Starting phenix.real_space_refine on Sun Sep 13 13:56:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ef1_9043/09_2026/6ef1_9043.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ef1_9043/09_2026/6ef1_9043.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ef1_9043/09_2026/6ef1_9043.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ef1_9043/09_2026/6ef1_9043.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6ef1_9043/09_2026/6ef1_9043.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ef1_9043/09_2026/6ef1_9043.cif" model { file = "/net/cci-nas-00/data/ceres_data/6ef1_9043/09_2026/6ef1_9043.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ef1_9043/09_2026/6ef1_9043.cif" } resolution = 4.73 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 66 5.16 5 C 14899 2.51 5 N 4080 2.21 5 O 4597 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23658 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 1818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1818 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 10, 'TRANS': 228} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 3, 'HIS:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 49 Chain: "B" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1801 Classifications: {'peptide': 250} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 12, 'TRANS': 237} Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 10, 'GLN:plan1': 1, 'PHE:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 64 Chain: "C" Number of atoms: 1738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1738 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 5, 'TRANS': 232} Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 7, 'GLN:plan1': 2, 'ASP:plan': 4, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 74 Chain: "D" Number of atoms: 1669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1669 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 10, 'TRANS': 223} Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 195 Unresolved non-hydrogen dihedrals: 133 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 4, 'GLN:plan1': 3, 'GLU:plan': 10, 'ASN:plan1': 3, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 98 Chain: "E" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1725 Classifications: {'peptide': 242} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 4, 'TRANS': 237} Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 164 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 17, 'ARG:plan': 3, 'PHE:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 103 Chain: "F" Number of atoms: 1736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1736 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 6, 'TRANS': 226} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 2, 'GLN:plan1': 2, 'ASP:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "G" Number of atoms: 1822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1822 Classifications: {'peptide': 243} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 9, 'TRANS': 233} Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 1, 'GLU:plan': 5, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 39 Chain: "H" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1764 Classifications: {'peptide': 254} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 13, 'TRANS': 240} Chain breaks: 1 Unresolved non-hydrogen bonds: 219 Unresolved non-hydrogen angles: 265 Unresolved non-hydrogen dihedrals: 183 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLU:plan': 9, 'PHE:plan': 5, 'ASP:plan': 6, 'ARG:plan': 6, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 117 Chain: "I" Number of atoms: 1918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1918 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 11, 'TRANS': 259} Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 225 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 12, 'ASN:plan1': 4, 'ARG:plan': 4, 'TYR:plan': 1, 'PHE:plan': 1, 'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 103 Chain: "J" Number of atoms: 1923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 1923 Classifications: {'peptide': 273} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 12, 'TRANS': 260} Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 226 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 10, 'ARG:plan': 9, 'ASN:plan1': 4, 'GLN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 114 Chain: "K" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 1856 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 263} Unresolved non-hydrogen bonds: 306 Unresolved non-hydrogen angles: 376 Unresolved non-hydrogen dihedrals: 242 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ASP:plan': 16, 'GLU:plan': 7, 'ASN:plan1': 5, 'ARG:plan': 14, 'GLN:plan1': 4, 'PHE:plan': 3} Unresolved non-hydrogen planarities: 195 Chain: "L" Number of atoms: 1867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 1867 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 249} Chain breaks: 1 Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 235 Unresolved non-hydrogen dihedrals: 165 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASN:plan1': 1, 'PHE:plan': 3, 'GLN:plan1': 3, 'GLU:plan': 8, 'ASP:plan': 3, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 109 Chain: "M" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1756 Classifications: {'peptide': 262} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 10, 'TRANS': 251} Unresolved non-hydrogen bonds: 278 Unresolved non-hydrogen angles: 338 Unresolved non-hydrogen dihedrals: 230 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'ASP:plan': 8, 'PHE:plan': 6, 'ARG:plan': 8, 'GLN:plan1': 6, 'GLU:plan': 6, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 151 Chain: "s" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 87 Classifications: {'peptide': 15} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 14} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "H" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.49, per 1000 atoms: 0.23 Number of scatterers: 23658 At special positions: 0 Unit cell: (135.96, 140.08, 126.69, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 66 16.00 P 16 15.00 O 4597 8.00 N 4080 7.00 C 14899 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.85 Conformation dependent library (CDL) restraints added in 1.2 seconds 6524 Ramachandran restraints generated. 3262 Oldfield, 0 Emsley, 3262 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6088 Finding SS restraints... Secondary structure from input PDB file: 137 helices and 29 sheets defined 43.7% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 25 through 36 removed outlier: 3.539A pdb=" N TYR A 30 " --> pdb=" O TYR A 26 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ALA A 31 " --> pdb=" O GLN A 27 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS A 33 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR A 35 " --> pdb=" O ALA A 31 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ASN A 36 " --> pdb=" O PHE A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 109 removed outlier: 3.684A pdb=" N ASN A 92 " --> pdb=" O PRO A 88 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA A 93 " --> pdb=" O ASP A 89 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N PHE A 104 " --> pdb=" O GLU A 100 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS A 107 " --> pdb=" O GLU A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 130 removed outlier: 3.783A pdb=" N LEU A 117 " --> pdb=" O PRO A 113 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE A 127 " --> pdb=" O ASN A 123 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR A 128 " --> pdb=" O LEU A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 190 removed outlier: 3.936A pdb=" N ILE A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N THR A 180 " --> pdb=" O GLN A 176 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ASN A 181 " --> pdb=" O GLU A 177 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HIS A 185 " --> pdb=" O ASN A 181 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS A 188 " --> pdb=" O ASN A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 201 Processing helix chain 'A' and resid 202 through 214 removed outlier: 3.557A pdb=" N ALA A 206 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE A 211 " --> pdb=" O ILE A 207 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASP A 212 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU A 214 " --> pdb=" O MET A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 246 removed outlier: 3.727A pdb=" N ARG A 244 " --> pdb=" O ASN A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 250 Processing helix chain 'B' and resid 18 through 23 removed outlier: 3.660A pdb=" N ASP B 22 " --> pdb=" O LEU B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 31 Processing helix chain 'B' and resid 79 through 96 removed outlier: 3.816A pdb=" N VAL B 84 " --> pdb=" O PRO B 80 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N LEU B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASP B 87 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N VAL B 92 " --> pdb=" O LYS B 88 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N HIS B 94 " --> pdb=" O ARG B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 102 Processing helix chain 'B' and resid 106 through 119 removed outlier: 3.973A pdb=" N LEU B 110 " --> pdb=" O PRO B 106 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS B 116 " --> pdb=" O SER B 112 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ILE B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 167 through 179 removed outlier: 4.045A pdb=" N GLU B 176 " --> pdb=" O LYS B 172 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N LYS B 177 " --> pdb=" O THR B 173 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG B 178 " --> pdb=" O PHE B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 199 removed outlier: 3.800A pdb=" N ILE B 191 " --> pdb=" O ASP B 187 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU B 198 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N SER B 199 " --> pdb=" O THR B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 223 removed outlier: 3.929A pdb=" N LEU B 222 " --> pdb=" O ASN B 218 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLY B 223 " --> pdb=" O PRO B 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 218 through 223' Processing helix chain 'B' and resid 239 through 249 removed outlier: 4.052A pdb=" N ILE B 243 " --> pdb=" O THR B 239 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN B 244 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG B 246 " --> pdb=" O GLU B 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 29 removed outlier: 3.648A pdb=" N ALA C 25 " --> pdb=" O GLN C 21 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU C 27 " --> pdb=" O GLU C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 32 No H-bonds generated for 'chain 'C' and resid 30 through 32' Processing helix chain 'C' and resid 84 through 103 removed outlier: 3.593A pdb=" N ILE C 88 " --> pdb=" O ALA C 84 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASN C 89 " --> pdb=" O GLU C 85 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE C 93 " --> pdb=" O ASN C 89 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR C 98 " --> pdb=" O HIS C 94 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU C 99 " --> pdb=" O ALA C 95 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N THR C 101 " --> pdb=" O ASN C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 112 removed outlier: 3.707A pdb=" N LEU C 111 " --> pdb=" O PRO C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 124 removed outlier: 4.059A pdb=" N GLN C 120 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY C 121 " --> pdb=" O ASP C 117 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR C 122 " --> pdb=" O ILE C 118 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR C 123 " --> pdb=" O LYS C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 180 removed outlier: 3.681A pdb=" N THR C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU C 175 " --> pdb=" O ALA C 171 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU C 176 " --> pdb=" O ALA C 172 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN C 177 " --> pdb=" O GLN C 173 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N MET C 178 " --> pdb=" O THR C 174 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ASP C 179 " --> pdb=" O LEU C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 201 removed outlier: 4.669A pdb=" N GLU C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N LEU C 192 " --> pdb=" O ASP C 188 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA C 193 " --> pdb=" O ALA C 189 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU C 194 " --> pdb=" O ILE C 190 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS C 199 " --> pdb=" O LYS C 195 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR C 200 " --> pdb=" O THR C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 209 No