Starting phenix.real_space_refine on Mon Oct 26 00:47:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9toi_56098/10_2026/9toi_56098.cif Found real_map, /net/cci-nas-00/data/ceres_data/9toi_56098/10_2026/9toi_56098.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9toi_56098/10_2026/9toi_56098.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9toi_56098/10_2026/9toi_56098.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9toi_56098/10_2026/9toi_56098.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9toi_56098/10_2026/9toi_56098.map" } resolution = 3.3 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= 0.003 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 58 5.16 5 C 12006 2.51 5 N 3162 2.21 5 O 3412 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s 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: 18638 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1447 Classifications: {'peptide': 205} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 9, 'TRANS': 195} Chain breaks: 1 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 8, 'GLN:plan1': 1, 'ASN:plan1': 3, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 75 Chain: "B" Number of atoms: 1447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1447 Classifications: {'peptide': 205} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 9, 'TRANS': 195} Chain breaks: 1 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 8, 'GLN:plan1': 1, 'ASN:plan1': 3, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 75 Chain: "C" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1580 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 10, 'TRANS': 211} Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 10, 'GLN:plan1': 1, 'ASN:plan1': 3, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 86 Chain: "D" Number of atoms: 1574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1574 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 10, 'TRANS': 211} Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 10, 'GLN:plan1': 1, 'ASN:plan1': 3, 'ASP:plan': 11, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 91 Chain: "E" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1580 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 10, 'TRANS': 211} Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 10, 'GLN:plan1': 1, 'ASN:plan1': 3, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 86 Chain: "F" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1580 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 10, 'TRANS': 211} Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 10, 'GLN:plan1': 1, 'ASN:plan1': 3, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 86 Chain: "G" Number of atoms: 1562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1562 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 10, 'TRANS': 209} Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 9, 'GLN:plan1': 1, 'ASN:plan1': 3, 'ASP:plan': 11, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 87 Chain: "H" Number of atoms: 1564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1564 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 10, 'TRANS': 208} Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 139 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 9, 'GLN:plan1': 1, 'ASN:plan1': 3, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 82 Chain: "I" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1580 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 10, 'TRANS': 211} Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 10, 'GLN:plan1': 1, 'ASN:plan1': 3, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 86 Chain: "J" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1580 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 10, 'TRANS': 211} Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 10, 'GLN:plan1': 1, 'ASN:plan1': 3, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 86 Chain: "K" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1580 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 10, 'TRANS': 211} Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 10, 'GLN:plan1': 1, 'ASN:plan1': 3, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 86 Chain: "L" Number of atoms: 1564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1564 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 10, 'TRANS': 208} Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 139 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 9, 'GLN:plan1': 1, 'ASN:plan1': 3, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 82 Time building chain proxies: 4.16, per 1000 atoms: 0.22 Number of scatterers: 18638 At special positions: 0 Unit cell: (140.8, 137.5, 110, 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 58 16.00 O 3412 8.00 N 3162 7.00 C 12006 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS H 126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 108 " - pdb=" SG CYS I 126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 108 " - pdb=" SG CYS J 126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 108 " - pdb=" SG CYS K 126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 108 " - pdb=" SG CYS L 126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 108 " - pdb=" SG CYS G 126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.75 Conformation dependent library (CDL) restraints added in 871.1 milliseconds 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4912 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 28 sheets defined 8.5% alpha, 48.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 78 through 82 Processing helix chain 'A' and resid 154 through 167 removed outlier: 4.268A 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: 4.370A 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: 4.439A 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 155 through 167 Processing helix chain 'E' and resid 78 through 82 Processing helix chain 'E' and resid 154 through 167 removed outlier: 4.444A 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 155 through 167 Processing helix chain 'G' and resid 78 through 82 Processing helix chain 'G' and resid 154 through 167 removed outlier: 4.445A 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: 4.436A 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 155 through 167 Processing helix chain 'J' and resid 78 through 82 Processing helix chain 'J' and resid 155 through 167 Processing helix chain 'K' and resid 78 through 82 Processing helix chain 'K' and resid 155 through 167 Processing helix chain 'L' and resid 78 through 82 Processing helix chain 'L' and resid 154 through 167 removed outlier: 4.359A pdb=" N ASP L 158 " --> pdb=" O ASN L 154 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 109 through 115 removed outlier: 6.784A pdb=" N THR A 147 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE A 112 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ALA A 145 " --> pdb=" O ILE A 112 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LYS A 114 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N SER A 143 " --> pdb=" O LYS A 114 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N SER A 211 " --> pdb=" O SER A 191 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N SER A 191 " --> pdb=" O SER A 211 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ASP A 213 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N VAL A 189 " --> pdb=" O ASP A 213 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N LYS A 215 " --> pdb=" O SER A 187 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N SER A 187 " --> pdb=" O LYS A 215 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ALA A 171 " --> pdb=" O GLU A 12 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N SER A 102 " --> pdb=" O ARG A 13 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ARG A 15 " --> pdb=" O ILE A 100 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ILE A 100 " --> pdb=" O ARG A 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 109 through 115 removed outlier: 6.784A pdb=" N THR A 147 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE A 112 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ALA A 145 " --> pdb=" O ILE A 112 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LYS A 114 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N SER A 143 " --> pdb=" O LYS A 114 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 202 through 219 current: chain 'A' and resid 61 through 67 removed outlier: 6.734A pdb=" N THR A 74 " --> pdb=" O LYS A 65 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N VAL A 67 " --> pdb=" O SER A 72 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N SER A 72 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ALA A 24 " --> pdb=" O THR A 34 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA A 24 " --> pdb=" O GLY A 93 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N GLY A 93 " --> pdb=" O ALA A 24 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 109 through 115 removed outlier: 6.664A pdb=" N THR B 147 " --> pdb=" O SER B 110 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ILE B 112 " --> pdb=" O ALA B 145 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ALA B 145 " --> pdb=" O ILE B 112 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LYS B 114 " --> pdb=" O SER B 143 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N SER B 143 " --> pdb=" O LYS B 114 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N SER B 187 " --> pdb=" O ASP B 213 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LYS B 215 " --> pdb=" O ALA B 185 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ALA B 185 " --> pdb=" O LYS B 215 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N VAL B 217 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ILE B 183 " --> pdb=" O VAL B 217 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ALA B 171 " --> pdb=" O GLU B 12 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N SER B 102 " --> pdb=" O ARG B 13 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ARG B 15 " --> pdb=" O ILE B 100 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE B 100 " --> pdb=" O ARG B 15 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N THR B 96 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N PHE B 46 " --> pdb=" O ILE B 100 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N THR B 74 " --> pdb=" O LYS B 65 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N VAL B 67 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N SER B 72 " --> pdb=" O VAL B 67 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ALA B 24 " --> pdb=" O THR B 34 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 119 through 120 removed outlier: 3.578A pdb=" N PHE B 138 " --> pdb=" O GLN B 120 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 109 through 115 removed outlier: 6.763A pdb=" N THR C 147 " --> pdb=" O SER C 110 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ILE C 112 " --> pdb=" O ALA C 145 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ALA C 145 " --> pdb=" O ILE C 112 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LYS C 114 " --> pdb=" O SER C 143 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N SER C 143 " --> pdb=" O LYS C 114 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N SER C 187 " --> pdb=" O ASP C 213 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LYS C 215 " --> pdb=" O ALA C 185 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ALA C 185 " --> pdb=" O LYS C 215 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N VAL C 217 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ILE C 183 " --> pdb=" O VAL C 217 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ALA C 171 " --> pdb=" O GLU C 12 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N SER C 102 " --> pdb=" O ARG C 13 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ARG C 15 " --> pdb=" O ILE C 100 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ILE C 100 " --> pdb=" O ARG C 15 