.8650 (mtt) cc_final: 0.8036 (mpp) REVERT: L 174 MET cc_start: 0.8501 (tpp) cc_final: 0.8251 (tpp) REVERT: L 193 ASP cc_start: 0.8742 (t0) cc_final: 0.8381 (p0) REVERT: M 193 ASP cc_start: 0.8531 (t0) cc_final: 0.8257 (t0) REVERT: N 88 LYS cc_start: 0.9295 (tppt) cc_final: 0.8881 (tppt) REVERT: N 99 LYS cc_start: 0.9479 (OUTLIER) cc_final: 0.9256 (ttpp) REVERT: N 193 ASP cc_start: 0.8423 (t0) cc_final: 0.8058 (t0) REVERT: O 88 LYS cc_start: 0.9277 (tppt) cc_final: 0.8927 (tppt) REVERT: O 99 LYS cc_start: 0.9464 (tttt) cc_final: 0.9194 (ttpp) REVERT: O 193 ASP cc_start: 0.8446 (t0) cc_final: 0.7996 (t0) REVERT: O 204 GLU cc_start: 0.8041 (pm20) cc_final: 0.7766 (pm20) REVERT: P 193 ASP cc_start: 0.8510 (t0) cc_final: 0.8233 (t0) REVERT: Q 88 LYS cc_start: 0.9275 (tppt) cc_final: 0.8828 (tppt) REVERT: Q 193 ASP cc_start: 0.8389 (t0) cc_final: 0.8061 (t0) REVERT: R 88 LYS cc_start: 0.9237 (tppt) cc_final: 0.8876 (tppt) REVERT: R 99 LYS cc_start: 0.9490 (tttt) cc_final: 0.9269 (ttpp) REVERT: R 193 ASP cc_start: 0.8353 (t0) cc_final: 0.7972 (t0) REVERT: R 204 GLU cc_start: 0.8092 (pm20) cc_final: 0.7832 (pm20) outliers start: 52 outliers final: 28 residues processed: 278 average time/residue: 0.1957 time to fit residues: 84.8113 Evaluate side-chains 246 residues out of total 3438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 212 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 122 TYR Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 122 TYR Chi-restraints excluded: chain D residue 88 LYS Chi-restraints excluded: chain D residue 122 TYR Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 138 PHE Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain F residue 122 TYR Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 88 LYS Chi-restraints excluded: chain G residue 127 LEU Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 173 TYR Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain I residue 137 THR Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 88 LYS Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 173 TYR Chi-restraints excluded: chain K residue 137 THR Chi-restraints excluded: chain L residue 137 THR Chi-restraints excluded: chain M residue 122 TYR Chi-restraints excluded: chain M residue 219 MET Chi-restraints excluded: chain N residue 68 THR Chi-restraints excluded: chain N residue 99 LYS Chi-restraints excluded: chain O residue 122 TYR Chi-restraints excluded: chain P residue 122 TYR Chi-restraints excluded: chain Q residue 68 THR Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 122 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: [37, 81, 63, 74, 231, 45, 119, 391, 240, 82, 197] chunk 37 optimal weight: 10.0000 chunk 81 optimal weight: 7.9990 chunk 63 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 chunk 231 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 119 optimal weight: 20.0000 chunk 391 optimal weight: 5.9990 chunk 240 optimal weight: 20.0000 chunk 82 optimal weight: 2.9990 chunk 197 optimal weight: 9.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 120 GLN E 120 GLN ** G 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 GLN H 120 GLN ** J 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 120 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.038764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.031854 restraints weight = 191863.838| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 3.96 r_work: 0.2825 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 28992 Z= 0.276 Angle : 0.518 8.166 39768 Z= 0.281 Chirality : 0.044 0.151 5004 Planarity : 0.004 0.047 4986 Dihedral : 4.366 17.476 4266 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.70 % Allowed : 14.93 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.13), residues: 3978 helix: 2.61 (0.37), residues: 234 sheet: 0.03 (0.12), residues: 1872 loop : -0.22 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 184 TYR 0.019 0.002 TYR I 173 PHE 0.016 0.001 PHE J 150 TRP 0.004 0.001 TRP P 54 HIS 0.003 0.001 HIS L 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00568 / 0.28 (28980) covalent geometry : angle 0.51745 / 0.28 (39744) SS BOND : bond 0.00075 / 0.04 ( 12) SS BOND : angle 1.05428 / 0.72 ( 24) hydrogen bonds : bond 0.03103 / 2.12 ( 1062) hydrogen bonds : angle 5.24954 / 3.73 ( 2754) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7956 Ramachandran restraints generated. 3978 Oldfield, 0 Emsley, 3978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7956 Ramachandran restraints generated. 3978 Oldfield, 0 Emsley, 3978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 223 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 ASP cc_start: 0.8446 (t0) cc_final: 0.8209 (t0) REVERT: B 137 THR cc_start: 0.6771 (OUTLIER) cc_final: 0.6272 (p) REVERT: B 193 ASP cc_start: 0.8369 (t0) cc_final: 0.7793 (p0) REVERT: C 193 ASP cc_start: 0.9045 (t0) cc_final: 0.8039 (p0) REVERT: D 137 THR cc_start: 0.6676 (OUTLIER) cc_final: 0.6349 (p) REVERT: D 193 ASP cc_start: 0.8440 (t0) cc_final: 0.8166 (t0) REVERT: E 137 THR cc_start: 0.6786 (OUTLIER) cc_final: 0.6282 (p) REVERT: E 193 ASP cc_start: 0.8350 (t0) cc_final: 0.7773 (p0) REVERT: F 193 ASP cc_start: 0.9044 (t0) cc_final: 0.8052 (p0) REVERT: G 173 TYR cc_start: 0.8975 (OUTLIER) cc_final: 0.8270 (p90) REVERT: G 193 ASP cc_start: 0.8816 (t0) cc_final: 0.8291 (p0) REVERT: H 164 ASP cc_start: 0.9125 (t70) cc_final: 0.8639 (m-30) REVERT: H 174 MET cc_start: 0.8518 (tpp) cc_final: 0.8180 (tpp) REVERT: H 193 ASP cc_start: 0.8802 (t0) cc_final: 0.8193 (p0) REVERT: H 204 GLU cc_start: 0.8640 (pm20) cc_final: 0.8417 (pm20) REVERT: I 146 TYR cc_start: 0.9065 (m-80) cc_final: 0.8512 (m-80) REVERT: I 174 MET cc_start: 0.8584 (tpp) cc_final: 0.8235 (tpp) REVERT: I 193 ASP cc_start: 0.8755 (t0) cc_final: 0.8255 (p0) REVERT: I 219 MET cc_start: 0.7999 (mpp) cc_final: 0.7611 (mpp) REVERT: J 173 TYR cc_start: 0.8939 (OUTLIER) cc_final: 0.8330 (p90) REVERT: J 193 ASP cc_start: 0.8806 (t0) cc_final: 0.8283 (p0) REVERT: J 219 MET cc_start: 0.7933 (mpp) cc_final: 0.7499 (mpp) REVERT: K 65 LYS cc_start: 0.9045 (ptpp) cc_final: 0.8773 (ptpp) REVERT: K 164 ASP cc_start: 0.9101 (t0) cc_final: 0.8872 (t70) REVERT: K 174 MET cc_start: 0.8564 (tpp) cc_final: 0.8341 (tpp) REVERT: K 219 MET cc_start: 0.8681 (mtt) cc_final: 0.7970 (mpp) REVERT: L 174 MET cc_start: 0.8558 (tpp) cc_final: 0.8263 (tpp) REVERT: L 193 ASP cc_start: 0.8730 (t0) cc_final: 0.8229 (p0) REVERT: M 193 ASP cc_start: 0.8566 (t0) cc_final: 0.8200 (t0) REVERT: N 88 LYS cc_start: 0.9363 (tppt) cc_final: 0.8891 (tppt) REVERT: N 99 LYS cc_start: 0.9521 (OUTLIER) cc_final: 0.9285 (ttpp) REVERT: N 193 ASP cc_start: 0.8476 (t0) cc_final: 0.8072 (t0) REVERT: O 99 LYS cc_start: 0.9487 (tttt) cc_final: 0.9227 (ttpp) REVERT: O 193 ASP cc_start: 0.8473 (t0) cc_final: 0.8010 (t0) REVERT: O 204 GLU cc_start: 0.8022 (pm20) cc_final: 0.7747 (pm20) REVERT: P 193 ASP cc_start: 0.8550 (t0) cc_final: 0.8190 (t0) REVERT: Q 88 LYS cc_start: 0.9355 (tppt) cc_final: 0.8868 (tppt) REVERT: Q 193 ASP cc_start: 0.8436 (t0) cc_final: 0.8030 (t0) REVERT: R 99 LYS cc_start: 0.9505 (tttt) cc_final: 0.9279 (ttpp) REVERT: R 193 ASP cc_start: 0.8345 (t0) cc_final: 0.7914 (t0) REVERT: R 200 MET cc_start: 0.9025 (OUTLIER) cc_final: 0.8817 (mmm) REVERT: R 204 GLU cc_start: 0.8034 (pm20) cc_final: 0.7730 (pm20) outliers start: 46 outliers final: 30 residues processed: 258 average time/residue: 0.2007 time to fit residues: 80.8428 Evaluate side-chains 243 residues out of total 3438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 206 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 TYR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 122 TYR Chi-restraints excluded: chain D residue 122 TYR Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain F residue 122 TYR Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 127 LEU Chi-restraints excluded: chain G residue 173 TYR Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain I residue 137 THR Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 173 TYR Chi-restraints excluded: chain K residue 120 GLN Chi-restraints excluded: chain K residue 137 THR Chi-restraints excluded: chain L residue 137 THR Chi-restraints excluded: chain M residue 122 TYR Chi-restraints excluded: chain M residue 137 THR Chi-restraints excluded: chain M residue 219 MET Chi-restraints excluded: chain N residue 99 LYS Chi-restraints excluded: chain N residue 137 THR Chi-restraints excluded: chain O residue 122 TYR Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain P residue 122 TYR Chi-restraints excluded: chain P residue 137 THR Chi-restraints excluded: chain P residue 219 MET Chi-restraints excluded: chain Q residue 137 THR Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 122 TYR Chi-restraints excluded: chain R residue 137 THR Chi-restraints excluded: chain R residue 200 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: [58, 281, 79, 80, 118, 382, 257, 214, 87, 170, 341] chunk 58 optimal weight: 9.9990 chunk 281 optimal weight: 0.9980 chunk 79 optimal weight: 7.9990 chunk 80 optimal weight: 9.9990 chunk 118 optimal weight: 10.0000 chunk 382 optimal weight: 8.9990 chunk 257 optimal weight: 10.0000 chunk 214 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 170 optimal weight: 4.9990 chunk 341 optimal weight: 20.0000 overall best weight: 6.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 120 GLN ** J 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 120 GLN P 125 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.038857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.031820 restraints weight = 192038.072| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 4.10 r_work: 0.2827 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 28992 Z= 0.254 Angle : 0.506 8.994 39768 Z= 0.274 Chirality : 0.044 0.147 5004 Planarity : 0.004 0.046 4986 Dihedral : 4.315 17.144 4266 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.44 % Allowed : 15.19 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.13), residues: 3978 helix: 2.66 (0.37), residues: 234 sheet: -0.03 (0.12), residues: 1872 loop : -0.24 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG J 133 TYR 0.019 0.001 TYR I 173 PHE 0.017 0.001 PHE G 150 TRP 0.003 0.001 TRP A 103 HIS 0.003 0.001 HIS R 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.25 (28980) covalent geometry : angle 0.50608 / 0.27 (39744) SS BOND : bond 0.00053 / 0.04 ( 12) SS BOND : angle 0.80491 / 0.58 ( 24) hydrogen bonds : bond 0.02960 / 2.02 ( 1062) hydrogen bonds : angle 5.23604 / 3.71 ( 2754) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7956 Ramachandran restraints generated. 