H-bonds generated for 'chain 'C' and resid 207 through 209' Processing helix chain 'C' and resid 231 through 242 removed outlier: 3.825A pdb=" N VAL C 240 " --> pdb=" O LYS C 236 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS C 241 " --> pdb=" O ASP C 237 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N THR C 242 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 24 removed outlier: 4.240A pdb=" N LEU D 24 " --> pdb=" O VAL D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 100 removed outlier: 3.605A pdb=" N ILE D 84 " --> pdb=" O ALA D 80 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LEU D 85 " --> pdb=" O ASP D 81 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE D 86 " --> pdb=" O SER D 82 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU D 87 " --> pdb=" O ARG D 83 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N LEU D 98 " --> pdb=" O GLN D 94 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU D 100 " --> pdb=" O HIS D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 120 removed outlier: 3.580A pdb=" N GLN D 117 " --> pdb=" O VAL D 113 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLN D 118 " --> pdb=" O ALA D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 175 removed outlier: 4.097A pdb=" N VAL D 171 " --> pdb=" O ASN D 167 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU D 175 " --> pdb=" O VAL D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 178 No H-bonds generated for 'chain 'D' and resid 176 through 178' Processing helix chain 'D' and resid 187 through 204 removed outlier: 4.008A pdb=" N LEU D 199 " --> pdb=" O THR D 195 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N GLU D 201 " --> pdb=" O ARG D 197 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N VAL D 202 " --> pdb=" O SER D 198 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN D 204 " --> pdb=" O LEU D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 225 through 238 removed outlier: 3.546A pdb=" N ILE D 229 " --> pdb=" O SER D 225 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N THR D 234 " --> pdb=" O ASN D 230 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLN D 235 " --> pdb=" O GLN D 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 28 Processing helix chain 'E' and resid 30 through 34 Processing helix chain 'E' and resid 81 through 103 removed outlier: 4.075A pdb=" N ALA E 85 " --> pdb=" O LEU E 81 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG E 86 " --> pdb=" O THR E 82 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N SER E 87 " --> pdb=" O ALA E 83 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N MET E 88 " --> pdb=" O ASP E 84 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLU E 90 " --> pdb=" O ARG E 86 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N HIS E 91 " --> pdb=" O SER E 87 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR E 103 " --> pdb=" O HIS E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 120 removed outlier: 3.527A pdb=" N LEU E 112 " --> pdb=" O ASN E 108 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN E 114 " --> pdb=" O GLU E 110 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N SER E 115 " --> pdb=" O SER E 111 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL E 116 " --> pdb=" O LEU E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 123 No H-bonds generated for 'chain 'E' and resid 121 through 123' Processing helix chain 'E' and resid 175 through 186 removed outlier: 4.943A pdb=" N ALA E 181 " --> pdb=" O GLU E 177 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLU E 182 " --> pdb=" O GLY E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 205 removed outlier: 4.073A pdb=" N VAL E 200 " --> pdb=" O ALA E 196 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N LEU E 201 " --> pdb=" O GLU E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 248 removed outlier: 3.568A pdb=" N THR E 236 " --> pdb=" O ASP E 232 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA E 237 " --> pdb=" O ASN E 233 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LEU E 239 " --> pdb=" O LYS E 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 26 Processing helix chain 'F' and resid 26 through 32 removed outlier: 4.046A pdb=" N LYS F 30 " --> pdb=" O LEU F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 94 removed outlier: 3.604A pdb=" N VAL F 83 " --> pdb=" O PRO F 79 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU F 84 " --> pdb=" O ASP F 80 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER F 85 " --> pdb=" O ALA F 81 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLN F 90 " --> pdb=" O ASN F 86 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN F 91 " --> pdb=" O TYR F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 99 Processing helix chain 'F' and resid 104 through 121 removed outlier: 4.060A pdb=" N ALA F 108 " --> pdb=" O ALA F 104 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY F 109 " --> pdb=" O VAL F 105 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ASP F 114 " --> pdb=" O HIS F 110 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA F 116 " --> pdb=" O LEU F 112 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN F 117 " --> pdb=" O CYS F 113 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LYS F 118 " --> pdb=" O ASP F 114 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN F 119 " --> pdb=" O LYS F 115 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLN F 121 " --> pdb=" O GLN F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 174 removed outlier: 3.616A pdb=" N TYR F 171 " --> pdb=" O GLY F 167 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU F 172 " --> pdb=" O ALA F 168 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU F 173 " --> pdb=" O LYS F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 182 removed outlier: 3.761A pdb=" N ILE F 182 " --> pdb=" O PHE F 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 198 removed outlier: 3.914A pdb=" N LEU F 189 " --> pdb=" O ASN F 185 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA F 192 " --> pdb=" O GLU F 188 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLY F 193 " --> pdb=" O LEU F 189 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL F 194 " --> pdb=" O ILE F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 201 No H-bonds generated for 'chain 'F' and resid 199 through 201' Processing helix chain 'F' and resid 228 through 233 removed outlier: 3.948A pdb=" N ALA F 231 " --> pdb=" O GLU F 228 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS F 232 " --> pdb=" O ALA F 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 32 removed outlier: 4.016A pdb=" N GLU G 25 " --> pdb=" O ASN G 21 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LYS G 29 " --> pdb=" O GLU G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 96 removed outlier: 4.076A pdb=" N LEU G 88 " --> pdb=" O ASP G 84 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N VAL G 89 " --> pdb=" O GLY G 85 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLU G 94 " --> pdb=" O ASN G 90 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA G 96 " --> pdb=" O GLY G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 104 removed outlier: 5.096A pdb=" N LEU G 102 " --> pdb=" O SER G 98 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TYR G 103 " --> pdb=" O PHE G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 115 Processing helix chain 'G' and resid 118 through 123 Processing helix chain 'G' and resid 168 through 181 removed outlier: 3.902A pdb=" N ALA G 172 " --> pdb=" O GLY G 168 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA G 174 " --> pdb=" O GLN G 170 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ASP G 181 " --> pdb=" O GLU G 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 188 through 204 removed outlier: 3.615A pdb=" N ALA G 192 " --> pdb=" O SER G 188 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS G 194 " --> pdb=" O ARG G 190 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA G 197 " --> pdb=" O VAL G 193 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE G 199 " --> pdb=" O GLN G 195 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE G 200 " --> pdb=" O ALA G 196 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR G 201 " --> pdb=" O ALA G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 208 removed outlier: 3.953A pdb=" N LYS G 208 " --> pdb=" O GLU G 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 205 through 208' Processing helix chain 'G' and resid 233 through 248 removed outlier: 3.571A pdb=" N GLN G 237 " --> pdb=" O GLY G 233 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LYS G 245 " --> pdb=" O ASP G 241 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU G 246 " --> pdb=" O PHE G 242 " (cutoff:3.500A) Processing helix chain 'H' and resid 218 through 231 Proline residue: H 228 - end of helix Processing helix chain 'H' and resid 231 through 239 removed outlier: 3.910A pdb=" N LEU H 238 " --> pdb=" O ARG H 234 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 268 removed outlier: 3.628A pdb=" N VAL H 263 " --> pdb=" O CYS H 259 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA H 264 " --> pdb=" O ALA H 260 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN H 265 " --> pdb=" O ARG H 261 " (cutoff:3.500A) Processing helix chain 'H' and resid 275 through 280 Processing helix chain 'H' and resid 287 through 299 removed outlier: 4.414A pdb=" N VAL H 291 " --> pdb=" O GLY H 287 " (cutoff:3.500A) Processing helix chain 'H' and resid 328 through 344 removed outlier: 3.727A pdb=" N THR H 332 " --> pdb=" O GLU H 328 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLN H 339 " --> pdb=" O GLU H 335 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU H 340 " --> pdb=" O LEU H 336 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N GLY H 342 " --> pdb=" O THR H 338 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N PHE H 343 " --> pdb=" O GLN H 339 " (cutoff:3.500A) Processing helix chain 'H' and resid 381 through 393 removed outlier: 3.885A pdb=" N ILE H 391 " --> pdb=" O ASN H 387 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N HIS H 392 " --> pdb=" O ILE H 388 " (cutoff:3.500A) Processing helix chain 'H' and resid 404 through 409 removed outlier: 3.631A pdb=" N SER H 408 " --> pdb=" O TRP H 404 " (cutoff:3.500A) Processing helix chain 'H' and resid 416 through 434 removed outlier: 4.196A pdb=" N THR H 424 " --> pdb=" O ARG H 420 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU H 425 " --> pdb=" O SER H 421 " (cutoff:3.500A) Processing helix chain 'H' and resid 440 through 453 removed outlier: 3.954A pdb=" N ALA H 446 " --> pdb=" O ASP H 442 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N LYS H 449 " --> pdb=" O LYS H 445 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE H 451 " --> pdb=" O VAL H 447 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER H 452 " --> pdb=" O ASP H 448 " (cutoff:3.500A) Processing helix chain 'I' and resid 168 through 172 removed outlier: 3.645A pdb=" N LYS I 172 " --> pdb=" O VAL I 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 168 through 172' Processing helix chain 'I' and resid 188 through 198 Processing helix chain 'I' and resid 199 through 203 Processing helix chain 'I' and resid 205 through 211 removed outlier: 3.600A pdb=" N MET I 211 " --> pdb=" O LEU I 207 " (cutoff:3.500A) Processing helix chain 'I' and resid 230 through 240 Processing helix chain 'I' and resid 248 through 253 Processing helix chain 'I' and resid 258 through 272 removed outlier: 3.556A pdb=" N ARG I 265 " --> pdb=" O PRO I 261 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLN I 266 " --> pdb=" O ARG I 262 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE I 267 " --> pdb=" O LEU I 263 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N PHE I 268 " --> pdb=" O CYS I 264 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS I 269 " --> pdb=" O ARG I 265 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL I 270 " --> pdb=" O GLN I 266 " (cutoff:3.500A) Processing helix chain 'I' and resid 283 through 287 removed outlier: 4.451A pdb=" N ALA I 286 " --> pdb=" O GLU I 283 " (cutoff:3.500A) Processing helix chain 'I' and resid 299 through 314 removed outlier: 4.000A pdb=" N GLN I 303 " --> pdb=" O GLU I 299 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU I 307 " --> pdb=" O GLN I 303 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU I 308 " --> pdb=" O ARG I 304 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN I 312 " --> pdb=" O GLU I 308 " (cutoff:3.500A) Processing helix chain 'I' and resid 355 through 366 removed outlier: 3.756A pdb=" N ILE I 361 " --> pdb=" O THR I 357 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LEU I 362 " --> pdb=" O LYS I 358 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY I 363 " --> pdb=" O LYS I 359 " (cutoff:3.500A) Processing helix chain 'I' and resid 388 through 390 No H-bonds generated for 'chain 'I' and resid 388 through 390' Processing helix chain 'I' and resid 391 through 405 removed outlier: 4.025A