Starting phenix.real_space_refine on Sat Sep 12 12:26:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ch9_30372/09_2026/7ch9_30372.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ch9_30372/09_2026/7ch9_30372.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ch9_30372/09_2026/7ch9_30372.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ch9_30372/09_2026/7ch9_30372.map" model { file = "/net/cci-nas-00/data/ceres_data/7ch9_30372/09_2026/7ch9_30372.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ch9_30372/09_2026/7ch9_30372.cif" } resolution = 3.5 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= -0.005 sd= 1.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 44 5.16 5 C 10271 2.51 5 N 2669 2.21 5 O 2991 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 79 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15978 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 1088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1088 Classifications: {'peptide': 150} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 148} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1068 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 1, 'TRANS': 146} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 1079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1079 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 146} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 1083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1083 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 146} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 1090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1090 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 147} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 1070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1070 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 146} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "G" Number of atoms: 1928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1928 Classifications: {'peptide': 258} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 250} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "H" Number of atoms: 1908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1908 Classifications: {'peptide': 257} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 250} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "I" Number of atoms: 2015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2015 Classifications: {'peptide': 262} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 245} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "J" Number of atoms: 1991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1991 Classifications: {'peptide': 262} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 16, 'TRANS': 245} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'TYR:plan': 3, 'ARG:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 35 Chain: "K" Number of atoms: 721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 721 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "L" Number of atoms: 721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 721 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'LPP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'LPP:plan-1': 1, 'LPP:plan-2': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'LPP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'LPP:plan-1': 2, 'LPP:plan-2': 2} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'LPP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'LPP:plan-1': 2, 'LPP:plan-2': 2} Unresolved non-hydrogen planarities: 16 Chain: "E" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'LPP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'LPP:plan-1': 1, 'LPP:plan-2': 1} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'LPP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'LPP:plan-1': 1, 'LPP:plan-2': 1} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 81 Unusual residues: {'LPP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "H" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'LPP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.76, per 1000 atoms: 0.24 Number of scatterers: 15978 At special positions: 0 Unit cell: (101, 121, 146, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 44 16.00 P 3 15.00 O 2991 8.00 N 2669 7.00 C 10271 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.92 Conformation dependent library (CDL) restraints added in 840.7 milliseconds 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3784 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 21 sheets defined 45.0% alpha, 15.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 2 through 20 Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 138 through 143 Processing helix chain 'C' and resid 6 through 27 Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.571A pdb=" N LEU C 141 " --> pdb=" O VAL C 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 27 removed outlier: 3.794A pdb=" N ILE D 8 " --> pdb=" O ARG D 4 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N GLY D 9 " --> pdb=" O THR D 5 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 143 Processing helix chain 'E' and resid 3 through 20 removed outlier: 3.702A pdb=" N GLY E 17 " --> pdb=" O PHE E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 145 Processing helix chain 'E' and resid 145 through 150 removed outlier: 3.979A pdb=" N VAL E 150 " --> pdb=" O LEU E 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 7 Processing helix chain 'F' and resid 8 through 26 removed outlier: 3.535A pdb=" N LEU F 12 " --> pdb=" O ILE F 8 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU F 21 " --> pdb=" O GLY F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 144 Processing helix chain 'G' and resid 6 through 37 removed outlier: 3.527A pdb=" N VAL G 21 " --> pdb=" O GLY G 17 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY G 37 " --> pdb=" O HIS G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 56 removed outlier: 4.025A pdb=" N LEU G 48 " --> pdb=" O GLY G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 84 removed outlier: 3.504A pdb=" N ILE G 63 " --> pdb=" O SER G 59 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASN G 80 " --> pdb=" O LEU G 76 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER G 84 " --> pdb=" O ASN G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 89 No H-bonds generated for 'chain 'G' and resid 87 through 89' Processing helix chain 'G' and resid 90 through 102 removed outlier: 4.268A pdb=" N LEU G 100 " --> pdb=" O ALA G 96 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 116 removed outlier: 3.766A pdb=" N GLY G 114 " --> pdb=" O LEU G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 129 Processing helix chain 'G' and resid 134 through 139 removed outlier: 3.588A pdb=" N MET G 138 " --> pdb=" O SER G 134 " (cutoff:3.500A) Processing helix chain 'G' and resid 143 through 148 Processing helix chain 'G' and resid 148 through 157 removed outlier: 3.678A pdb=" N ILE G 157 " --> pdb=" O TRP G 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 158 through 179 removed outlier: 3.778A pdb=" N VAL G 177 " --> pdb=" O GLY G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 194 Processing helix chain 'G' and resid 198 through 221 removed outlier: 5.442A pdb=" N LEU G 204 " --> pdb=" O THR G 200 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ASN G 205 " --> pdb=" O GLU G 201 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE G 213 " --> pdb=" O LYS G 209 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE G 220 " --> pdb=" O VAL G 216 " (cutoff:3.500A) Processing helix chain 'G' and resid 222 through 227 Processing helix chain 'G' and resid 231 through 260 removed outlier: 3.798A pdb=" N SER G 236 " --> pdb=" O SER G 232 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N THR G 240 " --> pdb=" O SER G 236 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL G 243 " --> pdb=" O THR G 239 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 37 removed outlier: 3.847A pdb=" N GLY H 25 " --> pdb=" O VAL H 21 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY H 37 " --> pdb=" O HIS H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 56 Processing helix chain 'H' and resid 59 through 83 removed outlier: 3.866A pdb=" N ILE H 63 " --> pdb=" O SER H 59 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N VAL H 65 " --> pdb=" O ALA H 61 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASN H 80 " --> pdb=" O LEU H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 96 Processing helix chain 'H' and resid 102 through 116 removed outlier: 4.052A pdb=" N GLY H 114 " --> pdb=" O LEU H 110 " (cutoff:3.500A) Processing helix chain 'H' and resid 118 through 130 removed outlier: 3.656A pdb=" N MET H 127 " --> pdb=" O GLU H 123 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LYS H 128 " --> pdb=" O ILE H 124 " (cutoff:3.500A) Processing helix chain 'H' and resid 133 through 138 removed outlier: 3.501A pdb=" N GLU H 137 " --> pdb=" O LEU H 133 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N MET H 138 " --> pdb=" O SER H 134 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 133 through 138' Processing helix chain 'H' and resid 142 through 148 Processing helix chain 'H' and resid 148 through 157 removed outlier: 3.513A pdb=" N ILE H 157 " --> pdb=" O TRP H 153 " (cutoff:3.500A) Processing helix chain 'H' and resid 158 through 180 Processing helix chain 'H' and resid 185 through 196 Processing helix chain 'H' and resid 198 through 227 removed outlier: 5.230A pdb=" N LEU H 204 " --> pdb=" O THR H 200 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ASN H 205 " --> pdb=" O GLU H 201 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE H 213 " --> pdb=" O LYS H 209 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL H 217 " --> pdb=" O PHE H 213 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE H 220 " --> pdb=" O VAL H 216 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLY H 225 " --> pdb=" O ALA H 221 " (cutoff:3.500A) Processing helix chain 'H' and resid 232 through 261 removed outlier: 4.096A pdb=" N THR H 240 " --> pdb=" O SER H 236 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 55 removed outlier: 3.736A pdb=" N ILE I 54 " --> pdb=" O LEU I 50 " (cutoff:3.500A) Processing helix chain 'I' and resid 76 through 84 removed outlier: 4.414A pdb=" N ASP I 82 " --> pdb=" O GLY I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 101 through 108 Processing helix chain 'I' and resid 109 through 114 removed outlier: 3.601A pdb=" N HIS I 113 " --> pdb=" O PRO I 109 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 132 removed outlier: 3.627A pdb=" N ALA I 131 " --> pdb=" O MET I 127 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 145 Processing helix chain 'I' and resid 148 through 160 removed outlier: 4.041A pdb=" N ARG I 152 " --> pdb=" O GLY I 148 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA I 154 " --> pdb=" O LYS I 150 " (cutoff:3.500A) Processing helix chain 'I' and resid 176 through 195 removed outlier: 3.574A pdb=" N LEU I 183 " --> pdb=" O ALA I 179 " (cutoff:3.500A) Processing helix chain 'I' and resid 204 through 212 removed outlier: 4.844A pdb=" N SER I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE I 211 " --> pdb=" O GLU I 207 " (cutoff:3.500A) Processing helix chain 'I' and resid 228 through 234 Processing helix chain 'I' and resid 237 through 245 removed outlier: 3.624A pdb=" N LYS I 245 " --> pdb=" O ARG I 241 " (cutoff:3.500A) Processing helix chain 'I' and resid 260 through 267 Processing helix chain 'J' and resid 46 through 55 Processing helix chain 'J' and resid 71 through 75 removed outlier: 4.057A pdb=" N GLN J 74 " --> pdb=" O ASN J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 84 removed outlier: 3.873A pdb=" N ASP J 82 " --> pdb=" O GLY J 78 " (cutoff:3.500A) Processing helix chain 'J' and resid 101 through 108 Processing helix chain 'J' and resid 109 through 114 removed outlier: 3.677A pdb=" N HIS J 113 " --> pdb=" O PRO J 109 " (cutoff:3.500A) Processing helix chain 'J' and resid 117 through 131 removed outlier: 3.856A pdb=" N ARG J 122 " --> pdb=" O GLU J 118 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ASP J 123 " --> pdb=" O GLU J 119 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA J 131 " --> pdb=" O MET J 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 148 through 159 removed outlier: 4.151A pdb=" N ARG J 152 " --> pdb=" O GLY J 148 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALA J 154 " --> pdb=" O LYS J 150 " (cutoff:3.500A) Processing helix chain 'J' and resid 176 through 193 removed outlier: 4.001A pdb=" N VAL J 182 " --> pdb=" O ILE J 178 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN J 191 " --> pdb=" O ILE J 187 " (cutoff:3.500A) Processing helix chain 'J' and resid 204 through 212 Processing helix chain 'J' and resid 228 through 233 Processing helix chain 'J' and resid 237 through 244 Processing helix chain 'J' and resid 262 through 267 Processing helix chain 'K' and resid 23 through 34 removed outlier: 4.577A pdb=" N ALA K 27 " --> pdb=" O SER K 23 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ARG K 34 " --> pdb=" O GLU K 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 36 through 40 removed outlier: 3.542A pdb=" N SER K 39 " --> pdb=" O ILE K 36 " (cutoff:3.500A) Processing helix chain 'K' and resid 55 through 73 removed outlier: 3.786A pdb=" N ILE K 66 " --> pdb=" O LEU K 62 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP K 68 " --> pdb=" O ALA K 64 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA K 69 " --> pdb=" O PHE K 65 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS K 71 " --> pdb=" O ARG K 67 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 92 removed outlier: 4.055A pdb=" N SER K 92 " --> pdb=" O ILE K 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 24 through 34 removed outlier: 3.574A pdb=" N LEU L 28 " --> pdb=" O SER L 24 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG L 34 " --> pdb=" O GLU L 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 34 through 39 removed outlier: 3.793A pdb=" N SER L 39 " --> pdb=" O LEU L 35 " (cutoff:3.500A) Processing helix chain 'L' and resid 55 through 73 removed outlier: 3.629A pdb=" N ILE L 59 " --> pdb=" O SER L 55 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE L 66 " --> pdb=" O LEU L 62 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG L 67 " --> pdb=" O LEU L 63 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASP L 68 " --> pdb=" O ALA L 64 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 93 removed outlier: 3.830A pdb=" N SER L 92 " --> pdb=" O ILE L 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 68 through 74 removed outlier: 5.787A pdb=" N VAL A 68 " --> pdb=" O GLU A 85 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N GLU A 85 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR A 79 " --> pdb=" O ASP A 74 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N ILE A 129 " --> pdb=" O LYS A 41 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N TYR A 43 " --> pdb=" O ILE A 129 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 63 through 66 removed outlier: 5.412A pdb=" N THR A 64 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N LEU A 60 " --> pdb=" O THR A 64 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N GLU A 109 " --> pdb=" O ALA A 104 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA A 104 " --> pdb=" O GLU A 109 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ALA A 99 " --> pdb=" O GLN A 133 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 39 through 46 removed outlier: 6.640A pdb=" N ARG B 81 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N VAL B 71 " --> pdb=" O ARG B 81 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N THR B 83 " --> pdb=" O THR B 69 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 59 through 60 Processing sheet with id=AA5, first strand: chain 'B' and resid 99 through 103 Processing sheet with id=AA6, first strand: chain 'C' and resid 39 through 46 removed outlier: 6.459A pdb=" N GLU C 85 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N VAL C 68 " --> pdb=" O GLU C 85 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ASN C 87 " --> pdb=" O GLY C 66 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N GLY C 66 " --> pdb=" O ASN C 87 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N VAL C 58 " --> pdb=" O ILE C 65 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LYS C 57 " --> pdb=" O ILE C 112 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N ILE C 114 " --> pdb=" O LYS C 57 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N THR C 59 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N LYS C 110 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU C 102 " --> pdb=" O LYS C 110 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ILE C 112 " --> pdb=" O SER C 100 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N SER C 100 " --> pdb=" O ILE C 112 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE C 114 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N THR C 98 " --> pdb=" O ILE C 114 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 68 through 74 removed outlier: 6.565A pdb=" N THR D 83 " --> pdb=" O THR D 69 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N VAL D 71 " --> pdb=" O ARG D 81 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ARG D 81 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU D 73 " --> pdb=" O THR D 79 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N THR D 79 " --> pdb=" O LEU D 73 " (cutoff:3.500A) removed outlier: 9.236A pdb=" N ILE D 129 " --> pdb=" O LYS D 41 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N TYR D 43 " --> pdb=" O ILE D 129 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 58 through 60 removed outlier: 6.804A pdb=" N VAL D 58 " --> pdb=" O ILE D 65 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 110 through 115 removed outlier: 3.749A pdb=" N GLN D 133 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 68 through 70 removed outlier: 6.504A pdb=" N THR E 83 " --> pdb=" O THR E 69 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N ILE E 129 " --> pdb=" O LYS E 41 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N TYR E 43 " --> pdb=" O ILE E 129 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 63 through 66 removed outlier: 6.649A pdb=" N VAL E 58 " --> pdb=" O ILE E 65 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ALA E 99 " --> pdb=" O GLN E 133 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 128 through 129 removed outlier: 8.683A pdb=" N ILE F 129 " --> pdb=" O LYS F 41 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N TYR F 43 " --> pdb=" O ILE F 129 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR F 79 " --> pdb=" O ASP F 74 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N GLU F 85 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL F 68 " --> pdb=" O GLU F 85 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N THR F 64 " --> pdb=" O LEU F 60 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LEU F 60 " --> pdb=" O THR F 64 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY F 66 " --> pdb=" O VAL F 58 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LYS F 57 " --> pdb=" O ILE F 112 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N ILE F 114 " --> pdb=" O LYS F 57 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N THR F 59 " --> pdb=" O ILE F 114 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N GLU F 109 " --> pdb=" O ALA F 104 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA F 104 " --> pdb=" O GLU F 109 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ALA F 99 " --> pdb=" O GLN F 133 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 24 through 32 removed outlier: 6.505A pdb=" N ASP I 25 " --> pdb=" O THR I 15 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N THR I 15 " --> pdb=" O ASP I 25 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ILE I 27 " --> pdb=" O GLY I 13 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY I 13 " --> pdb=" O ILE I 27 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL I 29 " --> pdb=" O LEU I 11 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL I 9 " --> pdb=" O ILE I 31 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS I 12 " --> pdb=" O GLU I 64 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLU I 64 " --> pdb=" O LYS I 12 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N LEU I 14 " --> pdb=" O LYS I 62 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LYS I 62 " --> pdb=" O LEU I 14 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 87 through 88 removed outlier: 6.710A pdb=" N GLY I 88 " --> pdb=" O LEU I 167 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N ASP I 169 " --> pdb=" O GLY I 88 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N LEU I 166 " --> pdb=" O ILE I 199 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N VAL I 201 " --> pdb=" O LEU I 166 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N TYR I 168 " --> pdb=" O VAL I 201 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'I' and resid 215 through 219 removed outlier: 4.434A pdb=" N GLY I 225 " --> pdb=" O ILE I 217 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLY I 219 " --> pdb=" O VAL I 223 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N