Starting phenix.real_space_refine on Mon Jul 6 11:52:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pvy_17980/07_2026/8pvy_17980.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pvy_17980/07_2026/8pvy_17980.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pvy_17980/07_2026/8pvy_17980.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pvy_17980/07_2026/8pvy_17980.map" model { file = "/net/cci-nas-00/data/ceres_data/8pvy_17980/07_2026/8pvy_17980.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pvy_17980/07_2026/8pvy_17980.cif" } resolution = 3.02 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= 0.000 sd= 0.001 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: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 S 210 5.16 5 Cl 8 4.86 5 C 22750 2.51 5 N 6107 2.21 5 O 6657 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 35736 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 2027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2027 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 8, 'TRANS': 243} Chain breaks: 2 Chain: "B" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1937 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 5, 'TRANS': 231} Chain breaks: 1 Chain: "C" Number of atoms: 2026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2026 Classifications: {'peptide': 252} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 243} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1937 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 5, 'TRANS': 231} Chain breaks: 1 Chain: "E" Number of atoms: 3063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3063 Classifications: {'peptide': 383} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 28, 'TRANS': 354} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'PHE:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 15 Chain: "F" Number of atoms: 3065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3065 Classifications: {'peptide': 383} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 28, 'TRANS': 354} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'PHE:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "G" Number of atoms: 2027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2027 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 8, 'TRANS': 243} Chain breaks: 2 Chain: "H" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1937 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 5, 'TRANS': 231} Chain breaks: 1 Chain: "I" Number of atoms: 2027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2027 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 8, 'TRANS': 243} Chain breaks: 2 Chain: "J" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1937 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 5, 'TRANS': 231} Chain breaks: 1 Chain: "K" Number of atoms: 3072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3072 Classifications: {'peptide': 383} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 354} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "L" Number of atoms: 3071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3071 Classifications: {'peptide': 383} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 28, 'TRANS': 354} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 1879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1879 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 220} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'HIS:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "N" Number of atoms: 1889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1889 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 16, 'TRANS': 220} Chain: "O" Number of atoms: 1889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1889 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 16, 'TRANS': 220} Chain: "P" Number of atoms: 1879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1879 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 220} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'G1V': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {' ZN': 1, 'G1V': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.73, per 1000 atoms: 0.22 Number of scatterers: 35736 At special positions: 0 Unit cell: (214.39, 164.697, 195.932, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 Cl 8 17.00 S 210 16.00 O 6657 8.00 N 6107 7.00 C 22750 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.80 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" NE2 HIS C 122 " pdb="ZN ZN C 401 " - pdb=" NE2 HIS C 124 " 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8496 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 27 sheets defined 40.2% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 16 through 27 Processing helix chain 'A' and resid 93 through 112 Processing helix chain 'A' and resid 132 through 146 removed outlier: 3.979A pdb=" N MET A 145 " --> pdb=" O MET A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 234 removed outlier: 3.695A pdb=" N VAL A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU A 234 " --> pdb=" O GLU A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 252 removed outlier: 3.699A pdb=" N ILE A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 279 Processing helix chain 'A' and resid 279 through 312 Processing helix chain 'B' and resid 6 through 19 removed outlier: 3.560A pdb=" N ASN B 19 " --> pdb=" O PHE B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 84 Processing helix chain 'B' and resid 86 through 89 removed outlier: 4.122A pdb=" N LYS B 89 " --> pdb=" O ASP B 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 86 through 89' Processing helix chain 'B' and resid 106 through 121 removed outlier: 3.768A pdb=" N LYS B 114 " --> pdb=" O GLN B 110 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN B 115 " --> pdb=" O VAL B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 168 removed outlier: 3.607A pdb=" N ASN B 167 " --> pdb=" O ASN B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 193 removed outlier: 3.960A pdb=" N ALA B 186 " --> pdb=" O SER B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 252 removed outlier: 4.353A pdb=" N ARG B 207 " --> pdb=" O MET B 203 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA B 208 " --> pdb=" O LYS B 204 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE B 209 " --> pdb=" O ASP B 205 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL B 212 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU B 240 " --> pdb=" O SER B 236 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN B 247 " --> pdb=" O LYS B 243 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILE B 248 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N THR B 249 " --> pdb=" O ARG B 245 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N GLN B 250 " --> pdb=" O ARG B 246 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ARG B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 27 Processing helix chain 'C' and resid 93 through 112 Processing helix chain 'C' and resid 132 through 146 removed outlier: 3.930A pdb=" N MET C 145 " --> pdb=" O MET C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 233 removed outlier: 3.623A pdb=" N VAL C 233 " --> pdb=" O LEU C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 252 removed outlier: 4.594A pdb=" N LYS C 237 " --> pdb=" O VAL C 233 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU C 242 " --> pdb=" O ILE C 238 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU C 243 " --> pdb=" O LEU C 239 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ILE C 250 " --> pdb=" O ALA C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 279 Processing helix chain 'C' and resid 279 through 311 removed outlier: 3.639A pdb=" N GLU C 292 " --> pdb=" O GLU C 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 18 Processing helix chain 'D' and resid 76 through 84 Processing helix chain 'D' and resid 86 through 89 removed outlier: 4.129A pdb=" N LYS D 89 " --> pdb=" O ASP D 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 86 through 89' Processing helix chain 'D' and resid 106 through 121 removed outlier: 3.623A pdb=" N LYS D 114 " --> pdb=" O GLN D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 168 Processing helix chain 'D' and resid 182 through 192 removed outlier: 4.003A pdb=" N ALA D 186 " --> pdb=" O SER D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 196 Processing helix chain 'D' and resid 203 through 252 removed outlier: 3.718A pdb=" N ARG D 207 " --> pdb=" O MET D 203 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE D 209 " --> pdb=" O ASP D 205 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU D 228 " --> pdb=" O CYS D 224 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS D 229 " --> pdb=" O ALA D 225 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS D 252 " --> pdb=" O ILE D 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 8 removed outlier: 4.019A pdb=" N ALA E 6 " --> pdb=" O SER E 2 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN E 8 " --> pdb=" O GLU E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 24 removed outlier: 3.813A pdb=" N ILE E 18 " --> pdb=" O LEU E 14 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 133 removed outlier: 3.560A pdb=" N LEU E 115 " --> pdb=" O GLU E 111 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL E 116 " --> pdb=" O CYS E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 148 removed outlier: 4.320A pdb=" N GLU E 148 " --> pdb=" O THR E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 154 removed outlier: 3.562A pdb=" N ASN E 154 " --> pdb=" O GLN E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 227 removed outlier: 3.984A pdb=" N HIS E 227 " --> pdb=" O PRO E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 234 Processing helix chain 'E' and resid 249 through 280 removed outlier: 3.941A pdb=" N LEU E 256 " --> pdb=" O GLN E 252 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL E 264 " --> pdb=" O LYS E 260 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER E 280 " --> pdb=" O ALA E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 377 through 381 removed outlier: 4.347A pdb=" N ASN E 380 " --> pdb=" O ALA E 377 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY E 381 " --> pdb=" O PHE E 378 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 377 through 381' Processing helix chain 'F' and resid 3 through 8 removed outlier: 3.614A pdb=" N ASN F 8 " --> pdb=" O GLU F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 13 No H-bonds generated for 'chain 'F' and resid 11 through 13' Processing helix chain 'F' and resid 14 through 24 removed outlier: 3.702A pdb=" N ILE F 18 " --> pdb=" O LEU F 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 104 Processing helix chain 'F' and resid 111 through 133 removed outlier: 3.651A pdb=" N LEU F 115 " --> pdb=" O GLU F 111 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL F 116 " --> pdb=" O CYS F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 147 Processing helix chain 'F' and resid 222 through 228 removed outlier: 3.690A pdb=" N HIS F 227 " --> pdb=" O PRO F 223 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA F 228 " --> pdb=" O ARG F 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 245 through 279 Proline residue: F 251 - end of helix Processing helix chain 'F' and resid 357 through 362 removed outlier: 3.946A pdb=" N ARG F 361 " --> pdb=" O GLU F 357 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 27 Processing helix chain 'G' and resid 93 through 112 removed outlier: 3.672A pdb=" N LEU G 97 " --> pdb=" O SER G 93 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER G 98 " --> pdb=" O PRO G 94 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA G 99 " --> pdb=" O GLU G 95 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU G 110 " --> pdb=" O ARG G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 147 removed outlier: 3.831A pdb=" N MET G 145 " --> pdb=" O MET G 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 225 through 252 removed outlier: 3.563A pdb=" N SER G 231 " --> pdb=" O VAL G 227 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA G 232 " --> pdb=" O CYS G 228 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL G 233 " --> pdb=" O LEU G 229 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LEU G 235 " --> pdb=" O SER G 231 " (cutoff:3.500A) Proline residue: G 236 - end of helix removed outlier: 3.687A pdb=" N ILE G 250 " --> pdb=" O ALA G 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 257 through 312 removed outlier: 4.909A pdb=" N GLY G 281 " --> pdb=" O SER G 277 " (cutoff:3.500A) Proline