pdb=" N THR I 397 " --> pdb=" O GLN I 393 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA I 399 " --> pdb=" O MET I 395 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLY I 400 " --> pdb=" O CYS I 396 " (cutoff:3.500A) Processing helix chain 'I' and resid 414 through 416 No H-bonds generated for 'chain 'I' and resid 414 through 416' Processing helix chain 'I' and resid 417 through 423 Processing helix chain 'J' and resid 155 through 170 removed outlier: 4.864A pdb=" N GLU J 162 " --> pdb=" O LYS J 158 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N VAL J 163 " --> pdb=" O GLU J 159 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE J 164 " --> pdb=" O ILE J 160 " (cutoff:3.500A) Proline residue: J 167 - end of helix Processing helix chain 'J' and resid 170 through 178 removed outlier: 4.040A pdb=" N LEU J 177 " --> pdb=" O LEU J 173 " (cutoff:3.500A) Processing helix chain 'J' and resid 194 through 202 removed outlier: 3.844A pdb=" N ALA J 201 " --> pdb=" O LEU J 197 " (cutoff:3.500A) Processing helix chain 'J' and resid 224 through 239 removed outlier: 3.885A pdb=" N ARG J 228 " --> pdb=" O GLY J 224 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N MET J 229 " --> pdb=" O GLU J 225 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL J 235 " --> pdb=" O ARG J 231 " (cutoff:3.500A) Processing helix chain 'J' and resid 264 through 277 removed outlier: 3.566A pdb=" N VAL J 268 " --> pdb=" O GLY J 264 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG J 270 " --> pdb=" O SER J 266 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR J 271 " --> pdb=" O GLU J 267 " (cutoff:3.500A) Processing helix chain 'J' and resid 281 through 288 Processing helix chain 'J' and resid 301 through 305 Processing helix chain 'J' and resid 320 through 332 removed outlier: 4.016A pdb=" N GLU J 326 " --> pdb=" O ALA J 322 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ILE J 327 " --> pdb=" O ALA J 323 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU J 328 " --> pdb=" O ARG J 324 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ARG J 329 " --> pdb=" O ALA J 325 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE J 330 " --> pdb=" O GLU J 326 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N HIS J 331 " --> pdb=" O ILE J 327 " (cutoff:3.500A) Processing helix chain 'J' and resid 343 through 348 removed outlier: 4.547A pdb=" N ALA J 347 " --> pdb=" O LEU J 343 " (cutoff:3.500A) Processing helix chain 'J' and resid 355 through 372 removed outlier: 3.903A pdb=" N LYS J 359 " --> pdb=" O GLY J 355 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU J 364 " --> pdb=" O GLY J 360 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N MET J 367 " --> pdb=" O THR J 363 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR J 368 " --> pdb=" O GLU J 364 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA J 369 " --> pdb=" O ALA J 365 " (cutoff:3.500A) Processing helix chain 'J' and resid 378 through 384 Processing helix chain 'J' and resid 385 through 393 removed outlier: 3.872A pdb=" N VAL J 389 " --> pdb=" O ALA J 385 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASN J 391 " --> pdb=" O GLY J 387 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS J 392 " --> pdb=" O LYS J 388 " (cutoff:3.500A) Processing helix chain 'K' and resid 177 through 186 removed outlier: 5.426A pdb=" N GLU K 183 " --> pdb=" O MET K 179 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG K 185 " --> pdb=" O LYS K 181 " (cutoff:3.500A) Processing helix chain 'K' and resid 194 through 201 removed outlier: 3.540A pdb=" N TYR K 198 " --> pdb=" O GLN K 194 " (cutoff:3.500A) Processing helix chain 'K' and resid 218 through 223 removed outlier: 3.900A pdb=" N LEU K 222 " --> pdb=" O GLY K 218 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL K 223 " --> pdb=" O LYS K 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 218 through 223' Processing helix chain 'K' and resid 225 through 230 removed outlier: 4.044A pdb=" N THR K 230 " --> pdb=" O ALA K 227 " (cutoff:3.500A) Processing helix chain 'K' and resid 248 through 264 removed outlier: 3.980A pdb=" N ARG K 255 " --> pdb=" O PRO K 251 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASP K 256 " --> pdb=" O ARG K 252 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG K 259 " --> pdb=" O ARG K 255 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU K 263 " --> pdb=" O ARG K 259 " (cutoff:3.500A) Processing helix chain 'K' and resid 286 through 305 removed outlier: 3.707A pdb=" N GLU K 291 " --> pdb=" O GLY K 287 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N VAL K 292 " --> pdb=" O SER K 288 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLN K 293 " --> pdb=" O ASP K 289 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ILE K 295 " --> pdb=" O GLU K 291 " (cutoff:3.500A) Processing helix chain 'K' and resid 345 through 360 removed outlier: 3.672A pdb=" N ARG K 350 " --> pdb=" O ARG K 346 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LEU K 351 " --> pdb=" O ARG K 347 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N GLY K 354 " --> pdb=" O ARG K 350 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ILE K 356 " --> pdb=" O ILE K 352 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N ALA K 357 " --> pdb=" O PHE K 353 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS K 359 " --> pdb=" O THR K 355 " (cutoff:3.500A) Processing helix chain 'K' and resid 370 through 374 Processing helix chain 'K' and resid 381 through 386 Processing helix chain 'K' and resid 386 through 391 Processing helix chain 'K' and resid 403 through 414 removed outlier: 3.669A pdb=" N LEU K 407 " --> pdb=" O LEU K 403 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU K 408 " --> pdb=" O GLN K 404 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLU K 409 " --> pdb=" O SER K 405 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA K 410 " --> pdb=" O ASP K 406 " (cutoff:3.500A) Processing helix chain 'K' and resid 420 through 425 Processing helix chain 'L' and resid 167 through 172 Processing helix chain 'L' and resid 179 through 183 removed outlier: 3.953A pdb=" N GLY L 182 " --> pdb=" O THR L 179 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ILE L 183 " --> pdb=" O PHE L 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 179 through 183' Processing helix chain 'L' and resid 186 through 202 removed outlier: 3.510A pdb=" N ILE L 190 " --> pdb=" O LEU L 186 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG L 194 " --> pdb=" O ILE L 190 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU L 199 " --> pdb=" O GLU L 195 " (cutoff:3.500A) Proline residue: L 200 - end of helix Processing helix chain 'L' and resid 204 through 211 removed outlier: 3.798A pdb=" N GLN L 208 " --> pdb=" O PRO L 204 " (cutoff:3.500A) Processing helix chain 'L' and resid 227 through 240 removed outlier: 3.539A pdb=" N VAL L 235 " --> pdb=" O LEU L 231 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA L 236 " --> pdb=" O ALA L 232 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ALA L 237 " --> pdb=" O LYS L 233 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE L 239 " --> pdb=" O VAL L 235 " (cutoff:3.500A) Processing helix chain 'L' and resid 255 through 272 removed outlier: 3.675A pdb=" N SER L 259 " --> pdb=" O TYR L 255 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA L 260 " --> pdb=" O ILE L 256 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE L 263 " --> pdb=" O SER L 259 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ARG L 264 " --> pdb=" O ALA L 260 " (cutoff:3.500A) Processing helix chain 'L' and resid 282 through 286 removed outlier: 3.977A pdb=" N ALA L 285 " --> pdb=" O GLU L 282 " (cutoff:3.500A) Processing helix chain 'L' and resid 297 through 314 removed outlier: 3.938A pdb=" N ILE L 301 " --> pdb=" O ALA L 297 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N ARG L 303 " --> pdb=" O ARG L 299 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR L 304 " --> pdb=" O GLU L 300 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU L 309 " --> pdb=" O LEU L 305 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR L 310 " --> pdb=" O MET L 306 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP L 313 " --> pdb=" O LEU L 309 " (cutoff:3.500A) Processing helix chain 'L' and resid 333 through 339 removed outlier: 3.748A pdb=" N LEU L 337 " --> pdb=" O LEU L 333 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG L 339 " --> pdb=" O PRO L 335 " (cutoff:3.500A) Processing helix chain 'L' and resid 353 through 365 removed outlier: 4.634A pdb=" N GLU L 359 " --> pdb=" O ALA L 355 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N PHE L 361 " --> pdb=" O ARG L 357 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LYS L 362 " --> pdb=" O LEU L 358 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ILE L 363 " --> pdb=" O GLU L 359 " (cutoff:3.500A) Processing helix chain 'L' and resid 376 through 382 removed outlier: 3.582A pdb=" N VAL L 380 " --> pdb=" O PHE L 376 " (cutoff:3.500A) Processing helix chain 'L' and resid 387 through 402 removed outlier: 3.729A pdb=" N ILE L 391 " --> pdb=" O ASN L 387 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N PHE L 401 " --> pdb=" O GLU L 397 " (cutoff:3.500A) Processing helix chain 'L' and resid 411 through 416 removed outlier: 4.187A pdb=" N LEU L 415 " --> pdb=" O ASN L 411 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N MET L 416 " --> pdb=" O PRO L 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 411 through 416' Processing helix chain 'L' and resid 418 through 427 removed outlier: 3.549A pdb=" N ALA L 423 " --> pdb=" O VAL L 419 " (cutoff:3.500A) Processing helix chain 'M' and resid 186 through 189 Processing helix chain 'M' and resid 190 through 202 removed outlier: 3.625A pdb=" N GLU M 195 " --> pdb=" O GLU M 191 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA M 196 " --> pdb=" O GLU M 192 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU M 199 " --> pdb=" O GLU M 195 " (cutoff:3.500A) Proline residue: M 200 - end of helix Processing helix chain 'M' and resid 203 through 211 Processing helix chain 'M' and resid 227 through 234 Processing helix chain 'M' and resid 257 through 272 removed outlier: 3.535A pdb=" N ASP M 265 " --> pdb=" O LYS M 261 " (cutoff:3.500A) Processing helix chain 'M' and resid 282 through 287 Processing helix chain 'M' and resid 300 through 318 removed outlier: 4.038A pdb=" N ASP M 318 " --> pdb=" O GLY M 314 " (cutoff:3.500A) Processing helix chain 'M' and resid 335 through 339 removed outlier: 3.658A pdb=" N LEU M 338 " --> pdb=" O PRO M 335 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG M 339 " --> pdb=" O ALA M 336 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 335 through 339' Processing helix chain 'M' and resid 354 through 367 removed outlier: 3.692A pdb=" N LEU M 361 " --> pdb=" O ARG M 357 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN M 362 " --> pdb=" O ALA M 358 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LYS M 367 " --> pdb=" O ILE M 363 " (cutoff:3.500A) Processing helix chain 'M' and resid 375 through 383 removed outlier: 4.135A pdb=" N LEU M 379 " --> pdb=" O ASN M 375 " (cutoff:3.500A) Processing helix chain 'M' and resid 387 through 392 Processing helix chain 'M' and resid 398 through 406 removed outlier: 3.632A pdb=" N ALA M 402 " --> pdb=" O ALA M 398 " (cutoff:3.500A) Processing helix chain 'M' and resid 415 through 421 Processing sheet with id=AA1, first strand: chain 'A' and resid 169 through 171 removed outlier: 3.591A pdb=" N VAL A 45 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL A 52 " --> pdb=" O VAL A 45 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N THR A 51 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA A 228 " --> pdb=" O THR A 51 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER A 55 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE A 234 " --> pdb=" O VAL A 227 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 141 through 145 removed outlier: 3.703A pdb=" N LEU A 141 " --> pdb=" O THR A 157 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 161 through 164 removed outlier: 3.601A pdb=" N ALA B 46 " --> pdb=" O LEU B 35 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL B 43 " --> pdb=" O ILE B 214 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA B 212 " --> pdb=" O ILE B 45 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG B 236 " --> pdb=" O ILE B 213 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 64 through 68 removed outlier: 3.566A pdb=" N LEU B 67 " --> pdb=" O ILE B 71 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N GLY B 72 " --> pdb=" O ALA B 137 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA B 137 " --> pdb=" O GLY B 72 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU B 147 " --> pdb=" O TRP B 159 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TRP B 159 " --> pdb=" O LEU B 147 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 162 through 163 removed outlier: 4.234A pdb=" N THR C 34 " --> pdb=" O GLU C 49 