VAL I 223 " --> pdb=" O GLY I 219 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 24 through 27 removed outlier: 5.356A pdb=" N LEU J 14 " --> pdb=" O ASN J 26 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL J 9 " --> pdb=" O ILE J 31 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 24 through 27 removed outlier: 5.356A pdb=" N LEU J 14 " --> pdb=" O ASN J 26 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU J 64 " --> pdb=" O LYS J 12 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N LEU J 14 " --> pdb=" O LYS J 62 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LYS J 62 " --> pdb=" O LEU J 14 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 87 through 91 removed outlier: 3.542A pdb=" N GLY J 88 " --> pdb=" O ILE J 165 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N LEU J 166 " --> pdb=" O ILE J 199 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N VAL J 201 " --> pdb=" O LEU J 166 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N TYR J 168 " --> pdb=" O VAL J 201 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR J 37 " --> pdb=" O VAL J 200 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N TYR J 216 " --> pdb=" O VAL J 36 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N GLY J 38 " --> pdb=" O TYR J 216 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N VAL J 218 " --> pdb=" O GLY J 38 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N MET J 40 " --> pdb=" O VAL J 218 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILE J 215 " --> pdb=" O HIS J 226 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N HIS J 226 " --> pdb=" O ILE J 215 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ILE J 217 " --> pdb=" O LEU J 224 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 14 through 15 removed outlier: 6.853A pdb=" N LEU K 44 " --> pdb=" O SER K 77 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N ARG K 79 " --> pdb=" O LEU K 44 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N VAL K 46 " --> pdb=" O ARG K 79 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 19 through 20 Processing sheet with id=AC3, first strand: chain 'L' and resid 45 through 47 removed outlier: 6.507A pdb=" N VAL L 46 " --> pdb=" O ARG L 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 725 hydrogen bonds defined for protein. 2100 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: 2.73 Time building geometry restraints manager: 2.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2668 1.31 - 1.43: 3732 1.43 - 1.56: 9685 1.56 - 1.68: 4 1.68 - 1.81: 82 Bond restraints: 16171 Sorted by residual: bond pdb=" O5 LPP G 301 " pdb=" P1 LPP G 301 " ideal model delta sigma weight residual 2.278 1.606 0.672 2.00e-02 2.50e+03 1.13e+03 bond pdb=" O5 LPP H 301 " pdb=" P1 LPP H 301 " ideal model delta sigma weight residual 2.278 1.644 0.634 2.00e-02 2.50e+03 1.01e+03 bond pdb=" O5 LPP G 302 " pdb=" P1 LPP G 302 " ideal model delta sigma weight residual 2.278 1.647 0.631 2.00e-02 2.50e+03 9.94e+02 bond pdb=" O4 LPP G 302 " pdb=" P1 LPP G 302 " ideal model delta sigma weight residual 1.764 1.506 0.258 2.00e-02 2.50e+03 1.66e+02 bond pdb=" O4 LPP H 301 " pdb=" P1 LPP H 301 " ideal model delta sigma weight residual 1.764 1.508 0.256 2.00e-02 2.50e+03 1.64e+02 ... (remaining 16166 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.39: 21868 9.39 - 18.79: 10 18.79 - 28.18: 4 28.18 - 37.58: 5 37.58 - 46.97: 3 Bond angle restraints: 21890 Sorted by residual: angle pdb=" O4 LPP H 301 " pdb=" P1 LPP H 301 " pdb=" O5 LPP H 301 " ideal model delta sigma weight residual 62.99 109.96 -46.97 3.00e+00 1.11e-01 2.45e+02 angle pdb=" O4 LPP G 302 " pdb=" P1 LPP G 302 " pdb=" O5 LPP G 302 " ideal model delta sigma weight residual 62.99 109.70 -46.71 3.00e+00 1.11e-01 2.42e+02 angle pdb=" O4 LPP G 301 " pdb=" P1 LPP G 301 " pdb=" O5 LPP G 301 " ideal model delta sigma weight residual 62.99 102.89 -39.90 3.00e+00 1.11e-01 1.77e+02 angle pdb=" C6 LPP G 301 " pdb=" O5 LPP G 301 " pdb=" P1 LPP G 301 " ideal model delta sigma weight residual 82.33 119.15 -36.82 3.00e+00 1.11e-01 1.51e+02 angle pdb=" C6 LPP G 302 " pdb=" O5 LPP G 302 " pdb=" P1 LPP G 302 " ideal model delta sigma weight residual 82.33 118.55 -36.22 3.00e+00 1.11e-01 1.46e+02 ... (remaining 21885 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 8263 17.99 - 35.98: 1026 35.98 - 53.98: 307 53.98 - 71.97: 72 71.97 - 89.96: 20 Dihedral angle restraints: 9688 sinusoidal: 3740 harmonic: 5948 Sorted by residual: dihedral pdb=" CA PHE H 213 " pdb=" C PHE H 213 " pdb=" N ALA H 214 " pdb=" CA ALA H 214 " ideal model delta harmonic sigma weight residual 180.00 151.07 28.93 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA GLU L 43 " pdb=" C GLU L 43 " pdb=" N LEU L 44 " pdb=" CA LEU L 44 " ideal model delta harmonic sigma weight residual 180.00 155.58 24.42 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA LEU A 26 " pdb=" C LEU A 26 " pdb=" N ARG A 27 " pdb=" CA ARG A 27 " ideal model delta harmonic sigma weight residual 180.00 -158.11 -21.89 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 9685 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2263 0.059 - 0.119: 386 0.119 - 0.178: 34 0.178 - 0.237: 4 0.237 - 0.297: 2 Chirality restraints: 2689 Sorted by residual: chirality pdb=" C7 LPP H 301 " pdb=" C6 LPP H 301 " pdb=" C8 LPP H 301 " pdb=" O9 LPP H 301 " both_signs ideal model delta sigma weight residual False -2.69 -2.40 -0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" C7 LPP G 301 " pdb=" C6 LPP G 301 " pdb=" C8 LPP G 301 " pdb=" O9 LPP G 301 " both_signs ideal model delta sigma weight residual False -2.69 -2.44 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CA ILE C 142 " pdb=" N ILE C 142 " pdb=" C ILE C 142 " pdb=" CB ILE C 142 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.05e+00 ... (remaining 2686 not shown) Planarity restraints: 2753 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL G 212 " -0.026 2.00e-02 2.50e+03 5.27e-02 2.77e+01 pdb=" C VAL G 212 " 0.091 2.00e-02 2.50e+03 pdb=" O VAL G 212 " -0.034 2.00e-02 2.50e+03 pdb=" N PHE G 213 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG G 101 " -0.014 2.00e-02 2.50e+03 2.74e-02 7.53e+00 pdb=" C ARG G 101 " 0.047 2.00e-02 2.50e+03 pdb=" O ARG G 101 " -0.018 2.00e-02 2.50e+03 pdb=" N GLU G 102 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR J 256 " -0.032 5.00e-02 4.00e+02 4.77e-02 3.64e+00 pdb=" N PRO J 257 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO J 257 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO J 257 " -0.027 5.00e-02 4.00e+02 ... (remaining 2750 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 243 2.61 - 3.18: 15043 3.18 - 3.75: 25348 3.75 - 4.33: 33564 4.33 - 4.90: 54871 Nonbonded interactions: 129069 Sorted by model distance: nonbonded pdb=" OE1 GLN H 93 " pdb=" O28 LPP G 301 " model vdw 2.032 3.040 nonbonded pdb=" OG1 THR G 40 " pdb=" OG1 THR G 43 " model vdw 2.139 3.040 nonbonded pdb=" OG SER C 97 " pdb=" O SER C 115 " model vdw 2.145 3.040 nonbonded pdb=" OG1 THR G 121 " pdb=" O ALA G 221 " model vdw 2.157 3.040 nonbonded pdb=" N ASP E 76 " pdb=" OD1 ASP E 76 " model vdw 2.159 3.120 ... (remaining 129064 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 3 or (resid 4 through 5 and (name N or name CA or name C o \ r name O or name CB )) or resid 6 through 38 or (resid 39 and (name N or name CA \ or name C or name O or name CB )) or resid 40 or (resid 41 and (name N or name \ CA or name C or name O or name CB )) or resid 42 through 54 or (resid 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 or (resid 57 and ( \ name N or name CA or name C or name O or name CB )) or resid 58 or (resid 59 and \ (name N or name CA or name C or name O or name CB )) or resid 60 through 68 or \ (resid 69 through 70 and (name N or name CA or name C or name O or name CB )) or \ resid 71 through 72 or (resid 73 through 75 and (name N or name CA or name C or \ name O or name CB )) or resid 76 or (resid 77 through 78 and (name N or name CA \ or name C or name O or name CB )) or resid 79 through 91 or (resid 92 and (name \ N or name CA or name C or name O or name CB )) or resid 93 through 131 or (resi \ d 132 and (name N or name CA or name C or name O or name CB )) or resid 133 thro \ ugh 150)) selection = (chain 'B' and (resid 3 or (resid 4 through 5 and (name N or name CA or name C o \ r name O or name CB )) or resid 6 through 54 or (resid 55 and (name N or name CA \ or name C or name O or name CB )) or resid 56 or (resid 57 and (name N or name \ CA or name C or name O or name CB )) or resid 58 or (resid 59 and (name N or nam \ e CA or name C or name O or name CB )) or resid 60 through 68 or (resid 69 throu \ gh 70 and (name N or name CA or name C or name O or name CB )) or resid 71 throu \ gh 77 or (resid 78 and (name N or name CA or name C or name O or name CB )) or r \ esid 79 through 91 or (resid 92 and (name N or name CA or name C or name O or na \ me CB )) or resid 93 through 150)) selection = (chain 'C' and (resid 3 or (resid 4 through 5 and (name N or name CA or name C o \ r name O or name CB )) or resid 6 through 38 or (resid 39 and (name N or name CA \ or name C or name O or name CB )) or resid 40 or (resid 41 and (name N or name \ CA or name C or name O or name CB )) or resid 42 through 54 or (resid 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 or (resid 57 and ( \ name N or name CA or name C or name O or name CB )) or resid 58 or (resid 59 and \ (name N or name CA or name C or name O or name CB )) or resid 60 through 68 or \ (resid 69 through 70 and (name N or name CA or name C or name O or name CB )) or \ resid 71 through 72 or (resid 73 through 75 and (name N or name CA or name C or \ name O or name CB )) or resid 76 or (resid 77 through 78 and (name N or name CA \ or name C or name O or name CB )) or resid 79 through 131 or (resid 132 and (na \ me N or name CA or name C or name O or name CB )) or resid 133 through 150)) selection = (chain 'D' and (resid 3 through 4 or (resid 5 and (name N or name CA or name C o \ r name O or name CB )) or resid 6 through 38 or (resid 39 and (name N or name CA \ or name C or name O or name CB )) or resid 40 or (resid 41 and (name N or name \ CA or name C or name O or name CB )) or resid 42 through 54 or (resid 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 or (resid 57 and ( \ name N or name CA or name C or name O or name CB )) or resid 58 or (resid 59 and \ (name N or name CA or name C or name O or name CB )) or resid 60 through 68 or \ (resid 69 through 70 and (name N or name CA or name C or name O or name CB )) or \ resid 71 through 72 or (resid 73 through 75 and (name N or name CA or name C or \ name O or name CB )) or resid 76 or (resid 77 through 78 and (name