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU C 51 " --> pdb=" O THR C 96 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N VAL C 98 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N VAL C 49 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE C 100 " --> pdb=" O VAL C 47 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL C 47 " --> pdb=" O ILE C 100 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N THR C 74 " --> pdb=" O LYS C 65 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N VAL C 67 " --> pdb=" O SER C 72 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N SER C 72 " --> pdb=" O VAL C 67 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ALA C 24 " --> pdb=" O THR C 34 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA C 24 " --> pdb=" O GLY C 93 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N GLY C 93 " --> pdb=" O ALA C 24 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 119 through 124 removed outlier: 6.708A 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 116 removed outlier: 6.746A pdb=" N THR D 147 " --> pdb=" O SER D 110 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ILE D 112 " --> pdb=" O ALA D 145 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ALA D 145 " --> pdb=" O ILE D 112 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N LYS D 114 " --> pdb=" O SER D 143 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N SER D 143 " --> pdb=" O LYS D 114 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N THR D 142 " --> pdb=" O LEU D 212 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N SER D 187 " --> pdb=" O ASP D 213 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LYS D 215 " --> pdb=" O ALA D 185 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ALA D 185 " --> pdb=" O LYS D 215 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N VAL D 217 " --> pdb=" O ILE D 183 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ILE D 183 " --> pdb=" O VAL D 217 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA D 171 " --> pdb=" O GLU D 12 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N SER D 102 " --> pdb=" O ARG D 13 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ARG D 15 " --> pdb=" O ILE D 100 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE D 100 " --> pdb=" O ARG D 15 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ALA D 94 " --> pdb=" O SER D 52 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N SER D 52 " --> pdb=" O ALA D 94 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N THR D 96 " --> pdb=" O THR D 50 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N PHE D 46 " --> pdb=" O ILE D 100 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N THR D 74 " --> pdb=" O LYS D 65 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N VAL D 67 " --> pdb=" O SER D 72 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N SER D 72 " --> pdb=" O VAL D 67 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ALA D 24 " --> pdb=" O THR D 34 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA D 24 " --> pdb=" O GLY D 93 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N GLY D 93 " --> pdb=" O ALA D 24 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 119 through 124 removed outlier: 4.859A 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 116 removed outlier: 6.805A pdb=" N THR E 147 " --> pdb=" O SER E 110 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ILE E 112 " --> pdb=" O ALA E 145 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ALA E 145 " --> pdb=" O ILE E 112 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LYS E 114 " --> pdb=" O SER E 143 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N SER E 143 " --> pdb=" O LYS E 114 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N THR E 142 " --> pdb=" O LEU E 212 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N SER E 211 " --> pdb=" O SER E 191 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N SER E 191 " --> pdb=" O SER E 211 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ASP E 213 " --> pdb=" O VAL E 189 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N VAL E 189 " --> pdb=" O ASP E 213 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N LYS E 215 " --> pdb=" O SER E 187 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N SER E 187 " --> pdb=" O LYS E 215 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ALA E 171 " --> pdb=" O GLU E 12 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N SER E 102 " --> pdb=" O ARG E 13 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ARG E 15 " --> pdb=" O ILE E 100 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE E 100 " --> pdb=" O ARG E 15 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU E 51 " --> pdb=" O THR E 96 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N VAL E 98 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N VAL E 49 " --> pdb=" O VAL E 98 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE E 100 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL E 47 " --> pdb=" O ILE E 100 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N THR E 74 " --> pdb=" O LYS E 65 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N VAL E 67 " --> pdb=" O SER E 72 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N SER E 72 " --> pdb=" O VAL E 67 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ALA E 24 " --> pdb=" O THR E 34 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA E 24 " --> pdb=" O GLY E 93 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLY E 93 " --> pdb=" O ALA E 24 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 119 through 124 removed outlier: 4.905A 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 116 removed outlier: 6.827A pdb=" N THR F 147 " --> pdb=" O SER F 110 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ILE F 112 " --> pdb=" O ALA F 145 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ALA F 145 " --> pdb=" O ILE F 112 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N LYS F 114 " --> pdb=" O SER F 143 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N SER F 143 " --> pdb=" O LYS F 114 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N THR F 142 " --> pdb=" O LEU F 212 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N SER F 187 " --> pdb=" O ASP F 213 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LYS F 215 " --> pdb=" O ALA F 185 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ALA F 185 " --> pdb=" O LYS F 215 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N VAL F 217 " --> pdb=" O ILE F 183 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ILE F 183 " --> pdb=" O VAL F 217 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ALA F 171 " --> pdb=" O GLU F 12 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N SER F 102 " --> pdb=" O ARG F 13 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ARG F 15 " --> pdb=" O ILE F 100 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ILE F 100 " --> pdb=" O ARG F 15 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ALA F 94 " --> pdb=" O SER F 52 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N SER F 52 " --> pdb=" O ALA F 94 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N THR F 96 " --> pdb=" O THR F 50 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N PHE F 46 " --> pdb=" O ILE F 100 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N THR F 74 " --> pdb=" O LYS F 65 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N VAL F 67 " --> pdb=" O SER F 72 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N SER F 72 " --> pdb=" O VAL F 67 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ALA F 24 " --> pdb=" O THR F 34 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA F 24 " --> pdb=" O GLY F 93 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N GLY F 93 " --> pdb=" O ALA F 24 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 119 through 124 removed outlier: 4.568A 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: 6.782A pdb=" N THR G 147 " --> pdb=" O SER G 110 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ILE G 112 " --> pdb=" O ALA G 145 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ALA G 145 " --> pdb=" O ILE G 112 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LYS G 114 " --> pdb=" O SER G 143 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N SER G 143 " --> pdb=" O LYS G 114 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N SER G 187 " --> pdb=" O ASP G 213 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LYS G 215 " --> pdb=" O ALA G 185 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA G 185 " --> pdb=" O LYS G 215 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N VAL G 217 " --> pdb=" O ILE G 183 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE G 183 " --> pdb=" O VAL G 217 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA G 171 " --> pdb=" O GLU G 12 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N SER G 102 " --> pdb=" O ARG G 13 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ARG G 15 " --> pdb=" O ILE G 100 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE G 100 " --> pdb=" O ARG G 15 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU G 51 " --> pdb=" O THR G 96 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N VAL G 98 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N VAL G 49 " --> pdb=" O VAL G 98 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE G 100 " --> pdb=" O VAL G 47 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL G 47 " --> pdb=" O ILE G 100 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N THR G 74 " --> pdb=" O LYS G 65 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N VAL G 67 " --> pdb=" O SER G 72 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N SER G 72 " --> pdb=" O VAL G 67 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ALA G 24 " --> pdb=" O THR G 34 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA G 24 " --> pdb=" O GLY G 93 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N GLY G 93 " --> pdb=" O ALA G 24 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 119 through 124 removed outlier: 4.604A pdb=" N GLN G 120 " --> pdb=" O THR G 137 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 20 through 22 removed outlier: 3.784A pdb=" N GLU H 51 " --> pdb=" O THR H 96 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N VAL H 98 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N VAL H 49 " --> pdb=" O VAL H 98 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE H 100 " --> pdb=" O VAL H 47 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL H 47 " --> pdb=" O ILE H 100 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N THR H 74 " --> pdb=" O LYS H 65 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N VAL H 67 " --> pdb=" O SER H 72 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N SER H 72 " --> pdb=" O VAL H 67 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 20 through 22 removed outlier: 6.838A pdb=" N ILE H 100 " --> pdb=" O ARG H 15 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ARG H 15 " --> pdb=" O ILE H 100 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N SER H 102 " --> pdb=" O ARG H 13 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ALA H 171 " --> pdb=" O GLU H 12 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ILE H 183 " --> pdb=" O VAL H 217 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N VAL H 217 " --> pdb=" O ILE H 183 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ALA H 185 " --> pdb=" O LYS H 215 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LYS H 215 " --> pdb=" O ALA H 185 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N SER H 187 " --> pdb=" O ASP H 213 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N SER H 143 " --> pdb=" O LYS H 114 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LYS H 114 " --> pdb=" O SER H 143 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ALA H 145 " --> pdb=" O ILE H 112 