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA C 47 " --> pdb=" O ILE C 36 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE C 38 " --> pdb=" O VAL C 45 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N VAL C 45 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE C 216 " --> pdb=" O ILE C 44 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU C 46 " --> pdb=" O ALA C 214 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA C 214 " --> pdb=" O LEU C 46 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 68 through 70 removed outlier: 4.426A pdb=" N ASN C 70 " --> pdb=" O ILE C 73 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE C 73 " --> pdb=" O ASN C 70 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 76 through 79 Processing sheet with id=AA8, first strand: chain 'C' and resid 139 through 141 removed outlier: 4.148A pdb=" N GLY C 139 " --> pdb=" O GLN C 147 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP C 141 " --> pdb=" O GLY C 145 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 161 through 163 removed outlier: 3.913A pdb=" N GLN D 162 " --> pdb=" O GLY D 35 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY D 35 " --> pdb=" O GLN D 162 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL D 43 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL D 42 " --> pdb=" O VAL D 215 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR D 213 " --> pdb=" O LEU D 44 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 64 through 66 removed outlier: 3.524A pdb=" N VAL D 72 " --> pdb=" O ALA D 136 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA D 136 " --> pdb=" O VAL D 72 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 45 through 46 Processing sheet with id=AB3, first strand: chain 'E' and resid 45 through 46 removed outlier: 4.221A pdb=" N GLY E 39 " --> pdb=" O LYS E 170 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYS E 170 " --> pdb=" O GLY E 39 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 74 through 79 removed outlier: 3.507A pdb=" N GLY E 75 " --> pdb=" O ALA E 145 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR E 165 " --> pdb=" O HIS E 157 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU E 159 " --> pdb=" O THR E 163 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR E 163 " --> pdb=" O GLU E 159 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 220 through 223 removed outlier: 3.832A pdb=" N LYS E 229 " --> pdb=" O CYS E 221 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 37 through 38 removed outlier: 3.519A pdb=" N GLY F 37 " --> pdb=" O THR F 159 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 43 through 49 removed outlier: 3.727A pdb=" N ALA F 214 " --> pdb=" O LEU F 46 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR F 223 " --> pdb=" O ILE F 215 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 63 through 67 removed outlier: 6.801A pdb=" N ILE F 63 " --> pdb=" O LEU F 74 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N LEU F 74 " --> pdb=" O ILE F 63 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N LYS F 65 " --> pdb=" O LEU F 72 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU F 72 " --> pdb=" O LYS F 65 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP F 67 " --> pdb=" O MET F 70 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY F 71 " --> pdb=" O ILE F 135 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY F 131 " --> pdb=" O ALA F 75 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE F 134 " --> pdb=" O LEU F 145 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY F 136 " --> pdb=" O HIS F 143 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU F 144 " --> pdb=" O LEU F 156 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 162 through 164 removed outlier: 3.621A pdb=" N ALA G 163 " --> pdb=" O GLY G 39 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLY G 39 " --> pdb=" O ALA G 163 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLU G 215 " --> pdb=" O VAL G 50 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TRP G 218 " --> pdb=" O LYS G 229 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS G 229 " --> pdb=" O TRP G 218 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 53 through 54 removed outlier: 4.385A pdb=" N ASP G 211 " --> pdb=" O ILE G 54 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 74 through 80 removed outlier: 3.500A pdb=" N GLY G 75 " --> pdb=" O GLY G 139 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL G 77 " --> pdb=" O ILE G 137 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE G 137 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER G 135 " --> pdb=" O SER G 79 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLY G 140 " --> pdb=" O HIS G 147 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET G 150 " --> pdb=" O TRP G 158 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TRP G 158 " --> pdb=" O MET G 150 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 245 through 246 Processing sheet with id=AC4, first strand: chain 'H' and resid 248 through 249 Processing sheet with id=AC5, first strand: chain 'I' and resid 325 through 326 removed outlier: 7.233A pdb=" N VAL I 219 " --> pdb=" O MET I 326 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 186 through 188 Processing sheet with id=AC7, first strand: chain 'J' and resid 209 through 210 removed outlier: 5.775A pdb=" N LYS J 209 " --> pdb=" O ILE J 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'L' and resid 218 through 219 removed outlier: 3.836A pdb=" N LEU L 219 " --> pdb=" O ASP L 344 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N LYS L 346 " --> pdb=" O LEU L 219 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'L' and resid 276 through 277 removed outlier: 7.748A pdb=" N CYS L 276 " --> pdb=" O LYS L 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'M' and resid 219 through 221 removed outlier: 6.115A pdb=" N LEU M 219 " --> pdb=" O ILE M 347 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'M' and resid 278 through 279 removed outlier: 6.825A pdb=" N ILE M 278 " --> pdb=" O LEU M 324 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 738 hydrogen bonds defined for protein. 2109 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: 3.99 Time building geometry restraints manager: 2.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7952 1.34 - 1.46: 4983 1.46 - 1.58: 10974 1.58 - 1.70: 26 1.70 - 1.82: 106 Bond restraints: 24041 Sorted by residual: bond pdb=" C4 ATP J 501 " pdb=" C5 ATP J 501 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.89e+01 bond pdb=" C4 ATP K 501 " pdb=" C5 ATP K 501 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.11e+01 bond pdb=" C4 ATP I 501 " pdb=" C5 ATP I 501 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.05e+01 bond pdb=" C4 ATP H 501 " pdb=" C5 ATP H 501 " ideal model delta sigma weight residual 1.388 1.458 -0.070 1.00e-02 1.00e+04 4.92e+01 bond pdb=" C5 ATP J 501 " pdb=" C6 ATP J 501 " ideal model delta sigma weight residual 1.409 1.473 -0.064 1.00e-02 1.00e+04 4.07e+01 ... (remaining 24036 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.76: 32677 4.76 - 9.51: 115 9.51 - 14.27: 2 14.27 - 19.02: 4 19.02 - 23.78: 3 Bond angle restraints: 32801 Sorted by residual: angle pdb=" PA ATP H 501 " pdb=" O3A ATP H 501 " pdb=" PB ATP H 501 " ideal model delta sigma weight residual 136.83 113.05 23.78 1.00e+00 1.00e+00 5.65e+02 angle pdb=" PA ATP K 501 " pdb=" O3A ATP K 501 " pdb=" PB ATP K 501 " ideal model delta sigma weight residual 136.83 115.52 21.31 1.00e+00 1.00e+00 4.54e+02 angle pdb=" PB ATP K 501 " pdb=" O3B ATP K 501 " pdb=" PG ATP K 501 " ideal model delta sigma weight residual 139.87 119.34 20.53 1.00e+00 1.00e+00 4.21e+02 angle pdb=" PB ATP H 501 " pdb=" O3B ATP H 501 " pdb=" PG ATP H 501 " ideal model delta sigma weight residual 139.87 120.85 19.02 1.00e+00 1.00e+00 3.62e+02 angle pdb=" PB ATP I 501 " pdb=" O3B ATP I 501 " pdb=" PG ATP I 501 " ideal model delta sigma weight residual 139.87 123.53 16.34 1.00e+00 1.00e+00 2.67e+02 ... (remaining 32796 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.49: 13994 26.49 - 52.98: 316 52.98 - 79.48: 35 79.48 - 105.97: 3 105.97 - 132.46: 1 Dihedral angle restraints: 14349 sinusoidal: 4880 harmonic: 9469 Sorted by residual: dihedral pdb=" O1B ADP L 501 " pdb=" O3A ADP L 501 " pdb=" PB ADP L 501 " pdb=" PA ADP L 501 " ideal model delta sinusoidal sigma weight residual 300.00 167.54 132.46 1 2.00e+01 2.50e-03 4.02e+01 dihedral pdb=" CA MET J 149 " pdb=" C MET J 149 " pdb=" N VAL J 150 " pdb=" CA VAL J 150 " ideal model delta harmonic sigma weight residual 180.00 -149.98 -30.02 0 5.00e+00 4.00e-02 3.61e+01 dihedral pdb=" CA ALA J 347 " pdb=" C ALA J 347 " pdb=" N GLU J 348 " pdb=" CA GLU J 348 " ideal model delta harmonic sigma weight residual 180.00 150.81 29.19 0 5.00e+00 4.00e-02 3.41e+01 ... (remaining 14346 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 2519 0.044 - 0.088: 1054 0.088 - 0.132: 304 0.132 - 0.176: 51 0.176 - 0.220: 6 Chirality restraints: 3934 Sorted by residual: chirality pdb=" C2' ATP I 501 " pdb=" C1' ATP I 501 " pdb=" C3' ATP I 501 " pdb=" O2' ATP I 501 " both_signs ideal model delta sigma weight residual False -2.68 -2.46 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" C2' ATP H 501 " pdb=" C1' ATP H 501 " pdb=" C3' ATP H 501 " pdb=" O2' ATP H 501 " both_signs ideal model delta sigma weight residual False -2.68 -2.49 -0.19 2.00e-01 2.50e+01 8.96e-01 chirality pdb=" CG LEU L 415 " pdb=" CB LEU L 415 " pdb=" CD1 LEU L 415 " pdb=" CD2 LEU L 415 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.21e-01 ... (remaining 3931 not shown) Planarity restraints: 4254 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 106 " 0.055 5.00e-02 4.00e+02 8.26e-02 1.09e+01 pdb=" N PRO C 107 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO C 107 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 107 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER H 421 " -0.014 2.00e-02 2.50e+03 2.82e-02 7.93e+00 pdb=" C SER H 421 " 0.049 2.00e-02 2.50e+03 pdb=" O SER H 421 " -0.018 2.00e-02 2.50e+03 pdb=" N VAL H 422 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG B 128 " 0.044 5.00e-02 4.00e+02 6.65e-02 7.07e+00 pdb=" N PRO B 129 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO B 129 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 129 " 0.037 5.00e-02 4.00e+02 ... (remaining 4251 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 385 2.61 - 3.18: 24292 3.18 - 3.76: 34120 3.76 - 4.33: 47817 4.33 - 4.90: 71422 Nonbonded interactions: 178036 Sorted by model distance: nonbonded pdb=" O MET H 297 " pdb=" OG1 THR H 300 " model vdw 2.040 3.040 nonbonded pdb=" O ILE L 301 " pdb=" OG1 THR L 304 " model vdw 2.091 3.040 nonbonded pdb=" OG SER I 277 " pdb=" O ASP I 321 " model vdw 2.096 3.040 nonbonded pdb=" O ASN B 205 " pdb=" OG1 THR B 208 " model vdw 2.143 3.040 nonbonded pdb=" O GLU H 233 " pdb=" OG1 THR H 237 " model vdw 2.164 3.040 ... (remaining 178031 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.310 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: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.850 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.050 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 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 : 0.009 0.100 24041 Z= 0.403 Angle : 0.988 23.775 32801 Z= 0.604 Chirality : 0.051 0.220 3934 Planarity : 0.006 0.083 4254 Dihedral : 11.782 132.459 8261 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 14.47 % Favored : 85.50 % Rotamer: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -5.20 (0.12), residues: 3262 helix: -3.99 (0.09), residues: 1014 sheet: -4.14 (0.19), residues: 356 loop : -3.07 (0.14), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG D 58 TYR 0.024 0.003 TYR I 436 PHE 0.029 0.003 PHE E 123 TRP 0.023 0.003 TRP E 187 HIS 0.014 0.003 HIS G 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00862 / 0.40 (24041) covalent geometry : angle 0.98801 / 0.60 (32801) hydrogen bonds : bond 0.33113 / 22.23 ( 736) hydrogen bonds : angle 11.55024 / 8.05 ( 2109) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6524 Ramachandran restraints generated. 3262 Oldfield, 0 Emsley, 3262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6524 Ramachandran restraints generated. 