N or name CA \ or name C or name O or name CB )) or resid 79 through 91 or (resid 92 and (name \ N or name CA or name C or name O or name CB )) or resid 93 through 131 or (resi \ d 132 and (name N or name CA or name C or name O or name CB )) or resid 133 thro \ ugh 150)) selection = (chain 'E' and (resid 3 or (resid 4 through 5 and (name N or name CA or name C o \ r name O or name CB )) or resid 6 through 38 or (resid 39 and (name N or name CA \ or name C or name O or name CB )) or resid 40 or (resid 41 and (name N or name \ CA or name C or name O or name CB )) or resid 42 through 54 or (resid 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 or (resid 57 and ( \ name N or name CA or name C or name O or name CB )) or resid 58 or (resid 59 and \ (name N or name CA or name C or name O or name CB )) or resid 60 through 72 or \ (resid 73 through 75 and (name N or name CA or name C or name O or name CB )) or \ resid 76 or (resid 77 through 78 and (name N or name CA or name C or name O or \ name CB )) or resid 79 through 91 or (resid 92 and (name N or name CA or name C \ or name O or name CB )) or resid 93 through 131 or (resid 132 and (name N or nam \ e CA or name C or name O or name CB )) or resid 133 through 150)) selection = (chain 'F' and (resid 3 or (resid 4 through 5 and (name N or name CA or name C o \ r name O or name CB )) or resid 6 through 38 or (resid 39 and (name N or name CA \ or name C or name O or name CB )) or resid 40 or (resid 41 and (name N or name \ CA or name C or name O or name CB )) or resid 42 through 68 or (resid 69 through \ 70 and (name N or name CA or name C or name O or name CB )) or resid 71 through \ 72 or (resid 73 through 75 and (name N or name CA or name C or name O or name C \ B )) or resid 76 or (resid 77 through 78 and (name N or name CA or name C or nam \ e O or name CB )) or resid 79 through 91 or (resid 92 and (name N or name CA or \ name C or name O or name CB )) or resid 93 through 131 or (resid 132 and (name N \ or name CA or name C or name O or name CB )) or resid 133 through 150)) } ncs_group { reference = (chain 'G' and (resid 5 through 100 or (resid 101 through 102 and (name N or nam \ e CA or name C or name O or name CB )) or resid 103 through 191 or (resid 192 an \ d (name N or name CA or name C or name O or name CB )) or resid 193 through 228 \ or (resid 229 and (name N or name CA or name C or name O or name CB )) or resid \ 231 through 301)) selection = (chain 'H' and (resid 5 through 185 or (resid 186 and (name N or name CA or name \ C or name O or name CB )) or resid 187 through 262 or (resid 301 and (name C11 \ or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name \ C18 or name C19 or name C20 or name C21 or name C22 or name C29 or name C30 or n \ ame C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 \ or name C38 or name C39 or name C40 or name C41 or name C6 or name C7 or name C8 \ or name O10 or name O2 or name O27 or name O28 or name O3 or name O4 or name O5 \ or name O9 or name P1 )))) } ncs_group { reference = (chain 'I' and ((resid 6 through 8 and (name N or name CA or name C or name O or \ name CB )) or resid 9 through 29 or (resid 30 and (name N or name CA or name C \ or name O or name CB )) or resid 31 through 129 or (resid 130 through 131 and (n \ ame N or name CA or name C or name O or name CB )) or resid 132 through 134 or ( \ resid 135 and (name N or name CA or name C or name O or name CB )) or resid 136 \ through 215 or (resid 216 and (name N or name CA or name C or name O or name CB \ )) or resid 217 through 267)) selection = (chain 'J' and (resid 6 through 261 or (resid 262 through 263 and (name N or nam \ e CA or name C or name O or name CB )) or resid 264 through 267)) } ncs_group { reference = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.770 Find NCS groups from input model: 0.390 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:1.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 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 : 0.011 0.672 16171 Z= 0.555 Angle : 1.139 46.971 21890 Z= 0.539 Chirality : 0.045 0.297 2689 Planarity : 0.004 0.053 2753 Dihedral : 18.141 89.959 5904 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.57 % Favored : 90.43 % Rotamer: Outliers : 10.34 % Allowed : 27.08 % Favored : 62.58 % 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: -4.56 (0.14), residues: 2100 helix: -2.48 (0.14), residues: 857 sheet: -2.68 (0.27), residues: 294 loop : -3.65 (0.15), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 79 TYR 0.012 0.001 TYR D 111 PHE 0.019 0.002 PHE H 213 TRP 0.010 0.001 TRP H 181 HIS 0.003 0.001 HIS I 203 Details of bonding type rmsd/Z covalent geometry : bond 0.01097 / 0.56 (16171) covalent geometry : angle 1.13893 / 0.54 (21890) hydrogen bonds : bond 0.17937 / 12.02 ( 722) hydrogen bonds : angle 8.22897 / 5.65 ( 2100) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 705 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 532 time to evaluate : 0.693 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 7 GLU cc_start: 0.8534 (mt-10) cc_final: 0.8242 (mt-10) REVERT: A 86 ILE cc_start: 0.9285 (mp) cc_final: 0.9068 (mp) REVERT: A 110 LYS cc_start: 0.9281 (mtpp) cc_final: 0.9018 (mtpp) REVERT: A 124 LYS cc_start: 0.6503 (ttpp) cc_final: 0.6104 (mtpp) REVERT: B 7 GLU cc_start: 0.6653 (tt0) cc_final: 0.6304 (tm-30) REVERT: B 47 ASP cc_start: 0.8649 (t0) cc_final: 0.8427 (t0) REVERT: B 67 LYS cc_start: 0.8851 (ttmt) cc_final: 0.8364 (ttmt) REVERT: B 88 GLN cc_start: 0.8532 (mm110) cc_final: 0.8031 (mm110) REVERT: B 96 ASP cc_start: 0.7509 (p0) cc_final: 0.7083 (p0) REVERT: B 139 GLU cc_start: 0.8575 (mm-30) cc_final: 0.7896 (tp30) REVERT: C 55 ARG cc_start: 0.7650 (ttt90) cc_final: 0.7000 (ttt90) REVERT: C 60 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8431 (tp) REVERT: C 111 TYR cc_start: 0.8730 (p90) cc_final: 0.8385 (p90) REVERT: C 139 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8280 (tp30) REVERT: C 145 PHE cc_start: 0.7742 (m-80) cc_final: 0.7520 (m-10) REVERT: D 27 ARG cc_start: 0.8371 (mtt180) cc_final: 0.7146 (mtp180) REVERT: D 144 LYS cc_start: 0.9067 (ptmm) cc_final: 0.8758 (ptmm) REVERT: D 145 PHE cc_start: 0.8323 (m-80) cc_final: 0.7872 (m-80) REVERT: E 49 ILE cc_start: 0.8759 (pt) cc_final: 0.8538 (pt) REVERT: E 145 PHE cc_start: 0.8077 (m-80) cc_final: 0.7608 (m-80) REVERT: F 67 LYS cc_start: 0.8762 (ptpt) cc_final: 0.8341 (ptmt) REVERT: F 110 LYS cc_start: 0.9040 (mttm) cc_final: 0.8771 (mtpt) REVERT: F 145 PHE cc_start: 0.7439 (m-80) cc_final: 0.7212 (m-80) REVERT: G 80 ASN cc_start: 0.9051 (t0) cc_final: 0.8724 (t0) REVERT: G 94 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.7831 (ttt) REVERT: G 132 GLN cc_start: 0.8748 (tt0) cc_final: 0.8459 (tt0) REVERT: G 159 MET cc_start: 0.8547 (tpt) cc_final: 0.7874 (tpt) REVERT: G 161 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8772 (mm) REVERT: G 165 ILE cc_start: 0.8686 (mt) cc_final: 0.8336 (mp) REVERT: G 176 MET cc_start: 0.8552 (tmm) cc_final: 0.8106 (tmm) REVERT: G 201 GLU cc_start: 0.8150 (tp30) cc_final: 0.7730 (tp30) REVERT: G 227 ASP cc_start: 0.8094 (t70) cc_final: 0.7442 (t0) REVERT: G 233 GLU cc_start: 0.8279 (tp30) cc_final: 0.7959 (tp30) REVERT: H 8 GLU cc_start: 0.7806 (tt0) cc_final: 0.7355 (pt0) REVERT: H 9 ARG cc_start: 0.6639 (tpp80) cc_final: 0.5905 (ptt90) REVERT: H 85 TYR cc_start: 0.7557 (m-80) cc_final: 0.7335 (m-80) REVERT: H 94 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.8468 (ttt) REVERT: H 126 ASN cc_start: 0.8507 (OUTLIER) cc_final: 0.8276 (t0) REVERT: H 227 ASP cc_start: 0.8253 (t0) cc_final: 0.7636 (t0) REVERT: I 12 LYS cc_start: 0.7925 (mptp) cc_final: 0.7574 (mttt) REVERT: I 35 LYS cc_start: 0.8413 (mmpt) cc_final: 0.8043 (mptt) REVERT: I 75 LEU cc_start: 0.8451 (mt) cc_final: 0.8223 (mt) REVERT: I 202 SER cc_start: 0.8427 (OUTLIER) cc_final: 0.7749 (p) REVERT: J 62 LYS cc_start: 0.8913 (pttp) cc_final: 0.8608 (tppt) REVERT: J 64 GLU cc_start: 0.6633 (pm20) cc_final: 0.6350 (pm20) REVERT: J 165 ILE cc_start: 0.8763 (OUTLIER) cc_final: 0.8554 (pt) REVERT: J 172 PHE cc_start: 0.9007 (OUTLIER) cc_final: 0.8579 (p90) REVERT: J 242 GLN cc_start: 0.7909 (tt0) cc_final: 0.7539 (tt0) REVERT: K 8 GLU cc_start: 0.7401 (mm-30) cc_final: 0.7072 (tp30) REVERT: K 52 GLU cc_start: 0.8396 (pt0) cc_final: 0.7719 (tt0) REVERT: K 65 PHE cc_start: 0.8991 (m-10) cc_final: 0.8567 (m-10) REVERT: K 90 LYS cc_start: 0.8553 (ttpp) cc_final: 0.7867 (mmpt) REVERT: L 15 GLN cc_start: 0.6666 (pt0) cc_final: 0.6248 (pp30) REVERT: L 29 ARG cc_start: 0.8957 (tmt-80) cc_final: 0.8741 (tpt90) REVERT: L 31 GLN cc_start: 0.8342 (pt0) cc_final: 0.8082 (pt0) REVERT: L 37 ARG cc_start: 0.7902 (ttp80) cc_final: 0.7462 (tmm160) REVERT: L 53 ARG cc_start: 0.8050 (ttp80) cc_final: 0.7706 (ptm-80) REVERT: L 70 ARG cc_start: 0.7949 (ttt-90) cc_final: 0.7673 (ttp-110) outliers start: 173 outliers final: 121 residues processed: 670 average time/residue: 0.1414 time to fit residues: 138.1882 Evaluate side-chains 555 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 426 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 111 TYR Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 91 ASN Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain D residue 3 THR Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 148 ASN Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 91 ASN Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 91 ASN Chi-restraints excluded: chain F residue 92 ASN Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain G residue 83 ILE Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 94 MET Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 118 SER Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 126 ASN Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 217 VAL Chi-restraints excluded: chain G residue 218 THR Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 231 THR Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain G residue 254 ASP Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain H residue 27 SER Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 94 MET Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 118 SER Chi-restraints excluded: chain H residue 126 ASN Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain H residue 231 THR Chi-restraints excluded: chain H residue 240 THR Chi-restraints excluded: chain H residue 253 LEU Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 56 SER Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 167 LEU Chi-restraints excluded: chain I residue 202 SER Chi-restraints excluded: chain I residue 215 ILE Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 228 THR Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain J residue 121 ILE Chi-restraints excluded: chain J residue 165 ILE Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 203 HIS Chi-restraints excluded: chain J residue 215 ILE Chi-restraints excluded: chain J residue 218 VAL Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain L residue 84 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.0170 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.3980 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 4.