3978 Oldfield, 0 Emsley, 3978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7956 Ramachandran restraints generated. 3978 Oldfield, 0 Emsley, 3978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 3438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 226 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 ASP cc_start: 0.8477 (t0) cc_final: 0.8204 (t0) REVERT: B 137 THR cc_start: 0.7090 (OUTLIER) cc_final: 0.6818 (p) REVERT: B 193 ASP cc_start: 0.8463 (t0) cc_final: 0.7853 (p0) REVERT: C 193 ASP cc_start: 0.9054 (t0) cc_final: 0.8040 (p0) REVERT: D 134 GLN cc_start: 0.6674 (OUTLIER) cc_final: 0.6105 (mm-40) REVERT: D 137 THR cc_start: 0.6684 (OUTLIER) cc_final: 0.6397 (p) REVERT: D 193 ASP cc_start: 0.8452 (t0) cc_final: 0.8169 (t0) REVERT: E 137 THR cc_start: 0.7022 (OUTLIER) cc_final: 0.6766 (p) REVERT: E 193 ASP cc_start: 0.8449 (t0) cc_final: 0.7848 (p0) REVERT: F 193 ASP cc_start: 0.9062 (t0) cc_final: 0.8048 (p0) REVERT: G 173 TYR cc_start: 0.8891 (OUTLIER) cc_final: 0.8199 (p90) REVERT: H 164 ASP cc_start: 0.9130 (t70) cc_final: 0.8670 (m-30) REVERT: H 174 MET cc_start: 0.8541 (tpp) cc_final: 0.8246 (tpp) REVERT: I 146 TYR cc_start: 0.9053 (m-80) cc_final: 0.8496 (m-80) REVERT: I 174 MET cc_start: 0.8587 (tpp) cc_final: 0.8221 (tpp) REVERT: I 193 ASP cc_start: 0.8775 (t0) cc_final: 0.8208 (p0) REVERT: I 219 MET cc_start: 0.8023 (mpp) cc_final: 0.7685 (mpp) REVERT: J 173 TYR cc_start: 0.8886 (OUTLIER) cc_final: 0.8226 (p90) REVERT: J 193 ASP cc_start: 0.8802 (t0) cc_final: 0.8258 (p0) REVERT: J 219 MET cc_start: 0.7857 (mpp) cc_final: 0.7392 (mpp) REVERT: K 65 LYS cc_start: 0.9072 (ptpp) cc_final: 0.8574 (ptpp) REVERT: K 164 ASP cc_start: 0.9140 (t0) cc_final: 0.8901 (t70) REVERT: K 174 MET cc_start: 0.8560 (tpp) cc_final: 0.8295 (tpp) REVERT: K 193 ASP cc_start: 0.8853 (t0) cc_final: 0.8175 (p0) REVERT: K 219 MET cc_start: 0.8718 (mtt) cc_final: 0.8036 (mpp) REVERT: L 174 MET cc_start: 0.8573 (tpp) cc_final: 0.8227 (tpp) REVERT: L 193 ASP cc_start: 0.8775 (t0) cc_final: 0.8223 (p0) REVERT: L 219 MET cc_start: 0.8778 (mtm) cc_final: 0.8539 (mpp) REVERT: M 193 ASP cc_start: 0.8599 (t0) cc_final: 0.8199 (t0) REVERT: N 88 LYS cc_start: 0.9395 (tppt) cc_final: 0.8906 (tppt) REVERT: N 193 ASP cc_start: 0.8598 (t0) cc_final: 0.8242 (t0) REVERT: O 99 LYS cc_start: 0.9494 (tttt) cc_final: 0.9229 (ttpp) REVERT: O 193 ASP cc_start: 0.8530 (t0) cc_final: 0.8042 (t0) REVERT: O 204 GLU cc_start: 0.8009 (pm20) cc_final: 0.7804 (pm20) REVERT: P 193 ASP cc_start: 0.8579 (t0) cc_final: 0.8171 (t0) REVERT: Q 88 LYS cc_start: 0.9403 (tppt) cc_final: 0.8904 (tppt) REVERT: Q 193 ASP cc_start: 0.8577 (t0) cc_final: 0.8215 (t0) REVERT: R 88 LYS cc_start: 0.9363 (tppt) cc_final: 0.9129 (tptp) REVERT: R 99 LYS cc_start: 0.9527 (tttt) cc_final: 0.9300 (ttpp) REVERT: R 193 ASP cc_start: 0.8430 (t0) cc_final: 0.7997 (t0) REVERT: R 204 GLU cc_start: 0.8027 (pm20) cc_final: 0.7812 (pm20) outliers start: 39 outliers final: 24 residues processed: 254 average time/residue: 0.2035 time to fit residues: 79.8332 Evaluate side-chains 237 residues out of total 3438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 207 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 TYR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 122 TYR Chi-restraints excluded: chain D residue 88 LYS Chi-restraints excluded: chain D residue 122 TYR Chi-restraints excluded: chain D residue 134 GLN Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain F residue 122 TYR Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 127 LEU Chi-restraints excluded: chain G residue 173 TYR Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain I residue 137 THR Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 173 TYR Chi-restraints excluded: chain K residue 137 THR Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain M residue 122 TYR Chi-restraints excluded: chain M residue 219 MET Chi-restraints excluded: chain N residue 137 THR Chi-restraints excluded: chain O residue 122 TYR Chi-restraints excluded: chain P residue 122 TYR Chi-restraints excluded: chain P residue 219 MET Chi-restraints excluded: chain Q residue 137 THR Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 122 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: [348, 165, 227, 334, 53, 49, 166, 94, 13, 204, 322] chunk 348 optimal weight: 10.0000 chunk 165 optimal weight: 30.0000 chunk 227 optimal weight: 20.0000 chunk 334 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 49 optimal weight: 0.9990 chunk 166 optimal weight: 5.9990 chunk 94 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 204 optimal weight: 9.9990 chunk 322 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 120 GLN M 125 GLN N 125 GLN O 125 GLN Q 125 GLN R 125 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.038738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.031734 restraints weight = 191608.556| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 4.05 r_work: 0.2822 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 28992 Z= 0.254 Angle : 0.517 9.052 39768 Z= 0.279 Chirality : 0.044 0.146 5004 Planarity : 0.004 0.046 4986 Dihedral : 4.311 16.912 4266 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.41 % Allowed : 15.78 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.09 (0.13), residues: 3978 helix: 2.65 (0.37), residues: 234 sheet: -0.09 (0.12), residues: 1872 loop : -0.24 (0.15), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG J 133 TYR 0.019 0.001 TYR I 173 PHE 0.014 0.001 PHE G 150 TRP 0.005 0.001 TRP O 54 HIS 0.003 0.001 HIS R 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.25 (28980) covalent geometry : angle 0.51638 / 0.28 (39744) SS BOND : bond 0.00060 / 0.04 ( 12) SS BOND : angle 0.74196 / 0.49 ( 24) hydrogen bonds : bond 0.02937 / 2.01 ( 1062) hydrogen bonds : angle 5.23912 / 3.71 ( 2754) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7956 Ramachandran restraints generated. 