3262 Oldfield, 0 Emsley, 3262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 607 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 TYR cc_start: 0.8545 (m-10) cc_final: 0.8098 (m-80) REVERT: B 130 PHE cc_start: 0.8179 (m-80) cc_final: 0.7899 (m-80) REVERT: C 110 ILE cc_start: 0.8561 (mt) cc_final: 0.8256 (mm) REVERT: C 233 GLN cc_start: 0.8890 (pp30) cc_final: 0.8290 (pp30) REVERT: D 44 LEU cc_start: 0.8684 (mt) cc_final: 0.8472 (mm) REVERT: D 176 GLU cc_start: 0.8392 (mt-10) cc_final: 0.8162 (mt-10) REVERT: D 230 ASN cc_start: 0.8072 (m110) cc_final: 0.7621 (m-40) REVERT: E 235 LYS cc_start: 0.8043 (mtmt) cc_final: 0.7709 (mtpt) REVERT: F 73 SER cc_start: 0.8566 (p) cc_final: 0.8090 (m) REVERT: F 91 GLN cc_start: 0.9156 (mm110) cc_final: 0.8698 (tp40) REVERT: F 146 GLU cc_start: 0.7572 (tp30) cc_final: 0.7119 (tp30) REVERT: G 14 VAL cc_start: 0.8624 (t) cc_final: 0.8351 (m) REVERT: G 26 TYR cc_start: 0.8343 (m-10) cc_final: 0.8047 (m-80) REVERT: G 51 GLU cc_start: 0.8387 (tt0) cc_final: 0.7971 (tt0) REVERT: G 84 ASP cc_start: 0.8553 (t70) cc_final: 0.8212 (t0) REVERT: G 86 ARG cc_start: 0.7303 (ttt-90) cc_final: 0.6712 (ttt-90) REVERT: G 132 PHE cc_start: 0.8863 (m-10) cc_final: 0.8648 (m-10) REVERT: G 135 SER cc_start: 0.8911 (m) cc_final: 0.8628 (t) REVERT: H 304 CYS cc_start: 0.7433 (t) cc_final: 0.6819 (p) REVERT: H 310 GLU cc_start: 0.9141 (mp0) cc_final: 0.8570 (mp0) REVERT: H 356 ASN cc_start: 0.9309 (t160) cc_final: 0.9100 (t0) REVERT: I 254 GLN cc_start: 0.7681 (mp10) cc_final: 0.7264 (mp10) REVERT: I 255 LYS cc_start: 0.7077 (mmtm) cc_final: 0.6193 (mmtm) REVERT: I 263 LEU cc_start: 0.9144 (mt) cc_final: 0.8943 (mt) REVERT: I 308 GLU cc_start: 0.8338 (tm-30) cc_final: 0.7986 (mm-30) REVERT: J 204 HIS cc_start: 0.8063 (t70) cc_final: 0.7556 (t-90) REVERT: J 207 ASP cc_start: 0.8474 (m-30) cc_final: 0.8002 (t0) REVERT: J 236 MET cc_start: 0.8952 (tpt) cc_final: 0.8635 (tpp) REVERT: J 282 PHE cc_start: 0.9211 (p90) cc_final: 0.8912 (p90) REVERT: J 364 GLU cc_start: 0.9066 (tt0) cc_final: 0.8700 (tt0) REVERT: K 182 GLN cc_start: 0.9205 (tm-30) cc_final: 0.8840 (tm-30) REVERT: L 191 ARG cc_start: 0.8987 (mtp180) cc_final: 0.8415 (mmm160) REVERT: L 199 LEU cc_start: 0.9198 (mm) cc_final: 0.8892 (mm) REVERT: L 317 ASN cc_start: 0.7993 (t0) cc_final: 0.7446 (p0) REVERT: L 362 LYS cc_start: 0.9213 (mmtm) cc_final: 0.8907 (mmtp) REVERT: L 363 ILE cc_start: 0.8950 (pt) cc_final: 0.8629 (tt) REVERT: L 400 PHE cc_start: 0.7258 (m-10) cc_final: 0.6976 (m-80) REVERT: M 188 LYS cc_start: 0.7402 (mttt) cc_final: 0.7066 (tppt) REVERT: M 290 ARG cc_start: 0.5659 (pmt170) cc_final: 0.5430 (mtm180) REVERT: M 397 GLU cc_start: 0.8837 (mp0) cc_final: 0.8503 (mp0) REVERT: M 433 TYR cc_start: 0.8035 (m-10) cc_final: 0.7794 (m-10) outliers start: 0 outliers final: 0 residues processed: 607 average time/residue: 0.1785 time to fit residues: 161.9357 Evaluate side-chains 366 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 366 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 0.6980 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 41 ASN B 139 HIS C 125 HIS ** D 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 231 GLN ** E 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 91 HIS F 21 GLN F 86 ASN ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 413 ASN I 365 HIS I 418 GLN J 156 GLN J 204 HIS J 331 HIS K 182 GLN ** K 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 412 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.074945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.062772 restraints weight = 99315.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.064128 restraints weight = 67209.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.065108 restraints weight = 48971.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.065857 restraints weight = 37900.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.066391 restraints weight = 30688.777| |-----------------------------------------------------------------------------| r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 24041 Z= 0.181 Angle : 0.746 8.645 32801 Z= 0.388 Chirality : 0.047 0.369 3934 Planarity : 0.006 0.114 4254 Dihedral : 7.931 105.265 3539 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 0.14 % Allowed : 4.26 % Favored : 95.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -4.30 (0.13), residues: 3262 helix: -2.60 (0.12), residues: 1192 sheet: -3.29 (0.21), residues: 411 loop : -2.93 (0.15), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG M 342 TYR 0.022 0.002 TYR B 82 PHE 0.026 0.002 PHE L 207 TRP 0.033 0.003 TRP H 404 HIS 0.009 0.002 HIS E 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.18 (24041) covalent geometry : angle 0.74645 / 0.39 (32801) hydrogen bonds : bond 0.05742 / 3.79 ( 736) hydrogen bonds : angle 7.28316 / 5.15 ( 2109) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6524 Ramachandran restraints generated. 3262 Oldfield, 0 Emsley, 3262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6524 Ramachandran restraints generated. 3262 Oldfield, 0 Emsley, 3262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 538 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 TYR cc_start: 0.8716 (m-80) cc_final: 0.8382 (m-80) REVERT: A 42 SER cc_start: 0.8944 (p) cc_final: 0.8336 (m) REVERT: A 55 SER cc_start: 0.7781 (p) cc_final: 0.7106 (p) REVERT: A 224 GLU cc_start: 0.7258 (tt0) cc_final: 0.7052 (tp30) REVERT: B 23 TYR cc_start: 0.8656 (m-10) cc_final: 0.8268 (m-10) REVERT: B 82 TYR cc_start: 0.8915 (t80) cc_final: 0.8531 (t80) REVERT: B 134 LEU cc_start: 0.8684 (pp) cc_final: 0.8209 (pp) REVERT: C 77 VAL cc_start: 0.8517 (t) cc_final: 0.7942 (p) REVERT: C 110 ILE cc_start: 0.8932 (mt) cc_final: 0.8664 (mm) REVERT: C 242 THR cc_start: 0.9173 (m) cc_final: 0.8902 (t) REVERT: D 66 LYS cc_start: 0.9018 (ptmt) cc_final: 0.8797 (ttpt) REVERT: D 81 ASP cc_start: 0.8677 (m-30) cc_final: 0.8185 (m-30) REVERT: D 111 ARG cc_start: 0.8169 (ttp-110) cc_final: 0.7819 (ttm110) REVERT: D 230 ASN cc_start: 0.7560 (m110) cc_final: 0.7250 (m-40) REVERT: E 166 ARG cc_start: 0.8604 (ttt90) cc_final: 0.7983 (tpt-90) REVERT: E 183 LEU cc_start: 0.9380 (mt) cc_final: 0.9032 (mm) REVERT: F 73 SER cc_start: 0.8904 (p) cc_final: 0.8269 (m) REVERT: F 155 GLU cc_start: 0.8345 (mm-30) cc_final: 0.8136 (mm-30) REVERT: G 38 ILE cc_start: 0.8539 (pt) cc_final: 0.8286 (mp) REVERT: G 51 GLU cc_start: 0.8796 (tt0) cc_final: 0.8569 (tt0) REVERT: G 84 ASP cc_start: 0.8679 (t70) cc_final: 0.8354 (t0) REVERT: G 135 SER cc_start: 0.8630 (m) cc_final: 0.8124 (t) REVERT: H 210 ASP cc_start: 0.8529 (m-30) cc_final: 0.8280 (m-30) REVERT: H 310 GLU cc_start: 0.8954 (mp0) cc_final: 0.8621 (mp0) REVERT: I 254 GLN cc_start: 0.8113 (mp10) cc_final: 0.7739 (mp10) REVERT: I 326 MET cc_start: 0.7248 (tpt) cc_final: 0.6884 (tpt) REVERT: I 421 GLU cc_start: 0.8987 (tt0) cc_final: 0.8520 (pt0) REVERT: J 149 MET cc_start: 0.8162 (tpp) cc_final: 0.7835 (tpp) REVERT: J 204 HIS cc_start: 0.8224 (t-90) cc_final: 0.7689 (t70) REVERT: J 207 ASP cc_start: 0.8118 (m-30) cc_final: 0.7772 (t0) REVERT: J 282 PHE cc_start: 0.8745 (p90) cc_final: 0.8495 (p90) REVERT: J 329 ARG cc_start: 0.7899 (ttm-80) cc_final: 0.7642 (ttm110) REVERT: J 367 MET cc_start: 0.9382 (mtp) cc_final: 0.8895 (mtp) REVERT: K 304 ASP cc_start: 0.9308 (t70) cc_final: 0.8706 (t0) REVERT: K 387 MET cc_start: 0.8324 (ptm) cc_final: 0.7982 (ttp) REVERT: L 191 ARG cc_start: 0.9074 (mtp180) cc_final: 0.8817 (mtp180) REVERT: L 194 ARG cc_start: 0.7624 (ttp80) cc_final: 0.7192 (ttp-110) REVERT: L 263 ILE cc_start: 0.9214 (pt) cc_final: 0.8997 (pt) REVERT: L 317 ASN cc_start: 0.8118 (t0) cc_final: 0.7566 (p0) REVERT: L 363 ILE cc_start: 0.8688 (pt) cc_final: 0.8380 (tt) REVERT: L 400 PHE cc_start: 0.7483 (m-10) cc_final: 0.7277 (m-10) REVERT: L 416 MET cc_start: 0.8738 (mmt) cc_final: 0.8305 (mmm) REVERT: M 188 LYS cc_start: 0.7627 (mttt) cc_final: 0.7208 (tppt) REVERT: M 377 GLN cc_start: 0.8598 (mp10) cc_final: 0.8263 (mp10) REVERT: M 390 GLN cc_start: 0.8900 (mm110) cc_final: 0.8608 (mp10) REVERT: s 114 GLU cc_start: 0.8507 (pp20) cc_final: 0.8010 (tp30) outliers start: 3 outliers final: 0 residues processed: 540 average time/residue: 0.1479 time to fit residues: 126.5411 Evaluate side-chains 374 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 374 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 133 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 153 optimal weight: 0.9980 chunk 270 optimal weight: 7.9990 chunk 80 optimal weight: 10.0000 chunk 143 optimal weight: 6.9990 chunk 173 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 82 optimal weight: 0.3980 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 209 HIS B 41 ASN ** C 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 21 GLN ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 192 GLN J 269 GLN K 182 GLN K 293 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.074006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.061878 restraints weight = 98625.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.063257 restraints weight = 65659.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.064245 restraints weight = 47232.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.064965 restraints weight = 36195.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.065499 restraints weight = 29236.727| |-----------------------------------------------------------------------------| r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.116 24041 Z= 0.144 Angle : 0.665 8.865 32801 Z= 0.342 Chirality : 0.045 0.254 3934 Planarity : 0.005 0.047 4254 Dihedral : 7.068 96.511 3539 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.36 % Favored : 92.61 % Rotamer: Outliers : 0.14 % Allowed : 4.21 % Favored : 95.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -3.61 (0.13), residues: 3262 helix: -1.99 (0.13), residues: 1252 sheet: -2.78 (0.22), residues: 435 loop : -2.59 (0.15), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 381 TYR 0.018 0.001 TYR L 221 PHE 0.020 0.002 PHE G 138 TRP 0.016 0.002 TRP H 404 HIS 0.009 0.001 HIS E 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (24041) covalent geometry : angle 0.66519 / 0.34 (32801) hydrogen bonds : bond 0.04384 / 2.90 ( 736) hydrogen bonds : angle 6.38261 / 4.52 ( 2109) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6524 Ramachandran restraints generated. 3262 Oldfield, 0 Emsley, 3262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6524 Ramachandran restraints generated. 3262 Oldfield, 0 Emsley, 3262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 503 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 TYR cc_start: 0.8752 (m-80) cc_final: 0.8482 (m-80) REVERT: A 42 SER cc_start: 0.8897 (p) cc_final: 0.8382 (m) REVERT: A 55 SER cc_start: 0.7827 (p) cc_final: 0.6992 (p) REVERT: A 65 ASP cc_start: 0.7241 (m-30) cc_final: 0.6830 (m-30) REVERT: A 221 ASN cc_start: 0.8261 (p0) cc_final: 0.7792 (p0) REVERT: A 224 GLU cc_start: 0.7488 (tt0) cc_final: 0.7109 (tp30) REVERT: B 23 TYR cc_start: 0.8635 (m-10) cc_final: 0.8349 (m-80) REVERT: B 35 LEU cc_start: 0.9094 (pt) cc_final: 0.8872 (pt) REVERT: B 82 TYR cc_start: 0.8836 (t80) cc_final: 0.8336 (t80) REVERT: B 87 ASP cc_start: 0.8573 (m-30) cc_final: 0.8343 (m-30) REVERT: B 134 LEU cc_start: 0.8656 (pp) cc_final: 0.8112 (pp) REVERT: C 77 VAL cc_start: 0.8590 (t) cc_final: 0.8103 (p) REVERT: C 117 ASP cc_start: 0.8492 (m-30) cc_final: 0.8290 (m-30) REVERT: C 233 GLN cc_start: 0.9174 (pp30) cc_final: 0.8969 (pp30) REVERT: C 242 THR cc_start: 0.9212 (m) cc_final: 0.8909 (t) REVERT: D 230 ASN cc_start: 0.7577 (m110) cc_final: 0.7200 (m-40) REVERT: E 183 LEU cc_start: 0.9382 (mt) cc_final: 0.9050 (mm) REVERT: F 73 SER cc_start: 0.8911 (p) cc_final: 0.8052 (m) REVERT: F 146 GLU cc_start: 0.7492 (tp30) cc_final: 0.7280 (tp30) REVERT: F 155 GLU cc_start: 0.8441 (mm-30) cc_final: 0.8094 (mm-30) REVERT: G 84 ASP cc_start: 0.8644 (t70) cc_final: 0.8376 (t0) REVERT: G 135 SER cc_start: 0.8499 (m) cc_final: 0.7936 (t) REVERT: H 210 ASP cc_start: 0.8532 (m-30) cc_final: 0.8311 (m-30) REVERT: H 294 LEU cc_start: 0.9387 (tp) cc_final: 0.9120 (tp) REVERT: H 297 MET cc_start: 0.8785 (tmm) cc_final: 0.8220 (ppp) REVERT: H 310 GLU cc_start: 0.8911 (mp0) cc_final: 0.8583 (mp0) REVERT: I 192 GLN cc_start: 0.9077 (OUTLIER) cc_final: 0.8367 (pp30) REVERT: I 196 GLU cc_start: 0.8730 (mt-10) cc_final: 0.8460 (mt-10) REVERT: I 254 GLN cc_start: 0.8099 (mp10) cc_final: 0.7751 (mp10) REVERT: I 391 ASP cc_start: 0.8722 (p0) cc_final: 0.8491 (p0) REVERT: I 421 GLU cc_start: 0.8929 (tt0) cc_final: 0.8483 (pt0) REVERT: J 149 MET cc_start: 0.8067 (tpp) cc_final: 0.7864 (tpp) REVERT: J 269 GLN cc_start: 0.9284 (tm130) cc_final: 0.9043 (tm-30) REVERT: J 282 PHE cc_start: 0.8765 (p90) cc_final: 0.8538 (p90) REVERT: J 297 LEU cc_start: 0.9210 (tp) cc_final: 0.8994 (tp) REVERT: J 326 GLU cc_start: 0.8497 (mp0) cc_final: 0.8255 (mp0) REVERT: J 350 MET cc_start: 0.7244 (tmm) cc_final: 0.7019 (tmm) REVERT: J 364 GLU cc_start: 0.8831 (tt0) cc_final: 0.8630 (mm-30) REVERT: J 367 MET cc_start: 0.9377 (mtp) cc_final: 0.8129 (mtp) REVERT: K 178 ASP cc_start: 0.8855 (p0) cc_final: 0.8519 (p0) REVERT: K 241 GLU cc_start: 0.8409 (mt-10) cc_final: 0.7762 (tm-30) REVERT: K 304 ASP cc_start: 0.9483 (t70) cc_final: 0.8776 (t0) REVERT: L 191 ARG cc_start: 0.9016 (mtp180) cc_final: 0.8736 (ptm160) REVERT: L 194 ARG cc_start: 0.7598 (ttp80) cc_final: 0.7099 (ttp-110) REVERT: L 199 LEU cc_start: 0.9210 (mp) cc_final: 0.8984 (mp) REVERT: L 219 LEU cc_start: 0.9022 (pt) cc_final: 0.8800 (pp) REVERT: L 263 ILE cc_start: 0.9330 (pt) cc_final: 0.9070 (pt) REVERT: L 267 PHE cc_start: 0.8676 (m-80) cc_final: 0.8076 (m-80) REVERT: L 317 ASN cc_start: 0.8286 (t0) cc_final: 0.7802 (p0) REVERT: L 363 ILE cc_start: 0.8655 (pt) cc_final: 0.8325 (tt) REVERT: L 400 PHE cc_start: 0.7458 (m-10) cc_final: 0.7163 (m-10) REVERT: L 416 MET cc_start: 0.8744 (mmt) cc_final: 0.8306 (mmm) REVERT: M 188 LYS cc_start: 0.7719 (mttt) cc_final: 0.7107 (tppt) REVERT: M 400 MET cc_start: 0.8980 (mmm) cc_final: 0.8766 (mmm) REVERT: s 114 GLU cc_start: 0.8337 (pp20) cc_final: 0.8043 (tp30) outliers start: 3 outliers final: 0 residues processed: 505 average time/residue: 0.1500 time to fit residues: 119.5720 Evaluate side-chains 377 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 376 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 277 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 312 optimal weight: 7.9990 chunk 227 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 chunk 191 optimal weight: 6.9990 chunk 286 optimal weight: 4.9990 chunk 109 optimal weight: 0.0000 chunk 69 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 305 optimal weight: 5.9990 overall best weight: 3.