residue: G 282 - end of helix Processing helix chain 'H' and resid 6 through 20 Processing helix chain 'H' and resid 76 through 84 removed outlier: 3.644A pdb=" N ILE H 83 " --> pdb=" O SER H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 89 removed outlier: 3.777A pdb=" N LYS H 89 " --> pdb=" O ASP H 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 86 through 89' Processing helix chain 'H' and resid 106 through 121 removed outlier: 3.693A pdb=" N LYS H 114 " --> pdb=" O GLN H 110 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 169 removed outlier: 3.781A pdb=" N SER H 169 " --> pdb=" O GLY H 166 " (cutoff:3.500A) Processing helix chain 'H' and resid 182 through 193 removed outlier: 3.587A pdb=" N VAL H 188 " --> pdb=" O SER H 184 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE H 189 " --> pdb=" O TYR H 185 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LYS H 190 " --> pdb=" O ALA H 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 203 through 252 removed outlier: 4.068A pdb=" N ARG H 207 " --> pdb=" O MET H 203 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL H 212 " --> pdb=" O ALA H 208 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA H 225 " --> pdb=" O GLN H 221 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER H 230 " --> pdb=" O ASP H 226 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LYS H 243 " --> pdb=" O ALA H 239 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE H 248 " --> pdb=" O LEU H 244 " (cutoff:3.500A) Processing helix chain 'I' and resid 16 through 27 Processing helix chain 'I' and resid 93 through 111 Processing helix chain 'I' and resid 132 through 146 removed outlier: 4.489A pdb=" N MET I 145 " --> pdb=" O MET I 141 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP I 146 " --> pdb=" O TYR I 142 " (cutoff:3.500A) Processing helix chain 'I' and resid 225 through 233 removed outlier: 3.905A pdb=" N VAL I 233 " --> pdb=" O LEU I 229 " (cutoff:3.500A) Processing helix chain 'I' and resid 234 through 252 removed outlier: 3.851A pdb=" N ARG I 249 " --> pdb=" O ASP I 245 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ILE I 250 " --> pdb=" O ALA I 246 " (cutoff:3.500A) Processing helix chain 'I' and resid 257 through 279 removed outlier: 3.538A pdb=" N GLN I 275 " --> pdb=" O ASN I 271 " (cutoff:3.500A) Processing helix chain 'I' and resid 279 through 306 removed outlier: 3.536A pdb=" N LEU I 291 " --> pdb=" O LEU I 287 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU I 292 " --> pdb=" O GLU I 288 " (cutoff:3.500A) Processing helix chain 'J' and resid 6 through 20 Processing helix chain 'J' and resid 76 through 84 removed outlier: 3.756A pdb=" N ASP J 81 " --> pdb=" O GLU J 77 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE J 83 " --> pdb=" O SER J 79 " (cutoff:3.500A) Processing helix chain 'J' and resid 86 through 89 removed outlier: 4.395A pdb=" N LYS J 89 " --> pdb=" O ASP J 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 86 through 89' Processing helix chain 'J' and resid 106 through 121 removed outlier: 3.533A pdb=" N LYS J 114 " --> pdb=" O GLN J 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 164 through 168 removed outlier: 3.517A pdb=" N ASN J 167 " --> pdb=" O ASN J 164 " (cutoff:3.500A) Processing helix chain 'J' and resid 182 through 193 removed outlier: 3.763A pdb=" N ALA J 186 " --> pdb=" O SER J 182 " (cutoff:3.500A) Processing helix chain 'J' and resid 203 through 252 removed outlier: 3.860A pdb=" N ARG J 207 " --> pdb=" O MET J 203 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU J 240 " --> pdb=" O SER J 236 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN J 242 " --> pdb=" O GLN J 238 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LYS J 243 " --> pdb=" O ALA J 239 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE J 248 " --> pdb=" O LEU J 244 " (cutoff:3.500A) Processing helix chain 'K' and resid 11 through 13 No H-bonds generated for 'chain 'K' and resid 11 through 13' Processing helix chain 'K' and resid 14 through 24 removed outlier: 3.629A pdb=" N ILE K 18 " --> pdb=" O LEU K 14 " (cutoff:3.500A) Processing helix chain 'K' and resid 111 through 133 removed outlier: 3.598A pdb=" N GLU K 119 " --> pdb=" O LEU K 115 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG K 133 " --> pdb=" O CYS K 129 " (cutoff:3.500A) Processing helix chain 'K' and resid 135 through 148 removed outlier: 4.151A pdb=" N GLU K 148 " --> pdb=" O THR K 144 " (cutoff:3.500A) Processing helix chain 'K' and resid 148 through 153 removed outlier: 3.540A pdb=" N GLU K 153 " --> pdb=" O PRO K 149 " (cutoff:3.500A) Processing helix chain 'K' and resid 222 through 230 Processing helix chain 'K' and resid 230 through 236 Processing helix chain 'K' and resid 245 through 261 Proline residue: K 251 - end of helix Processing helix chain 'K' and resid 262 through 277 removed outlier: 3.607A pdb=" N GLU K 273 " --> pdb=" O HIS K 269 " (cutoff:3.500A) Processing helix chain 'K' and resid 278 through 282 removed outlier: 3.805A pdb=" N HIS K 281 " --> pdb=" O PHE K 278 " (cutoff:3.500A) Processing helix chain 'K' and resid 358 through 365 removed outlier: 4.083A pdb=" N TYR K 365 " --> pdb=" O ARG K 361 " (cutoff:3.500A) Processing helix chain 'K' and resid 368 through 375 removed outlier: 3.904A pdb=" N GLU K 375 " --> pdb=" O PRO K 371 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 10 removed outlier: 3.760A pdb=" N ASN L 8 " --> pdb=" O GLU L 4 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG L 9 " --> pdb=" O VAL L 5 " (cutoff:3.500A) Processing helix chain 'L' and resid 14 through 24 removed outlier: 3.529A pdb=" N ILE L 18 " --> pdb=" O LEU L 14 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 132 Processing helix chain 'L' and resid 133 through 135 No H-bonds generated for 'chain 'L' and resid 133 through 135' Processing helix chain 'L' and resid 136 through 148 removed outlier: 3.501A pdb=" N GLU L 148 " --> pdb=" O THR L 144 " (cutoff:3.500A) Processing helix chain 'L' and resid 222 through 230 Processing helix chain 'L' and resid 245 through 277 Proline residue: L 251 - end of helix removed outlier: 3.735A pdb=" N THR L 258 " --> pdb=" O CYS L 254 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N TYR L 263 " --> pdb=" O ASN L 259 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N VAL L 264 " --> pdb=" O LYS L 260 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ILE L 265 " --> pdb=" O VAL L 261 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA L 277 " --> pdb=" O GLU L 273 " (cutoff:3.500A) Processing helix chain 'L' and resid 278 through 282 Processing helix chain 'L' and resid 358 through 365 removed outlier: 3.639A pdb=" N ALA L 362 " --> pdb=" O MET L 358 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TYR L 365 " --> pdb=" O ARG L 361 " (cutoff:3.500A) Processing helix chain 'L' and resid 366 through 368 No H-bonds generated for 'chain 'L' and resid 366 through 368' Processing helix chain 'L' and resid 369 through 374 removed outlier: 4.377A pdb=" N PHE L 373 " --> pdb=" O PHE L 369 " (cutoff:3.500A) Processing helix chain 'M' and resid 102 through 107 removed outlier: 3.987A pdb=" N LEU M 107 " --> pdb=" O GLU M 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 119 through 137 removed outlier: 4.050A pdb=" N VAL M 123 " --> pdb=" O ASN M 119 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS M 137 " --> pdb=" O ARG M 133 " (cutoff:3.500A) Processing helix chain 'M' and resid 162 through 169 removed outlier: 3.595A pdb=" N LEU M 166 " --> pdb=" O ASP M 162 " (cutoff:3.500A) Processing helix chain 'M' and resid 184 through 194 removed outlier: 3.814A pdb=" N LYS M 193 " --> pdb=" O LEU M 189 " (cutoff:3.500A) Processing helix chain 'M' and resid 229 through 238 removed outlier: 3.960A pdb=" N MET M 235 " --> pdb=" O PRO M 231 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N CYS M 238 " --> pdb=" O LYS M 234 " (cutoff:3.500A) Processing helix chain 'M' and resid 250 through 255 removed outlier: 4.529A pdb=" N GLU M 254 " --> pdb=" O ASN M 250 " (cutoff:3.500A) Processing helix chain 'M' and resid 259 through 269 Processing helix chain 'M' and resid 270 through 272 No H-bonds generated for 'chain 'M' and resid 270 through 272' Processing helix chain 'M' and resid 290 through 294 Processing helix chain 'M' and resid 310 through 317 removed outlier: 3.775A pdb=" N SER M 314 " --> pdb=" O HIS M 310 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU M 317 " --> pdb=" O TYR M 313 " (cutoff:3.500A) Processing helix chain 'N' and resid 103 through 107 removed outlier: 3.764A pdb=" N LEU N 107 " --> pdb=" O GLU N 104 " (cutoff:3.500A) Processing helix chain 'N' and resid 119 through 135 removed outlier: 3.858A pdb=" N VAL N 123 " --> pdb=" O ASN N 119 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN N 125 " --> pdb=" O LEU N 121 " (cutoff:3.500A) Processing helix chain 'N' and resid 162 through 169 removed outlier: 3.793A pdb=" N LEU N 166 " --> pdb=" O ASP N 162 " (cutoff:3.500A) Processing helix chain 'N' and resid 183 through 192 removed outlier: 4.117A pdb=" N PHE N 187 " --> pdb=" O LEU N 183 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN N 192 " --> pdb=" O SER N 188 " (cutoff:3.500A) Processing helix chain 'N' and resid 201 through 205 removed outlier: 3.566A pdb=" N THR N 204 " --> pdb=" O ASN N 201 " (cutoff:3.500A) Processing helix chain 'N' and resid 233 through 238 Processing helix chain 'N' and resid 258 through 269 removed outlier: 4.180A pdb=" N LYS N 262 " --> pdb=" O GLU N 258 " (cutoff:3.500A) Processing helix chain 'N' and resid 270 through 272 No H-bonds generated for 'chain 'N' and resid 270 through 272' Processing helix chain 'N' and resid 289 through 291 No H-bonds generated for 'chain 'N' and resid 289 through 291' Processing helix chain 'N' and resid 292 through 298 removed outlier: 3.885A pdb=" N LYS N 297 " --> pdb=" O ASN N 293 " (cutoff:3.500A) Processing helix chain 'N' and resid 307 through 311 Processing helix chain 'O' and resid 119 through 133 Processing helix chain 'O' and resid 163 through 170 Processing helix chain 'O' and resid 183 through 192 removed outlier: 3.775A pdb=" N PHE O 187 " --> pdb=" O LEU O 183 " (cutoff:3.500A) Processing helix chain 'O' and resid 199 through 204 removed outlier: 3.567A pdb=" N VAL O 202 " --> pdb=" O THR O 199 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLN O 203 " --> pdb=" O GLU O 200 " (cutoff:3.500A) Processing helix chain 'O' and resid 229 through 237 removed outlier: 4.002A pdb=" N MET O 235 " --> pdb=" O PRO O 231 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN O 237 " --> pdb=" O LYS O 233 " (cutoff:3.500A) Processing helix chain 'O' and resid 249 through 255 removed outlier: 4.074A pdb=" N GLU O 253 " --> pdb=" O HIS O 249 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLU O 254 " --> pdb=" O ASN O 250 " (cutoff:3.500A) Processing helix chain 'O' and resid 258 through 269 removed outlier: 4.400A pdb=" N LYS O 262 " --> pdb=" O GLU O 258 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N MET O 264 " --> pdb=" O SER O 260 " (cutoff:3.500A) Processing helix chain 'O' and resid 270 through 272 No H-bonds generated for 'chain 'O' and resid 270 through 272' Processing helix chain 'O' and resid 283 through 286 Processing helix chain 'O' and resid 288 through 298 removed outlier: 3.515A pdb=" N ASN O 293 " --> pdb=" O LEU O 289 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N CYS O 294 " --> pdb=" O GLU O 290 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N MET O 295 " --> pdb=" O LEU O 291 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS O 297 " --> pdb=" O ASN O 293 " (cutoff:3.500A) Processing helix chain 'O' and resid 307 through 311 Processing helix chain 'P' and resid 103 through 107 removed outlier: 3.684A pdb=" N SER P 106 " --> pdb=" O GLU P 103 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU P 107 " --> pdb=" O GLU P 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 103 through 107' Processing helix chain 'P' and resid 119 through 134 removed outlier: 4.199A pdb=" N VAL P 123 " --> pdb=" O ASN P 119 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN P 125 " --> pdb=" O LEU P 121 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR P 134 " --> pdb=" O MET P 130 " (cutoff:3.500A) Processing helix chain 'P' and resid 135 through 137 No H-bonds generated for 'chain 'P' and resid 135 through 137' Processing helix chain 'P' and resid 162 through 169 removed outlier: 4.044A pdb=" N LEU P 166 " --> pdb=" O ASP P 162 " (cutoff:3.500A) Processing helix chain 'P' and resid 183 through 194 removed outlier: 4.376A pdb=" N PHE P 187 " --> pdb=" O