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ILE H 112 " --> pdb=" O ALA H 145 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N THR H 147 " --> pdb=" O SER H 110 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 119 through 124 removed outlier: 4.863A pdb=" N GLN H 120 " --> pdb=" O THR H 137 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 109 through 116 removed outlier: 6.801A pdb=" N THR I 147 " --> pdb=" O SER I 110 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ILE I 112 " --> pdb=" O ALA I 145 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ALA I 145 " --> pdb=" O ILE I 112 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LYS I 114 " --> pdb=" O SER I 143 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N SER I 143 " --> pdb=" O LYS I 114 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N THR I 142 " --> pdb=" O LEU I 212 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N SER I 187 " --> pdb=" O ASP I 213 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N LYS I 215 " --> pdb=" O ALA I 185 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ALA I 185 " --> pdb=" O LYS I 215 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N VAL I 217 " --> pdb=" O ILE I 183 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ILE I 183 " --> pdb=" O VAL I 217 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ALA I 171 " --> pdb=" O GLU I 12 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N SER I 102 " --> pdb=" O ARG I 13 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ARG I 15 " --> pdb=" O ILE I 100 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE I 100 " --> pdb=" O ARG I 15 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU I 51 " --> pdb=" O THR I 96 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N VAL I 98 " --> pdb=" O VAL I 49 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N VAL I 49 " --> pdb=" O VAL I 98 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE I 100 " --> pdb=" O VAL I 47 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL I 47 " --> pdb=" O ILE I 100 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N THR I 74 " --> pdb=" O LYS I 65 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N VAL I 67 " --> pdb=" O SER I 72 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N SER I 72 " --> pdb=" O VAL I 67 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ALA I 24 " --> pdb=" O THR I 34 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA I 24 " --> pdb=" O GLY I 93 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N GLY I 93 " --> pdb=" O ALA I 24 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 119 through 124 removed outlier: 6.853A pdb=" N GLN I 120 " --> pdb=" O THR I 137 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 103 through 105 removed outlier: 6.720A pdb=" N ALA J 171 " --> pdb=" O GLU J 12 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL J 189 " --> pdb=" O SER J 211 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER J 211 " --> pdb=" O VAL J 189 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N SER J 143 " --> pdb=" O LYS J 114 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LYS J 114 " --> pdb=" O SER J 143 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ALA J 145 " --> pdb=" O ILE J 112 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ILE J 112 " --> pdb=" O ALA J 145 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N THR J 147 " --> pdb=" O SER J 110 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 103 through 105 removed outlier: 6.720A pdb=" N ALA J 171 " --> pdb=" O GLU J 12 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 20 through 25 removed outlier: 4.406A pdb=" N ALA J 24 " --> pdb=" O THR J 34 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N SER J 72 " --> pdb=" O VAL J 67 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N VAL J 67 " --> pdb=" O SER J 72 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N THR J 74 " --> pdb=" O LYS J 65 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ARG J 60 " --> pdb=" O VAL J 49 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N VAL J 49 " --> pdb=" O VAL J 98 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N VAL J 98 " --> pdb=" O VAL J 49 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU J 51 " --> pdb=" O THR J 96 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N GLY J 93 " --> pdb=" O ALA J 24 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA J 24 " --> pdb=" O GLY J 93 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 119 through 124 removed outlier: 4.807A pdb=" N GLN J 120 " --> pdb=" O THR J 137 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 103 through 105 removed outlier: 6.489A pdb=" N ALA K 171 " --> pdb=" O GLU K 12 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ILE K 183 " --> pdb=" O VAL K 217 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N VAL K 217 " --> pdb=" O ILE K 183 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ALA K 185 " --> pdb=" O LYS K 215 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N LYS K 215 " --> pdb=" O ALA K 185 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N SER K 187 " --> pdb=" O ASP K 213 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP K 111 " --> pdb=" O THR K 147 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ASP K 149 " --> pdb=" O VAL K 109 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N VAL K 109 " --> pdb=" O ASP K 149 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 20 through 25 removed outlier: 4.496A pdb=" N ALA K 24 " --> pdb=" O THR K 34 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N SER K 72 " --> pdb=" O VAL K 67 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N VAL K 67 " --> pdb=" O SER K 72 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N THR K 74 " --> pdb=" O LYS K 65 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N VAL K 49 " --> pdb=" O VAL K 98 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N VAL K 98 " --> pdb=" O VAL K 49 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU K 51 " --> pdb=" O THR K 96 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLY K 93 " --> pdb=" O ALA K 24 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA K 24 " --> pdb=" O GLY K 93 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 119 through 124 removed outlier: 4.963A pdb=" N GLN K 120 " --> pdb=" O THR K 137 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 109 through 116 removed outlier: 6.769A pdb=" N THR L 147 " --> pdb=" O SER L 110 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ILE L 112 " --> pdb=" O ALA L 145 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA L 145 " --> pdb=" O ILE L 112 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N LYS L 114 " --> pdb=" O SER L 143 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N SER L 143 " --> pdb=" O LYS L 114 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N THR L 142 " --> pdb=" O LEU L 212 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N SER L 211 " --> pdb=" O SER L 191 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N SER L 191 " --> pdb=" O SER L 211 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ASP L 213 " --> pdb=" O VAL L 189 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N VAL L 189 " --> pdb=" O ASP L 213 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N LYS L 215 " --> pdb=" O SER L 187 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N SER L 187 " --> pdb=" O LYS L 215 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ALA L 171 " --> pdb=" O GLU L 12 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N SER L 102 " --> pdb=" O ARG L 13 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ARG L 15 " --> pdb=" O ILE L 100 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ILE L 100 " --> pdb=" O ARG L 15 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU L 51 " --> pdb=" O THR L 96 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N VAL L 98 " --> pdb=" O VAL L 49 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N VAL L 49 " --> pdb=" O VAL L 98 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE L 100 " --> pdb=" O VAL L 47 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL L 47 " --> pdb=" O ILE L 100 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N THR L 74 " --> pdb=" O LYS L 65 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N VAL L 67 " --> pdb=" O SER L 72 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N SER L 72 " --> pdb=" O VAL L 67 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ALA L 24 " --> pdb=" O THR L 34 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 119 through 124 removed outlier: 4.777A pdb=" N GLN L 120 " --> pdb=" O THR L 137 " (cutoff:3.500A) 686 hydrogen bonds defined for protein. 1812 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: 3.74 Time building geometry restraints manager: 2.24 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: 5944 1.35 - 1.47: 4656 1.47 - 1.59: 8310 1.59 - 1.71: 0 1.71 - 1.83: 94 Bond restraints: 19004 Sorted by residual: bond pdb=" N SER I 128 " pdb=" CA SER I 128 " ideal model delta sigma weight residual 1.458 1.473 -0.015 1.77e-02 3.19e+03 7.07e-01 bond pdb=" CA CYS E 108 " pdb=" C CYS E 108 " ideal model delta sigma weight residual 1.531 1.522 0.009 1.08e-02 8.57e+03 6.83e-01 bond pdb=" N SER J 211 " pdb=" CA SER J 211 " ideal model delta sigma weight residual 1.461 1.451 0.010 1.30e-02 5.92e+03 6.46e-01 bond pdb=" CB CYS A 108 " pdb=" SG CYS A 108 " ideal model delta sigma weight residual 1.808 1.833 -0.025 3.30e-02 9.18e+02 5.93e-01 bond pdb=" CB LYS K 8 " pdb=" CG LYS K 8 " ideal model delta sigma weight residual 1.520 1.542 -0.022 3.00e-02 1.11e+03 5.20e-01 ... (remaining 18999 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 25508 1.29 - 2.58: 442 2.58 - 3.87: 77 3.87 - 5.16: 17 5.16 - 6.45: 5 Bond angle restraints: 26049 Sorted by residual: angle pdb=" C MET F 200 " pdb=" N ASN F 201 " pdb=" CA ASN F 201 " ideal model delta sigma weight residual 121.54 126.19 -4.65 1.91e+00 2.74e-01 5.92e+00 angle pdb=" N CYS E 108 " pdb=" CA CYS E 108 " pdb=" C CYS E 108 " ideal model delta sigma weight residual 111.02 113.82 -2.80 1.25e+00 6.40e-01 5.03e+00 angle pdb=" CA CYS E 108 " pdb=" C CYS E 108 " pdb=" N VAL E 109 " ideal model delta sigma weight residual 114.17 117.60 -3.43 1.55e+00 4.16e-01 4.90e+00 angle pdb=" CA CYS H 108 " pdb=" C CYS H 108 " pdb=" N VAL H 109 " ideal model delta sigma weight residual 114.17 117.21 -3.04 1.45e+00 4.76e-01 4.40e+00 angle pdb=" N THR L 137 " pdb=" CA THR L 137 " pdb=" C THR L 137 " ideal model delta sigma weight residual 110.80 106.38 4.42 2.13e+00 2.20e-01 4.30e+00 ... (remaining 26044 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.92: 10516 16.92 - 33.84: 566 33.84 - 50.76: 104 50.76 - 67.69: 19 67.69 - 84.61: 16 Dihedral angle restraints: 11221 sinusoidal: 3607 harmonic: 7614 Sorted by residual: dihedral pdb=" CA CYS E 108 " pdb=" C CYS E 108 " pdb=" N VAL E 109 " pdb=" CA VAL E 109 " ideal model delta harmonic sigma weight residual 180.00 157.14 22.86 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA LEU I 127 " pdb=" C LEU I 127 " pdb=" N SER I 128 " pdb=" CA SER I 128 " ideal model delta harmonic sigma weight residual 180.00 -160.96 -19.04 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA ASN A 59 " pdb=" CB ASN A 59 " pdb=" CG ASN A 59 " pdb=" OD1 ASN A 59 " ideal model delta sinusoidal sigma weight residual -90.00 -161.72 71.72 2 2.00e+01 2.50e-03 1.08e+01 ... (remaining 11218 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1920 0.028 - 0.055: 815 0.055 - 0.083: 172 0.083 - 0.111: 242 0.111 - 0.139: 124 Chirality restraints: 3273 Sorted by residual: chirality pdb=" CA ILE G 135 " pdb=" N ILE G 135 " pdb=" C ILE G 135 " pdb=" CB ILE G 135 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.80e-01 chirality pdb=" CA ILE J 135 " pdb=" N ILE J 135 " pdb=" C ILE J 135 " pdb=" CB ILE J 135 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.73e-01 chirality