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 176 GLN A 185 HIS E 23 GLN ** G 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 170 GLN I 192 GLN I 204 HIS K 182 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.071367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.058460 restraints weight = 98131.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.060030 restraints weight = 62909.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.061165 restraints weight = 44222.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.061990 restraints weight = 33071.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.062586 restraints weight = 26123.960| |-----------------------------------------------------------------------------| r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.4166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 24041 Z= 0.176 Angle : 0.684 9.358 32801 Z= 0.350 Chirality : 0.046 0.205 3934 Planarity : 0.004 0.047 4254 Dihedral : 6.791 91.975 3539 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 0.14 % Allowed : 4.57 % Favored : 95.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -3.18 (0.14), residues: 3262 helix: -1.59 (0.14), residues: 1252 sheet: -2.34 (0.23), residues: 437 loop : -2.44 (0.15), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 381 TYR 0.023 0.002 TYR L 221 PHE 0.025 0.002 PHE B 12 TRP 0.013 0.002 TRP H 404 HIS 0.010 0.001 HIS E 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.18 (24041) covalent geometry : angle 0.68397 / 0.35 (32801) hydrogen bonds : bond 0.04017 / 2.69 ( 736) hydrogen bonds : angle 6.14320 / 4.35 ( 2109) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6524 Ramachandran restraints generated. 3262 Oldfield, 0 Emsley, 3262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6524 Ramachandran restraints generated. 3262 Oldfield, 0 Emsley, 3262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 473 time to evaluate : 0.870 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 42 SER cc_start: 0.8930 (p) cc_final: 0.8448 (m) REVERT: A 55 SER cc_start: 0.8036 (p) cc_final: 0.7294 (p) REVERT: A 65 ASP cc_start: 0.7345 (m-30) cc_final: 0.7072 (m-30) REVERT: A 135 ARG cc_start: 0.8546 (ttp-170) cc_final: 0.7941 (ttt-90) REVERT: A 175 GLN cc_start: 0.7266 (pp30) cc_final: 0.7053 (pp30) REVERT: A 212 ASP cc_start: 0.7120 (m-30) cc_final: 0.6435 (t0) REVERT: A 221 ASN cc_start: 0.8311 (p0) cc_final: 0.8012 (p0) REVERT: A 224 GLU cc_start: 0.7674 (tt0) cc_final: 0.7178 (tp30) REVERT: B 23 TYR cc_start: 0.8642 (m-10) cc_final: 0.8236 (m-10) REVERT: B 134 LEU cc_start: 0.8526 (pp) cc_final: 0.8101 (pp) REVERT: C 242 THR cc_start: 0.9214 (m) cc_final: 0.8968 (t) REVERT: D 111 ARG cc_start: 0.7974 (mtm-85) cc_final: 0.6815 (mtm-85) REVERT: D 230 ASN cc_start: 0.7695 (m110) cc_final: 0.7487 (m-40) REVERT: E 50 VAL cc_start: 0.8878 (m) cc_final: 0.8471 (p) REVERT: E 183 LEU cc_start: 0.9398 (mt) cc_final: 0.9144 (mm) REVERT: F 148 GLN cc_start: 0.6123 (mm-40) cc_final: 0.5690 (mm-40) REVERT: G 26 TYR cc_start: 0.8274 (m-80) cc_final: 0.7912 (m-10) REVERT: G 74 ILE cc_start: 0.8678 (mt) cc_final: 0.8294 (mm) REVERT: G 84 ASP cc_start: 0.8737 (t70) cc_final: 0.8342 (t0) REVERT: G 135 SER cc_start: 0.8389 (m) cc_final: 0.8147 (m) REVERT: H 210 ASP cc_start: 0.8676 (m-30) cc_final: 0.8453 (m-30) REVERT: H 294 LEU cc_start: 0.9481 (tp) cc_final: 0.9252 (tp) REVERT: H 297 MET cc_start: 0.8948 (tmm) cc_final: 0.8444 (ppp) REVERT: I 192 GLN cc_start: 0.9168 (OUTLIER) cc_final: 0.8674 (pp30) REVERT: I 254 GLN cc_start: 0.8180 (mp10) cc_final: 0.7735 (mp10) REVERT: I 340 ARG cc_start: 0.7209 (mtm180) cc_final: 0.6762 (mtm180) REVERT: I 380 LEU cc_start: 0.8953 (mt) cc_final: 0.8687 (mp) REVERT: I 391 ASP cc_start: 0.8853 (p0) cc_final: 0.8600 (p0) REVERT: I 416 PHE cc_start: 0.8925 (t80) cc_final: 0.8605 (t80) REVERT: J 149 MET cc_start: 0.8603 (tpp) cc_final: 0.8138 (tpp) REVERT: J 269 GLN cc_start: 0.9393 (tm-30) cc_final: 0.9111 (tm-30) REVERT: J 282 PHE cc_start: 0.8863 (p90) cc_final: 0.8641 (p90) REVERT: J 350 MET cc_start: 0.7525 (tmm) cc_final: 0.7291 (tmm) REVERT: J 367 MET cc_start: 0.9371 (mtp) cc_final: 0.8301 (mtp) REVERT: K 178 ASP cc_start: 0.8990 (p0) cc_final: 0.8697 (p0) REVERT: K 304 ASP cc_start: 0.9505 (t70) cc_final: 0.8934 (t0) REVERT: L 191 ARG cc_start: 0.9019 (mtp180) cc_final: 0.8420 (mtp85) REVERT: L 194 ARG cc_start: 0.7647 (ttp80) cc_final: 0.7335 (ttp-110) REVERT: L 263 ILE cc_start: 0.9345 (pt) cc_final: 0.9014 (pt) REVERT: L 267 PHE cc_start: 0.8741 (m-80) cc_final: 0.8046 (m-80) REVERT: L 282 GLU cc_start: 0.7944 (tp30) cc_final: 0.7709 (tp30) REVERT: L 317 ASN cc_start: 0.8240 (t0) cc_final: 0.7741 (p0) REVERT: L 397 GLU cc_start: 0.8619 (pp20) cc_final: 0.8302 (pp20) REVERT: L 400 PHE cc_start: 0.7494 (m-10) cc_final: 0.7188 (m-10) REVERT: L 416 MET cc_start: 0.8794 (mmt) cc_final: 0.8386 (mmm) REVERT: M 188 LYS cc_start: 0.7714 (mttt) cc_final: 0.6724 (tppt) REVERT: s 114 GLU cc_start: 0.8394 (pp20) cc_final: 0.8155 (tp30) outliers start: 3 outliers final: 0 residues processed: 475 average time/residue: 0.1382 time to fit residues: 105.5568 Evaluate side-chains 368 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 367 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 192 optimal weight: 0.9990 chunk 157 optimal weight: 0.9980 chunk 80 optimal weight: 0.4980 chunk 168 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 45 optimal weight: 8.9990 chunk 92 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 219 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 41 ASN G 12 ASN G 23 GLN G 207 ASN I 192 GLN J 204 HIS J 240 HIS J 269 GLN ** K 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 228 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.073482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.060926 restraints weight = 97207.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.062323 restraints weight = 65123.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.063289 restraints weight = 47113.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.064052 restraints weight = 36434.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.064546 restraints weight = 29527.904| |-----------------------------------------------------------------------------| r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.4584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24041 Z= 0.114 Angle : 0.639 10.775 32801 Z= 0.319 Chirality : 0.044 0.302 3934 Planarity : 0.004 0.051 4254 Dihedral : 6.327 85.493 3539 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 0.05 % Allowed : 2.67 % Favored : 97.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -2.82 (0.14), residues: 3262 helix: -1.36 (0.14), residues: 1274 sheet: -2.04 (0.23), residues: 440 loop : -2.20 (0.16), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 367 TYR 0.019 0.001 TYR L 221 PHE 0.020 0.002 PHE A 32 TRP 0.014 0.001 TRP H 404 HIS 0.013 0.001 HIS J 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (24041) covalent geometry : angle 0.63930 / 0.32 (32801) hydrogen bonds : bond 0.03468 / 2.30 ( 736) hydrogen bonds : angle 5.69665 / 4.04 ( 2109) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6524 Ramachandran restraints generated. 3262 Oldfield, 0 Emsley, 3262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6524 Ramachandran restraints generated. 3262 Oldfield, 0 Emsley, 3262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 502 time to evaluate : 0.933 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 42 SER cc_start: 0.8793 (p) cc_final: 0.8399 (m) REVERT: A 55 SER cc_start: 0.7945 (p) cc_final: 0.7294 (p) REVERT: A 65 ASP cc_start: 0.7213 (m-30) cc_final: 0.6981 (m-30) REVERT: A 221 ASN cc_start: 0.8362 (p0) cc_final: 0.7998 (p0) REVERT: A 224 GLU cc_start: 0.7562 (tt0) cc_final: 0.7090 (tp30) REVERT: B 23 TYR cc_start: 0.8592 (m-10) cc_final: 0.8218 (m-10) REVERT: B 134 LEU cc_start: 0.8641 (pp) cc_final: 0.8032 (pp) REVERT: C 12 ILE cc_start: 0.7560 (tp) cc_final: 0.6896 (pt) REVERT: C 77 VAL cc_start: 0.8713 (t) cc_final: 0.8292 (p) REVERT: C 242 THR cc_start: 0.9123 (m) cc_final: 0.8914 (t) REVERT: D 111 ARG cc_start: 0.7962 (mtm-85) cc_final: 0.6788 (mtm-85) REVERT: D 133 THR cc_start: 0.8140 (p) cc_final: 0.7907 (t) REVERT: D 230 ASN cc_start: 0.7572 (m110) cc_final: 0.7349 (m-40) REVERT: E 53 ARG cc_start: 0.7286 (ttm-80) cc_final: 0.6550 (tpp-160) REVERT: E 88 MET cc_start: 0.8174 (ptp) cc_final: 0.7916 (mtp) REVERT: E 180 GLN cc_start: 0.7971 (pm20) cc_final: 0.7662 (pm20) REVERT: E 183 LEU cc_start: 0.9338 (mt) cc_final: 0.9113 (mm) REVERT: F 117 GLN cc_start: 0.8348 (mm110) cc_final: 0.8082 (tp40) REVERT: F 148 GLN cc_start: 0.5979 (mm-40) cc_final: 0.5610 (mm-40) REVERT: G 84 ASP cc_start: 0.8699 (t70) cc_final: 0.8182 (t0) REVERT: G 135 SER cc_start: 0.8290 (m) cc_final: 0.7991 (m) REVERT: H 210 ASP cc_start: 0.8690 (m-30) cc_final: 0.8406 (m-30) REVERT: H 294 LEU cc_start: 0.9415 (tp) cc_final: 0.9159 (tp) REVERT: H 310 GLU cc_start: 0.8927 (mp0) cc_final: 0.8441 (mp0) REVERT: H 356 ASN cc_start: 0.9492 (t0) cc_final: 0.9249 (t0) REVERT: I 254 GLN cc_start: 0.8240 (mp10) cc_final: 0.7793 (mp10) REVERT: I 255 LYS cc_start: 0.6993 (mmtm) cc_final: 0.5972 (mmtm) REVERT: I 383 THR cc_start: 0.8822 (m) cc_final: 0.8607 (p) REVERT: I 391 ASP cc_start: 0.8741 (p0) cc_final: 0.8450 (p0) REVERT: I 421 GLU cc_start: 0.8868 (mt-10) cc_final: 0.8372 (mt-10) REVERT: J 137 MET cc_start: 0.7762 (tpt) cc_final: 0.7525 (tpp) REVERT: J 149 MET cc_start: 0.8287 (tpp) cc_final: 0.8012 (tpp) REVERT: J 269 GLN cc_start: 0.9313 (tm130) cc_final: 0.9053 (tm-30) REVERT: J 282 PHE cc_start: 0.8800 (p90) cc_final: 0.8531 (p90) REVERT: J 350 MET cc_start: 0.7335 (tmm) cc_final: 0.7096 (tmm) REVERT: J 364 GLU cc_start: 0.8972 (tp30) cc_final: 0.7821 (mm-30) REVERT: J 367 MET cc_start: 0.9316 (mtp) cc_final: 0.8544 (mtp) REVERT: K 304 ASP cc_start: 0.9503 (t70) cc_final: 0.9017 (t0) REVERT: K 389 GLU cc_start: 0.8107 (tp30) cc_final: 0.7900 (tp30) REVERT: K 393 ARG cc_start: 0.7294 (mmp80) cc_final: 0.7063 (mmm160) REVERT: L 191 ARG cc_start: 0.8998 (mtp180) cc_final: 0.8783 (ptm160) REVERT: L 194 ARG cc_start: 0.7620 (ttp80) cc_final: 0.7149 (ttp-110) REVERT: L 228 LYS cc_start: 0.9292 (mtmm) cc_final: 0.8258 (mtmt) REVERT: L 282 GLU cc_start: 0.7937 (tp30) cc_final: 0.7632 (mm-30) REVERT: L 397 GLU cc_start: 0.8451 (pp20) cc_final: 0.8217 (pp20) REVERT: L 400 PHE cc_start: 0.7492 (m-10) cc_final: 0.7187 (m-10) REVERT: L 416 MET cc_start: 0.8713 (mmt) cc_final: 0.8348 (mmm) REVERT: M 188 LYS cc_start: 0.7348 (mttt) cc_final: 0.6615 (tppt) REVERT: M 205 ASP cc_start: 0.8829 (t0) cc_final: 0.8432 (t0) REVERT: M 209 ASP cc_start: 0.8940 (m-30) cc_final: 0.8590 (m-30) outliers start: 1 outliers final: 0 residues processed: 503 average time/residue: 0.1416 time to fit residues: 114.1388 Evaluate side-chains 367 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 367 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 296 optimal weight: 0.0050 chunk 116 optimal weight: 0.6980 chunk 87 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 195 optimal weight: 0.8980 chunk 321 optimal weight: 8.9990 chunk 258 optimal weight: 0.9990 chunk 289 optimal weight: 3.9990 chunk 89 optimal weight: 8.9990 chunk 154 optimal weight: 3.9990 chunk 191 optimal weight: 5.9990 overall best weight: 1.1198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 209 HIS I 192 GLN I 239 GLN J 240 HIS K 194 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.073338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.060801 restraints weight = 97905.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.062207 restraints weight = 65061.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.063197 restraints weight = 46858.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.063947 restraints weight = 36187.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.064447 restraints weight = 29146.145| |-----------------------------------------------------------------------------| r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.4913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 24041 Z= 0.108 Angle : 0.622 9.378 32801 Z= 0.310 Chirality : 0.044 0.247 3934 Planarity : 0.004 0.047 4254 Dihedral : 6.050 76.828 3539 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 0.09 % Allowed : 2.85 % Favored : 97.