LEU P 183 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU P 189 " --> pdb=" O GLY P 185 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS P 193 " --> pdb=" O LEU P 189 " (cutoff:3.500A) Processing helix chain 'P' and resid 199 through 204 removed outlier: 4.496A pdb=" N GLN P 203 " --> pdb=" O GLU P 200 " (cutoff:3.500A) Processing helix chain 'P' and resid 229 through 237 removed outlier: 4.770A pdb=" N MET P 235 " --> pdb=" O PRO P 231 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN P 237 " --> pdb=" O LYS P 233 " (cutoff:3.500A) Processing helix chain 'P' and resid 249 through 255 removed outlier: 4.146A pdb=" N GLU P 253 " --> pdb=" O HIS P 249 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLU P 254 " --> pdb=" O ASN P 250 " (cutoff:3.500A) Processing helix chain 'P' and resid 258 through 268 removed outlier: 4.512A pdb=" N LYS P 262 " --> pdb=" O GLU P 258 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP P 263 " --> pdb=" O MET P 259 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET P 264 " --> pdb=" O SER P 260 " (cutoff:3.500A) Processing helix chain 'P' and resid 269 through 272 Processing helix chain 'P' and resid 290 through 293 Processing helix chain 'P' and resid 294 through 299 Processing sheet with id=AA1, first strand: chain 'A' and resid 212 through 213 removed outlier: 4.247A pdb=" N LEU B 147 " --> pdb=" O ILE B 158 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 216 through 219 removed outlier: 3.846A pdb=" N GLU A 15 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N SER A 76 " --> pdb=" O GLU A 15 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N ILE A 74 " --> pdb=" O GLU A 41 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLU A 41 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 80 " --> pdb=" O MET A 35 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N MET A 35 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY A 119 " --> pdb=" O CYS A 38 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N GLY A 40 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N VAL A 117 " --> pdb=" O GLY A 40 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N CYS A 156 " --> pdb=" O HIS A 124 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE A 153 " --> pdb=" O THR A 171 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N PHE A 157 " --> pdb=" O ARG A 167 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ARG A 167 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU A 159 " --> pdb=" O THR A 165 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N THR A 165 " --> pdb=" O GLU A 159 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE B 132 " --> pdb=" O ARG B 98 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU B 28 " --> pdb=" O ILE B 92 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N TRP B 94 " --> pdb=" O GLY B 26 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N GLY B 26 " --> pdb=" O TRP B 94 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ARG B 96 " --> pdb=" O HIS B 24 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N HIS B 24 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N GLU B 25 " --> pdb=" O PRO B 61 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N PHE B 27 " --> pdb=" O HIS B 59 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N HIS B 59 " --> pdb=" O PHE B 27 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N LEU B 29 " --> pdb=" O HIS B 57 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ALA B 2 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N ILE B 56 " --> pdb=" O ALA B 2 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N SER B 4 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ASN B 58 " --> pdb=" O SER B 4 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 212 through 213 removed outlier: 3.878A pdb=" N LEU D 147 " --> pdb=" O ILE D 158 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 216 through 219 removed outlier: 6.325A pdb=" N VAL C 12 " --> pdb=" O HIS C 217 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL C 219 " --> pdb=" O VAL C 12 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LEU C 14 " --> pdb=" O VAL C 219 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU C 15 " --> pdb=" O ILE C 74 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N SER C 76 " --> pdb=" O GLU C 15 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE C 39 " --> pdb=" O HIS C 75 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N VAL C 77 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU C 37 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ILE C 79 " --> pdb=" O MET C 35 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N MET C 35 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY C 119 " --> pdb=" O CYS C 38 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N GLY C 40 " --> pdb=" O VAL C 117 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N VAL C 117 " --> pdb=" O GLY C 40 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N CYS C 156 " --> pdb=" O HIS C 124 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE C 153 " --> pdb=" O THR C 171 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N PHE C 157 " --> pdb=" O ARG C 167 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ARG C 167 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLU C 159 " --> pdb=" O THR C 165 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N THR C 165 " --> pdb=" O GLU C 159 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL D 126 " --> pdb=" O ILE D 92 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU D 28 " --> pdb=" O ILE D 92 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N TRP D 94 " --> pdb=" O GLY D 26 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLY D 26 " --> pdb=" O TRP D 94 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ARG D 96 " --> pdb=" O HIS D 24 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N HIS D 24 " --> pdb=" O ARG D 96 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N GLU D 25 " --> pdb=" O PRO D 61 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N PHE D 27 " --> pdb=" O HIS D 59 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N HIS D 59 " --> pdb=" O PHE D 27 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LEU D 29 " --> pdb=" O HIS D 57 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ALA D 2 " --> pdb=" O ILE D 54 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N ILE D 56 " --> pdb=" O ALA D 2 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N SER D 4 " --> pdb=" O ILE D 56 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N ASN D 58 " --> pdb=" O SER D 4 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 36 through 41 removed outlier: 6.452A pdb=" N ILE E 37 " --> pdb=" O HIS E 59 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N HIS E 59 " --> pdb=" O ILE E 37 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ASP E 39 " --> pdb=" O LYS E 57 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LYS E 57 " --> pdb=" O ASP E 39 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 61 through 62 Processing sheet with id=AA7, first strand: chain 'E' and resid 175 through 176 Processing sheet with id=AA8, first strand: chain 'F' and resid 36 through 41 removed outlier: 6.101A pdb=" N ILE F 37 " --> pdb=" O HIS F 59 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N HIS F 59 " --> pdb=" O ILE F 37 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N ASP F 39 " --> pdb=" O LYS F 57 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LYS F 57 " --> pdb=" O ASP F 39 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 61 through 62 Processing sheet with id=AB1, first strand: chain 'F' and resid 175 through 176 Processing sheet with id=AB2, first strand: chain 'G' and resid 212 through 213 removed outlier: 4.217A pdb=" N LEU J 147 " --> pdb=" O ILE J 158 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 216 through 219 removed outlier: 6.260A pdb=" N VAL G 12 " --> pdb=" O HIS G 217 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL G 219 " --> pdb=" O VAL G 12 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LEU G 14 " --> pdb=" O VAL G 219 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU G 15 " --> pdb=" O ILE G 74 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N SER G 76 " --> pdb=" O GLU G 15 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N ILE G 74 " --> pdb=" O GLU G 41 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N GLU G 41 " --> pdb=" O ILE G 74 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY G 119 " --> pdb=" O CYS G 38 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLY G 40 " --> pdb=" O VAL G 117 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N VAL G 117 " --> pdb=" O GLY G 40 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL G 150 " --> pdb=" O VAL G 118 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N CYS G 156 " --> pdb=" O HIS G 124 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE G 153 " --> pdb=" O THR G 171 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N PHE G 157 " --> pdb=" O ARG G 167 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ARG G 167 " --> pdb=" O PHE G 157 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLU G 159 " --> pdb=" O THR G 165 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N THR G 165 " --> pdb=" O GLU G 159 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE J 132 " --> pdb=" O ARG J 98 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU J 28 " --> pdb=" O ILE J 92 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N TRP J 94 " --> pdb=" O GLY J 26 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N GLY J 26 " --> pdb=" O TRP J 94 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ARG J 96 " --> pdb=" O HIS J 24 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N HIS J 24 " --> pdb=" O ARG J 96 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N GLU J 25 " --> pdb=" O PRO J 61 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N PHE J 27 " --> pdb=" O HIS J 59 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N HIS J 59 " --> pdb=" O PHE J 27 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LEU J 29 " --> pdb=" O HIS J 57 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ALA J 3 " --> pdb=" O ALA J 161 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 157 through 158 removed outlier: 4.165A pdb=" N LEU H 147 " --> pdb=" O ILE H 158 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 160 through 161 removed outlier: 6.694A pdb=" N ALA H 3 " --> pdb=" O ALA H 161 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ALA H 2 " --> pdb=" O ILE H 54 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N ILE H 56 " --> pdb=" O ALA H 2 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N SER H 4 " --> pdb=" O ILE H 56 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N ASN H 58 " --> pdb=" O SER H 4 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LEU H 29 " --> pdb=" O HIS H 57 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N HIS H 59 " --> pdb=" O PHE H 27 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N PHE H 27 " --> pdb=" O HIS H 59 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N GLU H 25 " --> pdb=" O PRO H 61 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N HIS H 24 " --> pdb=" O ARG H 96 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ARG H 96 " --> pdb=" O HIS H 24 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N GLY H 26 " --> pdb=" O TRP H 94 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N TRP H 94 " --> pdb=" O GLY H 26 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU H 28 " --> pdb=" O ILE H 92 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL H 126 " --> pdb=" O ILE H 92 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE H 132 " --> pdb=" O ARG H 98 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N ARG I 167 " --> pdb=" O PHE I 157 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N PHE I 157 " --> pdb=" O ARG I 167 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N CYS I 156 " --> pdb=" O HIS I 124 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N VAL I 117 " --> pdb=" O GLY I 40 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N GLY I 40 " --> pdb=" O VAL I 117 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY I 119 " --> pdb=" O CYS I 38 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR I 121 " --> pdb=" O GLY I 36 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLU I 41 " --> pdb=" O ILE I 74 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ILE I 74 " --> pdb=" O GLU I 41 