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 0.0570 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 ASN C 35 ASN C 148 ASN E 92 ASN E 133 GLN F 88 GLN G 89 GLN G 93 GLN G 224 GLN ** H 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 224 GLN ** I 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 105 ASN I 191 ASN J 191 ASN J 255 HIS L 31 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.132331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.099671 restraints weight = 32919.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.103197 restraints weight = 15880.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.105529 restraints weight = 10383.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.106728 restraints weight = 8091.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.107758 restraints weight = 7084.352| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16171 Z= 0.138 Angle : 0.682 9.420 21890 Z= 0.346 Chirality : 0.044 0.194 2689 Planarity : 0.004 0.051 2753 Dihedral : 12.273 67.200 2665 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 8.79 % Allowed : 29.17 % Favored : 62.04 % 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: -3.26 (0.16), residues: 2100 helix: -1.02 (0.17), residues: 864 sheet: -2.29 (0.30), residues: 263 loop : -3.25 (0.16), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 239 TYR 0.019 0.001 TYR F 111 PHE 0.016 0.002 PHE H 213 TRP 0.011 0.001 TRP J 66 HIS 0.003 0.001 HIS C 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (16171) covalent geometry : angle 0.68164 / 0.35 (21890) hydrogen bonds : bond 0.03932 / 2.69 ( 722) hydrogen bonds : angle 5.70585 / 3.97 ( 2100) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 484 time to evaluate : 0.641 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 52 VAL cc_start: 0.8909 (t) cc_final: 0.8614 (p) REVERT: A 106 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8815 (tt) REVERT: A 124 LYS cc_start: 0.6779 (ttpp) cc_final: 0.6341 (mtpp) REVERT: B 7 GLU cc_start: 0.6467 (tt0) cc_final: 0.6138 (tm-30) REVERT: B 47 ASP cc_start: 0.8664 (t0) cc_final: 0.8369 (t0) REVERT: B 48 ASN cc_start: 0.8904 (t0) cc_final: 0.8697 (t0) REVERT: B 87 ASN cc_start: 0.8587 (m-40) cc_final: 0.8152 (p0) REVERT: B 88 GLN cc_start: 0.8542 (mm110) cc_final: 0.8337 (mm110) REVERT: B 139 GLU cc_start: 0.8508 (mm-30) cc_final: 0.7902 (tp30) REVERT: C 7 GLU cc_start: 0.6598 (tp30) cc_final: 0.6090 (pt0) REVERT: C 43 TYR cc_start: 0.8552 (m-10) cc_final: 0.8307 (m-80) REVERT: C 74 ASP cc_start: 0.8167 (OUTLIER) cc_final: 0.7713 (p0) REVERT: C 133 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7945 (mp10) REVERT: D 8 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.7963 (mm) REVERT: D 27 ARG cc_start: 0.8431 (mtt180) cc_final: 0.7225 (mtp180) REVERT: F 67 LYS cc_start: 0.8620 (ptpt) cc_final: 0.8246 (ptmt) REVERT: F 110 LYS cc_start: 0.9092 (mttm) cc_final: 0.8719 (mtpt) REVERT: G 50 LYS cc_start: 0.8950 (tptp) cc_final: 0.8722 (tptm) REVERT: G 80 ASN cc_start: 0.8982 (t0) cc_final: 0.8640 (t0) REVERT: G 89 GLN cc_start: 0.8133 (mm110) cc_final: 0.7837 (mp10) REVERT: G 127 MET cc_start: 0.8257 (mtt) cc_final: 0.7984 (ttm) REVERT: G 165 ILE cc_start: 0.8421 (mt) cc_final: 0.8037 (mp) REVERT: G 176 MET cc_start: 0.8412 (tmm) cc_final: 0.7953 (tmm) REVERT: G 227 ASP cc_start: 0.7877 (t70) cc_final: 0.7366 (t0) REVERT: H 8 GLU cc_start: 0.7834 (tt0) cc_final: 0.7467 (pt0) REVERT: H 9 ARG cc_start: 0.6524 (tpp80) cc_final: 0.5829 (ptt90) REVERT: H 26 ARG cc_start: 0.8801 (ttp-110) cc_final: 0.8458 (ttp-110) REVERT: H 89 GLN cc_start: 0.8916 (mp10) cc_final: 0.8634 (pm20) REVERT: H 93 GLN cc_start: 0.8279 (tt0) cc_final: 0.7926 (tt0) REVERT: H 227 ASP cc_start: 0.8133 (t0) cc_final: 0.7509 (t0) REVERT: H 233 GLU cc_start: 0.8306 (tp30) cc_final: 0.7737 (mp0) REVERT: I 12 LYS cc_start: 0.7976 (mptp) cc_final: 0.7694 (mttt) REVERT: I 35 LYS cc_start: 0.8222 (mmpt) cc_final: 0.7867 (mptt) REVERT: I 101 ASP cc_start: 0.8326 (p0) cc_final: 0.8050 (p0) REVERT: I 105 ASN cc_start: 0.7976 (OUTLIER) cc_final: 0.7367 (m-40) REVERT: J 17 LYS cc_start: 0.7192 (ptpp) cc_final: 0.6875 (pttp) REVERT: J 62 LYS cc_start: 0.8843 (pttp) cc_final: 0.8585 (tppt) REVERT: J 144 GLU cc_start: 0.7705 (mp0) cc_final: 0.7413 (pt0) REVERT: J 241 ARG cc_start: 0.8669 (ttp80) cc_final: 0.7804 (mmm-85) REVERT: K 8 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7082 (tm-30) REVERT: K 13 GLU cc_start: 0.6886 (pm20) cc_final: 0.6194 (pm20) REVERT: K 52 GLU cc_start: 0.8430 (pt0) cc_final: 0.7823 (tt0) REVERT: K 87 GLU cc_start: 0.8731 (tt0) cc_final: 0.8486 (tt0) REVERT: K 90 LYS cc_start: 0.8562 (ttpp) cc_final: 0.7803 (mmpt) REVERT: L 15 GLN cc_start: 0.6662 (pt0) cc_final: 0.6297 (pp30) REVERT: L 53 ARG cc_start: 0.8117 (ttp80) cc_final: 0.7793 (ptm-80) REVERT: L 70 ARG cc_start: 0.7993 (ttt-90) cc_final: 0.7635 (ttp-110) outliers start: 147 outliers final: 81 residues processed: 589 average time/residue: 0.1274 time to fit residues: 110.9370 Evaluate side-chains 529 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 442 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 111 TYR Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 133 GLN Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain E residue 43 TYR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 40 TYR Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 83 ILE Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain G residue 218 THR Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain G residue 254 ASP Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain H residue 253 LEU Chi-restraints excluded: chain I residue 10 GLU Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 56 SER Chi-restraints excluded: chain I residue 62 LYS Chi-restraints excluded: chain I residue 71 ASN Chi-restraints excluded: chain I residue 105 ASN Chi-restraints excluded: chain I residue 121 ILE Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain I residue 149 MET Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 215 ILE Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 266 LEU Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 203 HIS Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 236 ASP Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 52 GLU Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 81 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 159 optimal weight: 0.0000 chunk 64 optimal weight: 2.9990 chunk 147 optimal weight: 0.8980 chunk 187 optimal weight: 6.9990 chunk 120 optimal weight: 0.9990 chunk 69 optimal weight: 7.9990 chunk 22 optimal weight: 9.9990 chunk 19 optimal weight: 0.7980 chunk 46 optimal weight: 0.2980 chunk 50 optimal weight: 10.0000 chunk 165 optimal weight: 2.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 35 ASN E 133 GLN ** G 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 105 ASN ** I 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.134362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.102532 restraints weight = 33251.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.106219 restraints weight = 15713.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.108549 restraints weight = 10124.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.110078 restraints weight = 7821.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.110793 restraints weight = 6707.343| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16171 Z= 0.128 Angle : 0.671 10.184 21890 Z= 0.337 Chirality : 0.044 0.196 2689 Planarity : 0.004 0.053 2753 Dihedral : 10.852 64.753 2548 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 8.43 % Allowed : 30.25 % Favored : 61.33 % 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: -2.71 (0.17), residues: 2100 helix: -0.50 (0.17), residues: 879 sheet: -2.07 (0.30), residues: 257 loop : -3.02 (0.16), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 75 TYR 0.017 0.001 TYR A 111 PHE 0.024 0.002 PHE C 13 TRP 0.009 0.001 TRP I 66 HIS 0.002 0.001 HIS I 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (16171) covalent geometry : angle 0.67135 / 0.34 (21890) hydrogen bonds : bond 0.03509 / 2.39 ( 722) hydrogen bonds : angle 5.34651 / 3.73 ( 2100) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 489 time to evaluate : 0.588 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 52 VAL cc_start: 0.8885 (t) cc_final: 0.8655 (p) REVERT: A 106 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8760 (tt) REVERT: A 124 LYS cc_start: 0.6816 (ttpp) cc_final: 0.6487 (mtpp) REVERT: A 133 GLN cc_start: 0.8666 (tp-100) cc_final: 0.8448 (tp-100) REVERT: B 7 GLU cc_start: 0.6486 (tt0) cc_final: 0.6200 (tm-30) REVERT: B 47 ASP cc_start: 0.8594 (t0) cc_final: 0.8283 (t0) REVERT: B 48 ASN cc_start: 0.8951 (t0) cc_final: 0.8563 (t0) REVERT: B 85 GLU cc_start: 0.7961 (tp30) cc_final: 0.7613 (tp30) REVERT: B 139 GLU cc_start: 0.8389 (mm-30) cc_final: 0.7927 (tp30) REVERT: B 144 LYS cc_start: 0.8307 (ptmt) cc_final: 0.8052 (ptmm) REVERT: C 7 GLU cc_start: 0.6771 (tp30) cc_final: 0.6084 (pt0) REVERT: C 85 GLU cc_start: 0.6522 (mm-30) cc_final: 0.6308 (mm-30) REVERT: C 133 GLN cc_start: 0.8020 (OUTLIER) cc_final: 0.7720 (mp10) REVERT: C 138 LEU cc_start: 0.8529 (mt) cc_final: 0.8196 (mt) REVERT: C 140 ASP cc_start: 0.8674 (m-30) cc_final: 0.8036 (t0) REVERT: D 27 ARG cc_start: 0.8370 (mtt180) cc_final: 0.7108 (mtp180) REVERT: D 144 LYS cc_start: 0.8881 (ptmm) cc_final: 0.8426 (ptmm) REVERT: D 145 PHE cc_start: 0.7821 (m-80) cc_final: 0.7321 (m-80) REVERT: F 47 ASP cc_start: 0.8325 (m-30) cc_final: 0.8051 (t0) REVERT: F 110 LYS cc_start: 0.9079 (mttm) cc_final: 0.8734 (mttt) REVERT: F 136 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8707 (pt) REVERT: F 144 LYS cc_start: 0.8457 (tmmt) cc_final: 0.8157 (tttt) REVERT: G 80 ASN cc_start: 0.8942 (t0) cc_final: 0.8509 (t0) REVERT: G 89 GLN cc_start: 0.8024 (mm110) cc_final: 0.7803 (mp10) REVERT: G 165 ILE cc_start: 0.8446 (mt) cc_final: 0.8069 (mp) REVERT: G 176 MET cc_start: 0.8440 (tmm) cc_final: 0.8146 (tmm) REVERT: G 194 GLN cc_start: 0.7959 (pt0) cc_final: 0.7711 (mt0) REVERT: G 227 ASP cc_start: 0.7783 (t70) cc_final: 0.7333 (t0) REVERT: H 8 GLU cc_start: 0.7847 (tt0) cc_final: 0.7453 (pt0) REVERT: H 9 ARG cc_start: 0.6548 (tpp80) cc_final: 0.5731 (ptm-80) REVERT: H 79 TYR cc_start: 0.8717 (t80) cc_final: 0.8014 (t80) REVERT: H 93 GLN cc_start: 0.8287 (tt0) cc_final: 0.8043 (tt0) REVERT: H 127 MET cc_start: 0.7775 (mtt) cc_final: 0.7568 (mtp) REVERT: H 227 ASP cc_start: 0.8021 (t0) cc_final: 0.7459 (t0) REVERT: I 12 LYS cc_start: 0.7936 (mptp) cc_final: 0.7664 (mttt) REVERT: I 35 LYS cc_start: 0.8289 (mmpt) cc_final: 0.7936 (mptt) REVERT: I 93 SER cc_start: 0.9052 (t) cc_final: 0.8400 (p) REVERT: I 105 ASN cc_start: 0.7826 (OUTLIER) cc_final: 0.7593 (t0) REVERT: I 134 LEU cc_start: 0.8868 (tm) cc_final: 0.8666 (tm) REVERT: J 17 LYS cc_start: 0.7225 (ptpp) cc_final: 0.6950 (pttp) REVERT: J 62 LYS cc_start: 0.8948 (pttp) cc_final: 0.8635 (tppt) REVERT: J 175 GLN cc_start: 0.6178 (OUTLIER) cc_final: 0.5729 (pm20) REVERT: J 232 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7539 (mp) REVERT: J 243 PHE cc_start: 0.8636 (t80) cc_final: 0.8325 (t80) REVERT: K 3 GLN cc_start: 0.7870 (mm-40) cc_final: 0.7605 (mm-40) REVERT: K 8 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.7168 (tm-30) REVERT: K 13 GLU cc_start: 0.6999 (pm20) cc_final: 0.6294 (pm20) REVERT: K 29 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7778 (tmm-80) REVERT: K 34 ARG cc_start: 0.6965 (mtp85) cc_final: 0.6680 (mtp85) REVERT: K 52 GLU cc_start: 0.8394 (pt0) cc_final: 0.7769 (tt0) REVERT: K 87 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8471 (tt0) REVERT: K 90 LYS cc_start: 0.8544 (ttpp) cc_final: 0.7782 (mmpt) REVERT: L 15 GLN cc_start: 0.6970 (pt0) cc_final: 0.6579 (pp30) REVERT: L 31 GLN cc_start: 0.8236 (pt0) cc_final: 0.7740 (pp30) REVERT: L 53 ARG cc_start: 0.8106 (ttp80) cc_final: 0.7799 (ptm-80) REVERT: L 70 ARG cc_start: 0.7928 (ttt-90) cc_final: 0.7650 (ttp-170) outliers start: 141 outliers final: 88 residues processed: 588 average time/residue: 0.1268 time to fit residues: 110.3456 Evaluate side-chains 526 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 429 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 111 TYR Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 133 GLN Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 112 ILE Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 125 ASP Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain H residue 30 PHE Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain H residue 258 THR Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain I residue 10 GLU Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 56 SER Chi-restraints excluded: chain I residue 62 LYS Chi-restraints excluded: chain I residue 105 ASN Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain I residue 149 MET Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 228 THR Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain I residue 266 LEU Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain J residue 175 GLN Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 215 ILE Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 232 LEU Chi-restraints excluded: chain J residue 236 ASP Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 29 ARG Chi-restraints excluded: chain K residue 83 ASP Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 52 GLU Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 81 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 61 optimal weight: 8.9990 chunk 162 optimal weight: 9.9990 chunk 138 optimal weight: 7.9990 chunk 195 optimal weight: 10.0000 chunk 164 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 chunk 153 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 9 optimal weight: 20.0000 chunk 25 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 35 ASN E 133 GLN ** H 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 105 ASN ** I 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 71 ASN ** J 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.131655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.099612 restraints weight = 32991.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.103154 restraints weight = 15946.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.105430 restraints weight = 10329.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.106804 restraints weight = 8013.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.107636 restraints weight = 6948.888| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 16171 Z= 0.177 Angle : 0.688 10.752 21890 Z= 0.346 Chirality : 0.044 0.206 2689 Planarity : 0.004 0.051 2753 Dihedral : 10.103 59.046 2527 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer: Outliers : 9.32 % Allowed : 31.80 % Favored : 58.88 % 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: -2.54 (0.17), residues: 2100 helix: -0.35 (0.17), residues: 892 sheet: -1.98 (0.30), residues: 263 loop : -2.97 (0.17), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 75 TYR 0.016 0.001 TYR E 111 PHE 0.020 0.002 PHE C 13 TRP 0.011 0.001 TRP G 219 HIS 0.004 0.001 HIS I 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 (16171) covalent geometry : angle 0.68769 / 0.35 (21890) hydrogen bonds : bond 0.03487 / 2.37 ( 722) hydrogen bonds : angle 5.29399 / 3.69 ( 2100) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 449 time to evaluate : 0.726 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 52 VAL cc_start: 0.9109 (t) cc_final: 0.8901 (p) REVERT: A 106 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8765 (tt) REVERT: A 124 LYS cc_start: 0.6730 (ttpp) cc_final: 0.6385 (mtpp) REVERT: B 7 GLU cc_start: 0.6653 (tt0) cc_final: 0.6377 (tm-30) REVERT: B 40 TYR cc_start: 0.6539 (m-80) cc_final: 0.6224 (m-80) REVERT: B 47 ASP cc_start: 0.8578 (t0) cc_final: 0.8284 (t0) REVERT: B 48 ASN cc_start: 0.8986 (t0) cc_final: 0.8616 (t0) REVERT: B 85 GLU cc_start: 0.7812 (tp30) cc_final: 0.7392 (tp30) REVERT: B 139 GLU cc_start: 0.8454 (mm-30) cc_final: 0.7906 (tp30) REVERT: C 111 TYR cc_start: 0.8754 (p90) cc_final: 0.8553 (p90) REVERT: C 133 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7729 (mp10) REVERT: C 140 ASP cc_start: 0.8704 (m-30) cc_final: 0.8143 (t0) REVERT: D 27 ARG cc_start: 0.8366 (mtt180) cc_final: 0.7100 (mtp180) REVERT: D 57 LYS cc_start: 0.8483 (mmtm) cc_final: 0.8118 (ttpt) REVERT: D 125 ASP cc_start: 0.6423 (OUTLIER) cc_final: 0.6052 (t70) REVERT: D 131 ASP cc_start: 0.8291 (p0) cc_final: 0.7931 (p0) REVERT: D 140 ASP cc_start: 0.7997 (m-30) cc_final: 0.7727 (m-30) REVERT: E 7 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7138 (mt-10) REVERT: E 13 PHE cc_start: 0.6850 (m-80) cc_final: 0.6571 (m-10) REVERT: E 91 ASN cc_start: 0.8244 (OUTLIER) cc_final: 0.7986 (m-40) REVERT: F 67 LYS cc_start: 0.8588 (ptmt) cc_final: 0.8350 (ttpt) REVERT: F 85 GLU cc_start: 0.7630 (mm-30) cc_final: 0.7301 (mm-30) REVERT: F 88 GLN cc_start: 0.8838 (tp-100) cc_final: 0.8334 (tt0) REVERT: F 110 LYS cc_start: 0.9108 (mttm) cc_final: 0.8779 (mttt) REVERT: F 136 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8723 (pt) REVERT: G 36 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8834 (pp) REVERT: G 50 LYS cc_start: 0.8944 (tptp) cc_final: 0.8670 (tptm) REVERT: G 80 ASN cc_start: 0.8981 (t0) cc_final: 0.8586 (t0) REVERT: G 89 GLN cc_start: 0.8110 (mm110) cc_final: 0.7909 (mp10) REVERT: G 159 MET cc_start: 0.8351 (tpt) cc_final: 0.7772 (tpt) REVERT: G 165 ILE cc_start: 0.8509 (mt) cc_final: 0.8115 (mp) REVERT: G 176 MET cc_start: 0.8479 (tmm) cc_final: 0.7958 (tmm) REVERT: G 194 GLN cc_start: 0.8016 (pt0) cc_final: 0.7805 (mt0) REVERT: G 201 GLU cc_start: 0.8419 (tp30) cc_final: 0.8168 (tp30) REVERT: G 227 ASP cc_start: 0.7736 (t70) cc_final: 0.7303 (t0) REVERT: H 8 GLU cc_start: 0.7820 (tt0) cc_final: 0.7447 (pt0) REVERT: H 9 ARG cc_start: 0.6510 (tpp80) cc_final: 0.5711 (ptm-80) REVERT: H 58 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8899 (mp) REVERT: H 79 TYR cc_start: 0.8624 (t80) cc_final: 0.8380 (t80) REVERT: H 89 GLN cc_start: 0.8915 (pm20) cc_final: 0.8441 (mt0) REVERT: H 93 GLN cc_start: 0.8240 (tt0) cc_final: 0.7932 (tt0) REVERT: H 127 MET cc_start: 0.8035 (mtt) cc_final: 0.7833 (mtp) REVERT: H 227 ASP cc_start: 0.8095 (t0) cc_final: 0.7476 (t0) REVERT: H 233 GLU cc_start: 0.8354 (tm-30) cc_final: 0.8140 (tm-30) REVERT: I 35 LYS cc_start: 0.8304 (mmpt) cc_final: 0.7980 (mptt) REVERT: I 40 MET cc_start: 0.7647 (mtp) cc_final: 0.7403 (mtp) REVERT: I 57 GLN cc_start: 0.8715 (OUTLIER) cc_final: 0.7373 (tm-30) REVERT: I 239 ARG cc_start: 0.7998 (mtm-85) cc_final: 0.7789 (mtm-85) REVERT: J 17 LYS cc_start: 0.7201 (ptpp) cc_final: 0.6938 (pttp) REVERT: J 62 LYS cc_start: 0.8935 (pttp) cc_final: 0.8628 (tppt) REVERT: J 83 MET cc_start: 0.8648 (tpp) cc_final: 0.8001 (tpp) REVERT: J 175 GLN cc_start: 0.6258 (OUTLIER) cc_final: 0.5592 (pm20) REVERT: J 232 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7527 (mp) REVERT: J 241 ARG cc_start: 0.8650 (ttp80) cc_final: 0.7788 (mmm-85) REVERT: J 243 PHE cc_start: 0.8610 (t80) cc_final: 0.8249 (t80) REVERT: K 8 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7235 (tm-30) REVERT: K 13 GLU cc_start: 0.6887 (pm20) cc_final: 0.6381 (pm20) REVERT: K 29 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7837 (tmm-80) REVERT: K 52 GLU cc_start: 0.8408 (pt0) cc_final: 0.7803 (tt0) REVERT: K 90 LYS cc_start: 0.8616 (ttpp) cc_final: 0.7808 (mmpt) REVERT: L 15 GLN cc_start: 0.7061 (pt0) cc_final: 0.6760 (pp30) REVERT: L 37 ARG cc_start: 0.8319 (tmm160) cc_final: 0.7808 (tmm-80) REVERT: L 53 ARG cc_start: 0.8110 (ttp80) cc_final: 0.7791 (ptm-80) REVERT: L 70 ARG cc_start: 0.7915 (ttt-90) cc_final: 0.7643 (ttp-170) outliers start: 156 outliers final: 108 residues processed: 561 average time/residue: 0.1286 time to fit residues: 106.4844 Evaluate side-chains 535 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 416 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 111 TYR Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 133 GLN Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain E residue 43 TYR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 91 ASN Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 126 ASN Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain G residue 229 GLU Chi-restraints excluded: chain G residue 232 SER Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain H residue 19 ASP Chi-restraints excluded: chain H residue 30 PHE Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain H residue 258 THR Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain I residue 10 GLU Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 56 SER Chi-restraints excluded: chain I residue 57 GLN Chi-restraints excluded: chain I residue 62 LYS Chi-restraints excluded: chain I residue 121 ILE Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain I residue 127 MET Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 215 ILE Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 228 THR Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain I residue 266 LEU Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 104 GLU Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain J residue 165 ILE Chi-restraints excluded: chain J residue 175 GLN Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 215 ILE Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 232 LEU Chi-restraints excluded: chain K residue 29 ARG Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 66 ILE Chi-restraints excluded: chain K residue 83 ASP Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 52 GLU Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain L residue 83 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 2 optimal weight: 7.9990 chunk 59 optimal weight: 0.8980 chunk 137 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 112 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 166 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 157 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 35 ASN E 88 GLN E 133 GLN ** G 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 191 ASN L 31 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.131262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.099446 restraints weight = 32878.