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -2.52 (0.14), residues: 3262 helix: -1.17 (0.14), residues: 1265 sheet: -1.77 (0.24), residues: 439 loop : -2.02 (0.16), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 340 TYR 0.019 0.001 TYR L 221 PHE 0.031 0.002 PHE H 343 TRP 0.014 0.001 TRP H 404 HIS 0.009 0.001 HIS G 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (24041) covalent geometry : angle 0.62233 / 0.31 (32801) hydrogen bonds : bond 0.03245 / 2.16 ( 736) hydrogen bonds : angle 5.48967 / 3.89 ( 2109) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6524 Ramachandran restraints generated. 3262 Oldfield, 0 Emsley, 3262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6524 Ramachandran restraints generated. 3262 Oldfield, 0 Emsley, 3262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 479 time to evaluate : 0.714 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 42 SER cc_start: 0.8838 (p) cc_final: 0.8442 (m) REVERT: A 55 SER cc_start: 0.8058 (p) cc_final: 0.7252 (p) REVERT: A 65 ASP cc_start: 0.7155 (m-30) cc_final: 0.6806 (m-30) REVERT: A 221 ASN cc_start: 0.8331 (p0) cc_final: 0.7942 (p0) REVERT: A 224 GLU cc_start: 0.7456 (tt0) cc_final: 0.6956 (tp30) REVERT: B 23 TYR cc_start: 0.8611 (m-10) cc_final: 0.8264 (m-10) REVERT: B 134 LEU cc_start: 0.8737 (pp) cc_final: 0.8133 (pp) REVERT: C 12 ILE cc_start: 0.7534 (tp) cc_final: 0.6868 (pt) REVERT: C 73 ILE cc_start: 0.7874 (mt) cc_final: 0.7648 (mt) REVERT: C 77 VAL cc_start: 0.8658 (t) cc_final: 0.8176 (m) REVERT: C 242 THR cc_start: 0.9178 (m) cc_final: 0.8921 (t) REVERT: D 25 GLU cc_start: 0.8327 (tp30) cc_final: 0.8049 (tp30) REVERT: D 111 ARG cc_start: 0.8072 (mtm-85) cc_final: 0.6923 (mtm-85) REVERT: D 230 ASN cc_start: 0.7707 (m110) cc_final: 0.7499 (m-40) REVERT: F 148 GLN cc_start: 0.6168 (mm-40) cc_final: 0.5957 (mm-40) REVERT: G 130 ARG cc_start: 0.8316 (ttp80) cc_final: 0.7716 (ttp80) REVERT: G 135 SER cc_start: 0.8127 (m) cc_final: 0.7902 (m) REVERT: H 210 ASP cc_start: 0.8745 (m-30) cc_final: 0.8502 (m-30) REVERT: H 310 GLU cc_start: 0.8953 (mp0) cc_final: 0.8443 (mp0) REVERT: H 356 ASN cc_start: 0.9524 (t0) cc_final: 0.9283 (t0) REVERT: I 254 GLN cc_start: 0.8166 (mp10) cc_final: 0.7755 (mp10) REVERT: I 395 MET cc_start: 0.9479 (mmt) cc_final: 0.9228 (mmm) REVERT: I 421 GLU cc_start: 0.9091 (mt-10) cc_final: 0.8528 (mt-10) REVERT: J 149 MET cc_start: 0.8421 (tpp) cc_final: 0.8104 (tpp) REVERT: J 269 GLN cc_start: 0.9385 (tm-30) cc_final: 0.9112 (tm-30) REVERT: J 282 PHE cc_start: 0.8775 (p90) cc_final: 0.8553 (p90) REVERT: K 304 ASP cc_start: 0.9492 (t70) cc_final: 0.9022 (t0) REVERT: L 194 ARG cc_start: 0.7795 (ttp80) cc_final: 0.7221 (ttp-110) REVERT: L 263 ILE cc_start: 0.9347 (pt) cc_final: 0.9044 (pt) REVERT: L 282 GLU cc_start: 0.7999 (tp30) cc_final: 0.7606 (mm-30) REVERT: L 397 GLU cc_start: 0.8402 (pp20) cc_final: 0.8149 (pp20) REVERT: L 400 PHE cc_start: 0.7479 (m-10) cc_final: 0.7196 (m-10) REVERT: L 416 MET cc_start: 0.8767 (mmt) cc_final: 0.8406 (mmm) REVERT: M 188 LYS cc_start: 0.7452 (mttt) cc_final: 0.6645 (tppt) REVERT: M 205 ASP cc_start: 0.8842 (t0) cc_final: 0.8415 (t0) REVERT: M 209 ASP cc_start: 0.8944 (m-30) cc_final: 0.8561 (m-30) REVERT: M 411 LYS cc_start: 0.8405 (ttmm) cc_final: 0.7828 (tptt) outliers start: 2 outliers final: 1 residues processed: 481 average time/residue: 0.1348 time to fit residues: 105.4777 Evaluate side-chains 376 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 375 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 224 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 chunk 47 optimal weight: 6.9990 chunk 116 optimal weight: 8.9990 chunk 16 optimal weight: 4.9990 chunk 320 optimal weight: 20.0000 chunk 279 optimal weight: 20.0000 chunk 214 optimal weight: 5.9990 chunk 290 optimal weight: 0.8980 chunk 21 optimal weight: 10.0000 chunk 250 optimal weight: 0.3980 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 41 ASN F 5 ASN G 127 ASN ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 192 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.071192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.058190 restraints weight = 98450.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.059674 restraints weight = 64509.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.060737 restraints weight = 46002.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.061509 restraints weight = 34975.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.062086 restraints weight = 28123.540| |-----------------------------------------------------------------------------| r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.5142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 24041 Z= 0.156 Angle : 0.659 9.700 32801 Z= 0.333 Chirality : 0.045 0.240 3934 Planarity : 0.004 0.046 4254 Dihedral : 5.997 79.734 3539 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 0.05 % Allowed : 2.22 % Favored : 97.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -2.35 (0.14), residues: 3262 helix: -1.00 (0.14), residues: 1264 sheet: -1.56 (0.23), residues: 456 loop : -1.99 (0.16), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 381 TYR 0.034 0.002 TYR E 167 PHE 0.020 0.002 PHE I 416 TRP 0.043 0.003 TRP M 376 HIS 0.008 0.001 HIS M 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (24041) covalent geometry : angle 0.65850 / 0.33 (32801) hydrogen bonds : bond 0.03514 / 2.32 ( 736) hydrogen bonds : angle 5.58285 / 3.95 ( 2109) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6524 Ramachandran restraints generated. 3262 Oldfield, 0 Emsley, 3262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6524 Ramachandran restraints generated. 3262 Oldfield, 0 Emsley, 3262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 459 time to evaluate : 0.898 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 42 SER cc_start: 0.8909 (p) cc_final: 0.8435 (m) REVERT: A 55 SER cc_start: 0.8102 (p) cc_final: 0.7368 (p) REVERT: A 65 ASP cc_start: 0.7270 (m-30) cc_final: 0.6907 (m-30) REVERT: A 81 MET cc_start: 0.7595 (ttp) cc_final: 0.7391 (ttm) REVERT: A 210 MET cc_start: 0.8547 (tpp) cc_final: 0.8286 (tpp) REVERT: A 221 ASN cc_start: 0.8367 (p0) cc_final: 0.8074 (p0) REVERT: A 224 GLU cc_start: 0.7677 (tt0) cc_final: 0.7100 (tp30) REVERT: B 23 TYR cc_start: 0.8654 (m-10) cc_final: 0.8298 (m-10) REVERT: B 134 LEU cc_start: 0.8616 (pp) cc_final: 0.8121 (pp) REVERT: C 12 ILE cc_start: 0.7609 (tp) cc_final: 0.6911 (pt) REVERT: C 73 ILE cc_start: 0.8018 (mt) cc_final: 0.7806 (mt) REVERT: C 242 THR cc_start: 0.9210 (m) cc_final: 0.8974 (t) REVERT: D 25 GLU cc_start: 0.8449 (tp30) cc_final: 0.8148 (tp30) REVERT: D 111 ARG cc_start: 0.8126 (mtm-85) cc_final: 0.7058 (mtm-85) REVERT: D 230 ASN cc_start: 0.7692 (m110) cc_final: 0.7416 (m-40) REVERT: F 117 GLN cc_start: 0.8193 (mm-40) cc_final: 0.7778 (tp40) REVERT: F 148 GLN cc_start: 0.6325 (mm-40) cc_final: 0.6041 (mm-40) REVERT: G 135 SER cc_start: 0.8281 (m) cc_final: 0.8076 (m) REVERT: H 210 ASP cc_start: 0.8937 (m-30) cc_final: 0.8616 (m-30) REVERT: H 310 GLU cc_start: 0.9009 (mp0) cc_final: 0.8568 (mp0) REVERT: H 356 ASN cc_start: 0.9553 (t0) cc_final: 0.9309 (t0) REVERT: H 399 GLU cc_start: 0.9047 (tt0) cc_final: 0.8470 (tm-30) REVERT: I 254 GLN cc_start: 0.8163 (mp10) cc_final: 0.7901 (mp10) REVERT: I 383 THR cc_start: 0.8876 (m) cc_final: 0.8664 (p) REVERT: J 149 MET cc_start: 0.8503 (tpp) cc_final: 0.8288 (tpp) REVERT: J 269 GLN cc_start: 0.9412 (tm-30) cc_final: 0.9102 (tm-30) REVERT: J 282 PHE cc_start: 0.8810 (p90) cc_final: 0.8598 (p90) REVERT: J 367 MET cc_start: 0.9254 (mtp) cc_final: 0.8773 (mtp) REVERT: K 389 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7904 (tp30) REVERT: L 194 ARG cc_start: 0.7797 (ttp80) cc_final: 0.7209 (ttp-110) REVERT: L 279 PHE cc_start: 0.8899 (t80) cc_final: 0.8640 (t80) REVERT: L 282 GLU cc_start: 0.8013 (tp30) cc_final: 0.7579 (mm-30) REVERT: L 400 PHE cc_start: 0.7589 (m-10) cc_final: 0.7306 (m-10) REVERT: L 416 MET cc_start: 0.8807 (mmt) cc_final: 0.8408 (mmm) REVERT: M 188 LYS cc_start: 0.7541 (mttt) cc_final: 0.6622 (tppt) REVERT: M 203 ARG cc_start: 0.9287 (mmm160) cc_final: 0.9086 (mmt-90) REVERT: M 205 ASP cc_start: 0.8860 (t0) cc_final: 0.8433 (t0) REVERT: M 209 ASP cc_start: 0.8907 (m-30) cc_final: 0.8455 (m-30) REVERT: M 411 LYS cc_start: 0.8426 (ttmm) cc_final: 0.7916 (tptt) outliers start: 1 outliers final: 0 residues processed: 460 average time/residue: 0.1381 time to fit residues: 103.6054 Evaluate side-chains 352 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 352 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 204 optimal weight: 9.9990 chunk 116 optimal weight: 0.7980 chunk 247 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 chunk 167 optimal weight: 6.9990 chunk 305 optimal weight: 6.9990 chunk 223 optimal weight: 10.0000 chunk 261 optimal weight: 5.9990 chunk 183 optimal weight: 6.9990 chunk 313 optimal weight: 0.3980 chunk 71 optimal weight: 0.5980 overall best weight: 1.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 209 HIS B 41 ASN E 185 ASN F 5 ASN ** G 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 127 ASN ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 192 GLN L 393 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.071935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.058756 restraints weight = 97966.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.060291 restraints weight = 64013.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.061358 restraints weight = 45410.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.062142 restraints weight = 34645.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.062722 restraints weight = 27836.674| |-----------------------------------------------------------------------------| r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.5365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 24041 Z= 0.120 Angle : 0.638 9.798 32801 Z= 0.317 Chirality : 0.044 0.232 3934 Planarity : 0.004 0.046 4254 Dihedral : 5.817 81.075 3539 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 0.05 % Allowed : 1.68 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -2.24 (0.14), residues: 3262 helix: -0.93 (0.14), residues: 1263 sheet: -1.45 (0.24), residues: 458 loop : -1.93 (0.16), residues: 1541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG M 381 TYR 0.025 0.001 TYR A 30 PHE 0.031 0.002 PHE H 343 TRP 0.028 0.002 TRP M 376 HIS 0.009 0.001 HIS G 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (24041) covalent geometry : angle 0.63764 / 0.32 (32801) hydrogen bonds : bond 0.03190 / 2.12 ( 736) hydrogen bonds : angle 5.43933 / 3.86 ( 2109) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6524 Ramachandran restraints generated. 3262 Oldfield, 0 Emsley, 3262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6524 Ramachandran restraints generated. 3262 Oldfield, 0 Emsley, 3262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 467 time to evaluate : 0.892 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 42 SER cc_start: 0.8909 (p) cc_final: 0.8470 (m) REVERT: A 55 SER cc_start: 0.7999 (p) cc_final: 0.7341 (p) REVERT: A 65 ASP cc_start: 0.7179 (m-30) cc_final: 0.6829 (m-30) REVERT: A 221 ASN cc_start: 0.8455 (p0) cc_final: 0.8057 (p0) REVERT: A 224 GLU cc_start: 0.7556 (tt0) cc_final: 0.6846 (tp30) REVERT: B 87 ASP cc_start: 0.8509 (m-30) cc_final: 0.8258 (m-30) REVERT: B 134 LEU cc_start: 0.8712 (pp) cc_final: 0.8082 (pp) REVERT: C 12 ILE cc_start: 0.7623 (tp) cc_final: 0.6949 (pt) REVERT: C 73 ILE cc_start: 0.8014 (mt) cc_final: 0.7809 (mt) REVERT: C 77 VAL cc_start: 0.8573 (t) cc_final: 0.8125 (m) REVERT: C 242 THR cc_start: 0.9169 (m) cc_final: 0.8951 (t) REVERT: D 25 GLU cc_start: 0.8561 (tp30) cc_final: 0.8262 (tp30) REVERT: D 111 ARG cc_start: 0.8111 (mtm-85) cc_final: 0.7056 (mtm-85) REVERT: D 230 ASN cc_start: 0.7655 (m110) cc_final: 0.7352 (m-40) REVERT: E 180 GLN cc_start: 0.7871 (pm20) cc_final: 0.7667 (pm20) REVERT: F 117 GLN cc_start: 0.8129 (mm-40) cc_final: 0.7659 (tp40) REVERT: F 148 GLN cc_start: 0.6360 (mm-40) cc_final: 0.6024 (mm-40) REVERT: G 135 SER cc_start: 0.8150 (m) cc_final: 0.7946 (m) REVERT: G 211 ASP cc_start: 0.6457 (p0) cc_final: 0.5836 (m-30) REVERT: H 210 ASP cc_start: 0.9002 (m-30) cc_final: 0.8697 (m-30) REVERT: H 310 GLU cc_start: 0.8931 (mp0) cc_final: 0.8608 (mp0) REVERT: H 356 ASN cc_start: 0.9539 (t0) cc_final: 0.9313 (t0) REVERT: H 399 GLU cc_start: 0.9080 (tt0) cc_final: 0.8450 (tm-30) REVERT: I 254 GLN cc_start: 0.8149 (mp10) cc_final: 0.7707 (mp10) REVERT: I 383 THR cc_start: 0.8882 (m) cc_final: 0.8679 (p) REVERT: J 149 MET cc_start: 0.8515 (tpp) cc_final: 0.8268 (tpp) REVERT: J 150 VAL cc_start: 0.9240 (p) cc_final: 0.8981 (m) REVERT: J 269 GLN cc_start: 0.9414 (tm-30) cc_final: 0.9098 (tm-30) REVERT: J 367 MET cc_start: 0.9257 (mtp) cc_final: 0.8770 (mtp) REVERT: L 194 ARG cc_start: 0.7825 (ttp80) cc_final: 0.7230 (ttp-110) REVERT: L 279 PHE cc_start: 0.8965 (t80) cc_final: 0.8691 (t80) REVERT: L 282 GLU cc_start: 0.7971 (tp30) cc_final: 0.7509 (mm-30) REVERT: L 400 PHE cc_start: 0.7472 (m-10) cc_final: 0.7171 (m-10) REVERT: L 416 MET cc_start: 0.8829 (mmt) cc_final: 0.8413 (mmm) REVERT: M 188 LYS cc_start: 0.7528 (mttt) cc_final: 0.6585 (tppt) REVERT: M 205 ASP cc_start: 0.8828 (t0) cc_final: 0.8441 (t0) REVERT: M 209 ASP cc_start: 0.8918 (m-30) cc_final: 0.8574 (m-30) REVERT: M 411 LYS cc_start: 0.8478 (ttmm) cc_final: 0.7948 (tptt) outliers start: 1 outliers final: 0 residues processed: 468 average time/residue: 0.1359 time to fit residues: 104.1377 Evaluate side-chains 359 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 359 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 74 optimal weight: 7.9990 chunk 239 optimal weight: 5.9990 chunk 212 optimal weight: 9.9990 chunk 175 optimal weight: 5.9990 chunk 200 optimal weight: 0.0030 chunk 245 optimal weight: 8.9990 chunk 142 optimal weight: 0.6980 chunk 134 optimal weight: 5.9990 chunk 186 optimal weight: 9.9990 chunk 98 optimal weight: 7.9990 chunk 23 optimal weight: 20.0000 overall best weight: 3.