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE I 74 " --> pdb=" O HIS I 13 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU I 15 " --> pdb=" O ILE I 74 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N SER I 76 " --> pdb=" O GLU I 15 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N VAL I 12 " --> pdb=" O HIS I 217 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL I 219 " --> pdb=" O VAL I 12 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU I 14 " --> pdb=" O VAL I 219 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 36 through 41 removed outlier: 3.608A pdb=" N ARG K 36 " --> pdb=" O HIS K 59 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU K 40 " --> pdb=" O ARG K 55 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ARG K 55 " --> pdb=" O LEU K 40 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 61 through 62 Processing sheet with id=AB8, first strand: chain 'K' and resid 175 through 176 Processing sheet with id=AB9, first strand: chain 'L' and resid 36 through 41 removed outlier: 4.333A pdb=" N LEU L 40 " --> pdb=" O ARG L 55 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ARG L 55 " --> pdb=" O LEU L 40 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 158 through 159 removed outlier: 3.507A pdb=" N ALA L 171 " --> pdb=" O PHE L 207 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ALA L 201 " --> pdb=" O LEU L 177 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'M' and resid 155 through 160 removed outlier: 8.161A pdb=" N LEU M 156 " --> pdb=" O VAL M 148 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N VAL M 148 " --> pdb=" O LEU M 156 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N GLY M 158 " --> pdb=" O LEU M 146 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N LEU M 146 " --> pdb=" O GLY M 158 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N VAL M 216 " --> pdb=" O CYS M 98 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N TYR M 280 " --> pdb=" O PHE M 243 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N VAL M 245 " --> pdb=" O TYR M 280 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N VAL M 282 " --> pdb=" O VAL M 245 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N TYR M 247 " --> pdb=" O VAL M 282 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'M' and resid 110 through 111 Processing sheet with id=AC4, first strand: chain 'N' and resid 155 through 160 removed outlier: 5.697A pdb=" N GLY N 158 " --> pdb=" O LEU N 146 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N LEU N 146 " --> pdb=" O GLY N 158 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL N 95 " --> pdb=" O ALA N 145 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N VAL N 147 " --> pdb=" O VAL N 95 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ILE N 97 " --> pdb=" O VAL N 147 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE N 96 " --> pdb=" O ILE N 214 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N VAL N 216 " --> pdb=" O ILE N 96 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N TYR N 280 " --> pdb=" O PHE N 243 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N VAL N 245 " --> pdb=" O TYR N 280 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N VAL N 282 " --> pdb=" O VAL N 245 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N TYR N 247 " --> pdb=" O VAL N 282 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'N' and resid 110 through 111 Processing sheet with id=AC6, first strand: chain 'O' and resid 155 through 160 removed outlier: 8.066A pdb=" N LEU O 156 " --> pdb=" O VAL O 148 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N VAL O 148 " --> pdb=" O LEU O 156 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N GLY O 158 " --> pdb=" O LEU O 146 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N LEU O 146 " --> pdb=" O GLY O 158 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA O 145 " --> pdb=" O VAL O 95 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE O 97 " --> pdb=" O ALA O 145 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE O 96 " --> pdb=" O ILE O 214 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N VAL O 216 " --> pdb=" O ILE O 96 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N CYS O 98 " --> pdb=" O VAL O 216 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N TYR O 280 " --> pdb=" O PHE O 243 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N VAL O 245 " --> pdb=" O TYR O 280 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N VAL O 282 " --> pdb=" O VAL O 245 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N TYR O 247 " --> pdb=" O VAL O 282 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'O' and resid 110 through 111 removed outlier: 4.000A pdb=" N LEU O 110 " --> pdb=" O THR O 118 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'P' and resid 155 through 160 removed outlier: 3.545A pdb=" N LEU P 146 " --> pdb=" O LEU P 156 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLY P 158 " --> pdb=" O PHE P 144 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N PHE P 144 " --> pdb=" O GLY P 158 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL P 95 " --> pdb=" O ALA P 145 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N VAL P 147 " --> pdb=" O VAL P 95 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE P 97 " --> pdb=" O VAL P 147 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N VAL P 216 " --> pdb=" O CYS P 98 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N TYR P 280 " --> pdb=" O PHE P 243 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL P 245 " --> pdb=" O TYR P 280 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N VAL P 282 " --> pdb=" O VAL P 245 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N TYR P 247 " --> pdb=" O VAL P 282 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'P' and resid 110 through 111 removed outlier: 3.736A pdb=" N THR P 118 " --> pdb=" O LEU P 110 " (cutoff:3.500A) 1423 hydrogen bonds defined for protein. 4041 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: 6.38 Time building geometry restraints manager: 3.79 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: 11739 1.34 - 1.47: 8361 1.47 - 1.59: 16138 1.59 - 1.71: 5 1.71 - 1.83: 317 Bond restraints: 36560 Sorted by residual: bond pdb=" CAC G1V D 301 " pdb=" CAF G1V D 301 " ideal model delta sigma weight residual 1.482 1.323 0.159 2.00e-02 2.50e+03 6.33e+01 bond pdb=" CAC G1V I 402 " pdb=" CAF G1V I 402 " ideal model delta sigma weight residual 1.482 1.327 0.155 2.00e-02 2.50e+03 6.04e+01 bond pdb=" CBE G1V I 402 " pdb=" CBF G1V I 402 " ideal model delta sigma weight residual 1.498 1.355 0.143 2.00e-02 2.50e+03 5.10e+01 bond pdb=" CBD G1V I 402 " pdb=" CBE G1V I 402 " ideal model delta sigma weight residual 1.497 1.638 -0.141 2.00e-02 2.50e+03 4.97e+01 bond pdb=" CBD G1V I 402 " pdb=" CBF G1V I 402 " ideal model delta sigma weight residual 1.501 1.642 -0.141 2.00e-02 2.50e+03 4.94e+01 ... (remaining 36555 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.88: 49473 5.88 - 11.75: 49 11.75 - 17.63: 10 17.63 - 23.50: 0 23.50 - 29.38: 6 Bond angle restraints: 49538 Sorted by residual: angle pdb=" CBG G1V D 301 " pdb=" NBH G1V D 301 " pdb=" CBI G1V D 301 " ideal model delta sigma weight residual 107.83 137.21 -29.38 3.00e+00 1.11e-01 9.59e+01 angle pdb=" CBG G1V I 402 " pdb=" NBH G1V I 402 " pdb=" CBI G1V I 402 " ideal model delta sigma weight residual 107.83 136.56 -28.73 3.00e+00 1.11e-01 9.17e+01 angle pdb=" CBF G1V D 301 " pdb=" CBI G1V D 301 " pdb=" NBH G1V D 301 " ideal model delta sigma weight residual 103.30 74.88 28.42 3.00e+00 1.11e-01 8.97e+01 angle pdb=" CBF G1V I 402 " pdb=" CBI G1V I 402 " pdb=" NBH G1V I 402 " ideal model delta sigma weight residual 103.30 74.99 28.31 3.00e+00 1.11e-01 8.91e+01 angle pdb=" CBE G1V D 301 " pdb=" CBG G1V D 301 " pdb=" NBH G1V D 301 " ideal model delta sigma weight residual 103.30 75.41 27.89 3.00e+00 1.11e-01 8.64e+01 ... (remaining 49533 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 18560 17.92 - 35.85: 2576 35.85 - 53.77: 778 53.77 - 71.69: 173 71.69 - 89.61: 76 Dihedral angle restraints: 22163 sinusoidal: 9088 harmonic: 13075 Sorted by residual: dihedral pdb=" CA ILE N 96 " pdb=" C ILE N 96 " pdb=" N ILE N 97 " pdb=" CA ILE N 97 " ideal model delta harmonic sigma weight residual 180.00 -158.25 -21.75 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA SER N 102 " pdb=" C SER N 102 " pdb=" N GLU N 103 " pdb=" CA GLU N 103 " ideal model delta harmonic sigma weight residual -180.00 -158.49 -21.51 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA ASP N 100 " pdb=" C ASP N 100 " pdb=" N LEU N 101 " pdb=" CA LEU N 101 " ideal model delta harmonic sigma weight residual 180.00 -159.05 -20.95 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 22160 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 4737 0.060 - 0.120: 646 0.120 - 0.179: 73 0.179 - 0.239: 7 0.239 - 0.299: 3 Chirality restraints: 5466 Sorted by residual: chirality pdb=" CG LEU L 145 " pdb=" CB LEU L 145 " pdb=" CD1 LEU L 145 " pdb=" CD2 LEU L 145 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CA MET N 130 " pdb=" N MET N 130 " pdb=" C MET N 130 " pdb=" CB MET N 130 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CBF G1V I 402 " pdb=" CBD G1V I 402 " pdb=" CBE G1V I 402 " pdb=" CBI G1V I 402 " both_signs ideal model delta sigma weight residual True 2.62 -2.36 0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 5463 not shown) Planarity restraints: 6411 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAA G1V D 301 " -0.003 2.00e-02 2.50e+03 6.57e-02 1.08e+02 pdb=" CAB G1V D 301 " 0.105 2.00e-02 2.50e+03 pdb=" CAC G1V D 301 " -0.095 2.00e-02 2.50e+03 pdb=" CAF G1V D 301 " -0.010 2.00e-02 2.50e+03 pdb=" CAT G1V D 301 " -0.030 2.00e-02 2.50e+03 pdb=" CAV G1V D 301 " 0.077 2.00e-02 2.50e+03 pdb=" NAD G1V D 301 " -0.042 2.00e-02 2.50e+03 pdb=" NAE G1V D 301 " 0.083 2.00e-02 2.50e+03 pdb=" NAI G1V D 301 " 0.002 2.00e-02 2.50e+03 pdb=" OAU G1V D 301 " -0.087 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAA G1V I 402 " -0.009 2.00e-02 2.50e+03 5.59e-02 7.81e+01 pdb=" CAB G1V I 402 " 0.084 2.00e-02 2.50e+03 pdb=" CAC G1V I 402 " -0.077 2.00e-02 2.50e+03 pdb=" CAF G1V I 402 " -0.006 2.00e-02 2.50e+03 pdb=" CAT G1V I 402 " -0.036 2.00e-02 2.50e+03 pdb=" CAV G1V I 402 " 0.064 2.00e-02 2.50e+03 pdb=" NAD G1V I 402 " -0.038 2.00e-02 2.50e+03 pdb=" NAE G1V I 402 " 0.083 2.00e-02 2.50e+03 pdb=" NAI G1V I 402 " 0.003 2.00e-02 2.50e+03 pdb=" OAU G1V I 402 " -0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAJ G1V D 301 " -0.031 2.00e-02 2.50e+03 4.59e-02 4.75e+01 pdb=" CAL G1V D 301 " 0.114 2.00e-02 2.50e+03 pdb=" CAM G1V D 301 " -0.067 2.00e-02 2.50e+03 pdb=" CAN G1V D 301 " 0.002 2.00e-02 2.50e+03 pdb=" CAO G1V D 301 " 0.000 2.00e-02 2.50e+03 pdb=" CAP G1V D 301 " -0.002 2.00e-02 2.50e+03 pdb=" CAQ G1V D 301 " -0.001 2.00e-02 2.50e+03 pdb="CLAR G1V D 301 " 0.005 2.00e-02 2.50e+03 pdb="CLAS G1V D 301 " -0.022 2.00e-02 2.50e+03 ... (remaining 6408 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 391 2.63 - 3.20: 31053 3.20 - 3.77: 54413 3.77 - 4.33: 73775 4.33 - 4.90: 121850 Nonbonded interactions: 281482 Sorted by model distance: nonbonded pdb=" OD2 ASP C 135 " pdb="ZN ZN C 401 " model vdw 2.063 2.230 nonbonded pdb=" O VAL I 90 " pdb="ZN ZN I 401 " model vdw 2.076 2.230 nonbonded pdb=" OG1 THR F 298 " pdb=" OE2 GLU N 184 " model vdw 2.106 3.040 nonbonded pdb=" OE1 GLN H 103 " pdb=" OG SER H 131 " model vdw 2.153 3.040 nonbonded pdb=" OG SER O 102 " pdb=" O GLU O 174 " model vdw 2.184 3.040 ... (remaining 281477 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 265 or (resid 266 and (name N or name CA or name \ C or name O or name CB )) or resid 267 through 401)) selection = chain 'C' selection = (chain 'G' and (resid 7 through 265 or (resid 266 and (name N or name CA or name \ C or name O or name CB )) or resid 267 through 401)) selection = (chain 'I' and (resid 7 through 265 or (resid 266 and (name N or name CA or name \ C or name O or name CB )) or resid 267 through 401)) } ncs_group { reference = chain 'B' selection = (chain 'D' and resid 1 through 252) selection = chain 'H' selection = chain 'J' } ncs_group { reference = (chain 'E' and (resid 1 through 301 or (resid 302 and (name N or name CA or name \ C or name O or name CB )) or resid 303 through 305 or (resid 306 through 308 an \ d (name N or name CA or name C or name O or name CB )) or resid 309 through 327 \ or (resid 328 and (name N or name CA or name C or name O or name CB )) or resid \ 329 through 383)) selection = (chain 'F' and (resid 1 through 301 or (resid 302 and (name N or name CA or name \ C or