3978 Oldfield, 0 Emsley, 3978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7956 Ramachandran restraints generated. 3978 Oldfield, 0 Emsley, 3978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 3438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 216 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 GLN cc_start: 0.6737 (OUTLIER) cc_final: 0.6168 (mm-40) REVERT: A 193 ASP cc_start: 0.8483 (t0) cc_final: 0.8195 (t0) REVERT: B 137 THR cc_start: 0.7005 (OUTLIER) cc_final: 0.6694 (p) REVERT: B 193 ASP cc_start: 0.8492 (t0) cc_final: 0.7861 (p0) REVERT: C 193 ASP cc_start: 0.9045 (t0) cc_final: 0.8074 (p0) REVERT: D 134 GLN cc_start: 0.6675 (OUTLIER) cc_final: 0.6102 (mm-40) REVERT: D 137 THR cc_start: 0.6701 (OUTLIER) cc_final: 0.6382 (p) REVERT: D 193 ASP cc_start: 0.8467 (t0) cc_final: 0.8174 (t0) REVERT: E 137 THR cc_start: 0.6975 (OUTLIER) cc_final: 0.6696 (p) REVERT: E 193 ASP cc_start: 0.8475 (t0) cc_final: 0.7866 (p0) REVERT: E 200 MET cc_start: 0.8160 (mmp) cc_final: 0.7863 (mtt) REVERT: F 193 ASP cc_start: 0.9036 (t0) cc_final: 0.8049 (p0) REVERT: G 164 ASP cc_start: 0.9130 (t0) cc_final: 0.8700 (m-30) REVERT: G 173 TYR cc_start: 0.8922 (OUTLIER) cc_final: 0.8269 (p90) REVERT: G 193 ASP cc_start: 0.8690 (t0) cc_final: 0.8261 (p0) REVERT: G 197 ASN cc_start: 0.9374 (m-40) cc_final: 0.9135 (m-40) REVERT: H 137 THR cc_start: 0.5338 (OUTLIER) cc_final: 0.5128 (p) REVERT: H 164 ASP cc_start: 0.9130 (t70) cc_final: 0.8666 (m-30) REVERT: H 174 MET cc_start: 0.8596 (tpp) cc_final: 0.8246 (tpp) REVERT: H 193 ASP cc_start: 0.8787 (t0) cc_final: 0.8234 (p0) REVERT: I 146 TYR cc_start: 0.9093 (m-80) cc_final: 0.8614 (m-80) REVERT: I 174 MET cc_start: 0.8541 (tpp) cc_final: 0.8202 (tpp) REVERT: I 193 ASP cc_start: 0.8754 (t0) cc_final: 0.8216 (p0) REVERT: I 219 MET cc_start: 0.8036 (mpp) cc_final: 0.7693 (mpp) REVERT: J 173 TYR cc_start: 0.8896 (OUTLIER) cc_final: 0.8215 (p90) REVERT: J 219 MET cc_start: 0.7908 (mpp) cc_final: 0.7455 (mpp) REVERT: K 65 LYS cc_start: 0.9067 (ptpp) cc_final: 0.8561 (ptpp) REVERT: K 137 THR cc_start: 0.5762 (OUTLIER) cc_final: 0.5538 (p) REVERT: K 164 ASP cc_start: 0.9083 (t0) cc_final: 0.8864 (t70) REVERT: K 174 MET cc_start: 0.8503 (tpp) cc_final: 0.8201 (tpp) REVERT: K 193 ASP cc_start: 0.8830 (t0) cc_final: 0.8183 (p0) REVERT: L 174 MET cc_start: 0.8524 (tpp) cc_final: 0.8226 (tpp) REVERT: L 193 ASP cc_start: 0.8798 (t0) cc_final: 0.8237 (p0) REVERT: L 219 MET cc_start: 0.8793 (mtm) cc_final: 0.8574 (mpp) REVERT: M 193 ASP cc_start: 0.8639 (t0) cc_final: 0.8201 (t0) REVERT: N 88 LYS cc_start: 0.9411 (tppt) cc_final: 0.8942 (tppt) REVERT: N 193 ASP cc_start: 0.8610 (t0) cc_final: 0.8269 (t0) REVERT: N 200 MET cc_start: 0.8904 (mmt) cc_final: 0.8583 (mmm) REVERT: O 89 TYR cc_start: 0.9465 (m-80) cc_final: 0.9261 (m-80) REVERT: O 99 LYS cc_start: 0.9511 (tttt) cc_final: 0.9257 (ttpp) REVERT: O 134 GLN cc_start: 0.7598 (mp10) cc_final: 0.7143 (mp-120) REVERT: O 193 ASP cc_start: 0.8546 (t0) cc_final: 0.8063 (t0) REVERT: P 193 ASP cc_start: 0.8603 (t0) cc_final: 0.8167 (t0) REVERT: Q 88 LYS cc_start: 0.9408 (tppt) cc_final: 0.8923 (tppt) REVERT: Q 193 ASP cc_start: 0.8605 (t0) cc_final: 0.8255 (t0) REVERT: R 99 LYS cc_start: 0.9548 (tttt) cc_final: 0.9320 (ttpp) REVERT: R 134 GLN cc_start: 0.7635 (mp10) cc_final: 0.7219 (mp-120) REVERT: R 193 ASP cc_start: 0.8445 (t0) cc_final: 0.8002 (t0) REVERT: R 204 GLU cc_start: 0.8028 (pm20) cc_final: 0.7827 (pm20) outliers start: 38 outliers final: 23 residues processed: 248 average time/residue: 0.1971 time to fit residues: 76.4931 Evaluate side-chains 238 residues out of total 3438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 206 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 122 TYR Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 122 TYR Chi-restraints excluded: chain D residue 88 LYS Chi-restraints excluded: chain D residue 122 TYR Chi-restraints excluded: chain D residue 134 GLN Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain F residue 122 TYR Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 173 TYR Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 173 TYR Chi-restraints excluded: chain K residue 137 THR Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain M residue 122 TYR Chi-restraints excluded: chain M residue 137 THR Chi-restraints excluded: chain M residue 219 MET Chi-restraints excluded: chain N residue 137 THR Chi-restraints excluded: chain O residue 122 TYR Chi-restraints excluded: chain P residue 122 TYR Chi-restraints excluded: chain P residue 137 THR Chi-restraints excluded: chain P residue 219 MET Chi-restraints excluded: chain Q residue 137 THR Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 