pdb=" CB ILE K 25 " pdb=" CA ILE K 25 " pdb=" CG1 ILE K 25 " pdb=" CG2 ILE K 25 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.14 2.00e-01 2.50e+01 4.69e-01 ... (remaining 3270 not shown) Planarity restraints: 3264 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE K 210 " -0.008 2.00e-02 2.50e+03 1.55e-02 2.40e+00 pdb=" C ILE K 210 " 0.027 2.00e-02 2.50e+03 pdb=" O ILE K 210 " -0.010 2.00e-02 2.50e+03 pdb=" N SER K 211 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR H 137 " -0.007 2.00e-02 2.50e+03 1.50e-02 2.25e+00 pdb=" C THR H 137 " 0.026 2.00e-02 2.50e+03 pdb=" O THR H 137 " -0.010 2.00e-02 2.50e+03 pdb=" N PHE H 138 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE G 106 " -0.024 5.00e-02 4.00e+02 3.61e-02 2.09e+00 pdb=" N PRO G 107 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO G 107 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO G 107 " -0.020 5.00e-02 4.00e+02 ... (remaining 3261 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 9177 2.98 - 3.46: 17419 3.46 - 3.94: 29791 3.94 - 4.42: 31869 4.42 - 4.90: 57376 Nonbonded interactions: 145632 Sorted by model distance: nonbonded pdb=" O GLU G 12 " pdb=" OH TYR G 163 " model vdw 2.496 3.040 nonbonded pdb=" O ASN D 197 " pdb=" OD1 ASN D 197 " model vdw 2.502 3.040 nonbonded pdb=" NE1 TRP F 54 " pdb=" O PRO F 90 " model vdw 2.568 3.120 nonbonded pdb=" O ASP G 193 " pdb=" OG1 THR G 206 " model vdw 2.580 3.040 nonbonded pdb=" N ASP D 130 " pdb=" OD1 ASP D 130 " model vdw 2.581 3.120 ... (remaining 145627 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 2 through 220) selection = (chain 'B' and resid 2 through 220) selection = (chain 'C' and (resid 2 through 121 or resid 137 through 220)) selection = (chain 'D' and (resid 2 through 121 or resid 137 through 220)) selection = (chain 'E' and (resid 2 through 121 or resid 137 through 220)) selection = (chain 'F' and (resid 2 through 121 or resid 137 through 220)) selection = (chain 'G' and (resid 2 through 121 or resid 137 through 220)) selection = (chain 'H' and (resid 2 through 121 or resid 137 through 220)) selection = (chain 'I' and (resid 2 through 121 or resid 137 through 220)) selection = (chain 'J' and (resid 2 through 121 or resid 137 through 220)) selection = (chain 'K' and (resid 2 through 121 or resid 137 through 220)) selection = (chain 'L' and (resid 2 through 121 or resid 137 through 220)) } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.320 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: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.520 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.040 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 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 : 0.002 0.025 19010 Z= 0.089 Angle : 0.472 6.452 26061 Z= 0.252 Chirality : 0.045 0.139 3273 Planarity : 0.004 0.036 3264 Dihedral : 11.845 84.607 6291 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.57 % Allowed : 10.34 % Favored : 88.08 % 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: 0.44 (0.16), residues: 2594 helix: 1.65 (0.45), residues: 156 sheet: 0.46 (0.14), residues: 1166 loop : 0.07 (0.16), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 15 TYR 0.013 0.001 TYR L 122 PHE 0.009 0.001 PHE B 150 TRP 0.006 0.001 TRP D 54 HIS 0.003 0.001 HIS E 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00180 / 0.09 (19004) covalent geometry : angle 0.47156 / 0.25 (26049) SS BOND : bond 0.00170 / 0.10 ( 6) SS BOND : angle 1.02029 / 0.52 ( 12) hydrogen bonds : bond 0.15306 / 10.85 ( 662) hydrogen bonds : angle 7.95417 / 5.68 ( 1812) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 443 time to evaluate : 0.769 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 8 LYS cc_start: 0.8857 (mtpp) cc_final: 0.8595 (mtpp) REVERT: A 105 GLU cc_start: 0.8546 (tt0) cc_final: 0.8243 (tt0) REVERT: A 121 TYR cc_start: 0.7235 (m-80) cc_final: 0.6590 (t80) REVERT: A 154 ASN cc_start: 0.8990 (t0) cc_final: 0.8784 (t0) REVERT: A 193 ASP cc_start: 0.8399 (t0) cc_final: 0.8121 (t0) REVERT: B 121 TYR cc_start: 0.5110 (OUTLIER) cc_final: 0.4688 (m-80) REVERT: C 89 TYR cc_start: 0.9103 (m-10) cc_final: 0.8722 (m-10) REVERT: D 134 GLN cc_start: 0.8454 (mt0) cc_final: 0.7933 (mm-40) REVERT: D 138 PHE cc_start: 0.8805 (p90) cc_final: 0.8357 (p90) REVERT: G 85 ASN cc_start: 0.8901 (t0) cc_final: 0.8679 (t0) REVERT: H 88 LYS cc_start: 0.8997 (mtpp) cc_final: 0.8770 (pttm) REVERT: H 144 ILE cc_start: 0.9305 (mt) cc_final: 0.9071 (tt) REVERT: J 173 TYR cc_start: 0.8744 (p90) cc_final: 0.8512 (p90) REVERT: J 219 MET cc_start: 0.8053 (mtm) cc_final: 0.7700 (mpp) REVERT: L 193 ASP cc_start: 0.8702 (t0) cc_final: 0.8105 (t0) outliers start: 28 outliers final: 9 residues processed: 463 average time/residue: 0.1662 time to fit residues: 110.2250 Evaluate side-chains 334 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 324 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain B residue 121 TYR Chi-restraints excluded: chain D residue 108 CYS Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain K residue 49 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: [197, 215, 20, 132, 248, 207, 155, 244, 183, 111, 71] chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.2980 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 9.9990 chunk 111 optimal weight: 9.9990 chunk 71 optimal weight: 9.9990 overall best weight: 4.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 GLN B 220 GLN C 125 GLN D 120 GLN D 125 GLN F 125 GLN G 59 ASN G 87 ASN H 220 GLN I 30 ASN I 120 GLN ** I 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.059452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.047429 restraints weight = 72667.721| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 3.84 r_work: 0.2679 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 19010 Z= 0.227 Angle : 0.543 8.076 26061 Z= 0.288 Chirality : 0.045 0.176 3273 Planarity : 0.004 0.041 3264 Dihedral : 4.735 51.075 2803 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.54 % Allowed : 13.94 % Favored : 82.52 % 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: 0.50 (0.16), residues: 2594 helix: 1.89 (0.45), residues: 156 sheet: 0.42 (0.14), residues: 1145 loop : 0.20 (0.17), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 60 TYR 0.021 0.002 TYR J 173 PHE 0.023 0.002 PHE H 192 TRP 0.009 0.001 TRP L 54 HIS 0.004 0.001 HIS A 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.23 (19004) covalent geometry : angle 0.54239 / 0.29 (26049) SS BOND : bond 0.00225 / 0.13 ( 6) SS BOND : angle 1.19491 / 0.61 ( 12) hydrogen bonds : bond 0.03502 / 2.51 ( 662) hydrogen bonds : angle 5.47351 / 3.92 ( 1812) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 331 time to evaluate : 0.717 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: A 8 LYS cc_start: 0.8954 (mtpp) cc_final: 0.8615 (mtpp) REVERT: A 121 TYR cc_start: 0.7346 (m-80) cc_final: 0.6452 (t80) REVERT: A 154 ASN cc_start: 0.9139 (t0) cc_final: 0.8910 (t0) REVERT: A 193 ASP cc_start: 0.8741 (t0) cc_final: 0.8403 (t0) REVERT: B 193 ASP cc_start: 0.9335 (t0) cc_final: 0.8587 (p0) REVERT: C 88 LYS cc_start: 0.9638 (ttmm) cc_final: 0.9366 (ttpp) REVERT: C 121 TYR cc_start: 0.9329 (m-80) cc_final: 0.8986 (m-80) REVERT: D 134 GLN cc_start: 0.8944 (mt0) cc_final: 0.8242 (mm-40) REVERT: D 138 PHE cc_start: 0.9217 (p90) cc_final: 0.8419 (p90) REVERT: D 204 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8407 (mt-10) REVERT: E 131 ARG cc_start: 0.8577 (ptm-80) cc_final: 0.7950 (ptm-80) REVERT: E 134 GLN cc_start: 0.9263 (mm110) cc_final: 0.8955 (mm-40) REVERT: E 204 GLU cc_start: 0.8297 (mm-30) cc_final: 0.8051 (mm-30) REVERT: F 133 ARG cc_start: 0.8770 (ptp90) cc_final: 0.8465 (ptp90) REVERT: F 178 LYS cc_start: 0.9353 (mmmt) cc_final: 0.9104 (mtmt) REVERT: G 8 LYS cc_start: 0.6655 (mmpt) cc_final: 0.6077 (mmpt) REVERT: G 60 ARG cc_start: 0.8929 (mmm-85) cc_final: 0.8590 (mmm-85) REVERT: G 85 ASN cc_start: 0.9182 (t0) cc_final: 0.8715 (t0) REVERT: G 124 LYS cc_start: 0.9171 (OUTLIER) cc_final: 0.8718 (ptmm) REVERT: G 134 GLN cc_start: 0.8743 (mp10) cc_final: 0.8443 (mp10) REVERT: G 163 TYR cc_start: 0.8931 (m-10) cc_final: 0.8531 (m-80) REVERT: H 60 ARG cc_start: 0.9056 (mmm-85) cc_final: 0.8691 (mmm-85) REVERT: H 122 TYR cc_start: 0.9395 (t80) cc_final: 0.9045 (t80) REVERT: H 193 ASP cc_start: 0.8359 (t0) cc_final: 0.8122 (p0) REVERT: I 88 LYS cc_start: 0.9544 (ptmt) cc_final: 0.9164 (ptmt) REVERT: I 89 TYR cc_start: 0.9043 (m-80) cc_final: 0.8632 (m-10) REVERT: I 124 LYS cc_start: 0.9168 (ptmm) cc_final: 0.8708 (pttt) REVERT: I 150 PHE cc_start: 0.8919 (t80) cc_final: 0.8531 (t80) REVERT: I 178 LYS cc_start: 0.9085 (mtmt) cc_final: 0.8523 (pttt) REVERT: J 134 GLN cc_start: 0.9408 (mt0) cc_final: 0.9164 (mm-40) REVERT: J 174 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.8166 (tmm) REVERT: J 219 MET cc_start: 0.8702 (mtm) cc_final: 0.8129 (mtm) REVERT: K 105 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7792 (tm-30) REVERT: K 173 TYR cc_start: 0.7888 (p90) cc_final: 0.7617 (p90) REVERT: K 193 ASP cc_start: 0.8892 (p0) cc_final: 0.8445 (p0) REVERT: K 219 MET cc_start: 0.8254 (mpp) cc_final: 0.7700 (mpp) REVERT: L 89 TYR cc_start: 0.9130 (m-80) cc_final: 0.8861 (m-80) REVERT: L 193 ASP cc_start: 0.8779 (t0) cc_final: 0.8525 (t0) REVERT: L 197 ASN cc_start: 0.9160 (t0) cc_final: 0.8526 (t0) REVERT: L 204 GLU cc_start: 0.8586 (mm-30) cc_final: 0.8249 (mm-30) outliers start: 63 outliers final: 42 residues processed: 379 average time/residue: 0.1600 time to fit residues: 87.7053 Evaluate side-chains 342 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 298 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 108 CYS Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 108 CYS Chi-restraints excluded: chain D residue 126 CYS Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain F residue 59 ASN Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 124 LYS Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 135 ILE Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain J residue 61 VAL Chi-restraints excluded: chain J residue 73 ILE Chi-restraints excluded: chain J residue 174 MET Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 95 SER Chi-restraints excluded: chain K residue 172 LEU Chi-restraints excluded: chain L residue 137 THR Chi-restraints excluded: chain L residue 176 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: [209, 30, 98, 173, 112, 165, 138, 36, 47, 74, 166] chunk 209 optimal weight: 9.9990 chunk 30 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 chunk 173 optimal weight: 20.0000 chunk 112 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 36 optimal weight: 0.0170 chunk 47 optimal weight: 8.9990 chunk 74 optimal weight: 9.9990 chunk 166 optimal weight: 4.9990 overall best weight: 2.5824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 125 GLN H 197 ASN I 125 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.059736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.047736 restraints weight = 72983.723| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 3.83 r_work: 0.2691 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19010 Z= 0.146 Angle : 0.483 9.249 26061 Z= 0.258 Chirality : 0.045 0.164 3273 Planarity : 0.004 0.040 3264 Dihedral : 4.366 51.306 2799 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.54 % Allowed : 14.73 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.49 (0.16), residues: 2594 helix: 1.92 (0.45), residues: 156 sheet: 0.40 (0.14), residues: 1141 loop : 0.19 (0.17), residues: 1297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 60 TYR 0.015 0.001 TYR H 173 PHE 0.023 0.001 PHE L 150 TRP 0.004 0.001 TRP H 54 HIS 0.002 0.001 HIS F 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 (19004) covalent geometry : angle 0.48203 / 0.26 (26049) SS BOND : bond 0.00432 / 0.26 ( 6) SS BOND : angle 1.27632 / 0.69 ( 12) hydrogen bonds : bond 0.02899 / 2.07 ( 662) hydrogen bonds : angle 5.22507 / 3.73 ( 1812) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 325 time to evaluate : 0.668 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: A 8 LYS cc_start: 0.8924 (mtpp) cc_final: 0.8553 (mtpp) REVERT: A 87 ASN cc_start: 0.9464 (m-40) cc_final: 0.9015 (t0) REVERT: A 121 TYR cc_start: 0.7483 (m-80) cc_final: 0.6411 (t80) REVERT: A 154 ASN cc_start: 0.9138 (t0) cc_final: 0.8912 (t0) REVERT: A 193 ASP cc_start: 0.8777 (t0) cc_final: 0.8442 (t0) REVERT: B 193 ASP cc_start: 0.9325 (t0) cc_final: 0.8562 (p0) REVERT: C 88 LYS cc_start: 0.9615 (ttmm) cc_final: 0.9357 (ttpp) REVERT: C 121 TYR cc_start: 0.9249 (m-80) cc_final: 0.8939 (m-80) REVERT: C 178 LYS cc_start: 0.9180 (mtmm) cc_final: 0.8941 (mtmm) REVERT: C 187 SER cc_start: 0.9325 (t) cc_final: 0.9071 (p) REVERT: D 122 TYR cc_start: 0.8277 (t80) cc_final: 0.7993 (t80) REVERT: D 134 GLN cc_start: 0.8980 (mt0) cc_final: 0.8282 (mm-40) REVERT: D 138 PHE cc_start: 0.9229 (p90) cc_final: 0.8443 (p90) REVERT: E 124 LYS cc_start: 0.8835 (ptmt) cc_final: 0.8576 (ptmt) REVERT: E 131 ARG cc_start: 0.8600 (ptm-80) cc_final: 0.8121 (ptm-80) REVERT: E 134 GLN cc_start: 0.9272 (mm110) cc_final: 0.8927 (mm-40) REVERT: E 204 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7950 (mm-30) REVERT: F 68 THR cc_start: 0.8538 (OUTLIER) cc_final: 0.8326 (m) REVERT: F 133 ARG cc_start: 0.8919 (ptp90) cc_final: 0.8633 (ptp90) REVERT: G 8 LYS cc_start: 0.6150 (mmpt) cc_final: 0.5543 (mmpt) REVERT: G 60 ARG cc_start: 0.8893 (mmm-85) cc_final: 0.8682 (mmm-85) REVERT: G 85 ASN cc_start: 0.9245 (t0) cc_final: 0.8789 (t0) REVERT: G 124 LYS cc_start: 0.9166 (OUTLIER) cc_final: 0.8745 (ptmm) REVERT: G 134 GLN cc_start: 0.8785 (mp10) cc_final: 0.8407 (mp10) REVERT: G 163 TYR cc_start: 0.8988 (m-10) cc_final: 0.8677 (m-80) REVERT: H 60 ARG cc_start: 0.9055 (mmm-85) cc_final: 0.8680 (mmm-85) REVERT: H 144 ILE cc_start: 0.9329 (mm) cc_final: 0.8694 (tt) REVERT: H 193 ASP cc_start: 0.8455 (t0) cc_final: 0.8173 (p0) REVERT: I 8 LYS cc_start: 0.8961 (mtpt) cc_final: 0.8539 (mmtt) REVERT: I 88 LYS cc_start: 0.9527 (ptmt) cc_final: 0.9257 (ptmt) REVERT: I 124 LYS cc_start: 0.9195 (ptmm) cc_final: 0.8792 (pttt) REVERT: I 150 PHE cc_start: 0.8981 (t80) cc_final: 0.8583 (t80) REVERT: I 178 LYS cc_start: 0.9072 (mtmt) cc_final: 0.8507 (pttt) REVERT: I 192 PHE cc_start: 0.9002 (t80) cc_final: 0.8770 (t80) REVERT: J 8 LYS cc_start: 0.8799 (mmmm) cc_final: 0.8561 (mmmm) REVERT: J 65 LYS cc_start: 0.9401 (ttpp) cc_final: 0.9176 (ptmm) REVERT: J 88 LYS cc_start: 0.9386 (ttpp) cc_final: 0.9173 (ttpp) REVERT: J 134 GLN cc_start: 0.9431 (mt0) cc_final: 0.9144 (mm-40) REVERT: J 137 THR cc_start: 0.8608 (OUTLIER) cc_final: 0.8187 (p) REVERT: J 174 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.8088 (tmm) REVERT: J 219 MET cc_start: 0.8719 (mtm) cc_final: 0.8102 (mtm) REVERT: K 105 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7664 (tm-30) REVERT: K 173 TYR cc_start: 0.7974 (p90) cc_final: 0.7588 (p90) REVERT: L 89 TYR cc_start: 0.9095 (m-80) cc_final: 0.8646 (m-80) REVERT: L 193 ASP cc_start: 0.8739 (t0) cc_final: 0.8342 (t0) REVERT: L 197 ASN cc_start: 0.9258 (t0) cc_final: 0.8571 (t0) REVERT: L 204 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8486 (mm-30) outliers start: 63 outliers final: 43 residues processed: 372 average time/residue: 0.1578 time to fit residues: 84.7725 Evaluate side-chains 349 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 302 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 108 CYS Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain C residue 108 CYS Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain D residue 108 CYS Chi-restraints excluded: chain D residue 126 CYS Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 200 MET Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 124 LYS Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 149 ASP Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 61 VAL Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 174 MET Chi-restraints excluded: chain J residue 193 ASP Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 95 SER Chi-restraints excluded: chain K residue 172 LEU Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain L residue 137 THR Chi-restraints excluded: chain L residue 176 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: [178, 143, 58, 186, 96, 117, 61, 52, 65, 67, 155] chunk 178 optimal weight: 30.0000 chunk 143 optimal weight: 8.9990 chunk 58 optimal weight: 10.0000 chunk 186 optimal weight: 10.0000 chunk 96 optimal weight: 9.9990 chunk 117 optimal weight: 8.9990 chunk 61 optimal weight: 3.9990 chunk 52 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 chunk 67 optimal weight: 9.9990 chunk 155 optimal weight: 10.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 GLN H 134 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.056794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.045122 restraints weight = 75638.351| |-----------------------------------------------------------------------------| r_work (start): 0.2733 rms_B_bonded: 3.77 r_work: 0.2619 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.077 19010 Z= 0.370 Angle : 0.606 7.444 26061 Z= 0.322 Chirality : 0.046 0.159 3273 Planarity : 0.004 0.045 3264 Dihedral : 4.799 51.658 2799 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.50 % Allowed : 14.90 % Favored : 80.61 % 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: 0.24 (0.16), residues: 2594 helix: 1.82 (0.43), residues: 156 sheet: 0.23 (0.15), residues: 1083 loop : 0.02 (0.17), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 184 TYR 0.023 0.002 TYR J 173 PHE 0.024 0.002 PHE A 150 TRP 0.009 0.002 TRP H 103 HIS 0.005 0.001 HIS J 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00809 / 0.37 (19004) covalent geometry : angle 0.60486 / 0.32 (26049) SS BOND : bond 0.00770 / 0.38 ( 6) SS BOND : angle 1.67539 / 0.84 ( 12) hydrogen bonds : bond 0.03740 / 2.69 ( 662) hydrogen bonds : angle 5.50456 / 3.92 ( 1812) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 282 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8950 (mtpp) cc_final: 0.8690 (mtpp) REVERT: A 87 ASN cc_start: 0.9529 (m-40) cc_final: 0.9198 (t0) REVERT: A 105 GLU cc_start: 0.9124 (tt0) cc_final: 0.8564 (tt0) REVERT: A 193 ASP cc_start: 0.8816 (t0) cc_final: 0.8544 (t0) REVERT: B 193 ASP cc_start: 0.9318 (t0) cc_final: 0.8488 (p0) REVERT: C 88 LYS cc_start: 0.9591 (ttmm) cc_final: 0.9378 (ttpp) REVERT: D 122 TYR cc_start: 0.8501 (t80) cc_final: 0.8168 (t80) REVERT: D 134 GLN cc_start: 0.9137 (mt0) cc_final: 0.8361 (mm-40) REVERT: D 200 MET cc_start: 0.9225 (mmm) cc_final: 0.8145 (mmm) REVERT: E 134 GLN cc_start: 0.9290 (mm110) cc_final: 0.8968 (mm-40) REVERT: E 204 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7791 (mm-30) REVERT: E 216 TYR cc_start: 0.9362 (m-10) cc_final: 0.9105 (m-10) REVERT: F 130 ASP cc_start: 0.9481 (p0) cc_final: 0.9045 (p0) REVERT: F 150 PHE cc_start: 0.9253 (t80) cc_final: 0.9040 (t80) REVERT: F 193 ASP cc_start: 0.8670 (t0) cc_final: 0.8214 (t0) REVERT: G 8 LYS cc_start: 0.6098 (mmpt) cc_final: 0.5424 (mmpt) REVERT: G 60 ARG cc_start: 0.8917 (mmm-85) cc_final: 0.8688 (mmm-85) REVERT: G 85 ASN cc_start: 0.9318 (t0) cc_final: 0.8869 (t0) REVERT: G 124 LYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8606 (ptmm) REVERT: G 134 GLN cc_start: 0.8851 (mp10) cc_final: 0.8510 (mp10) REVERT: G 163 TYR cc_start: 0.9086 (m-10) cc_final: 0.8686 (m-80) REVERT: H 105 GLU cc_start: 0.9207 (pm20) cc_final: 0.8988 (tt0) REVERT: H 144 ILE cc_start: 0.9434 (mm) cc_final: 0.8784 (tt) REVERT: H 193 ASP cc_start: 0.8572 (t0) cc_final: 0.8073 (p0) REVERT: I 8 LYS cc_start: 0.8971 (mtpt) cc_final: 0.8559 (mmtt) REVERT: I 88 LYS cc_start: 0.9570 (ptmt) cc_final: 0.9367 (ttpt) REVERT: I 124 LYS cc_start: 0.9088 (ptmm) cc_final: 0.8774 (pttm) REVERT: I 216 TYR cc_start: 0.9193 (m-80) cc_final: 0.8990 (m-80) REVERT: J 8 LYS cc_start: 0.8919 (mmmm) cc_final: 0.8634 (mmmm) REVERT: J 88 LYS cc_start: 0.9526 (ttpp) cc_final: 0.9272 (ttpp) REVERT: J 137 THR cc_start: 0.8611 (OUTLIER) cc_final: 0.8186 (p) REVERT: J 174 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.8114 (tmm) REVERT: J 219 MET cc_start: 0.8953 (mtm) cc_final: 0.8294 (mtm) REVERT: K 105 GLU cc_start: 0.8054 (tm-30) cc_final: 0.7762 (tm-30) REVERT: K 121 TYR cc_start: 0.9542 (m-10) cc_final: 0.9303 (m-10) REVERT: K 173 TYR cc_start: 0.8069 (p90) cc_final: 0.7638 (p90) REVERT: K 219 MET cc_start: 0.8685 (mpp) cc_final: 0.7706 (mpp) REVERT: L 89 TYR cc_start: 0.9312 (m-80) cc_final: 0.8925 (m-80) REVERT: L 131 ARG cc_start: 0.9462 (ptp-170) cc_final: 0.9252 (ptp-110) REVERT: L 139 LYS cc_start: 0.8903 (mtpp) cc_final: 0.8267 (mtpp) REVERT: L 193 ASP cc_start: 0.8736 (t0) cc_final: 0.8440 (t0) REVERT: L 197 ASN cc_start: 0.9300 (t0) cc_final: 0.8569 (t0) REVERT: L 204 GLU cc_start: 0.8950 (mm-30) cc_final: 0.8619 (mm-30) outliers start: 80 outliers final: 60 residues processed: 343 average time/residue: 0.1590 time to fit residues: 79.7372 Evaluate side-chains 333 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 270 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 108 CYS Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain C residue 108 CYS Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain D residue 108 CYS Chi-restraints excluded: chain D residue 126 CYS Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 200 MET Chi-restraints excluded: chain F residue 59 ASN Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 219 MET Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 124 LYS Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 59 ASN Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 59 ASN Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 149 ASP Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 61 VAL Chi-restraints excluded: chain J residue 73 ILE Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 174 MET Chi-restraints excluded: chain J residue 193 ASP Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 95 SER Chi-restraints excluded: chain K residue 172 LEU Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 137 THR Chi-restraints excluded: chain L residue 176 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: [183, 29, 121, 18, 150, 202, 158, 191, 225, 219, 11] chunk 183 optimal weight: 0.9990 chunk 29 optimal weight: 7.9990 chunk 121 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 150 optimal weight: 10.0000 chunk 202 optimal weight: 20.0000 chunk 158 optimal weight: 5.9990 chunk 191 optimal weight: 9.9990 chunk 225 optimal weight: 0.8980 chunk 219 optimal weight: 0.0670 chunk 11 optimal weight: 4.9990 overall best weight: 2.