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.102934 restraints weight = 15815.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.105178 restraints weight = 10269.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.106590 restraints weight = 7985.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.107444 restraints weight = 6891.658| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 16171 Z= 0.187 Angle : 0.699 11.119 21890 Z= 0.351 Chirality : 0.044 0.227 2689 Planarity : 0.004 0.060 2753 Dihedral : 9.796 59.839 2522 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.48 % Favored : 90.52 % Rotamer: Outliers : 10.04 % Allowed : 32.34 % Favored : 57.62 % 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: -2.42 (0.17), residues: 2100 helix: -0.23 (0.18), residues: 899 sheet: -2.11 (0.29), residues: 279 loop : -2.88 (0.17), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 75 TYR 0.016 0.001 TYR A 111 PHE 0.025 0.002 PHE C 13 TRP 0.010 0.001 TRP G 219 HIS 0.004 0.001 HIS I 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.19 (16171) covalent geometry : angle 0.69941 / 0.35 (21890) hydrogen bonds : bond 0.03469 / 2.37 ( 722) hydrogen bonds : angle 5.21568 / 3.63 ( 2100) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 444 time to evaluate : 0.621 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 106 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8749 (tt) REVERT: A 124 LYS cc_start: 0.6789 (ttpp) cc_final: 0.6446 (mtpp) REVERT: B 7 GLU cc_start: 0.6528 (tt0) cc_final: 0.6272 (tm-30) REVERT: B 40 TYR cc_start: 0.6639 (m-80) cc_final: 0.6334 (m-80) REVERT: B 47 ASP cc_start: 0.8606 (t0) cc_final: 0.8308 (t0) REVERT: B 48 ASN cc_start: 0.8994 (t0) cc_final: 0.8670 (t0) REVERT: B 85 GLU cc_start: 0.7773 (tp30) cc_final: 0.7392 (tp30) REVERT: B 139 GLU cc_start: 0.8435 (mm-30) cc_final: 0.7879 (tp30) REVERT: C 133 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7733 (mp10) REVERT: C 140 ASP cc_start: 0.8650 (m-30) cc_final: 0.8124 (t0) REVERT: D 27 ARG cc_start: 0.8417 (mtt180) cc_final: 0.7156 (mtm180) REVERT: D 57 LYS cc_start: 0.8470 (mmtm) cc_final: 0.8147 (ttpt) REVERT: D 98 THR cc_start: 0.8324 (OUTLIER) cc_final: 0.7533 (t) REVERT: D 100 SER cc_start: 0.9130 (t) cc_final: 0.8664 (p) REVERT: D 125 ASP cc_start: 0.6309 (OUTLIER) cc_final: 0.6014 (t70) REVERT: D 131 ASP cc_start: 0.8285 (p0) cc_final: 0.7863 (p0) REVERT: D 140 ASP cc_start: 0.8006 (m-30) cc_final: 0.7744 (m-30) REVERT: E 7 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7201 (mt-10) REVERT: E 91 ASN cc_start: 0.8221 (OUTLIER) cc_final: 0.7940 (m-40) REVERT: F 38 ASP cc_start: 0.6469 (t0) cc_final: 0.5942 (p0) REVERT: F 47 ASP cc_start: 0.8388 (m-30) cc_final: 0.8015 (t0) REVERT: F 85 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7406 (mm-30) REVERT: F 89 ASN cc_start: 0.9065 (p0) cc_final: 0.8791 (p0) REVERT: F 110 LYS cc_start: 0.9113 (mttm) cc_final: 0.8700 (mtpt) REVERT: G 36 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8857 (pp) REVERT: G 50 LYS cc_start: 0.8976 (tptp) cc_final: 0.8700 (tptm) REVERT: G 80 ASN cc_start: 0.9002 (t0) cc_final: 0.8626 (t0) REVERT: G 159 MET cc_start: 0.8453 (tpt) cc_final: 0.7838 (tpt) REVERT: G 165 ILE cc_start: 0.8535 (mt) cc_final: 0.8164 (mp) REVERT: G 176 MET cc_start: 0.8502 (tmm) cc_final: 0.7962 (tmm) REVERT: G 194 GLN cc_start: 0.7962 (pt0) cc_final: 0.7749 (mt0) REVERT: G 201 GLU cc_start: 0.8397 (tp30) cc_final: 0.8131 (tp30) REVERT: G 227 ASP cc_start: 0.7708 (t70) cc_final: 0.7292 (t0) REVERT: H 8 GLU cc_start: 0.7783 (tt0) cc_final: 0.7439 (pt0) REVERT: H 9 ARG cc_start: 0.6552 (tpp80) cc_final: 0.5673 (ptm-80) REVERT: H 58 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8915 (mp) REVERT: H 79 TYR cc_start: 0.8582 (t80) cc_final: 0.8184 (t80) REVERT: H 227 ASP cc_start: 0.8223 (t0) cc_final: 0.7545 (t0) REVERT: H 233 GLU cc_start: 0.8386 (tm-30) cc_final: 0.8169 (tm-30) REVERT: H 262 PHE cc_start: 0.6913 (OUTLIER) cc_final: 0.5523 (m-80) REVERT: I 35 LYS cc_start: 0.8396 (mmpt) cc_final: 0.8020 (mptt) REVERT: I 57 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.7361 (tm-30) REVERT: I 239 ARG cc_start: 0.7929 (mtm-85) cc_final: 0.7656 (mtm-85) REVERT: J 17 LYS cc_start: 0.7131 (ptpp) cc_final: 0.6931 (pttp) REVERT: J 62 LYS cc_start: 0.8937 (pttp) cc_final: 0.8604 (tppt) REVERT: J 83 MET cc_start: 0.8674 (tpp) cc_final: 0.8060 (tpp) REVERT: J 175 GLN cc_start: 0.6278 (OUTLIER) cc_final: 0.5613 (pm20) REVERT: J 232 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7585 (mp) REVERT: J 243 PHE cc_start: 0.8619 (t80) cc_final: 0.8250 (t80) REVERT: J 262 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.8680 (tpt-90) REVERT: K 8 GLU cc_start: 0.7689 (mm-30) cc_final: 0.7284 (tm-30) REVERT: K 13 GLU cc_start: 0.6945 (pm20) cc_final: 0.6477 (pm20) REVERT: K 34 ARG cc_start: 0.6844 (OUTLIER) cc_final: 0.6644 (mmt180) REVERT: K 52 GLU cc_start: 0.8439 (pt0) cc_final: 0.7891 (tt0) REVERT: K 90 LYS cc_start: 0.8718 (ttpp) cc_final: 0.7886 (mmpt) REVERT: L 15 GLN cc_start: 0.7188 (pt0) cc_final: 0.6853 (pp30) REVERT: L 37 ARG cc_start: 0.8382 (tmm160) cc_final: 0.7879 (tmm-80) REVERT: L 53 ARG cc_start: 0.8054 (ttp80) cc_final: 0.7721 (ptm-80) REVERT: L 70 ARG cc_start: 0.7956 (ttt-90) cc_final: 0.7666 (ttp-170) outliers start: 168 outliers final: 120 residues processed: 569 average time/residue: 0.1269 time to fit residues: 107.3556 Evaluate side-chains 548 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 415 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 111 TYR Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 40 TYR Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 67 LYS Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 133 GLN Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain E residue 43 TYR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 88 GLN Chi-restraints excluded: chain E residue 91 ASN Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 126 ASN Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain G residue 218 THR Chi-restraints excluded: chain G residue 229 GLU Chi-restraints excluded: chain G residue 232 SER Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain H residue 30 PHE Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain H residue 201 GLU Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 253 LEU Chi-restraints excluded: chain H residue 258 THR Chi-restraints excluded: chain H residue 262 PHE Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 56 SER Chi-restraints excluded: chain I residue 57 GLN Chi-restraints excluded: chain I residue 62 LYS Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 121 ILE Chi-restraints excluded: chain I residue 127 MET Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 215 ILE Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 228 THR Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 104 GLU Chi-restraints excluded: chain J residue 149 MET Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain J residue 165 ILE Chi-restraints excluded: chain J residue 175 GLN Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 215 ILE Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 232 LEU Chi-restraints excluded: chain J residue 236 ASP Chi-restraints excluded: chain J residue 262 ARG Chi-restraints excluded: chain K residue 34 ARG Chi-restraints excluded: chain K residue 37 ARG Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 66 ILE Chi-restraints excluded: chain K residue 83 ASP Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 52 GLU Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain L residue 83 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 165 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 128 optimal weight: 8.9990 chunk 89 optimal weight: 0.9980 chunk 204 optimal weight: 0.9980 chunk 82 optimal weight: 6.9990 chunk 182 optimal weight: 10.0000 chunk 99 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 chunk 124 optimal weight: 0.0870 chunk 93 optimal weight: 4.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 88 GLN C 35 ASN E 133 GLN ** G 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.134307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.102621 restraints weight = 32625.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.106277 restraints weight = 15514.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.108700 restraints weight = 10001.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.110149 restraints weight = 7686.