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 5 ASN ** G 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 127 ASN H 392 HIS I 192 GLN ** I 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 240 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.069669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.056628 restraints weight = 98956.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.058072 restraints weight = 65002.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.059105 restraints weight = 46477.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.059856 restraints weight = 35596.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.060418 restraints weight = 28744.423| |-----------------------------------------------------------------------------| r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.5526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 24041 Z= 0.186 Angle : 0.695 9.793 32801 Z= 0.353 Chirality : 0.045 0.200 3934 Planarity : 0.004 0.046 4254 Dihedral : 6.012 84.139 3539 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 0.05 % Allowed : 1.45 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -2.29 (0.14), residues: 3262 helix: -0.96 (0.14), residues: 1274 sheet: -1.31 (0.24), residues: 447 loop : -2.03 (0.15), residues: 1541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG M 381 TYR 0.028 0.002 TYR E 167 PHE 0.029 0.002 PHE A 218 TRP 0.030 0.002 TRP M 376 HIS 0.020 0.002 HIS G 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.19 (24041) covalent geometry : angle 0.69487 / 0.35 (32801) hydrogen bonds : bond 0.03568 / 2.38 ( 736) hydrogen bonds : angle 5.63361 / 3.97 ( 2109) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6524 Ramachandran restraints generated. 3262 Oldfield, 0 Emsley, 3262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6524 Ramachandran restraints generated. 3262 Oldfield, 0 Emsley, 3262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 444 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 SER cc_start: 0.8911 (p) cc_final: 0.8511 (m) REVERT: A 55 SER cc_start: 0.8158 (p) cc_final: 0.7457 (p) REVERT: A 65 ASP cc_start: 0.7229 (m-30) cc_final: 0.6878 (m-30) REVERT: A 221 ASN cc_start: 0.8371 (p0) cc_final: 0.7961 (p0) REVERT: A 224 GLU cc_start: 0.7496 (tt0) cc_final: 0.6813 (tp30) REVERT: B 134 LEU cc_start: 0.8623 (pp) cc_final: 0.8092 (pp) REVERT: C 12 ILE cc_start: 0.7619 (tp) cc_final: 0.6901 (pt) REVERT: D 25 GLU cc_start: 0.8609 (tp30) cc_final: 0.8330 (tp30) REVERT: D 111 ARG cc_start: 0.8178 (mtm-85) cc_final: 0.7146 (mtm-85) REVERT: D 230 ASN cc_start: 0.7687 (m110) cc_final: 0.7394 (m-40) REVERT: F 117 GLN cc_start: 0.8078 (mm-40) cc_final: 0.7682 (tp40) REVERT: F 148 GLN cc_start: 0.6392 (mm-40) cc_final: 0.6096 (mm-40) REVERT: G 84 ASP cc_start: 0.8865 (t0) cc_final: 0.8519 (t0) REVERT: G 135 SER cc_start: 0.8394 (m) cc_final: 0.8177 (m) REVERT: H 210 ASP cc_start: 0.9045 (m-30) cc_final: 0.8731 (m-30) REVERT: H 294 LEU cc_start: 0.9476 (tp) cc_final: 0.9212 (tp) REVERT: H 310 GLU cc_start: 0.8968 (mp0) cc_final: 0.8638 (mp0) REVERT: H 356 ASN cc_start: 0.9556 (t0) cc_final: 0.9311 (t0) REVERT: H 399 GLU cc_start: 0.9091 (tt0) cc_final: 0.8531 (tm-30) REVERT: I 254 GLN cc_start: 0.8071 (mp10) cc_final: 0.7620 (mp10) REVERT: I 255 LYS cc_start: 0.7286 (mmtm) cc_final: 0.6461 (mmtm) REVERT: J 137 MET cc_start: 0.7739 (tpt) cc_final: 0.7489 (tpp) REVERT: J 149 MET cc_start: 0.8570 (tpp) cc_final: 0.8307 (tpp) REVERT: J 269 GLN cc_start: 0.9421 (tm-30) cc_final: 0.9092 (tm-30) REVERT: J 367 MET cc_start: 0.9276 (mtp) cc_final: 0.8774 (mtp) REVERT: K 408 GLU cc_start: 0.9192 (mp0) cc_final: 0.8964 (mp0) REVERT: L 194 ARG cc_start: 0.7855 (ttp80) cc_final: 0.7234 (ttp-110) REVERT: L 282 GLU cc_start: 0.7968 (tp30) cc_final: 0.7500 (mm-30) REVERT: L 394 CYS cc_start: 0.9211 (t) cc_final: 0.8985 (t) REVERT: L 400 PHE cc_start: 0.7483 (m-10) cc_final: 0.7239 (m-10) REVERT: L 416 MET cc_start: 0.8887 (mmt) cc_final: 0.8472 (mmm) REVERT: M 188 LYS cc_start: 0.7516 (mttt) cc_final: 0.6558 (tppt) REVERT: M 205 ASP cc_start: 0.8829 (t0) cc_final: 0.8450 (t0) REVERT: M 209 ASP cc_start: 0.8870 (m-30) cc_final: 0.8523 (m-30) REVERT: M 411 LYS cc_start: 0.8545 (ttmm) cc_final: 0.8004 (tptt) outliers start: 1 outliers final: 0 residues processed: 445 average time/residue: 0.1307 time to fit residues: 95.2264 Evaluate side-chains 357 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 357 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 132 optimal weight: 8.9990 chunk 68 optimal weight: 5.9990 chunk 241 optimal weight: 0.4980 chunk 63 optimal weight: 1.9990 chunk 94 optimal weight: 0.0970 chunk 297 optimal weight: 0.0070 chunk 50 optimal weight: 2.9990 chunk 202 optimal weight: 9.9990 chunk 52 optimal weight: 4.9990 chunk 235 optimal weight: 7.9990 chunk 96 optimal weight: 0.8980 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 127 ASN I 192 GLN ** I 239 GLN ** 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 = 0.3107 r_free = 0.3107 target = 0.071933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.059043 restraints weight = 97733.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.060468 restraints weight = 64569.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.061495 restraints weight = 46448.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.062189 restraints weight = 35648.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.062770 restraints weight = 29144.788| |-----------------------------------------------------------------------------| r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.5753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 24041 Z= 0.115 Angle : 0.652 9.867 32801 Z= 0.323 Chirality : 0.044 0.184 3934 Planarity : 0.004 0.046 4254 Dihedral : 5.655 85.281 3539 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 0.05 % Allowed : 0.36 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -2.01 (0.14), residues: 3262 helix: -0.79 (0.14), residues: 1274 sheet: -1.13 (0.25), residues: 442 loop : -1.81 (0.16), residues: 1546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG M 381 TYR 0.024 0.001 TYR A 30 PHE 0.033 0.002 PHE H 343 TRP 0.033 0.002 TRP H 404 HIS 0.018 0.001 HIS G 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 (24041) covalent geometry : angle 0.65241 / 0.32 (32801) hydrogen bonds : bond 0.03070 / 2.06 ( 736) hydrogen bonds : angle 5.34044 / 3.78 ( 2109) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6524 Ramachandran restraints generated. 3262 Oldfield, 0 Emsley, 3262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6524 Ramachandran restraints generated. 3262 Oldfield, 0 Emsley, 3262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 476 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 SER cc_start: 0.8874 (p) cc_final: 0.8474 (m) REVERT: A 55 SER cc_start: 0.8078 (p) cc_final: 0.7327 (p) REVERT: A 65 ASP cc_start: 0.7286 (m-30) cc_final: 0.6924 (m-30) REVERT: A 221 ASN cc_start: 0.8461 (p0) cc_final: 0.8054 (p0) REVERT: A 224 GLU cc_start: 0.7504 (tt0) cc_final: 0.6875 (tp30) REVERT: B 134 LEU cc_start: 0.8600 (pp) cc_final: 0.8008 (pp) REVERT: C 12 ILE cc_start: 0.7652 (tp) cc_final: 0.6985 (pt) REVERT: C 39 MET cc_start: 0.7456 (ttm) cc_final: 0.6688 (tmm) REVERT: C 73 ILE cc_start: 0.7969 (mt) cc_final: 0.7687 (mp) REVERT: C 77 VAL cc_start: 0.8562 (t) cc_final: 0.7972 (m) REVERT: D 25 GLU cc_start: 0.8602 (tp30) cc_final: 0.8334 (tp30) REVERT: D 111 ARG cc_start: 0.8056 (mtm-85) cc_final: 0.6921 (mtm-85) REVERT: D 234 THR cc_start: 0.8213 (p) cc_final: 0.7914 (p) REVERT: E 53 ARG cc_start: 0.7242 (ttm-80) cc_final: 0.6584 (tpp-160) REVERT: E 117 CYS cc_start: 0.8206 (m) cc_final: 0.7531 (t) REVERT: F 6 TYR cc_start: 0.7749 (m-80) cc_final: 0.7534 (m-10) REVERT: F 117 GLN cc_start: 0.7932 (mm-40) cc_final: 0.7630 (tp40) REVERT: F 148 GLN cc_start: 0.6342 (mm-40) cc_final: 0.6041 (mm-40) REVERT: F 155 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8165 (mm-30) REVERT: G 84 ASP cc_start: 0.8889 (t0) cc_final: 0.8594 (t0) REVERT: G 135 SER cc_start: 0.8211 (m) cc_final: 0.7937 (m) REVERT: G 211 ASP cc_start: 0.6525 (p0) cc_final: 0.5739 (m-30) REVERT: H 310 GLU cc_start: 0.8874 (mp0) cc_final: 0.8570 (mp0) REVERT: H 356 ASN cc_start: 0.9543 (t0) cc_final: 0.9311 (t0) REVERT: H 399 GLU cc_start: 0.9082 (tt0) cc_final: 0.8499 (tm-30) REVERT: I 255 LYS cc_start: 0.7342 (mmtm) cc_final: 0.6448 (mmtm) REVERT: I 350 PHE cc_start: 0.8051 (m-10) cc_final: 0.7756 (m-10) REVERT: J 149 MET cc_start: 0.8478 (tpp) cc_final: 0.8206 (tpp) REVERT: J 150 VAL cc_start: 0.9225 (p) cc_final: 0.8953 (m) REVERT: J 181 GLN cc_start: 0.9029 (mt0) cc_final: 0.8569 (tp40) REVERT: J 269 GLN cc_start: 0.9415 (tm-30) cc_final: 0.9082 (tm-30) REVERT: J 367 MET cc_start: 0.9210 (mtp) cc_final: 0.8818 (mtp) REVERT: J 391 ASN cc_start: 0.8536 (m110) cc_final: 0.8297 (m110) REVERT: K 408 GLU cc_start: 0.9152 (mp0) cc_final: 0.8939 (mp0) REVERT: L 194 ARG cc_start: 0.7853 (ttp80) cc_final: 0.7323 (ttp-110) REVERT: L 198 GLU cc_start: 0.8542 (pp20) cc_final: 0.7866 (pm20) REVERT: L 199 LEU cc_start: 0.9241 (mp) cc_final: 0.8721 (mp) REVERT: L 207 PHE cc_start: 0.7876 (m-10) cc_final: 0.7495 (m-80) REVERT: L 282 GLU cc_start: 0.7920 (tp30) cc_final: 0.7493 (mm-30) REVERT: L 394 CYS cc_start: 0.9116 (t) cc_final: 0.8895 (t) REVERT: L 400 PHE cc_start: 0.7333 (m-10) cc_final: 0.7046 (m-10) REVERT: L 416 MET cc_start: 0.8822 (mmt) cc_final: 0.8400 (mmm) REVERT: M 188 LYS cc_start: 0.7520 (mttt) cc_final: 0.6539 (tppt) REVERT: M 205 ASP cc_start: 0.8818 (t0) cc_final: 0.8434 (t0) REVERT: M 209 ASP cc_start: 0.8818 (m-30) cc_final: 0.8460 (m-30) REVERT: M 411 LYS cc_start: 0.8546 (ttmm) cc_final: 0.7993 (tptt) outliers start: 1 outliers final: 0 residues processed: 477 average time/residue: 0.1378 time to fit residues: 106.8258 Evaluate side-chains 371 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 371 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 129 optimal weight: 10.0000 chunk 322 optimal weight: 20.0000 chunk 236 optimal weight: 10.0000 chunk 136 optimal weight: 0.9990 chunk 118 optimal weight: 8.9990 chunk 161 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 302 optimal weight: 9.9990 chunk 181 optimal weight: 0.0030 overall best weight: 3.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 41 ASN F 5 ASN ** G 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 192 GLN ** I 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 156 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.069568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.056811 restraints weight = 97493.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.058210 restraints weight = 64563.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.059194 restraints weight = 46458.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.059920 restraints weight = 35769.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.060448 restraints weight = 29011.484| |-----------------------------------------------------------------------------| r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.5851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 24041 Z= 0.168 Angle : 0.684 10.460 32801 Z= 0.344 Chirality : 0.045 0.176 3934 Planarity : 0.004 0.055 4254 Dihedral : 5.821 88.474 3539 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 0.05 % Allowed : 0.41 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -2.05 (0.14), residues: 3262 helix: -0.76 (0.14), residues: 1275 sheet: -1.30 (0.24), residues: 455 loop : -1.85 (0.16), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG M 381 TYR 0.028 0.002 TYR E 167 PHE 0.024 0.002 PHE A 218 TRP 0.037 0.003 TRP C 160 HIS 0.015 0.001 HIS G 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 (24041) covalent geometry : angle 0.68427 / 0.34 (32801) hydrogen bonds : bond 0.03348 / 2.24 ( 736) hydrogen bonds : angle 5.48860 / 3.87 ( 2109) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3438.81 seconds wall clock time: 60 minutes 20.15 seconds (3620.15 seconds total)