name O or name CB )) or resid 303 through 327 or (resid 328 and (name N or \ name CA or name C or name O or name CB )) or resid 329 through 332 or (resid 33 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 334 through \ 365 or (resid 366 and (name N or name CA or name C or name O or name CB )) or re \ sid 367 through 379 or (resid 380 and (name N or name CA or name C or name O or \ name CB )) or resid 381 through 383)) selection = (chain 'K' and (resid 1 through 301 or (resid 302 and (name N or name CA or name \ C or name O or name CB )) or resid 303 through 306 or (resid 307 through 308 an \ d (name N or name CA or name C or name O or name CB )) or resid 309 through 327 \ or (resid 328 and (name N or name CA or name C or name O or name CB )) or resid \ 329 through 332 or (resid 333 and (name N or name CA or name C or name O or name \ CB )) or resid 334 through 365 or (resid 366 and (name N or name CA or name C o \ r name O or name CB )) or resid 367 through 379 or (resid 380 and (name N or nam \ e CA or name C or name O or name CB )) or resid 381 through 383)) selection = (chain 'L' and (resid 1 through 305 or (resid 306 through 308 and (name N or nam \ e CA or name C or name O or name CB )) or resid 309 through 332 or (resid 333 an \ d (name N or name CA or name C or name O or name CB )) or resid 334 through 365 \ or (resid 366 and (name N or name CA or name C or name O or name CB )) or resid \ 367 through 379 or (resid 380 and (name N or name CA or name C or name O or name \ CB )) or resid 381 through 383)) } ncs_group { reference = (chain 'M' and (resid 81 through 113 or (resid 114 and (name N or name CA or nam \ e C or name O or name CB )) or resid 115 through 312 or (resid 313 and (name N o \ r name CA or name C or name O or name CB )) or resid 314 through 317)) selection = (chain 'N' and (resid 81 through 113 or (resid 114 and (name N or name CA or nam \ e C or name O or name CB )) or resid 115 through 141 or (resid 142 and (name N o \ r name CA or name C or name O or name CB )) or resid 143 through 291 or (resid 2 \ 92 and (name N or name CA or name C or name O or name CB )) or resid 293 through \ 312 or (resid 313 and (name N or name CA or name C or name O or name CB )) or r \ esid 314 through 317)) selection = (chain 'O' and (resid 81 through 113 or (resid 114 and (name N or name CA or nam \ e C or name O or name CB )) or resid 115 through 141 or (resid 142 and (name N o \ r name CA or name C or name O or name CB )) or resid 143 through 291 or (resid 2 \ 92 and (name N or name CA or name C or name O or name CB )) or resid 293 through \ 312 or (resid 313 and (name N or name CA or name C or name O or name CB )) or r \ esid 314 through 317)) selection = (chain 'P' and (resid 81 through 141 or (resid 142 and (name N or name CA or nam \ e C or name O or name CB )) or resid 143 through 291 or (resid 292 and (name N o \ r name CA or name C or name O or name CB )) or resid 293 through 317)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.85 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.960 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: 0.020 Extract box with map and model: 1.000 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 33.000 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.060 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: 0.000 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6817 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 : 0.004 0.159 36562 Z= 0.185 Angle : 0.709 29.380 49538 Z= 0.329 Chirality : 0.043 0.299 5466 Planarity : 0.004 0.120 6411 Dihedral : 18.899 89.614 13667 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 0.15 % Allowed : 30.76 % Favored : 69.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.13), residues: 4380 helix: 0.98 (0.14), residues: 1522 sheet: -0.71 (0.20), residues: 664 loop : -1.94 (0.13), residues: 2194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 82 TYR 0.022 0.001 TYR K 274 PHE 0.030 0.001 PHE N 131 TRP 0.017 0.001 TRP L 303 HIS 0.007 0.001 HIS E 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.19 (36560) covalent geometry : angle 0.70915 / 0.33 (49538) hydrogen bonds : bond 0.18337 / 12.74 ( 1399) hydrogen bonds : angle 6.43466 / 4.62 ( 4041) metal coordination : bond 0.00402 / 0.19 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 195 time to evaluate : 1.284 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: L 155 MET cc_start: 0.5435 (tpt) cc_final: 0.5081 (tpt) outliers start: 6 outliers final: 0 residues processed: 200 average time/residue: 0.2211 time to fit residues: 72.5184 Evaluate side-chains 145 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 432 optimal weight: 40.0000 chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 6.9990 chunk 401 optimal weight: 10.0000 chunk 424 optimal weight: 30.0000 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 ASN C 143 GLN C 174 GLN C 302 GLN D 24 HIS E 125 HIS ** E 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 183 ASN ** H 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 294 ASN J 137 ASN K 183 ASN L 266 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.097248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.066048 restraints weight = 161334.353| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 5.99 r_work: 0.2999 rms_B_bonded: 5.02 restraints_weight: 2.0000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.089 36562 Z= 0.298 Angle : 0.703 14.637 49538 Z= 0.357 Chirality : 0.045 0.249 5466 Planarity : 0.004 0.055 6411 Dihedral : 5.240 81.480 4851 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 3.74 % Allowed : 27.80 % Favored : 68.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.13), residues: 4380 helix: 1.05 (0.13), residues: 1518 sheet: -0.73 (0.21), residues: 637 loop : -1.92 (0.13), residues: 2225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.001 ARG J 245 TYR 0.024 0.002 TYR I 170 PHE 0.029 0.002 PHE N 131 TRP 0.030 0.002 TRP E 165 HIS 0.011 0.001 HIS M 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00689 / 0.30 (36560) covalent geometry : angle 0.70296 / 0.36 (49538) hydrogen bonds : bond 0.05767 / 3.89 ( 1399) hydrogen bonds : angle 5.17362 / 3.74 ( 4041) metal coordination : bond 0.00686 / 0.34 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 149 time to evaluate : 1.425 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 32 GLU cc_start: 0.9120 (OUTLIER) cc_final: 0.8735 (pm20) REVERT: C 87 LYS cc_start: 0.8263 (mmtm) cc_final: 0.7951 (mmmm) REVERT: C 289 ASP cc_start: 0.9094 (m-30) cc_final: 0.8875 (m-30) REVERT: D 1 MET cc_start: 0.6780 (mmt) cc_final: 0.6227 (tpp) REVERT: F 139 MET cc_start: 0.8830 (tmm) cc_final: 0.8448 (tmm) REVERT: G 35 MET cc_start: 0.9375 (ptt) cc_final: 0.9097 (ptt) REVERT: G 145 MET cc_start: 0.9059 (mtm) cc_final: 0.8741 (tmm) REVERT: H 144 GLU cc_start: 0.9082 (OUTLIER) cc_final: 0.8460 (mt-10) REVERT: I 115 MET cc_start: 0.7556 (mmm) cc_final: 0.7132 (mmm) REVERT: I 309 MET cc_start: 0.7185 (pmm) cc_final: 0.6981 (pmm) REVERT: K 71 ILE cc_start: 0.9233 (OUTLIER) cc_final: 0.8974 (mt) REVERT: M 127 MET cc_start: -0.4469 (mmt) cc_final: -0.4703 (mmm) outliers start: 149 outliers final: 56 residues processed: 291 average time/residue: 0.2099 time to fit residues: 103.0716 Evaluate side-chains 198 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 139 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 141 MET Chi-restraints excluded: chain C residue 209 TYR Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 140 PHE Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain F residue 34 CYS Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 254 CYS Chi-restraints excluded: chain F residue 368 THR Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 144 GLU Chi-restraints excluded: chain H residue 165 LEU Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 123 SER Chi-restraints excluded: chain I residue 171 THR Chi-restraints excluded: chain I residue 177 GLN Chi-restraints excluded: chain I residue 243 GLU Chi-restraints excluded: chain I residue 259 VAL Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain K residue 11 SER Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 112 CYS Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 157 ILE Chi-restraints excluded: chain L residue 174 LEU Chi-restraints excluded: chain L residue 284 THR Chi-restraints excluded: chain M residue 130 MET Chi-restraints excluded: chain M residue 210 VAL Chi-restraints excluded: chain M residue 303 LEU Chi-restraints excluded: chain M residue 316 LEU Chi-restraints excluded: chain N residue 110 LEU Chi-restraints excluded: chain N residue 127 MET Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain N residue 211 VAL Chi-restraints excluded: chain N residue 265 PHE Chi-restraints excluded: chain O residue 103 GLU Chi-restraints excluded: chain O residue 301 HIS Chi-restraints excluded: chain P residue 126 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 184 optimal weight: 8.9990 chunk 225 optimal weight: 9.9990 chunk 409 optimal weight: 50.0000 chunk 231 optimal weight: 2.9990 chunk 181 optimal weight: 4.9990 chunk 244 optimal weight: 7.9990 chunk 78 optimal weight: 0.0020 chunk 323 optimal weight: 6.9990 chunk 169 optimal weight: 50.0000 chunk 382 optimal weight: 20.0000 chunk 343 optimal weight: 40.0000 overall best weight: 4.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 174 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.097769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.067658 restraints weight = 161127.695| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 5.54 r_work: 0.3075 rms_B_bonded: 5.48 restraints_weight: 2.0000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 36562 Z= 0.183 Angle : 0.609 17.185 49538 Z= 0.308 Chirality : 0.043 0.256 5466 Planarity : 0.004 0.050 6411 Dihedral : 5.116 82.893 4851 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 2.91 % Allowed : 28.35 % Favored : 68.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.13), residues: 4380 helix: 1.35 (0.13), residues: 1519 sheet: -0.72 (0.20), residues: 670 loop : -1.84 (0.13), residues: 2191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 33 TYR 0.022 0.001 TYR K 274 PHE 0.065 0.001 PHE N 131 TRP 0.023 0.001 TRP E 165 HIS 0.007 0.001 HIS M 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 (36560) covalent geometry : angle 0.60909 / 0.31 (49538) hydrogen bonds : bond 0.05132 / 3.49 ( 1399) hydrogen bonds : angle 4.79158 / 3.47 ( 4041) metal coordination : bond 0.00403 / 0.20 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 147 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 ASP cc_start: 0.8883 (m-30) cc_final: 0.8678 (m-30) REVERT: C 87 LYS cc_start: 0.8415 (mmtm) cc_final: 0.8084 (mmmm) REVERT: E 169 PHE cc_start: 0.7370 (OUTLIER) cc_final: 0.7056 (t80) REVERT: F 139 MET cc_start: 0.8692 (tmm) cc_final: 0.8260 (tmm) REVERT: F 147 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.8598 (mp0) REVERT: F 190 LYS cc_start: 0.4942 (OUTLIER) cc_final: 0.4490 (pttm) REVERT: G 35 MET cc_start: 0.9390 (ptt) cc_final: 0.9152 (ptt) REVERT: G 145 MET cc_start: 0.9129 (mtm) cc_final: 0.8869 (tmm) REVERT: H 144 GLU cc_start: 0.9075 (OUTLIER) cc_final: 0.8505 (mt-10) REVERT: I 115 MET cc_start: 0.7673 (mmm) cc_final: 0.7260 (mmm) REVERT: K 71 ILE cc_start: 0.9167 (OUTLIER) cc_final: 0.8920 (mt) REVERT: K 302 MET cc_start: 0.3732 (mmt) cc_final: 0.1355 (tpp) REVERT: M 127 MET cc_start: -0.4402 (mmt) cc_final: -0.4637 (mmm) outliers start: 116 outliers final: 55 residues processed: 254 average time/residue: 0.1859 time to fit residues: 80.4617 Evaluate side-chains 205 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 145 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 141 MET Chi-restraints excluded: chain C residue 209 TYR Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 140 PHE Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 169 PHE Chi-restraints excluded: chain E residue 194 GLU Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 190 LYS Chi-restraints excluded: chain F residue 254 CYS Chi-restraints excluded: chain F residue 368 THR Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain H residue 144 GLU Chi-restraints excluded: chain H residue 227 VAL Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 123 SER Chi-restraints excluded: chain J residue 6 SER Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 11 SER Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 112 CYS Chi-restraints excluded: chain K residue 370 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 108 SER Chi-restraints excluded: chain L residue 157 ILE Chi-restraints excluded: chain L residue 174 LEU Chi-restraints excluded: chain L residue 284 THR Chi-restraints excluded: chain L residue 286 VAL Chi-restraints excluded: chain M residue 210 VAL Chi-restraints excluded: chain M residue 303 LEU Chi-restraints excluded: chain M residue 316 LEU Chi-restraints excluded: chain N residue 127 MET Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain N residue 211 VAL Chi-restraints excluded: chain N residue 265 PHE Chi-restraints excluded: chain O residue 103 GLU Chi-restraints excluded: chain O residue 291 LEU Chi-restraints excluded: chain O residue 301 HIS Chi-restraints excluded: chain P residue 126 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 401 optimal weight: 9.9990 chunk 98 optimal weight: 0.6980 chunk 237 optimal weight: 3.9990 chunk 304 optimal weight: 50.0000 chunk 72 optimal weight: 6.9990 chunk 114 optimal weight: 40.0000 chunk 305 optimal weight: 50.0000 chunk 421 optimal weight: 0.4980 chunk 294 optimal weight: 20.0000 chunk 77 optimal weight: 9.9990 chunk 63 optimal weight: 4.9990 overall best weight: 3.