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.058547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.046767 restraints weight = 73260.509| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 3.87 r_work: 0.2660 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19010 Z= 0.132 Angle : 0.493 12.388 26061 Z= 0.261 Chirality : 0.045 0.152 3273 Planarity : 0.004 0.038 3264 Dihedral : 4.343 52.639 2798 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.49 % Allowed : 16.25 % Favored : 80.27 % 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: 0.28 (0.16), residues: 2594 helix: 2.01 (0.45), residues: 156 sheet: 0.24 (0.15), residues: 1132 loop : 0.04 (0.17), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 133 TYR 0.015 0.001 TYR G 146 PHE 0.024 0.001 PHE L 150 TRP 0.004 0.001 TRP C 103 HIS 0.002 0.000 HIS E 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (19004) covalent geometry : angle 0.49144 / 0.26 (26049) SS BOND : bond 0.00505 / 0.31 ( 6) SS BOND : angle 1.62679 / 0.93 ( 12) hydrogen bonds : bond 0.02683 / 1.92 ( 662) hydrogen bonds : angle 5.21381 / 3.70 ( 1812) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 314 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8897 (mtpp) cc_final: 0.8650 (mtpp) REVERT: A 87 ASN cc_start: 0.9529 (m-40) cc_final: 0.9224 (t0) REVERT: A 105 GLU cc_start: 0.9117 (tt0) cc_final: 0.8553 (tt0) REVERT: A 121 TYR cc_start: 0.7582 (m-80) cc_final: 0.6001 (t80) REVERT: A 193 ASP cc_start: 0.8726 (t0) cc_final: 0.8457 (t0) REVERT: B 193 ASP cc_start: 0.9354 (t0) cc_final: 0.8501 (p0) REVERT: C 88 LYS cc_start: 0.9606 (ttmm) cc_final: 0.9340 (ttpp) REVERT: C 134 GLN cc_start: 0.8925 (tt0) cc_final: 0.8645 (tt0) REVERT: C 187 SER cc_start: 0.9386 (t) cc_final: 0.9134 (p) REVERT: D 122 TYR cc_start: 0.8524 (t80) cc_final: 0.8197 (t80) REVERT: D 134 GLN cc_start: 0.9075 (mt0) cc_final: 0.8339 (mm-40) REVERT: D 200 MET cc_start: 0.9257 (mmm) cc_final: 0.7993 (mmm) REVERT: E 124 LYS cc_start: 0.8899 (ptmt) cc_final: 0.8618 (ptmt) REVERT: E 133 ARG cc_start: 0.8537 (ttp-110) cc_final: 0.8315 (ttp-110) REVERT: E 134 GLN cc_start: 0.9198 (mm110) cc_final: 0.8803 (mm-40) REVERT: E 204 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7812 (mm-30) REVERT: F 120 GLN cc_start: 0.8927 (mm110) cc_final: 0.8723 (mm110) REVERT: F 150 PHE cc_start: 0.9202 (t80) cc_final: 0.8927 (t80) REVERT: F 178 LYS cc_start: 0.9339 (mmmt) cc_final: 0.9123 (mtmt) REVERT: G 8 LYS cc_start: 0.5968 (mmpt) cc_final: 0.5372 (mmpt) REVERT: G 60 ARG cc_start: 0.8843 (mmm-85) cc_final: 0.8559 (mmm-85) REVERT: G 85 ASN cc_start: 0.9259 (t0) cc_final: 0.8764 (t0) REVERT: G 124 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8572 (ptmm) REVERT: G 134 GLN cc_start: 0.8922 (mp10) cc_final: 0.8633 (mp10) REVERT: G 163 TYR cc_start: 0.9103 (m-10) cc_final: 0.8702 (m-80) REVERT: G 204 GLU cc_start: 0.8629 (pp20) cc_final: 0.8159 (pp20) REVERT: H 60 ARG cc_start: 0.8993 (mmm-85) cc_final: 0.8596 (mmm-85) REVERT: H 105 GLU cc_start: 0.9196 (pm20) cc_final: 0.8965 (tt0) REVERT: H 144 ILE cc_start: 0.9321 (mm) cc_final: 0.8733 (tt) REVERT: H 193 ASP cc_start: 0.8509 (t0) cc_final: 0.8099 (p0) REVERT: I 8 LYS cc_start: 0.9003 (mtpt) cc_final: 0.8549 (mmtt) REVERT: I 124 LYS cc_start: 0.9171 (ptmm) cc_final: 0.8794 (pttm) REVERT: I 216 TYR cc_start: 0.9057 (m-80) cc_final: 0.8831 (m-80) REVERT: J 8 LYS cc_start: 0.8814 (mmmm) cc_final: 0.8575 (mmmm) REVERT: J 65 LYS cc_start: 0.9387 (ttpp) cc_final: 0.9148 (ptmm) REVERT: J 88 LYS cc_start: 0.9473 (ttpp) cc_final: 0.9203 (ttpp) REVERT: J 137 THR cc_start: 0.8466 (OUTLIER) cc_final: 0.8001 (p) REVERT: J 174 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.8057 (tmm) REVERT: J 178 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8432 (pttm) REVERT: J 219 MET cc_start: 0.8849 (mtm) cc_final: 0.8569 (mtm) REVERT: K 105 GLU cc_start: 0.7996 (tm-30) cc_final: 0.7698 (tm-30) REVERT: K 121 TYR cc_start: 0.9521 (m-10) cc_final: 0.9249 (m-10) REVERT: K 173 TYR cc_start: 0.8045 (p90) cc_final: 0.7524 (p90) REVERT: K 219 MET cc_start: 0.8565 (mpp) cc_final: 0.7650 (mpp) REVERT: L 89 TYR cc_start: 0.9259 (m-80) cc_final: 0.8860 (m-80) REVERT: L 131 ARG cc_start: 0.9418 (ptp-170) cc_final: 0.9169 (ptp-110) REVERT: L 193 ASP cc_start: 0.8779 (t0) cc_final: 0.8479 (t0) REVERT: L 197 ASN cc_start: 0.9354 (t0) cc_final: 0.8610 (t0) REVERT: L 204 GLU cc_start: 0.9039 (mm-30) cc_final: 0.8708 (mm-30) outliers start: 62 outliers final: 48 residues processed: 360 average time/residue: 0.1594 time to fit residues: 83.7206 Evaluate side-chains 343 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 291 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 108 CYS Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain D residue 108 CYS Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 200 MET Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 219 MET Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 124 LYS Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 219 MET Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 127 LEU Chi-restraints excluded: chain H residue 135 ILE Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 149 ASP Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 61 VAL Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 174 MET Chi-restraints excluded: chain J residue 178 LYS Chi-restraints excluded: chain J residue 193 ASP Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 95 SER Chi-restraints excluded: chain K residue 172 LEU Chi-restraints excluded: chain L residue 137 THR Chi-restraints excluded: chain L residue 173 TYR Chi-restraints excluded: chain L residue 176 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: [201, 91, 33, 242, 167, 100, 226, 116, 50, 53, 29] chunk 201 optimal weight: 20.0000 chunk 91 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 242 optimal weight: 6.9990 chunk 167 optimal weight: 0.3980 chunk 100 optimal weight: 0.4980 chunk 226 optimal weight: 20.0000 chunk 116 optimal weight: 4.9990 chunk 50 optimal weight: 0.0010 chunk 53 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 overall best weight: 2.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 ASN ** 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 = 0.3094 r_free = 0.3094 target = 0.058254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.046393 restraints weight = 72817.163| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 3.81 r_work: 0.2663 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19010 Z= 0.140 Angle : 0.487 10.185 26061 Z= 0.258 Chirality : 0.045 0.142 3273 Planarity : 0.004 0.039 3264 Dihedral : 4.178 53.835 2797 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.88 % Allowed : 16.64 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.26 (0.16), residues: 2594 helix: 2.01 (0.44), residues: 156 sheet: 0.22 (0.15), residues: 1144 loop : 0.02 (0.17), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 131 TYR 0.020 0.001 TYR B 146 PHE 0.023 0.001 PHE A 150 TRP 0.004 0.001 TRP H 54 HIS 0.002 0.000 HIS F 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (19004) covalent geometry : angle 0.48647 / 0.26 (26049) SS BOND : bond 0.00296 / 0.16 ( 6) SS BOND : angle 1.41170 / 0.79 ( 12) hydrogen bonds : bond 0.02604 / 1.85 ( 662) hydrogen bonds : angle 5.08193 / 3.61 ( 1812) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 300 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8938 (mtpp) cc_final: 0.8553 (mtpp) REVERT: A 87 ASN cc_start: 0.9486 (m-40) cc_final: 0.9218 (t0) REVERT: A 193 ASP cc_start: 0.8726 (t0) cc_final: 0.8486 (t0) REVERT: B 193 ASP cc_start: 0.9308 (t0) cc_final: 0.8504 (p0) REVERT: B 197 ASN cc_start: 0.9441 (t0) cc_final: 0.9176 (t0) REVERT: B 219 MET cc_start: 0.9221 (mtm) cc_final: 0.8924 (mtp) REVERT: C 88 LYS cc_start: 0.9592 (ttmm) cc_final: 0.9338 (ttpp) REVERT: C 121 TYR cc_start: 0.9231 (m-80) cc_final: 0.8922 (m-80) REVERT: C 187 SER cc_start: 0.9340 (t) cc_final: 0.9131 (p) REVERT: D 122 TYR cc_start: 0.8515 (t80) cc_final: 0.8207 (t80) REVERT: D 133 ARG cc_start: 0.8985 (mmm-85) cc_final: 0.8776 (mmm-85) REVERT: D 134 GLN cc_start: 0.9079 (mt0) cc_final: 0.8392 (mm-40) REVERT: D 200 MET cc_start: 0.9155 (mmm) cc_final: 0.8100 (mmm) REVERT: E 124 LYS cc_start: 0.8964 (ptmt) cc_final: 0.8710 (pttt) REVERT: E 134 GLN cc_start: 0.9155 (mm110) cc_final: 0.8711 (mm-40) REVERT: E 204 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7815 (mm-30) REVERT: F 150 PHE cc_start: 0.9168 (t80) cc_final: 0.8881 (t80) REVERT: F 178 LYS cc_start: 0.9294 (mmmt) cc_final: 0.9084 (mtmt) REVERT: G 8 LYS cc_start: 0.6186 (mmpt) cc_final: 0.5526 (mmpt) REVERT: G 60 ARG cc_start: 0.8824 (mmm-85) cc_final: 0.8531 (mmm-85) REVERT: G 85 ASN cc_start: 0.9254 (t0) cc_final: 0.8814 (t0) REVERT: G 124 LYS cc_start: 0.9019 (OUTLIER) cc_final: 0.8649 (ptmm) REVERT: G 134 GLN cc_start: 0.8898 (mp10) cc_final: 0.8622 (mp10) REVERT: G 163 TYR cc_start: 0.9068 (m-10) cc_final: 0.8737 (m-80) REVERT: G 204 GLU cc_start: 0.8648 (pp20) cc_final: 0.8243 (pp20) REVERT: H 60 ARG cc_start: 0.9008 (mmm-85) cc_final: 0.8788 (mmm-85) REVERT: H 144 ILE cc_start: 0.9366 (mm) cc_final: 0.8842 (tt) REVERT: H 193 ASP cc_start: 0.8567 (t0) cc_final: 0.8157 (p0) REVERT: I 8 LYS cc_start: 0.8990 (mtpt) cc_final: 0.8544 (mmtt) REVERT: I 124 LYS cc_start: 0.9182 (ptmm) cc_final: 0.8863 (pttm) REVERT: I 130 ASP cc_start: 0.9373 (p0) cc_final: 0.9138 (p0) REVERT: J 8 LYS cc_start: 0.8908 (mmmm) cc_final: 0.8640 (mmmm) REVERT: J 65 LYS cc_start: 0.9379 (ttpp) cc_final: 0.9144 (ptmm) REVERT: J 88 LYS cc_start: 0.9523 (ttpp) cc_final: 0.9194 (ttpp) REVERT: J 137 THR cc_start: 0.8630 (OUTLIER) cc_final: 0.8187 (p) REVERT: J 174 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.8142 (tmm) REVERT: J 178 LYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8546 (pttm) REVERT: J 219 MET cc_start: 0.8826 (mtm) cc_final: 0.8087 (mtm) REVERT: K 105 GLU cc_start: 0.7962 (tm-30) cc_final: 0.7661 (tm-30) REVERT: K 121 TYR cc_start: 0.9533 (m-10) cc_final: 0.9258 (m-10) REVERT: K 173 TYR cc_start: 0.8135 (p90) cc_final: 0.7604 (p90) REVERT: K 219 MET cc_start: 0.8590 (mpp) cc_final: 0.7667 (mpp) REVERT: L 89 TYR cc_start: 0.9166 (m-80) cc_final: 0.8872 (m-80) REVERT: L 130 ASP cc_start: 0.9605 (p0) cc_final: 0.9404 (p0) REVERT: L 193 ASP cc_start: 0.8773 (t0) cc_final: 0.8508 (t0) REVERT: L 197 ASN cc_start: 0.9386 (t0) cc_final: 0.8681 (t0) REVERT: L 204 GLU cc_start: 0.8944 (mm-30) cc_final: 0.8552 (mm-30) outliers start: 69 outliers final: 54 residues processed: 353 average time/residue: 0.1464 time to fit residues: 76.0661 Evaluate side-chains 345 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 287 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 108 CYS Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain D residue 108 CYS Chi-restraints excluded: chain D residue 126 CYS Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 200 MET Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 200 MET Chi-restraints excluded: chain F residue 219 MET Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 124 LYS Chi-restraints excluded: chain G residue 200 MET Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 219 MET Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 127 LEU Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 149 ASP Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 61 VAL Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 174 MET Chi-restraints excluded: chain J residue 178 LYS Chi-restraints excluded: chain J residue 193 ASP Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 95 SER Chi-restraints excluded: chain K residue 172 LEU Chi-restraints excluded: chain L residue 137 THR Chi-restraints excluded: chain L residue 173 TYR Chi-restraints excluded: chain L residue 176 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: [234, 185, 233, 41, 235, 97, 194, 4, 87, 247, 1] chunk 234 optimal weight: 10.0000 chunk 185 optimal weight: 5.9990 chunk 233 optimal weight: 6.9990 chunk 41 optimal weight: 0.4980 chunk 235 optimal weight: 9.9990 chunk 97 optimal weight: 9.9990 chunk 194 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 87 optimal weight: 8.9990 chunk 247 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 ASN ** 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 = 0.3075 r_free = 0.3075 target = 0.058030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.046335 restraints weight = 73904.818| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 3.79 r_work: 0.2641 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 19010 Z= 0.209 Angle : 0.519 8.288 26061 Z= 0.275 Chirality : 0.044 0.144 3273 Planarity : 0.004 0.038 3264 Dihedral : 4.266 51.268 2797 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.93 % Allowed : 17.43 % Favored : 78.64 % 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 (0.16), residues: 2594 helix: 2.03 (0.44), residues: 156 sheet: 0.17 (0.15), residues: 1159 loop : 0.00 (0.17), residues: 1279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG K 131 TYR 0.021 0.001 TYR J 173 PHE 0.030 0.001 PHE I 192 TRP 0.004 0.001 TRP J 54 HIS 0.001 0.001 HIS K 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.21 (19004) covalent geometry : angle 0.51854 / 0.27 (26049) SS BOND : bond 0.00222 / 0.13 ( 6) SS BOND : angle 1.30542 / 0.72 ( 12) hydrogen bonds : bond 0.02875 / 2.05 ( 662) hydrogen bonds : angle 5.15910 / 3.67 ( 1812) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 287 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8956 (mtpp) cc_final: 0.8677 (mtpp) REVERT: A 87 ASN cc_start: 0.9516 (m-40) cc_final: 0.9260 (t0) REVERT: A 105 GLU cc_start: 0.9086 (tt0) cc_final: 0.8561 (tt0) REVERT: A 193 ASP cc_start: 0.8709 (t0) cc_final: 0.8495 (t0) REVERT: B 193 ASP cc_start: 0.9288 (t0) cc_final: 0.8499 (p0) REVERT: B 219 MET cc_start: 0.9249 (mtm) cc_final: 0.8950 (mtp) REVERT: C 88 LYS cc_start: 0.9613 (ttmm) cc_final: 0.9372 (ttpp) REVERT: C 121 TYR cc_start: 0.9261 (m-80) cc_final: 0.8958 (m-80) REVERT: D 122 TYR cc_start: 0.8568 (t80) cc_final: 0.8258 (t80) REVERT: D 133 ARG cc_start: 0.9048 (mmm-85) cc_final: 0.8822 (mmm-85) REVERT: D 134 GLN cc_start: 0.9096 (mt0) cc_final: 0.8390 (mm-40) REVERT: D 200 MET cc_start: 0.9170 (mmm) cc_final: 0.7912 (mmm) REVERT: D 204 GLU cc_start: 0.8855 (pt0) cc_final: 0.8471 (pm20) REVERT: E 133 ARG cc_start: 0.8556 (ttp-110) cc_final: 0.8304 (ttp-110) REVERT: E 134 GLN cc_start: 0.9137 (mm110) cc_final: 0.8465 (mm-40) REVERT: E 204 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7711 (mm-30) REVERT: G 8 LYS cc_start: 0.5980 (mmpt) cc_final: 0.5287 (mmpt) REVERT: G 60 ARG cc_start: 0.8852 (mmm-85) cc_final: 0.8550 (mmm-85) REVERT: G 85 ASN cc_start: 0.9260 (t0) cc_final: 0.8812 (t0) REVERT: G 124 LYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8635 (ptmm) REVERT: G 134 GLN cc_start: 0.8904 (mp10) cc_final: 0.8635 (mp10) REVERT: G 163 TYR cc_start: 0.9082 (m-10) cc_final: 0.8762 (m-80) REVERT: G 204 GLU cc_start: 0.8679 (pp20) cc_final: 0.8340 (pp20) REVERT: H 60 ARG cc_start: 0.9024 (mmm-85) cc_final: 0.8797 (mmm-85) REVERT: H 144 ILE cc_start: 0.9407 (mm) cc_final: 0.8894 (tt) REVERT: H 193 ASP cc_start: 0.8591 (t0) cc_final: 0.8164 (p0) REVERT: I 8 LYS cc_start: 0.8984 (mtpt) cc_final: 0.8549 (mmtt) REVERT: I 88 LYS cc_start: 0.9558 (ttpt) cc_final: 0.9268 (tmmt) REVERT: I 124 LYS cc_start: 0.9187 (ptmm) cc_final: 0.8837 (pttm) REVERT: I 130 ASP cc_start: 0.9346 (p0) cc_final: 0.9126 (p0) REVERT: J 65 LYS cc_start: 0.9399 (ttpp) cc_final: 0.9155 (ptmm) REVERT: J 88 LYS cc_start: 0.9564 (ttpp) cc_final: 0.9249 (ttpp) REVERT: J 174 MET cc_start: 0.8624 (tmm) cc_final: 0.8190 (tmm) REVERT: J 178 LYS cc_start: 0.8969 (pttm) cc_final: 0.8580 (pttm) REVERT: J 204 GLU cc_start: 0.9014 (pt0) cc_final: 0.8570 (tm-30) REVERT: J 219 MET cc_start: 0.8908 (mtm) cc_final: 0.8654 (mtm) REVERT: K 105 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7666 (tm-30) REVERT: K 121 TYR cc_start: 0.9527 (m-10) cc_final: 0.9245 (m-10) REVERT: K 173 TYR cc_start: 0.8125 (p90) cc_final: 0.7561 (p90) REVERT: K 219 MET cc_start: 0.8619 (mpp) cc_final: 0.7655 (mpp) REVERT: L 89 TYR cc_start: 0.9248 (m-80) cc_final: 0.8989 (m-80) REVERT: L 130 ASP cc_start: 0.9612 (p0) cc_final: 0.9398 (p0) REVERT: L 193 ASP cc_start: 0.8762 (t0) cc_final: 0.8452 (t0) REVERT: L 197 ASN cc_start: 0.9395 (t0) cc_final: 0.8702 (t0) REVERT: L 204 GLU cc_start: 0.8966 (mm-30) cc_final: 0.8679 (mm-30) outliers start: 70 outliers final: 61 residues processed: 339 average time/residue: 0.1526 time to fit residues: 76.0840 Evaluate side-chains 346 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 284 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 108 CYS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain D residue 108 CYS Chi-restraints excluded: chain D residue 126 CYS Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain E residue 8 LYS Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 59 ASN Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 174 MET Chi-restraints excluded: chain F residue 200 MET Chi-restraints excluded: chain F residue 219 MET Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 124 LYS Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 200 MET Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 219 MET Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 127 LEU Chi-restraints excluded: chain H residue 135 ILE Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 149 ASP Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 61 VAL Chi-restraints excluded: chain J residue 193 ASP Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 95 SER Chi-restraints excluded: chain K residue 172 LEU Chi-restraints excluded: chain L residue 137 THR Chi-restraints excluded: chain L residue 173 TYR Chi-restraints excluded: chain L residue 176 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: [195, 216, 51, 177, 153, 58, 152, 187, 22, 62, 219] chunk 195 optimal weight: 20.0000 chunk 216 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 chunk 177 optimal weight: 20.0000 chunk 153 optimal weight: 20.0000 chunk 58 optimal weight: 0.9990 chunk 152 optimal weight: 8.9990 chunk 187 optimal weight: 8.9990 chunk 22 optimal weight: 6.9990 chunk 62 optimal weight: 8.9990 chunk 219 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN ** I 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 218 HIS ** 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 = 0.3050 r_free = 0.3050 target = 0.056291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.044890 restraints weight = 74674.629| |-----------------------------------------------------------------------------| r_work (start): 0.2734 rms_B_bonded: 3.68 r_work: 0.2623 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 19010 Z= 0.320 Angle : 0.591 8.097 26061 Z= 0.315 Chirality : 0.045 0.149 3273 Planarity : 0.004 0.042 3264 Dihedral : 4.630 52.661 2797 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 4.05 % Allowed : 17.59 % Favored : 78.36 % 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 (0.16), residues: 2594 helix: 1.81 (0.43), residues: 156 sheet: -0.03 (0.15), residues: 1157 loop : -0.12 (0.17), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 131 TYR 0.025 0.002 TYR G 89 PHE 0.029 0.002 PHE A 150 TRP 0.007 0.001 TRP F 54 HIS 0.003 0.001 HIS J 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00698 / 0.32 (19004) covalent geometry : angle 0.59031 / 0.31 (26049) SS BOND : bond 0.00308 / 0.19 ( 6) SS BOND : angle 1.56069 / 0.83 ( 12) hydrogen bonds : bond 0.03421 / 2.45 ( 662) hydrogen bonds : angle 5.48414 / 3.89 ( 1812) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 278 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8996 (mtpp) cc_final: 0.8685 (mtpp) REVERT: A 87 ASN cc_start: 0.9473 (m-40) cc_final: 0.9263 (t0) REVERT: A 105 GLU cc_start: 0.9145 (tt0) cc_final: 0.8557 (tt0) REVERT: A 193 ASP cc_start: 0.8657 (t0) cc_final: 0.8436 (t0) REVERT: B 193 ASP cc_start: 0.9255 (t0) cc_final: 0.8484 (p0) REVERT: B 219 MET cc_start: 0.9199 (mtm) cc_final: 0.8960 (mtp) REVERT: C 121 TYR cc_start: 0.9274 (m-80) cc_final: 0.8824 (m-80) REVERT: C 134 GLN cc_start: 0.8892 (tt0) cc_final: 0.8503 (tt0) REVERT: D 122 TYR cc_start: 0.8636 (t80) cc_final: 0.8369 (t80) REVERT: D 134 GLN cc_start: 0.9179 (mt0) cc_final: 0.8426 (mm-40) REVERT: D 204 GLU cc_start: 0.8816 (pt0) cc_final: 0.8588 (pm20) REVERT: E 134 GLN cc_start: 0.9180 (mm110) cc_final: 0.8537 (mm-40) REVERT: E 216 TYR cc_start: 0.9342 (m-10) cc_final: 0.9113 (m-10) REVERT: F 193 ASP cc_start: 0.8684 (t0) cc_final: 0.8191 (t0) REVERT: G 8 LYS cc_start: 0.6063 (mmpt) cc_final: 0.5208 (mmpt) REVERT: G 60 ARG cc_start: 0.8893 (mmm-85) cc_final: 0.8605 (mmm-85) REVERT: G 85 ASN cc_start: 0.9298 (t0) cc_final: 0.8879 (t0) REVERT: G 124 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8571 (ptmm) REVERT: G 134 GLN cc_start: 0.8927 (mp10) cc_final: 0.8644 (mp10) REVERT: G 163 TYR cc_start: 0.9144 (m-10) cc_final: 0.8812 (m-80) REVERT: G 204 GLU cc_start: 0.8658 (pp20) cc_final: 0.8361 (pp20) REVERT: H 60 ARG cc_start: 0.9021 (mmm-85) cc_final: 0.8734 (mmm-85) REVERT: H 124 LYS cc_start: 0.9065 (ttpp) cc_final: 0.8671 (ttpp) REVERT: H 144 ILE cc_start: 0.9416 (mm) cc_final: 0.8864 (tt) REVERT: H 193 ASP cc_start: 0.8638 (t0) cc_final: 0.8175 (p0) REVERT: I 8 LYS cc_start: 0.8980 (mtpt) cc_final: 0.8487 (mmtt) REVERT: I 88 LYS cc_start: 0.9529 (ttpt) cc_final: 0.9233 (tmmt) REVERT: I 124 LYS cc_start: 0.9194 (ptmm) cc_final: 0.8813 (pttm) REVERT: I 130 ASP cc_start: 0.9300 (p0) cc_final: 0.9063 (p0) REVERT: J 8 LYS cc_start: 0.8934 (mmmm) cc_final: 0.8733 (ttmt) REVERT: J 88 LYS cc_start: 0.9576 (ttpp) cc_final: 0.9278 (ttpp) REVERT: J 174 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.8198 (tmm) REVERT: J 178 LYS cc_start: 0.8938 (pttm) cc_final: 0.8548 (pttm) REVERT: J 204 GLU cc_start: 0.9006 (pt0) cc_final: 0.8557 (tm-30) REVERT: J 219 MET cc_start: 0.9051 (mtm) cc_final: 0.8820 (mtm) REVERT: K 105 GLU cc_start: 0.8052 (tm-30) cc_final: 0.7711 (tm-30) REVERT: K 173 TYR cc_start: 0.8162 (p90) cc_final: 0.7565 (p90) REVERT: K 219 MET cc_start: 0.8650 (mpp) cc_final: 0.7640 (mpp) REVERT: L 89 TYR cc_start: 0.9271 (m-80) cc_final: 0.8959 (m-80) REVERT: L 130 ASP cc_start: 0.9621 (p0) cc_final: 0.9390 (p0) REVERT: L 131 ARG cc_start: 0.9419 (ptp-110) cc_final: 0.9210 (ttm110) REVERT: L 139 LYS cc_start: 0.8864 (mtpp) cc_final: 0.8214 (mtpp) REVERT: L 193 ASP cc_start: 0.8833 (t0) cc_final: 0.8497 (t0) REVERT: L 204 GLU cc_start: 0.8941 (mm-30) cc_final: 0.8673 (mm-30) outliers start: 72 outliers final: 59 residues processed: 334 average time/residue: 0.1551 time to fit residues: 75.9395 Evaluate side-chains 332 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 271 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 108 CYS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain D residue 108 CYS Chi-restraints excluded: chain D residue 126 CYS Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain E residue 8 LYS Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain F residue 59 ASN Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 174 MET Chi-restraints excluded: chain F residue 200 MET Chi-restraints excluded: chain F residue 219 MET Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 124 LYS Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 219 MET Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 127 LEU Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 59 ASN Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 149 ASP Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 61 VAL Chi-restraints excluded: chain J residue 174 MET Chi-restraints excluded: chain J residue 193 ASP Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 95 SER Chi-restraints excluded: chain K residue 172 LEU Chi-restraints excluded: chain L residue 137 THR Chi-restraints excluded: chain L residue 173 TYR Chi-restraints excluded: chain L residue 176 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: [23, 51, 217, 136, 4, 229, 207, 154, 184, 231, 70] chunk 23 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 chunk 217 optimal weight: 20.0000 chunk 136 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 229 optimal weight: 10.0000 chunk 207 optimal weight: 9.9990 chunk 154 optimal weight: 10.0000 chunk 184 optimal weight: 3.9990 chunk 231 optimal weight: 10.0000 chunk 70 optimal weight: 0.1980 overall best weight: 3.