122 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: [182, 171, 251, 321, 13, 73, 289, 7, 112, 38, 322] chunk 182 optimal weight: 20.0000 chunk 171 optimal weight: 4.9990 chunk 251 optimal weight: 30.0000 chunk 321 optimal weight: 30.0000 chunk 13 optimal weight: 0.7980 chunk 73 optimal weight: 8.9990 chunk 289 optimal weight: 30.0000 chunk 7 optimal weight: 20.0000 chunk 112 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 322 optimal weight: 9.9990 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 120 GLN Q 120 GLN R 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.038924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.031842 restraints weight = 192110.886| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 4.16 r_work: 0.2825 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 28992 Z= 0.209 Angle : 0.497 6.932 39768 Z= 0.267 Chirality : 0.044 0.147 5004 Planarity : 0.004 0.046 4986 Dihedral : 4.195 16.649 4266 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.11 % Allowed : 16.26 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.06 (0.13), residues: 3978 helix: 2.69 (0.37), residues: 234 sheet: -0.08 (0.12), residues: 1872 loop : -0.21 (0.15), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 133 TYR 0.019 0.001 TYR I 173 PHE 0.014 0.001 PHE G 150 TRP 0.004 0.001 TRP A 103 HIS 0.003 0.001 HIS R 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.21 (28980) covalent geometry : angle 0.49689 / 0.27 (39744) SS BOND : bond 0.00066 / 0.04 ( 12) SS BOND : angle 0.60646 / 0.42 ( 24) hydrogen bonds : bond 0.02720 / 1.86 ( 1062) hydrogen bonds : angle 5.16143 / 3.66 ( 2754) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7956 Ramachandran restraints generated. 3978 Oldfield, 0 Emsley, 3978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7956 Ramachandran restraints generated. 3978 Oldfield, 0 Emsley, 3978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 3438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 214 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 GLN cc_start: 0.6862 (OUTLIER) cc_final: 0.6295 (mm-40) REVERT: A 193 ASP cc_start: 0.8533 (t0) cc_final: 0.8206 (t0) REVERT: B 137 THR cc_start: 0.7036 (OUTLIER) cc_final: 0.6716 (p) REVERT: B 193 ASP cc_start: 0.8497 (t0) cc_final: 0.7911 (p0) REVERT: C 193 ASP cc_start: 0.9068 (t0) cc_final: 0.8074 (p0) REVERT: D 134 GLN cc_start: 0.6805 (OUTLIER) cc_final: 0.6230 (mm-40) REVERT: D 137 THR cc_start: 0.6777 (OUTLIER) cc_final: 0.6448 (p) REVERT: D 193 ASP cc_start: 0.8491 (t0) cc_final: 0.8169 (t0) REVERT: E 137 THR cc_start: 0.6969 (OUTLIER) cc_final: 0.6690 (p) REVERT: E 193 ASP cc_start: 0.8475 (t0) cc_final: 0.7891 (p0) REVERT: F 193 ASP cc_start: 0.9066 (t0) cc_final: 0.8037 (p0) REVERT: G 173 TYR cc_start: 0.8777 (OUTLIER) cc_final: 0.8096 (p90) REVERT: G 193 ASP cc_start: 0.8690 (t0) cc_final: 0.8194 (p0) REVERT: G 197 ASN cc_start: 0.9389 (m-40) cc_final: 0.9163 (m-40) REVERT: H 88 LYS cc_start: 0.9587 (ptpt) cc_final: 0.9194 (ptpp) REVERT: H 137 THR cc_start: 0.5809 (OUTLIER) cc_final: 0.5545 (p) REVERT: H 164 ASP cc_start: 0.9143 (t70) cc_final: 0.8663 (m-30) REVERT: H 174 MET cc_start: 0.8588 (tpp) cc_final: 0.8240 (tpp) REVERT: H 193 ASP cc_start: 0.8790 (t0) cc_final: 0.8204 (p0) REVERT: H 204 GLU cc_start: 0.8733 (pm20) cc_final: 0.8201 (pm20) REVERT: I 146 TYR cc_start: 0.9053 (m-80) cc_final: 0.8579 (m-80) REVERT: I 174 MET cc_start: 0.8520 (tpp) cc_final: 0.8163 (tpp) REVERT: I 193 ASP cc_start: 0.8808 (t0) cc_final: 0.8195 (p0) REVERT: I 219 MET cc_start: 0.8061 (mpp) cc_final: 0.7714 (mpp) REVERT: J 173 TYR cc_start: 0.8765 (OUTLIER) cc_final: 0.8034 (p90) REVERT: J 193 ASP cc_start: 0.8717 (t0) cc_final: 0.8246 (p0) REVERT: J 219 MET cc_start: 0.7900 (mpp) cc_final: 0.7448 (mpp) REVERT: K 65 LYS cc_start: 0.9085 (ptpp) cc_final: 0.8572 (ptpp) REVERT: K 137 THR cc_start: 0.5926 (OUTLIER) cc_final: 0.5702 (p) REVERT: K 164 ASP cc_start: 0.9097 (t0) cc_final: 0.8863 (t70) REVERT: K 174 MET cc_start: 0.8489 (tpp) cc_final: 0.8126 (tpp) REVERT: K 193 ASP cc_start: 0.8827 (t0) cc_final: 0.8174 (p0) REVERT: L 174 MET cc_start: 0.8526 (tpp) cc_final: 0.8210 (tpp) REVERT: L 193 ASP cc_start: 0.8813 (t0) cc_final: 0.8228 (p0) REVERT: L 219 MET cc_start: 0.8791 (mtm) cc_final: 0.8573 (mpp) REVERT: M 193 ASP cc_start: 0.8644 (t0) cc_final: 0.8174 (t0) REVERT: N 88 LYS cc_start: 0.9458 (tppt) cc_final: 0.8970 (tppt) REVERT: N 193 ASP cc_start: 0.8627 (t0) cc_final: 0.8284 (t0) REVERT: N 200 MET cc_start: 0.8948 (mmt) cc_final: 0.8693 (mmm) REVERT: O 99 LYS cc_start: 0.9501 (tttt) cc_final: 0.9234 (ttpp) REVERT: O 134 GLN cc_start: 0.7666 (mp10) cc_final: 0.7215 (mp-120) REVERT: O 193 ASP cc_start: 0.8568 (t0) cc_final: 0.8079 (t0) REVERT: P 193 ASP cc_start: 0.8600 (t0) cc_final: 0.8109 (t0) REVERT: Q 88 LYS cc_start: 0.9442 (tppt) cc_final: 0.8938 (tppt) REVERT: Q 193 ASP cc_start: 0.8608 (t0) cc_final: 0.8252 (t0) REVERT: R 88 LYS cc_start: 0.9395 (tppt) cc_final: 0.9036 (tppt) REVERT: R 99 LYS cc_start: 0.9535 (tttt) cc_final: 0.9298 (ttpp) REVERT: R 134 GLN cc_start: 0.7723 (mp10) cc_final: 0.7281 (mp-120) REVERT: R 193 ASP cc_start: 0.8458 (t0) cc_final: 0.8007 (t0) REVERT: R 204 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7759 (pm20) outliers start: 30 outliers final: 19 residues processed: 