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 GLN ** E 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.097966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.067015 restraints weight = 160801.975| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 5.13 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 36562 Z= 0.149 Angle : 0.579 15.204 49538 Z= 0.291 Chirality : 0.042 0.221 5466 Planarity : 0.004 0.049 6411 Dihedral : 4.921 83.527 4851 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 3.06 % Allowed : 28.53 % Favored : 68.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.13), residues: 4380 helix: 1.52 (0.13), residues: 1523 sheet: -0.59 (0.21), residues: 659 loop : -1.79 (0.13), residues: 2198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 96 TYR 0.022 0.001 TYR M 247 PHE 0.050 0.001 PHE N 131 TRP 0.031 0.001 TRP E 165 HIS 0.007 0.001 HIS E 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (36560) covalent geometry : angle 0.57922 / 0.29 (49538) hydrogen bonds : bond 0.04655 / 3.17 ( 1399) hydrogen bonds : angle 4.54906 / 3.30 ( 4041) metal coordination : bond 0.00309 / 0.15 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 151 time to evaluate : 1.507 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 31 LYS cc_start: 0.9130 (mmtm) cc_final: 0.8748 (pttt) REVERT: A 289 ASP cc_start: 0.8469 (m-30) cc_final: 0.8185 (m-30) REVERT: B 73 SER cc_start: 0.9560 (OUTLIER) cc_final: 0.8851 (p) REVERT: C 35 MET cc_start: 0.8374 (OUTLIER) cc_final: 0.8147 (mtm) REVERT: E 1 MET cc_start: -0.0329 (mmt) cc_final: -0.0574 (mtt) REVERT: E 114 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.9016 (mm) REVERT: F 139 MET cc_start: 0.8496 (tmm) cc_final: 0.7954 (tmm) REVERT: F 147 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8602 (mp0) REVERT: F 190 LYS cc_start: 0.5244 (OUTLIER) cc_final: 0.4862 (pttm) REVERT: G 35 MET cc_start: 0.7991 (ptt) cc_final: 0.7774 (ptt) REVERT: H 144 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8151 (mt-10) REVERT: I 115 MET cc_start: 0.7024 (mmm) cc_final: 0.6673 (mmm) REVERT: K 302 MET cc_start: 0.1234 (mmt) cc_final: -0.1483 (tpp) REVERT: M 127 MET cc_start: -0.4877 (mmt) cc_final: -0.5092 (mmm) outliers start: 122 outliers final: 62 residues processed: 263 average time/residue: 0.1994 time to fit residues: 88.1933 Evaluate side-chains 210 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 142 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 141 MET Chi-restraints excluded: chain C residue 209 TYR Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 140 PHE Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 322 GLN Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain F residue 190 LYS Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 368 THR Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain H residue 105 MET Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 144 GLU Chi-restraints excluded: chain H residue 165 LEU Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 123 SER Chi-restraints excluded: chain I residue 144 MET Chi-restraints excluded: chain I residue 216 ILE Chi-restraints excluded: chain J residue 6 SER Chi-restraints excluded: chain J residue 175 VAL Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 11 SER Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 334 THR Chi-restraints excluded: chain K residue 370 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 108 SER Chi-restraints excluded: chain L residue 284 THR Chi-restraints excluded: chain L residue 286 VAL Chi-restraints excluded: chain L residue 374 GLN Chi-restraints excluded: chain M residue 130 MET Chi-restraints excluded: chain M residue 210 VAL Chi-restraints excluded: chain M residue 303 LEU Chi-restraints excluded: chain M residue 316 LEU Chi-restraints excluded: chain N residue 127 MET Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain O residue 98 CYS Chi-restraints excluded: chain O residue 103 GLU Chi-restraints excluded: chain O residue 291 LEU Chi-restraints excluded: chain O residue 301 HIS Chi-restraints excluded: chain P residue 126 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 107 optimal weight: 0.9990 chunk 340 optimal weight: 40.0000 chunk 294 optimal weight: 20.0000 chunk 302 optimal weight: 0.0070 chunk 308 optimal weight: 40.0000 chunk 221 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 276 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 overall best weight: 2.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN ** E 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.098317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.069173 restraints weight = 161163.730| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 5.22 r_work: 0.3176 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 36562 Z= 0.117 Angle : 0.561 13.625 49538 Z= 0.282 Chirality : 0.042 0.270 5466 Planarity : 0.003 0.049 6411 Dihedral : 4.801 83.331 4851 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.86 % Allowed : 28.96 % Favored : 68.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.13), residues: 4380 helix: 1.74 (0.13), residues: 1517 sheet: -0.48 (0.21), residues: 659 loop : -1.72 (0.13), residues: 2204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 70 TYR 0.020 0.001 TYR K 274 PHE 0.042 0.001 PHE N 131 TRP 0.027 0.001 TRP E 165 HIS 0.007 0.001 HIS E 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (36560) covalent geometry : angle 0.56083 / 0.28 (49538) hydrogen bonds : bond 0.04335 / 2.97 ( 1399) hydrogen bonds : angle 4.39513 / 3.18 ( 4041) metal coordination : bond 0.00192 / 0.09 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 144 time to evaluate : 1.346 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 289 ASP cc_start: 0.8815 (m-30) cc_final: 0.8542 (m-30) REVERT: B 73 SER cc_start: 0.9546 (OUTLIER) cc_final: 0.8893 (p) REVERT: D 1 MET cc_start: 0.6327 (mmt) cc_final: 0.6111 (mmt) REVERT: F 139 MET cc_start: 0.8817 (tmm) cc_final: 0.8596 (tmm) REVERT: F 147 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.8580 (mp0) REVERT: F 190 LYS cc_start: 0.5065 (OUTLIER) cc_final: 0.4674 (pttm) REVERT: G 113 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7788 (ptp-170) REVERT: H 144 GLU cc_start: 0.8997 (OUTLIER) cc_final: 0.8542 (mt-10) REVERT: I 115 MET cc_start: 0.8010 (mmm) cc_final: 0.7631 (mmm) REVERT: J 84 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8550 (mp) REVERT: K 71 ILE cc_start: 0.9091 (OUTLIER) cc_final: 0.8851 (mt) REVERT: K 302 MET cc_start: 0.0794 (mmt) cc_final: -0.1738 (tpp) REVERT: M 127 MET cc_start: -0.4865 (mmt) cc_final: -0.5113 (mmm) outliers start: 114 outliers final: 58 residues processed: 250 average time/residue: 0.1921 time to fit residues: 82.1896 Evaluate side-chains 206 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 141 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 209 TYR Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 140 PHE Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 322 GLN Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain F residue 34 CYS Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain F residue 190 LYS Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 254 CYS Chi-restraints excluded: chain F residue 318 PHE Chi-restraints excluded: chain F residue 368 THR Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain G residue 113 ARG Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 218 ILE Chi-restraints excluded: chain H residue 105 MET Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 144 GLU Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 144 MET Chi-restraints excluded: chain I residue 177 GLN Chi-restraints excluded: chain J residue 6 SER Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 175 VAL Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 334 THR Chi-restraints excluded: chain K residue 370 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 53 CYS Chi-restraints excluded: chain L residue 108 SER Chi-restraints excluded: chain L residue 263 TYR Chi-restraints excluded: chain L residue 284 THR Chi-restraints excluded: chain L residue 286 VAL Chi-restraints excluded: chain L residue 374 GLN Chi-restraints excluded: chain M residue 130 MET Chi-restraints excluded: chain M residue 210 VAL Chi-restraints excluded: chain M residue 289 LEU Chi-restraints excluded: chain M residue 303 LEU Chi-restraints excluded: chain M residue 316 LEU Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain N residue 265 PHE Chi-restraints excluded: chain O residue 291 LEU Chi-restraints excluded: chain O residue 301 HIS Chi-restraints excluded: chain P residue 126 LYS Chi-restraints excluded: chain P residue 209 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 165 optimal weight: 0.7980 chunk 362 optimal weight: 20.0000 chunk 319 optimal weight: 50.0000 chunk 158 optimal weight: 5.9990 chunk 97 optimal weight: 10.0000 chunk 346 optimal weight: 50.0000 chunk 124 optimal weight: 0.1980 chunk 324 optimal weight: 6.9990 chunk 51 optimal weight: 9.9990 chunk 256 optimal weight: 5.9990 chunk 417 optimal weight: 7.9990 overall best weight: 3.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 294 ASN G 73 HIS ** H 171 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 = 0.4233 r_free = 0.4233 target = 0.091404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.061173 restraints weight = 143461.813| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 4.16 r_work: 0.3120 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 36562 Z= 0.164 Angle : 0.578 12.873 49538 Z= 0.290 Chirality : 0.042 0.168 5466 Planarity : 0.004 0.047 6411 Dihedral : 4.761 84.195 4851 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 3.14 % Allowed : 28.88 % Favored : 67.