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 ASN ** J 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.057050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.045480 restraints weight = 73508.945| |-----------------------------------------------------------------------------| r_work (start): 0.2765 rms_B_bonded: 3.80 r_work: 0.2653 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 19010 Z= 0.200 Angle : 0.540 9.882 26061 Z= 0.288 Chirality : 0.045 0.149 3273 Planarity : 0.004 0.039 3264 Dihedral : 4.406 53.328 2797 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.77 % Allowed : 18.38 % Favored : 77.85 % 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: 0.00 (0.16), residues: 2594 helix: 1.94 (0.44), residues: 156 sheet: -0.01 (0.15), residues: 1127 loop : -0.10 (0.17), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 131 TYR 0.036 0.001 TYR H 89 PHE 0.033 0.001 PHE I 192 TRP 0.003 0.001 TRP H 54 HIS 0.002 0.001 HIS J 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.20 (19004) covalent geometry : angle 0.53901 / 0.29 (26049) SS BOND : bond 0.00215 / 0.13 ( 6) SS BOND : angle 1.39931 / 0.76 ( 12) hydrogen bonds : bond 0.02860 / 2.04 ( 662) hydrogen bonds : angle 5.33901 / 3.79 ( 1812) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 288 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8940 (mtpp) cc_final: 0.8639 (mtpp) REVERT: A 65 LYS cc_start: 0.9475 (ttmm) cc_final: 0.9173 (ptmm) REVERT: A 87 ASN cc_start: 0.9483 (m-40) cc_final: 0.9258 (t0) REVERT: A 105 GLU cc_start: 0.9154 (tt0) cc_final: 0.8637 (tt0) REVERT: A 200 MET cc_start: 0.9294 (OUTLIER) cc_final: 0.9024 (tpt) REVERT: B 193 ASP cc_start: 0.9282 (t0) cc_final: 0.8467 (p0) REVERT: B 219 MET cc_start: 0.9275 (mtm) cc_final: 0.8965 (mtp) REVERT: C 121 TYR cc_start: 0.9295 (m-80) cc_final: 0.8884 (m-80) REVERT: C 133 ARG cc_start: 0.8900 (mtp85) cc_final: 0.8691 (mtp85) REVERT: D 122 TYR cc_start: 0.8640 (t80) cc_final: 0.8287 (t80) REVERT: D 134 GLN cc_start: 0.9134 (mt0) cc_final: 0.8387 (mm-40) REVERT: D 204 GLU cc_start: 0.8867 (pt0) cc_final: 0.8587 (pm20) REVERT: E 131 ARG cc_start: 0.8719 (ptm-80) cc_final: 0.8381 (ptm-80) REVERT: E 134 GLN cc_start: 0.9078 (mm110) cc_final: 0.8411 (mm-40) REVERT: F 178 LYS cc_start: 0.9324 (mmmt) cc_final: 0.9075 (mtmt) REVERT: G 8 LYS cc_start: 0.5791 (mmpt) cc_final: 0.5023 (mmpt) REVERT: G 60 ARG cc_start: 0.8852 (mmm-85) cc_final: 0.8534 (mmm-85) REVERT: G 85 ASN cc_start: 0.9274 (t0) cc_final: 0.8829 (t0) REVERT: G 124 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8523 (ptmm) REVERT: G 134 GLN cc_start: 0.8965 (mp10) cc_final: 0.8705 (mp10) REVERT: G 204 GLU cc_start: 0.8703 (pp20) cc_final: 0.8328 (pp20) REVERT: H 59 ASN cc_start: 0.9128 (m110) cc_final: 0.8467 (p0) REVERT: H 60 ARG cc_start: 0.9025 (mmm-85) cc_final: 0.8670 (mmm-85) REVERT: H 124 LYS cc_start: 0.9040 (ttpp) cc_final: 0.8626 (ttpp) REVERT: H 144 ILE cc_start: 0.9377 (mm) cc_final: 0.8832 (tt) REVERT: H 193 ASP cc_start: 0.8639 (t0) cc_final: 0.8212 (p0) REVERT: I 8 LYS cc_start: 0.8931 (mtpt) cc_final: 0.8445 (mmtt) REVERT: I 88 LYS cc_start: 0.9583 (ttpt) cc_final: 0.9299 (tmmt) REVERT: I 124 LYS cc_start: 0.9202 (ptmm) cc_final: 0.8792 (pttm) REVERT: I 130 ASP cc_start: 0.9298 (p0) cc_final: 0.9025 (p0) REVERT: I 184 ARG cc_start: 0.8992 (mtm-85) cc_final: 0.8568 (mtm-85) REVERT: J 8 LYS cc_start: 0.8870 (mmmm) cc_final: 0.8667 (ttmt) REVERT: J 65 LYS cc_start: 0.9370 (ttpp) cc_final: 0.9123 (ptmm) REVERT: J 88 LYS cc_start: 0.9578 (ttpp) cc_final: 0.9243 (ttpp) REVERT: J 174 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.8148 (tmm) REVERT: J 178 LYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8600 (pttm) REVERT: J 204 GLU cc_start: 0.8979 (pt0) cc_final: 0.8593 (tm-30) REVERT: J 219 MET cc_start: 0.9022 (mtm) cc_final: 0.8773 (mtm) REVERT: K 105 GLU cc_start: 0.7995 (tm-30) cc_final: 0.7690 (tm-30) REVERT: K 173 TYR cc_start: 0.8176 (p90) cc_final: 0.7572 (p90) REVERT: K 219 MET cc_start: 0.8576 (mpp) cc_final: 0.7527 (mpp) REVERT: L 89 TYR cc_start: 0.9256 (m-80) cc_final: 0.8984 (m-80) REVERT: L 139 LYS cc_start: 0.8835 (mtpp) cc_final: 0.8117 (mtpp) REVERT: L 193 ASP cc_start: 0.8833 (t0) cc_final: 0.8516 (t0) REVERT: L 197 ASN cc_start: 0.9370 (t0) cc_final: 0.8820 (t0) REVERT: L 204 GLU cc_start: 0.8988 (mm-30) cc_final: 0.8621 (mm-30) outliers start: 67 outliers final: 57 residues processed: 339 average time/residue: 0.1528 time to fit residues: 75.8982 Evaluate side-chains 344 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 283 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 108 CYS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain D residue 108 CYS Chi-restraints excluded: chain D residue 126 CYS Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 174 MET Chi-restraints excluded: chain F residue 200 MET Chi-restraints excluded: chain F residue 219 MET Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 124 LYS Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 219 MET Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 127 LEU Chi-restraints excluded: chain H residue 135 ILE Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 149 ASP Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 61 VAL Chi-restraints excluded: chain J residue 174 MET Chi-restraints excluded: chain J residue 178 LYS Chi-restraints excluded: chain J residue 193 ASP Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 95 SER Chi-restraints excluded: chain K residue 172 LEU Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 137 THR Chi-restraints excluded: chain L residue 173 TYR Chi-restraints excluded: chain L residue 176 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: [203, 75, 255, 254, 188, 158, 216, 136, 51, 13, 160] chunk 203 optimal weight: 9.9990 chunk 75 optimal weight: 0.9990 chunk 255 optimal weight: 3.9990 chunk 254 optimal weight: 1.9990 chunk 188 optimal weight: 0.3980 chunk 158 optimal weight: 7.9990 chunk 216 optimal weight: 10.0000 chunk 136 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 160 optimal weight: 6.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 ASN I 134 GLN ** J 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 = 0.3108 r_free = 0.3108 target = 0.058497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.047133 restraints weight = 72011.252| |-----------------------------------------------------------------------------| r_work (start): 0.2794 rms_B_bonded: 3.78 r_work: 0.2679 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19010 Z= 0.120 Angle : 0.527 10.542 26061 Z= 0.279 Chirality : 0.045 0.147 3273 Planarity : 0.004 0.040 3264 Dihedral : 4.168 52.755 2797 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.43 % Allowed : 19.39 % Favored : 77.18 % 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: 0.08 (0.16), residues: 2594 helix: 2.02 (0.45), residues: 156 sheet: 0.03 (0.15), residues: 1082 loop : -0.04 (0.17), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 131 TYR 0.042 0.001 TYR H 89 PHE 0.042 0.001 PHE I 192 TRP 0.006 0.001 TRP J 103 HIS 0.002 0.000 HIS F 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (19004) covalent geometry : angle 0.52698 / 0.28 (26049) SS BOND : bond 0.00148 / 0.09 ( 6) SS BOND : angle 1.10325 / 0.60 ( 12) hydrogen bonds : bond 0.02503 / 1.77 ( 662) hydrogen bonds : angle 5.13378 / 3.64 ( 1812) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 308 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8904 (mtpp) cc_final: 0.8648 (mtpp) REVERT: A 65 LYS cc_start: 0.9434 (ttmm) cc_final: 0.9155 (ptmm) REVERT: A 87 ASN cc_start: 0.9479 (m-40) cc_final: 0.9274 (t0) REVERT: A 105 GLU cc_start: 0.9093 (tt0) cc_final: 0.8567 (tt0) REVERT: B 193 ASP cc_start: 0.9283 (t0) cc_final: 0.8550 (p0) REVERT: B 195 VAL cc_start: 0.9740 (t) cc_final: 0.9505 (p) REVERT: B 219 MET cc_start: 0.9200 (mtm) cc_final: 0.8901 (mtp) REVERT: C 121 TYR cc_start: 0.9263 (m-80) cc_final: 0.8950 (m-80) REVERT: C 187 SER cc_start: 0.9356 (t) cc_final: 0.9130 (p) REVERT: D 122 TYR cc_start: 0.8581 (t80) cc_final: 0.8201 (t80) REVERT: D 134 GLN cc_start: 0.9058 (mt0) cc_final: 0.8295 (mm-40) REVERT: D 204 GLU cc_start: 0.8844 (pt0) cc_final: 0.8532 (pm20) REVERT: E 131 ARG cc_start: 0.8702 (ptm-80) cc_final: 0.8342 (ptm-80) REVERT: E 134 GLN cc_start: 0.9027 (mm110) cc_final: 0.8362 (mm-40) REVERT: F 150 PHE cc_start: 0.9193 (t80) cc_final: 0.8896 (t80) REVERT: F 178 LYS cc_start: 0.9230 (mmmt) cc_final: 0.9015 (mtmt) REVERT: G 8 LYS cc_start: 0.5828 (mmpt) cc_final: 0.5146 (mmpt) REVERT: G 85 ASN cc_start: 0.9230 (t0) cc_final: 0.8813 (t0) REVERT: G 124 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8484 (ptmm) REVERT: G 134 GLN cc_start: 0.8952 (mp10) cc_final: 0.8723 (mp10) REVERT: G 204 GLU cc_start: 0.8799 (pp20) cc_final: 0.8445 (pp20) REVERT: H 60 ARG cc_start: 0.8990 (mmm-85) cc_final: 0.8758 (mmm-85) REVERT: H 124 LYS cc_start: 0.9064 (ttpp) cc_final: 0.8684 (ttpp) REVERT: H 144 ILE cc_start: 0.9356 (mm) cc_final: 0.8851 (tt) REVERT: H 193 ASP cc_start: 0.8611 (t0) cc_final: 0.8220 (p0) REVERT: I 8 LYS cc_start: 0.8908 (mtpt) cc_final: 0.8420 (mmtt) REVERT: I 88 LYS cc_start: 0.9588 (ttpt) cc_final: 0.9321 (tmmt) REVERT: I 124 LYS cc_start: 0.9200 (ptmm) cc_final: 0.8885 (pttm) REVERT: I 197 ASN cc_start: 0.8995 (m110) cc_final: 0.8764 (p0) REVERT: I 207 ILE cc_start: 0.9637 (mp) cc_final: 0.9395 (mp) REVERT: J 65 LYS cc_start: 0.9367 (ttpp) cc_final: 0.9138 (ptmm) REVERT: J 88 LYS cc_start: 0.9580 (ttpp) cc_final: 0.9251 (ttpp) REVERT: J 174 MET cc_start: 0.8596 (OUTLIER) cc_final: 0.8145 (tmm) REVERT: J 178 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8626 (pttm) REVERT: J 204 GLU cc_start: 0.8896 (pt0) cc_final: 0.8584 (tm-30) REVERT: J 219 MET cc_start: 0.8928 (mtm) cc_final: 0.8264 (mtm) REVERT: K 89 TYR cc_start: 0.8145 (m-10) cc_final: 0.7901 (m-80) REVERT: K 105 GLU cc_start: 0.7932 (tm-30) cc_final: 0.7623 (tm-30) REVERT: K 131 ARG cc_start: 0.9064 (mtp-110) cc_final: 0.8837 (mmm-85) REVERT: K 173 TYR cc_start: 0.8196 (p90) cc_final: 0.7599 (p90) REVERT: K 219 MET cc_start: 0.8553 (mpp) cc_final: 0.7561 (mpp) REVERT: L 139 LYS cc_start: 0.8868 (mtpp) cc_final: 0.8166 (mtpp) REVERT: L 193 ASP cc_start: 0.8826 (t0) cc_final: 0.8530 (t0) REVERT: L 197 ASN cc_start: 0.9376 (t0) cc_final: 0.8830 (t0) REVERT: L 204 GLU cc_start: 0.8956 (mm-30) cc_final: 0.8591 (mm-30) outliers start: 61 outliers final: 52 residues processed: 354 average time/residue: 0.1523 time to fit residues: 78.7101 Evaluate side-chains 349 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 294 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 108 CYS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain D residue 108 CYS Chi-restraints excluded: chain D residue 126 CYS Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 200 MET Chi-restraints excluded: chain F residue 219 MET Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 124 LYS Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 219 MET Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 135 ILE Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 149 ASP Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 61 VAL Chi-restraints excluded: chain J residue 174 MET Chi-restraints excluded: chain J residue 178 LYS Chi-restraints excluded: chain J residue 193 ASP Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 95 SER Chi-restraints excluded: chain K residue 172 LEU Chi-restraints excluded: chain L residue 137 THR Chi-restraints excluded: chain L residue 173 TYR Chi-restraints excluded: chain L residue 176 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: [16, 12, 119, 134, 63, 227, 140, 224, 32, 76, 98] chunk 16 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 119 optimal weight: 8.9990 chunk 134 optimal weight: 3.9990 chunk 63 optimal weight: 9.9990 chunk 227 optimal weight: 10.0000 chunk 140 optimal weight: 9.9990 chunk 224 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 76 optimal weight: 8.9990 chunk 98 optimal weight: 7.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.055961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.044175 restraints weight = 75733.898| |-----------------------------------------------------------------------------| r_work (start): 0.2710 rms_B_bonded: 3.80 r_work: 0.2595 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 19010 Z= 0.341 Angle : 0.617 9.007 26061 Z= 0.328 Chirality : 0.045 0.160 3273 Planarity : 0.004 0.042 3264 Dihedral : 4.604 52.965 2797 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.32 % Allowed : 19.11 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.11 (0.16), residues: 2594 helix: 1.77 (0.43), residues: 156 sheet: -0.13 (0.15), residues: 1181 loop : -0.11 (0.17), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 131 TYR 0.037 0.002 TYR H 89 PHE 0.030 0.002 PHE A 150 TRP 0.007 0.001 TRP F 54 HIS 0.003 0.001 HIS K 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00746 / 0.34 (19004) covalent geometry : angle 0.61636 / 0.33 (26049) SS BOND : bond 0.00308 / 0.18 ( 6) SS BOND : angle 1.84451 / 0.94 ( 12) hydrogen bonds : bond 0.03393 / 2.43 ( 662) hydrogen bonds : angle 5.46416 / 3.87 ( 1812) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4052.48 seconds wall clock time: 70 minutes 11.58 seconds (4211.58 seconds total)