241 average time/residue: 0.2026 time to fit residues: 76.1004 Evaluate side-chains 230 residues out of total 3438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 201 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 TYR Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 122 TYR Chi-restraints excluded: chain D residue 122 TYR Chi-restraints excluded: chain D residue 134 GLN Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain F residue 122 TYR Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 173 TYR Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 173 TYR Chi-restraints excluded: chain K residue 137 THR Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain M residue 122 TYR Chi-restraints excluded: chain M residue 137 THR Chi-restraints excluded: chain M residue 219 MET Chi-restraints excluded: chain O residue 122 TYR Chi-restraints excluded: chain P residue 122 TYR Chi-restraints excluded: chain P residue 137 THR Chi-restraints excluded: chain P residue 219 MET Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 122 TYR Chi-restraints excluded: chain R residue 204 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: [215, 331, 242, 342, 274, 199, 41, 57, 378, 384, 377] chunk 215 optimal weight: 6.9990 chunk 331 optimal weight: 9.9990 chunk 242 optimal weight: 7.9990 chunk 342 optimal weight: 7.9990 chunk 274 optimal weight: 6.9990 chunk 199 optimal weight: 0.8980 chunk 41 optimal weight: 7.9990 chunk 57 optimal weight: 20.0000 chunk 378 optimal weight: 20.0000 chunk 384 optimal weight: 0.9990 chunk 377 optimal weight: 20.0000 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 119 GLN J 120 GLN ** K 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.038990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.031941 restraints weight = 192007.710| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 4.10 r_work: 0.2832 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 28992 Z= 0.190 Angle : 0.490 7.124 39768 Z= 0.263 Chirality : 0.044 0.144 5004 Planarity : 0.004 0.046 4986 Dihedral : 4.127 17.525 4266 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.26 % Allowed : 16.19 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.03 (0.13), residues: 3978 helix: 2.70 (0.37), residues: 234 sheet: -0.06 (0.12), residues: 1872 loop : -0.20 (0.15), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 133 TYR 0.019 0.001 TYR I 173 PHE 0.013 0.001 PHE G 150 TRP 0.004 0.001 TRP K 103 HIS 0.004 0.001 HIS O 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.19 (28980) covalent geometry : angle 0.48970 / 0.26 (39744) SS BOND : bond 0.00077 / 0.05 ( 12) SS BOND : angle 0.61596 / 0.41 ( 24) hydrogen bonds : bond 0.02654 / 1.82 ( 1062) hydrogen bonds : angle 5.12617 / 3.64 ( 2754) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7956 Ramachandran restraints generated. 3978 Oldfield, 0 Emsley, 3978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7956 Ramachandran restraints generated. 3978 Oldfield, 0 Emsley, 3978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 3438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 211 time to evaluate : 1.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 GLN cc_start: 0.6851 (OUTLIER) cc_final: 0.6294 (mm-40) REVERT: A 193 ASP cc_start: 0.8512 (t0) cc_final: 0.7880 (p0) REVERT: B 137 THR cc_start: 0.6883 (OUTLIER) cc_final: 0.6581 (p) REVERT: B 193 ASP cc_start: 0.8507 (t0) cc_final: 0.7897 (p0) REVERT: C 193 ASP cc_start: 0.9043 (t0) cc_final: 0.8081 (p0) REVERT: D 134 GLN cc_start: 0.6733 (OUTLIER) cc_final: 0.6190 (mm-40) REVERT: D 137 THR cc_start: 0.6468 (OUTLIER) cc_final: 0.6133 (p) REVERT: D 193 ASP cc_start: 0.8471 (t0) cc_final: 0.7850 (p0) REVERT: E 137 THR cc_start: 0.6963 (OUTLIER) cc_final: 0.6661 (p) REVERT: E 193 ASP cc_start: 0.8506 (t0) cc_final: 0.7914 (p0) REVERT: F 193 ASP cc_start: 0.9033 (t0) cc_final: 0.8069 (p0) REVERT: G 139 LYS cc_start: 0.8628 (tppt) cc_final: 0.8402 (tppt) REVERT: G 164 ASP cc_start: 0.9095 (t0) cc_final: 0.8691 (m-30) REVERT: G 173 TYR cc_start: 0.8804 (OUTLIER) cc_final: 0.8121 (p90) REVERT: G 193 ASP cc_start: 0.8720 (t0) cc_final: 0.8284 (p0) REVERT: G 197 ASN cc_start: 0.9388 (m-40) cc_final: 0.9170 (m-40) REVERT: H 137 THR cc_start: 0.5886 (OUTLIER) cc_final: 0.5647 (p) REVERT: H 164 ASP cc_start: 0.9104 (t70) cc_final: 0.8656 (m-30) REVERT: H 174 MET cc_start: 0.8615 (tpp) cc_final: 0.8347 (tpp) REVERT: H 193 ASP cc_start: 0.8763 (t0) cc_final: 0.8141 (p0) REVERT: H 204 GLU cc_start: 0.8691 (pm20) cc_final: 0.8216 (pm20) REVERT: I 146 TYR cc_start: 0.9089 (m-80) cc_final: 0.8631 (m-80) REVERT: I 174 MET cc_start: 0.8536 (tpp) cc_final: 0.8210 (tpp) REVERT: I 193 ASP cc_start: 0.8789 (t0) cc_final: 0.8213 (p0) REVERT: I 219 MET cc_start: 0.8103 (mpp) cc_final: 0.7775 (mpp) REVERT: J 173 TYR cc_start: 0.8785 (OUTLIER) cc_final: 0.8196 (p90) REVERT: J 193 ASP cc_start: 0.8660 (t0) cc_final: 0.8136 (p0) REVERT: J 219 MET cc_start: 0.7925 (mpp) cc_final: 0.7502 (mpp) REVERT: K 137 THR cc_start: 0.5934 (OUTLIER) cc_final: 0.5706 (p) REVERT: K 164 ASP cc_start: 0.9073 (t0) cc_final: 0.8849 (t70) REVERT: K 174 MET cc_start: 0.8598 (tpp) cc_final: 0.8275 (tpp) REVERT: K 193 ASP cc_start: 0.8825 (t0) cc_final: 0.8173 (p0) REVERT: L 146 TYR cc_start: 0.9043 (m-80) cc_final: 0.8419 (m-80) REVERT: L 174 MET cc_start: 