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.13), residues: 4380 helix: 1.75 (0.13), residues: 1516 sheet: -0.48 (0.21), residues: 669 loop : -1.73 (0.13), residues: 2195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 133 TYR 0.020 0.001 TYR K 274 PHE 0.039 0.001 PHE N 131 TRP 0.041 0.001 TRP E 165 HIS 0.009 0.001 HIS E 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 (36560) covalent geometry : angle 0.57846 / 0.29 (49538) hydrogen bonds : bond 0.04520 / 3.08 ( 1399) hydrogen bonds : angle 4.41312 / 3.19 ( 4041) metal coordination : bond 0.00422 / 0.21 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 142 time to evaluate : 1.568 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 289 ASP cc_start: 0.8848 (m-30) cc_final: 0.8577 (m-30) REVERT: D 1 MET cc_start: 0.6422 (mmt) cc_final: 0.5530 (tpp) REVERT: F 139 MET cc_start: 0.8926 (tmm) cc_final: 0.8384 (tmm) REVERT: F 147 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8587 (mp0) REVERT: F 190 LYS cc_start: 0.5220 (OUTLIER) cc_final: 0.4773 (pttm) REVERT: G 113 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.7985 (ptp-170) REVERT: H 144 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8429 (mt-10) REVERT: I 115 MET cc_start: 0.7874 (mmm) cc_final: 0.7494 (mmm) REVERT: I 163 THR cc_start: 0.9458 (OUTLIER) cc_final: 0.8913 (t) REVERT: J 84 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8620 (mp) REVERT: K 71 ILE cc_start: 0.9151 (OUTLIER) cc_final: 0.8891 (mt) REVERT: K 302 MET cc_start: 0.1327 (mmt) cc_final: -0.1302 (tpp) REVERT: M 127 MET cc_start: -0.4729 (mmt) cc_final: -0.4984 (mmm) outliers start: 125 outliers final: 82 residues processed: 258 average time/residue: 0.2126 time to fit residues: 93.4077 Evaluate side-chains 227 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 138 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 141 MET Chi-restraints excluded: chain C residue 209 TYR Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 140 PHE Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 322 GLN Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain F residue 34 CYS Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain F residue 136 SER Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 190 LYS Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 254 CYS Chi-restraints excluded: chain F residue 318 PHE Chi-restraints excluded: chain G residue 113 ARG Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 218 ILE Chi-restraints excluded: chain H residue 105 MET Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 144 GLU Chi-restraints excluded: chain H residue 165 LEU Chi-restraints excluded: chain H residue 227 VAL Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 123 SER Chi-restraints excluded: chain I residue 144 MET Chi-restraints excluded: chain I residue 156 CYS Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 216 ILE Chi-restraints excluded: chain J residue 6 SER Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 175 VAL Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 11 SER Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 334 THR Chi-restraints excluded: chain K residue 370 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 53 CYS Chi-restraints excluded: chain L residue 108 SER Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain L residue 263 TYR Chi-restraints excluded: chain L residue 284 THR Chi-restraints excluded: chain L residue 286 VAL Chi-restraints excluded: chain L residue 374 GLN Chi-restraints excluded: chain M residue 130 MET Chi-restraints excluded: chain M residue 210 VAL Chi-restraints excluded: chain M residue 289 LEU Chi-restraints excluded: chain M residue 303 LEU Chi-restraints excluded: chain M residue 316 LEU Chi-restraints excluded: chain N residue 102 SER Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain N residue 184 GLU Chi-restraints excluded: chain N residue 265 PHE Chi-restraints excluded: chain O residue 98 CYS Chi-restraints excluded: chain O residue 103 GLU Chi-restraints excluded: chain O residue 161 SER Chi-restraints excluded: chain O residue 291 LEU Chi-restraints excluded: chain P residue 126 LYS Chi-restraints excluded: chain P residue 209 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 190 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 187 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 183 optimal weight: 9.9990 chunk 391 optimal weight: 40.0000 chunk 134 optimal weight: 0.9980 chunk 173 optimal weight: 0.0040 chunk 198 optimal weight: 2.9990 overall best weight: 2.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 214 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.098088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.067636 restraints weight = 160878.614| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 5.24 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 36562 Z= 0.122 Angle : 0.554 9.962 49538 Z= 0.279 Chirality : 0.041 0.150 5466 Planarity : 0.003 0.048 6411 Dihedral : 4.682 84.153 4851 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.69 % Allowed : 29.08 % Favored : 68.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.13), residues: 4380 helix: 1.84 (0.14), residues: 1518 sheet: -0.35 (0.20), residues: 681 loop : -1.69 (0.13), residues: 2181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 133 TYR 0.020 0.001 TYR K 274 PHE 0.038 0.001 PHE L 317 TRP 0.035 0.001 TRP E 165 HIS 0.005 0.001 HIS M 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (36560) covalent geometry : angle 0.55357 / 0.28 (49538) hydrogen bonds : bond 0.04214 / 2.88 ( 1399) hydrogen bonds : angle 4.29244 / 3.10 ( 4041) metal coordination : bond 0.00249 / 0.12 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 141 time to evaluate : 1.424 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 289 ASP cc_start: 0.8501 (m-30) cc_final: 0.8205 (m-30) REVERT: B 73 SER cc_start: 0.9528 (OUTLIER) cc_final: 0.9282 (p) REVERT: D 1 MET cc_start: 0.6390 (mmt) cc_final: 0.5668 (tpp) REVERT: D 144 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8042 (mt-10) REVERT: F 139 MET cc_start: 0.8538 (tmm) cc_final: 0.7960 (tmm) REVERT: F 147 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8599 (mp0) REVERT: F 190 LYS cc_start: 0.5267 (OUTLIER) cc_final: 0.4910 (pttm) REVERT: G 113 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.8025 (ptp-170) REVERT: H 1 MET cc_start: 0.5201 (mmp) cc_final: 0.4732 (mmp) REVERT: H 144 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8167 (mt-10) REVERT: I 115 MET cc_start: 0.7105 (mmm) cc_final: 0.6781 (mmm) REVERT: I 145 MET cc_start: 0.8620 (ppp) cc_final: 0.8399 (ppp) REVERT: I 163 THR cc_start: 0.9285 (OUTLIER) cc_final: 0.8731 (t) REVERT: J 84 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8484 (mp) REVERT: K 71 ILE cc_start: 0.8847 (OUTLIER) cc_final: 0.8589 (mt) REVERT: K 302 MET cc_start: 0.1151 (mmt) cc_final: -0.1454 (tpp) REVERT: M 127 MET cc_start: -0.4807 (mmt) cc_final: -0.5067 (mmm) outliers start: 107 outliers final: 71 residues processed: 241 average time/residue: 0.2032 time to fit residues: 83.2104 Evaluate side-chains 218 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 138 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 141 MET Chi-restraints excluded: chain C residue 209 TYR Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 140 PHE Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 322 GLN Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain F residue 190 LYS Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 254 CYS Chi-restraints excluded: chain F residue 318 PHE Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain G residue 113 ARG Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 218 ILE Chi-restraints excluded: chain H residue 105 MET Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 144 GLU Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 123 SER Chi-restraints excluded: chain I residue 144 MET Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 216 ILE Chi-restraints excluded: chain I residue 270 LYS Chi-restraints excluded: chain I residue 273 CYS Chi-restraints excluded: chain J residue 6 SER Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 175 VAL Chi-restraints excluded: chain J residue 177 SER Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 334 THR Chi-restraints excluded: chain K residue 370 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 53 CYS Chi-restraints excluded: chain L residue 108 SER Chi-restraints excluded: chain L residue 205 VAL Chi-restraints excluded: chain L residue 227 HIS Chi-restraints excluded: chain L residue 263 TYR Chi-restraints excluded: chain L residue 284 THR Chi-restraints excluded: chain L residue 286 VAL Chi-restraints excluded: chain L residue 374 GLN Chi-restraints excluded: chain M residue 130 MET Chi-restraints excluded: chain M residue 210 VAL Chi-restraints excluded: chain M residue 289 LEU Chi-restraints excluded: chain M residue 303 LEU Chi-restraints excluded: chain N residue 102 SER Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain N residue 184 GLU Chi-restraints excluded: chain N residue 265 PHE Chi-restraints excluded: chain O residue 98 CYS Chi-restraints excluded: chain O residue 103 GLU Chi-restraints excluded: chain P residue 126 LYS Chi-restraints excluded: chain P residue 209 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 285 optimal weight: 20.0000 chunk 86 optimal weight: 3.9990 chunk 378 optimal weight: 30.0000 chunk 383 optimal weight: 50.0000 chunk 277 optimal weight: 0.9980 chunk 215 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 93 optimal weight: 0.8980 chunk 403 optimal weight: 9.9990 chunk 400 optimal weight: 10.0000 chunk 372 optimal weight: 4.9990 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 294 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.098089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.067692 restraints weight = 160555.173| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 4.94 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 36562 Z= 0.121 Angle : 0.555 10.916 49538 Z= 0.278 Chirality : 0.041 0.237 5466 Planarity : 0.003 0.047 6411 Dihedral : 4.586 83.928 4851 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.41 % Allowed : 29.31 % Favored : 68.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.13), residues: 4380 helix: 1.84 (0.13), residues: 1523 sheet: -0.28 (0.20), residues: 681 loop : -1.64 (0.13), residues: 2176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 133 TYR 0.020 0.001 TYR K 274 PHE 0.038 0.001 PHE N 131 TRP 0.031 0.001 TRP E 165 HIS 0.005 0.001 HIS M 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (36560) covalent geometry : angle 0.55496 / 0.28 (49538) hydrogen bonds : bond 0.04091 / 2.79 ( 1399) hydrogen bonds : angle 4.22624 / 3.06 ( 4041) metal coordination : bond 0.00254 / 0.13 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 139 time to evaluate : 1.461 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 289 ASP cc_start: 0.8453 (m-30) cc_final: 0.8144 (m-30) REVERT: B 73 SER cc_start: 0.9526 (OUTLIER) cc_final: 0.9304 (p) REVERT: D 1 MET cc_start: 0.6295 (mmt) cc_final: 0.6049 (mmt) REVERT: D 144 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8080 (mt-10) REVERT: F 139 MET cc_start: 0.8581 (tmm) cc_final: 0.7974 (tmm) REVERT: F 147 GLU cc_start: 0.8906 (OUTLIER) cc_final: 0.8606 (mp0) REVERT: F 190 LYS cc_start: 0.5260 (OUTLIER) cc_final: 0.4871 (pttm) REVERT: G 113 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.8045 (ptp-170) REVERT: G 145 MET cc_start: 0.9090 (ptp) cc_final: 0.8830 (tmm) REVERT: H 1 MET cc_start: 0.5195 (OUTLIER) cc_final: 0.4581 (mmp) REVERT: H 144 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8190 (mt-10) REVERT: I 115 MET cc_start: 0.7128 (mmm) cc_final: 0.6800 (mmm) REVERT: I 145 MET cc_start: 0.8656 (ppp) cc_final: 0.8427 (ppp) REVERT: J 84 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8463 (mp) REVERT: K 71 ILE cc_start: 0.8845 (OUTLIER) cc_final: 0.8584 (mt) REVERT: K 302 MET cc_start: 0.0804 (mmt) cc_final: -0.1716 (tpp) REVERT: M 127 MET cc_start: -0.4814 (mmt) cc_final: -0.5084 (mmm) outliers start: 96 outliers final: 73 residues processed: 227 average time/residue: 0.1989 time to fit residues: 77.1264 Evaluate side-chains 220 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 138 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 141 MET Chi-restraints excluded: chain C residue 209 TYR Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 140 PHE Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 322 GLN Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain F residue 34 CYS Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain F residue 136 SER Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain F residue 190 LYS Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 254 CYS Chi-restraints excluded: chain F residue 318 PHE Chi-restraints excluded: chain G residue 113 ARG Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 218 ILE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 105 MET Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 144 GLU Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 123 SER Chi-restraints excluded: chain I residue 156 CYS Chi-restraints excluded: chain I residue 270 LYS Chi-restraints excluded: chain I residue 273 CYS Chi-restraints excluded: chain I residue 301 LEU Chi-restraints excluded: chain J residue 6 SER Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 175 VAL Chi-restraints excluded: chain J residue 177 SER Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 334 THR Chi-restraints excluded: chain K residue 370 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 53 CYS Chi-restraints excluded: chain L residue 108 SER Chi-restraints excluded: chain L residue 205 VAL Chi-restraints excluded: chain L residue 227 HIS Chi-restraints excluded: chain L residue 263 TYR Chi-restraints excluded: chain L residue 284 THR Chi-restraints excluded: chain L residue 374 GLN Chi-restraints excluded: chain M residue 130 MET Chi-restraints excluded: chain M residue 210 VAL Chi-restraints excluded: chain M residue 289 LEU Chi-restraints excluded: chain M residue 303 LEU Chi-restraints excluded: chain M residue 316 LEU Chi-restraints excluded: chain N residue 102 SER Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain N residue 184 GLU Chi-restraints excluded: chain N residue 265 PHE Chi-restraints excluded: chain O residue 98 CYS Chi-restraints excluded: chain O residue 291 LEU Chi-restraints excluded: chain P residue 126 LYS Chi-restraints excluded: chain P residue 209 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 226 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 332 optimal weight: 10.0000 chunk 101 optimal weight: 0.9980 chunk 248 optimal weight: 9.9990 chunk 121 optimal weight: 10.0000 chunk 171 optimal weight: 4.9990 chunk 221 optimal weight: 7.9990 chunk 237 optimal weight: 1.9990 chunk 224 optimal weight: 6.9990 chunk 129 optimal weight: 8.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.097680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.066486 restraints weight = 160006.838| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 5.21 r_work: 0.3076 rms_B_bonded: 5.18 restraints_weight: 2.0000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 36562 Z= 0.150 Angle : 0.567 10.600 49538 Z= 0.284 Chirality : 0.042 0.257 5466 Planarity : 0.003 0.047 6411 Dihedral : 4.584 84.340 4851 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 2.59 % Allowed : 28.83 % Favored : 68.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.13), residues: 4380 helix: 1.88 (0.13), residues: 1508 sheet: -0.28 (0.20), residues: 681 loop : -1.59 (0.14), residues: 2191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG O 219 TYR 0.020 0.001 TYR K 274 PHE 0.039 0.001 PHE N 131 TRP 0.051 0.001 TRP E 165 HIS 0.005 0.001 HIS A 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (36560) covalent geometry : angle 0.56687 / 0.28 (49538) hydrogen bonds : bond 0.04250 / 2.89 ( 1399) hydrogen bonds : angle 4.25816 / 3.08 ( 4041) metal coordination : bond 0.00366 / 0.18 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 140 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 ASP cc_start: 0.8815 (m-30) cc_final: 0.8538 (m-30) REVERT: B 73 SER cc_start: 0.9557 (OUTLIER) cc_final: 0.9338 (p) REVERT: D 1 MET cc_start: 0.6357 (mmt) cc_final: 0.6065 (mmt) REVERT: D 144 GLU cc_start: 0.9185 (OUTLIER) cc_final: 0.8838 (mt-10) REVERT: F 139 MET cc_start: 0.8939 (tmm) cc_final: 0.8371 (tmm) REVERT: F 147 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8572 (mp0) REVERT: F 190 LYS cc_start: 0.5074 (OUTLIER) cc_final: 0.4648 (pttm) REVERT: G 113 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.7922 (ptp-170) REVERT: G 145 MET cc_start: 0.9081 (ptp) cc_final: 0.8819 (tmm) REVERT: H 1 MET cc_start: 0.5321 (OUTLIER) cc_final: 0.4632 (mmp) REVERT: H 144 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8444 (mt-10) REVERT: I 115 MET cc_start: 0.7833 (mmm) cc_final: 0.7436 (mmm) REVERT: I 145 MET cc_start: 0.8858 (ppp) cc_final: 0.8626 (ppp) REVERT: I 163 THR cc_start: 0.9411 (OUTLIER) cc_final: 0.8851 (t) REVERT: J 84 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8622 (mp) REVERT: K 71 ILE cc_start: 0.9120 (OUTLIER) cc_final: 0.8863 (mt) REVERT: K 302 MET cc_start: 0.4074 (mmt) cc_final: 0.1682 (tpp) REVERT: M 127 MET cc_start: -0.4059 (mmt) cc_final: -0.4377 (mmm) outliers start: 103 outliers final: 82 residues processed: 234 average time/residue: 0.2065 time to fit residues: 82.3091 Evaluate side-chains 229 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 137 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 245 ARG Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 141 MET Chi-restraints excluded: chain C residue 209 TYR Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 140 PHE Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 322 GLN Chi-restraints excluded: chain F residue 34 CYS Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain F residue 136 SER Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain F residue 190 LYS Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 254 CYS Chi-restraints excluded: chain F residue 318 PHE Chi-restraints excluded: chain G residue 113 ARG Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 218 ILE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 105 MET Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 144 GLU Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 123 SER Chi-restraints excluded: chain I residue 144 MET Chi-restraints excluded: chain I residue 156 CYS Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 216 ILE Chi-restraints excluded: chain I residue 270 LYS Chi-restraints excluded: chain I residue 273 CYS Chi-restraints excluded: chain I residue 301 LEU Chi-restraints excluded: chain J residue 6 SER Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 175 VAL Chi-restraints excluded: chain J residue 177 SER Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 66 THR Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 334 THR Chi-restraints excluded: chain K residue 370 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 53 CYS Chi-restraints excluded: chain L residue 108 SER Chi-restraints excluded: chain L residue 157 ILE Chi-restraints excluded: chain L residue 205 VAL Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain L residue 227 HIS Chi-restraints excluded: chain L residue 263 TYR Chi-restraints excluded: chain L residue 284 THR Chi-restraints excluded: chain L residue 374 GLN Chi-restraints excluded: chain M residue 130 MET Chi-restraints excluded: chain M residue 210 VAL Chi-restraints excluded: chain M residue 289 LEU Chi-restraints excluded: chain M residue 303 LEU Chi-restraints excluded: chain N residue 102 SER Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain N residue 184 GLU Chi-restraints excluded: chain O residue 98 CYS Chi-restraints excluded: chain O residue 161 SER Chi-restraints excluded: chain P residue 126 LYS Chi-restraints excluded: chain P residue 209 TYR Chi-restraints excluded: chain P residue 210 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 283 optimal weight: 1.9990 chunk 318 optimal weight: 20.0000 chunk 389 optimal weight: 30.0000 chunk 166 optimal weight: 30.0000 chunk 224 optimal weight: 10.0000 chunk 192 optimal weight: 9.9990 chunk 213 optimal weight: 0.6980 chunk 149 optimal weight: 1.9990 chunk 155 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.097972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.067360 restraints weight = 161041.919| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 5.10 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 36562 Z= 0.123 Angle : 0.558 10.321 49538 Z= 0.280 Chirality : 0.042 0.227 5466 Planarity : 0.003 0.048 6411 Dihedral : 4.551 84.179 4851 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 2.46 % Allowed : 28.96 % Favored : 68.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.13), residues: 4380 helix: 1.95 (0.14), residues: 1509 sheet: -0.23 (0.21), residues: 683 loop : -1.57 (0.14), residues: 2188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG O 219 TYR 0.019 0.001 TYR K 274 PHE 0.041 0.001 PHE N 131 TRP 0.031 0.001 TRP E 165 HIS 0.005 0.001 HIS M 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (36560) covalent geometry : angle 0.55751 / 0.28 (49538) hydrogen bonds : bond 0.04064 / 2.77 ( 1399) hydrogen bonds : angle 4.19432 / 3.03 ( 4041) metal coordination : bond 0.00277 / 0.13 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 138 time to evaluate : 1.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 ASP cc_start: 0.8428 (m-30) cc_final: 0.8115 (m-30) REVERT: B 73 SER cc_start: 0.9526 (OUTLIER) cc_final: 0.9305 (p) REVERT: D 1 MET cc_start: 0.6278 (mmt) cc_final: 0.6038 (mmt) REVERT: D 144 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8020 (mt-10) REVERT: F 139 MET cc_start: 0.8623 (tmm) cc_final: 0.8317 (tmm) REVERT: F 147 GLU cc_start: 0.8937 (OUTLIER) cc_final: 0.8610 (mp0) REVERT: F 190 LYS cc_start: 0.5347 (OUTLIER) cc_final: 0.4974 (pttm) REVERT: G 113 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.8050 (ptp-170) REVERT: G 145 MET cc_start: 0.9121 (ptp) cc_final: 0.8874 (tmm) REVERT: H 1 MET cc_start: 0.5249 (OUTLIER) cc_final: 0.4624 (mmp) REVERT: H 144 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8167 (mt-10) REVERT: I 115 MET cc_start: 0.7148 (mmm) cc_final: 0.6839 (mmm) REVERT: I 145 MET cc_start: 0.8714 (ppp) cc_final: 0.8489 (ppp) REVERT: I 163 THR cc_start: 0.9257 (OUTLIER) cc_final: 0.8692 (t) REVERT: J 84 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8496 (mp) REVERT: K 71 ILE cc_start: 0.8854 (OUTLIER) cc_final: 0.8575 (mt) REVERT: K 302 MET cc_start: 0.0983 (mmt) cc_final: -0.1605 (tpp) REVERT: M 127 MET cc_start: -0.4812 (mmt) cc_final: -0.5075 (mmm) outliers start: 98 outliers final: 81 residues processed: 227 average time/residue: 0.2060 time to fit residues: 79.9703 Evaluate side-chains 229 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 138 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 245 ARG Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 141 MET Chi-restraints excluded: chain C residue 209 TYR Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 140 PHE Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 322 GLN Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain F residue 34 CYS Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain F residue 190 LYS Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 254 CYS Chi-restraints excluded: chain F residue 318 PHE Chi-restraints excluded: chain G residue 113 ARG Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 218 ILE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 105 MET Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 144 GLU Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 123 SER Chi-restraints excluded: chain I residue 144 MET Chi-restraints excluded: chain I residue 156 CYS Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 216 ILE Chi-restraints excluded: chain I residue 270 LYS Chi-restraints excluded: chain I residue 273 CYS Chi-restraints excluded: chain I residue 301 LEU Chi-restraints excluded: chain J residue 6 SER Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 175 VAL Chi-restraints excluded: chain J residue 177 SER Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 66 THR Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 334 THR Chi-restraints excluded: chain K residue 370 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 53 CYS Chi-restraints excluded: chain L residue 108 SER Chi-restraints excluded: chain L residue 157 ILE Chi-restraints excluded: chain L residue 205 VAL Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain L residue 227 HIS Chi-restraints excluded: chain L residue 263 TYR Chi-restraints excluded: chain L residue 374 GLN Chi-restraints excluded: chain M residue 130 MET Chi-restraints excluded: chain M residue 210 VAL Chi-restraints excluded: chain M residue 289 LEU Chi-restraints excluded: chain M residue 303 LEU Chi-restraints excluded: chain N residue 102 SER Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain N residue 184 GLU Chi-restraints excluded: chain N residue 211 VAL Chi-restraints excluded: chain O residue 98 CYS Chi-restraints excluded: chain P residue 126 LYS Chi-restraints excluded: chain P residue 209 TYR Chi-restraints excluded: chain P residue 210 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 413 optimal weight: 10.0000 chunk 136 optimal weight: 8.9990 chunk 263 optimal weight: 9.9990 chunk 88 optimal weight: 1.9990 chunk 347 optimal weight: 7.9990 chunk 179 optimal weight: 10.0000 chunk 392 optimal weight: 5.9990 chunk 375 optimal weight: 0.0270 chunk 266 optimal weight: 5.9990 chunk 313 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 overall best weight: 3.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.097630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.067360 restraints weight = 160065.052| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 4.91 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 36562 Z= 0.145 Angle : 0.573 10.507 49538 Z= 0.287 Chirality : 0.042 0.204 5466 Planarity : 0.003 0.047 6411 Dihedral : 4.529 84.350 4851 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.51 % Allowed : 28.93 % Favored : 68.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.13), residues: 4380 helix: 1.93 (0.13), residues: 1509 sheet: -0.25 (0.21), residues: 683 loop : -1.58 (0.14), residues: 2188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 81 TYR 0.020 0.001 TYR K 274 PHE 0.046 0.001 PHE N 131 TRP 0.053 0.001 TRP E 165 HIS 0.006 0.001 HIS C 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (36560) covalent geometry : angle 0.57305 / 0.29 (49538) hydrogen bonds : bond 0.04199 / 2.85 ( 1399) hydrogen bonds : angle 4.23056 / 3.06 ( 4041) metal coordination : bond 0.00307 / 0.15 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10658.05 seconds wall clock time: 182 minutes 4.58 seconds (10924.58 seconds total)