0.8505 (tpp) cc_final: 0.8180 (tpp) REVERT: L 193 ASP cc_start: 0.8810 (t0) cc_final: 0.8271 (p0) REVERT: M 193 ASP cc_start: 0.8649 (t0) cc_final: 0.8165 (t0) REVERT: N 88 LYS cc_start: 0.9431 (tppt) cc_final: 0.8951 (tppt) REVERT: N 193 ASP cc_start: 0.8632 (t0) cc_final: 0.8306 (t0) REVERT: N 200 MET cc_start: 0.8830 (mmt) cc_final: 0.8608 (mmm) REVERT: O 99 LYS cc_start: 0.9553 (tttt) cc_final: 0.9270 (ttpp) REVERT: O 134 GLN cc_start: 0.7888 (mp10) cc_final: 0.7459 (mp-120) REVERT: O 193 ASP cc_start: 0.8572 (t0) cc_final: 0.8090 (t0) REVERT: P 193 ASP cc_start: 0.8620 (t0) cc_final: 0.8118 (t0) REVERT: Q 88 LYS cc_start: 0.9415 (tppt) cc_final: 0.8932 (tppt) REVERT: Q 193 ASP cc_start: 0.8614 (t0) cc_final: 0.8269 (t0) REVERT: R 88 LYS cc_start: 0.9373 (tppt) cc_final: 0.9014 (tppt) REVERT: R 99 LYS cc_start: 0.9551 (tttt) cc_final: 0.9310 (ttpp) REVERT: R 134 GLN cc_start: 0.7662 (mp10) cc_final: 0.7223 (mp-120) REVERT: R 193 ASP cc_start: 0.8451 (t0) cc_final: 0.8027 (t0) REVERT: R 204 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7778 (pm20) outliers start: 34 outliers final: 22 residues processed: 242 average time/residue: 0.2013 time to fit residues: 76.0430 Evaluate side-chains 234 residues out of total 3438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 202 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 TYR Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 122 TYR Chi-restraints excluded: chain D residue 122 TYR Chi-restraints excluded: chain D residue 134 GLN Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain F residue 122 TYR Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 173 TYR Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 173 TYR Chi-restraints excluded: chain K residue 137 THR Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain M residue 122 TYR Chi-restraints excluded: chain M residue 137 THR Chi-restraints excluded: chain M residue 219 MET Chi-restraints excluded: chain N residue 137 THR Chi-restraints excluded: chain O residue 122 TYR Chi-restraints excluded: chain P residue 122 TYR Chi-restraints excluded: chain P residue 137 THR Chi-restraints excluded: chain P residue 219 MET Chi-restraints excluded: chain Q residue 137 THR Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 122 TYR Chi-restraints excluded: chain R residue 204 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: [15, 239, 124, 4, 349, 120, 355, 146, 140, 52, 100] chunk 15 optimal weight: 9.9990 chunk 239 optimal weight: 20.0000 chunk 124 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 349 optimal weight: 9.9990 chunk 120 optimal weight: 0.9980 chunk 355 optimal weight: 6.9990 chunk 146 optimal weight: 6.9990 chunk 140 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 119 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.038955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.031925 restraints weight = 189325.108| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 4.07 r_work: 0.2828 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 28992 Z= 0.190 Angle : 0.491 6.892 39768 Z= 0.263 Chirality : 0.044 0.149 5004 Planarity : 0.004 0.047 4986 Dihedral : 4.090 17.671 4266 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.30 % Allowed : 16.15 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.01 (0.13), residues: 3978 helix: 2.71 (0.37), residues: 234 sheet: -0.05 (0.12), residues: 1872 loop : -0.18 (0.15), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 133 TYR 0.018 0.001 TYR I 173 PHE 0.013 0.001 PHE G 150 TRP 0.004 0.001 TRP K 103 HIS 0.003 0.001 HIS O 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.19 (28980) covalent geometry : angle 0.49050 / 0.26 (39744) SS BOND : bond 0.00083 / 0.05 ( 12) SS BOND : angle 0.63213 / 0.43 ( 24) hydrogen bonds : bond 0.02643 / 1.81 ( 1062) hydrogen bonds : angle 5.10707 / 3.63 ( 2754) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7956 Ramachandran restraints generated. 3978 Oldfield, 0 Emsley, 3978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7956 Ramachandran restraints generated. 3978 Oldfield, 0 Emsley, 3978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 3438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 205 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 GLN cc_start: 0.6778 (OUTLIER) cc_final: 0.6250 (mm-40) REVERT: A 193 ASP cc_start: 0.8540 (t0) cc_final: 0.7923 (p0) REVERT: B 137 THR cc_start: 0.6880 (OUTLIER) cc_final: 0.6570 (p) REVERT: B 193 ASP cc_start: 0.8468 (t0) cc_final: 0.7888 (p0) REVERT: C 193 ASP cc_start: 0.9002 (t0) cc_final: 0.8114 (p0) REVERT: D 134 GLN cc_start: 0.6691 (OUTLIER) cc_final: 0.6174 (mm-40) REVERT: D 137 THR cc_start: 0.6146 (OUTLIER) cc_final: 0.5851 (p) REVERT: D 193 ASP cc_start: 0.8496 (t0) cc_final: 0.7875 (p0) REVERT: E 137 THR cc_start: 0.6957 (OUTLIER) cc_final: 0.6651 (p) REVERT: E 193 ASP cc_start: 0.8471 (t0) cc_final: 0.7876 (p0) REVERT: F 193 ASP cc_start: 0.9015 (t0) cc_final: 0.8116 (p0) REVERT: G 139 LYS cc_start: 0.8659 (tppt) cc_final: 0.8453 (tppt) REVERT: G 164 ASP cc_start: 0.9083 (t0) cc_final: 0.8692 (m-30) REVERT: G 173 TYR cc_start: 0.8838 (OUTLIER) cc_final: 0.8049 (p90) REVERT: G 193 ASP cc_start: 0.8699 (t0) cc_final: 0.8287 (p0) REVERT: G 197 ASN cc_start: 0.9384 (m-40) cc_final: 0.9174 (m-40) REVERT: H 137 THR cc_start: 0.5938 (OUTLIER) cc_final: 0.5703 (p) REVERT: H 164 ASP cc_start: 0.9104 (t70) cc_final: 0.8847 (t0) REVERT: H 174 MET cc_start: 0.8575 (tpp) cc_final: 0.8315 (tpp) REVERT: H 193 ASP cc_start: 0.8774 (t0) cc_final: 0.8134 (p0) REVERT: I 146 TYR cc_start: 0.9089 (m-80) cc_final: 0.8633 (m-80) REVERT: I 174 MET cc_start: 0.8530 (tpp) cc_final: 0.8194 (tpp) REVERT: I 193 ASP cc_start: 0.8771 (t0) cc_final: 0.8212 (p0) REVERT: I 219 MET cc_start: 0.8085 (mpp) cc_final: 0.7753 (mpp) REVERT: J 173 TYR cc_start: 0.8805 (OUTLIER) cc_final: 0.8251 (p90) REVERT: J 193 ASP cc_start: 0.8633 (t0) cc_final: 0.8126 (p0) REVERT: J 219 MET cc_start: 0.7963 (mpp) cc_final: 0.7572 (mpp) REVERT: K 65 LYS cc_start: 0.9323 (ptmm) cc_final: 0.8987 (ptpp) REVERT: K 137 THR cc_start: 0.5835 (OUTLIER) cc_final: 0.5620 (p) REVERT: K 164 ASP cc_start: 0.9070 (t0) cc_final: 0.8853 (t70) REVERT: K 174 MET cc_start: 0.8555 (tpp) cc_final: 0.8239 (tpp) REVERT: K 193 ASP cc_start: 0.8813 (t0) cc_final: 0.8189 (p0) REVERT: L 146 TYR cc_start: 0.9053 (m-80) cc_final: 0.8449 (m-80) REVERT: L 174 MET cc_start: 0.8507 (tpp) cc_final: 0.8184 (tpp) REVERT: L 193 ASP cc_start: 0.8802 (t0) cc_final: 0.8272 (p0) REVERT: L 219 MET cc_start: 0.8414 (mpp) cc_final: 0.8000 (pmm) REVERT: M 193 ASP cc_start: 0.8706 (t0) cc_final: 0.8226 (t0) REVERT: N 88 LYS cc_start: 0.9445 (tppt) cc_final: 0.8986 (tppt) REVERT: N 193 ASP cc_start: 0.8618 (t0) cc_final: 0.8287 (t0) REVERT: N 200 MET cc_start: 0.8831 (mmt) cc_final: 0.8572 (mmm) REVERT: O 99 LYS cc_start: 0.9512 (tttt) cc_final: 0.9256 (ttpp) REVERT: O 134 GLN cc_start: 0.7757 (mp10) cc_final: 0.7359 (mp-120) REVERT: O 193 ASP cc_start: 0.8534 (t0) cc_final: 0.8063 (t0) REVERT: P 193 ASP cc_start: 0.8659 (t0) cc_final: 0.8140 (t0) REVERT: Q 88 LYS cc_start: 0.9450 (tppt) cc_final: 0.8982 (tppt) REVERT: Q 193 ASP cc_start: 0.8590 (t0) cc_final: 0.8240 (t0) REVERT: Q 200 MET cc_start: 0.8736 (mmt) cc_final: 0.8493 (mmm) REVERT: R 88 LYS cc_start: 0.9366 (tppt) cc_final: 0.9019 (tppt) REVERT: R 99 LYS cc_start: 0.9552 (tttt) cc_final: 0.9309 (ttpp) REVERT: R 134 GLN cc_start: 0.7818 (mp10) cc_final: 0.7424 (mp-120) REVERT: R 193 ASP cc_start: 0.8435 (t0) cc_final: 0.8028 (t0) REVERT: R 204 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7811 (pm20) outliers start: 35 outliers final: 24 residues processed: 237 average time/residue: 0.2007 time to fit residues: 74.0498 Evaluate side-chains 233 residues out of total 3438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 199 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 TYR Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain C residue 122 TYR Chi-restraints excluded: chain D residue 122 TYR Chi-restraints excluded: chain D residue 134 GLN Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain F residue 120 GLN Chi-restraints excluded: chain F residue 122 TYR Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 173 TYR Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 173 TYR Chi-restraints excluded: chain K residue 137 THR Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain M residue 122 TYR Chi-restraints excluded: chain M residue 137 THR Chi-restraints excluded: chain M residue 219 MET Chi-restraints excluded: chain N residue 137 THR Chi-restraints excluded: chain O residue 122 TYR Chi-restraints excluded: chain P residue 122 TYR Chi-restraints excluded: chain P residue 137 THR Chi-restraints excluded: chain P residue 219 MET Chi-restraints excluded: chain Q residue 137 THR Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 122 TYR Chi-restraints excluded: chain R residue 204 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: [351, 82, 99, 50, 76, 7, 114, 109, 221, 35, 268] chunk 351 optimal weight: 1.9990 chunk 82 optimal weight: 0.0040 chunk 99 optimal weight: 20.0000 chunk 50 optimal weight: 10.0000 chunk 76 optimal weight: 0.3980 chunk 7 optimal weight: 30.0000 chunk 114 optimal weight: 10.0000 chunk 109 optimal weight: 10.0000 chunk 221 optimal weight: 3.9990 chunk 35 optimal weight: 0.0370 chunk 268 optimal weight: 8.9990 overall best weight: 1.2874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.039809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.032797 restraints weight = 187500.531| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 4.00 r_work: 0.2872 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 28992 Z= 0.089 Angle : 0.466 9.293 39768 Z= 0.247 Chirality : 0.044 0.140 5004 Planarity : 0.004 0.045 4986 Dihedral : 3.752 17.262 4266 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.74 % Allowed : 16.48 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.15 (0.13), residues: 3978 helix: 2.60 (0.37), residues: 234 sheet: 0.21 (0.12), residues: 1800 loop : -0.21 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 133 TYR 0.017 0.001 TYR M 173 PHE 0.014 0.001 PHE G 150 TRP 0.005 0.001 TRP H 103 HIS 0.005 0.001 HIS O 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00203 / 0.09 (28980) covalent geometry : angle 0.46616 / 0.25 (39744) SS BOND : bond 0.00108 / 0.07 ( 12) SS BOND : angle 0.44587 / 0.31 ( 24) hydrogen bonds : bond 0.02157 / 1.48 ( 1062) hydrogen bonds : angle 4.85530 / 3.45 ( 2754) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5901.37 seconds wall clock time: 102 minutes 3.28 seconds (6123.28 seconds total)