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.110860 restraints weight = 6639.202| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16171 Z= 0.134 Angle : 0.682 11.173 21890 Z= 0.342 Chirality : 0.044 0.241 2689 Planarity : 0.004 0.065 2753 Dihedral : 9.446 59.292 2520 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 8.61 % Allowed : 34.07 % Favored : 57.32 % 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: -2.16 (0.18), residues: 2100 helix: -0.01 (0.18), residues: 897 sheet: -2.03 (0.30), residues: 275 loop : -2.72 (0.18), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 67 TYR 0.016 0.001 TYR E 111 PHE 0.056 0.002 PHE C 13 TRP 0.009 0.001 TRP I 66 HIS 0.002 0.000 HIS I 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (16171) covalent geometry : angle 0.68219 / 0.34 (21890) hydrogen bonds : bond 0.03261 / 2.22 ( 722) hydrogen bonds : angle 5.06116 / 3.53 ( 2100) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 464 time to evaluate : 0.493 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 52 VAL cc_start: 0.9218 (t) cc_final: 0.8906 (p) REVERT: A 106 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8708 (tt) REVERT: A 124 LYS cc_start: 0.6759 (ttpp) cc_final: 0.6461 (mtpp) REVERT: A 133 GLN cc_start: 0.8635 (tp-100) cc_final: 0.8429 (tp-100) REVERT: A 141 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.9123 (pp) REVERT: B 7 GLU cc_start: 0.6566 (tt0) cc_final: 0.6331 (tm-30) REVERT: B 47 ASP cc_start: 0.8497 (t0) cc_final: 0.8197 (t0) REVERT: B 48 ASN cc_start: 0.8976 (t0) cc_final: 0.8620 (t0) REVERT: B 85 GLU cc_start: 0.7757 (tp30) cc_final: 0.7429 (tp30) REVERT: B 86 ILE cc_start: 0.8699 (mp) cc_final: 0.8322 (mp) REVERT: B 139 GLU cc_start: 0.8341 (mm-30) cc_final: 0.7776 (tp30) REVERT: C 133 GLN cc_start: 0.7938 (OUTLIER) cc_final: 0.7604 (mp10) REVERT: C 140 ASP cc_start: 0.8616 (m-30) cc_final: 0.8080 (t0) REVERT: D 27 ARG cc_start: 0.8362 (mtt180) cc_final: 0.7104 (mtm180) REVERT: D 98 THR cc_start: 0.8409 (OUTLIER) cc_final: 0.7809 (t) REVERT: D 100 SER cc_start: 0.9005 (t) cc_final: 0.8650 (p) REVERT: D 131 ASP cc_start: 0.8085 (p0) cc_final: 0.7729 (p0) REVERT: D 140 ASP cc_start: 0.7929 (m-30) cc_final: 0.7692 (m-30) REVERT: E 7 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7175 (mt-10) REVERT: F 67 LYS cc_start: 0.8558 (ptmt) cc_final: 0.8238 (tttt) REVERT: G 36 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8815 (pp) REVERT: G 80 ASN cc_start: 0.8908 (t0) cc_final: 0.8596 (t0) REVERT: G 131 GLU cc_start: 0.7801 (mp0) cc_final: 0.7140 (mp0) REVERT: G 148 VAL cc_start: 0.8652 (OUTLIER) cc_final: 0.8358 (p) REVERT: G 159 MET cc_start: 0.8374 (tpt) cc_final: 0.7772 (tpt) REVERT: G 165 ILE cc_start: 0.8445 (mt) cc_final: 0.8013 (mp) REVERT: G 176 MET cc_start: 0.8451 (tmm) cc_final: 0.8122 (tmm) REVERT: G 227 ASP cc_start: 0.7685 (t70) cc_final: 0.7311 (t0) REVERT: H 9 ARG cc_start: 0.6557 (tpp80) cc_final: 0.5699 (ptm-80) REVERT: H 58 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8825 (mp) REVERT: H 227 ASP cc_start: 0.8211 (t0) cc_final: 0.7561 (t0) REVERT: H 262 PHE cc_start: 0.6942 (OUTLIER) cc_final: 0.5534 (m-80) REVERT: I 35 LYS cc_start: 0.8399 (mmpt) cc_final: 0.8031 (mptt) REVERT: I 40 MET cc_start: 0.7522 (mtp) cc_final: 0.7131 (mtp) REVERT: I 57 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.7207 (tm-30) REVERT: J 62 LYS cc_start: 0.8993 (pttp) cc_final: 0.8541 (tppt) REVERT: J 83 MET cc_start: 0.8641 (tpp) cc_final: 0.7967 (tpp) REVERT: J 175 GLN cc_start: 0.6081 (OUTLIER) cc_final: 0.5397 (pm20) REVERT: J 232 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7517 (mp) REVERT: J 243 PHE cc_start: 0.8570 (t80) cc_final: 0.8228 (t80) REVERT: K 8 GLU cc_start: 0.7619 (mm-30) cc_final: 0.7268 (tm-30) REVERT: K 29 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7915 (tmm-80) REVERT: K 52 GLU cc_start: 0.8435 (pt0) cc_final: 0.7917 (tt0) REVERT: K 90 LYS cc_start: 0.8662 (ttpp) cc_final: 0.7864 (mmpt) REVERT: L 15 GLN cc_start: 0.6954 (pt0) cc_final: 0.6750 (pp30) REVERT: L 37 ARG cc_start: 0.8313 (tmm160) cc_final: 0.7806 (tmm-80) REVERT: L 53 ARG cc_start: 0.8133 (ttp80) cc_final: 0.7824 (ptm-80) REVERT: L 67 ARG cc_start: 0.7675 (ptp90) cc_final: 0.7405 (ptp90) REVERT: L 70 ARG cc_start: 0.7955 (ttt-90) cc_final: 0.7663 (ttp-170) outliers start: 144 outliers final: 92 residues processed: 567 average time/residue: 0.1224 time to fit residues: 102.4284 Evaluate side-chains 530 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 426 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 111 TYR Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 40 TYR Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 67 LYS Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 133 GLN Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain E residue 43 TYR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 88 GLN Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain G residue 218 THR Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain H residue 30 PHE Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 262 PHE Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 56 SER Chi-restraints excluded: chain I residue 57 GLN Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 121 ILE Chi-restraints excluded: chain I residue 127 MET Chi-restraints excluded: chain I residue 149 MET Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 215 ILE Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 228 THR Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain J residue 165 ILE Chi-restraints excluded: chain J residue 175 GLN Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 210 SER Chi-restraints excluded: chain J residue 215 ILE Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 232 LEU Chi-restraints excluded: chain K residue 29 ARG Chi-restraints excluded: chain K residue 37 ARG Chi-restraints excluded: chain K residue 66 ILE Chi-restraints excluded: chain K residue 83 ASP Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 52 GLU Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain L residue 94 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 188 optimal weight: 9.9990 chunk 136 optimal weight: 0.5980 chunk 70 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 chunk 106 optimal weight: 0.5980 chunk 95 optimal weight: 0.7980 chunk 171 optimal weight: 0.8980 chunk 42 optimal weight: 6.9990 chunk 141 optimal weight: 20.0000 chunk 133 optimal weight: 0.5980 chunk 21 optimal weight: 9.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 88 GLN E 88 GLN E 91 ASN E 133 GLN ** G 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 242 GLN ** J 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 191 ASN ** L 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.134995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.103771 restraints weight = 32244.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.107450 restraints weight = 15191.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.109896 restraints weight = 9744.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.111314 restraints weight = 7447.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.112011 restraints weight = 6440.540| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.3911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 16171 Z= 0.132 Angle : 0.698 11.670 21890 Z= 0.348 Chirality : 0.045 0.247 2689 Planarity : 0.004 0.062 2753 Dihedral : 9.220 58.505 2511 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 8.55 % Allowed : 34.25 % Favored : 57.20 % 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: -2.02 (0.18), residues: 2100 helix: 0.16 (0.18), residues: 887 sheet: -1.90 (0.30), residues: 280 loop : -2.69 (0.18), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 67 TYR 0.018 0.001 TYR G 79 PHE 0.054 0.002 PHE C 13 TRP 0.010 0.001 TRP J 66 HIS 0.002 0.001 HIS I 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (16171) covalent geometry : angle 0.69767 / 0.35 (21890) hydrogen bonds : bond 0.03264 / 2.20 ( 722) hydrogen bonds : angle 5.02024 / 3.49 ( 2100) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 450 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 VAL cc_start: 0.9205 (t) cc_final: 0.8859 (p) REVERT: A 86 ILE cc_start: 0.9291 (mm) cc_final: 0.9034 (mm) REVERT: A 106 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8700 (tt) REVERT: A 124 LYS cc_start: 0.6798 (ttpp) cc_final: 0.6544 (mtpp) REVERT: A 133 GLN cc_start: 0.8643 (tp-100) cc_final: 0.8405 (tp-100) REVERT: B 7 GLU cc_start: 0.6751 (tt0) cc_final: 0.6458 (tm-30) REVERT: B 38 ASP cc_start: 0.7452 (t70) cc_final: 0.7158 (p0) REVERT: B 47 ASP cc_start: 0.8475 (t0) cc_final: 0.8203 (t0) REVERT: B 48 ASN cc_start: 0.8834 (t0) cc_final: 0.8567 (t0) REVERT: B 60 LEU cc_start: 0.8962 (tp) cc_final: 0.8515 (tp) REVERT: B 85 GLU cc_start: 0.7634 (tp30) cc_final: 0.7076 (tp30) REVERT: B 139 GLU cc_start: 0.8296 (mm-30) cc_final: 0.7746 (tp30) REVERT: C 133 GLN cc_start: 0.7945 (OUTLIER) cc_final: 0.7586 (mp10) REVERT: C 140 ASP cc_start: 0.8589 (m-30) cc_final: 0.8019 (t70) REVERT: D 27 ARG cc_start: 0.8283 (mtt180) cc_final: 0.7091 (mtm180) REVERT: D 98 THR cc_start: 0.8371 (OUTLIER) cc_final: 0.7787 (t) REVERT: D 100 SER cc_start: 0.8924 (t) cc_final: 0.8609 (p) REVERT: D 131 ASP cc_start: 0.8041 (p0) cc_final: 0.7683 (p0) REVERT: D 140 ASP cc_start: 0.7914 (m-30) cc_final: 0.7685 (m-30) REVERT: E 13 PHE cc_start: 0.6629 (m-10) cc_final: 0.6412 (m-10) REVERT: F 39 THR cc_start: 0.7556 (t) cc_final: 0.7308 (t) REVERT: F 41 LYS cc_start: 0.8859 (ttmt) cc_final: 0.8431 (tmmt) REVERT: F 47 ASP cc_start: 0.8328 (m-30) cc_final: 0.8032 (t0) REVERT: F 93 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8271 (mp) REVERT: G 19 ASP cc_start: 0.8475 (t0) cc_final: 0.8187 (t0) REVERT: G 36 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8856 (pp) REVERT: G 43 THR cc_start: 0.8777 (m) cc_final: 0.8269 (p) REVERT: G 50 LYS cc_start: 0.8956 (tptp) cc_final: 0.8738 (tptm) REVERT: G 80 ASN cc_start: 0.8866 (t0) cc_final: 0.8568 (t0) REVERT: G 148 VAL cc_start: 0.8579 (OUTLIER) cc_final: 0.8329 (p) REVERT: G 159 MET cc_start: 0.8303 (tpt) cc_final: 0.8024 (tpt) REVERT: G 165 ILE cc_start: 0.8448 (mt) cc_final: 0.8034 (mp) REVERT: G 176 MET cc_start: 0.8414 (tmm) cc_final: 0.8089 (tmm) REVERT: G 227 ASP cc_start: 0.7613 (t70) cc_final: 0.7291 (t0) REVERT: H 8 GLU cc_start: 0.7746 (tt0) cc_final: 0.7396 (pt0) REVERT: H 9 ARG cc_start: 0.6563 (tpp80) cc_final: 0.5598 (ptm-80) REVERT: H 147 ILE cc_start: 0.8954 (OUTLIER) cc_final: 0.8676 (tp) REVERT: H 198 GLN cc_start: 0.7377 (mm-40) cc_final: 0.6981 (tp-100) REVERT: H 227 ASP cc_start: 0.8164 (t0) cc_final: 0.7543 (t0) REVERT: H 262 PHE cc_start: 0.6932 (OUTLIER) cc_final: 0.5372 (m-80) REVERT: I 35 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.8035 (mptt) REVERT: I 40 MET cc_start: 0.7448 (mtp) cc_final: 0.7098 (mtp) REVERT: I 57 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.7176 (tm-30) REVERT: I 144 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8134 (mt-10) REVERT: J 62 LYS cc_start: 0.9010 (pttp) cc_final: 0.8547 (tppt) REVERT: J 83 MET cc_start: 0.8650 (tpp) cc_final: 0.8045 (tpp) REVERT: J 175 GLN cc_start: 0.5990 (OUTLIER) cc_final: 0.5341 (pm20) REVERT: J 222 ARG cc_start: 0.7643 (OUTLIER) cc_final: 0.7367 (ttp-110) REVERT: J 232 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7465 (mp) REVERT: J 243 PHE cc_start: 0.8575 (t80) cc_final: 0.8175 (t80) REVERT: K 7 ARG cc_start: 0.7698 (ppt170) cc_final: 0.7414 (ppt170) REVERT: K 8 GLU cc_start: 0.7602 (mm-30) cc_final: 0.7251 (tm-30) REVERT: K 29 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7903 (ttt180) REVERT: K 52 GLU cc_start: 0.8416 (pt0) cc_final: 0.7905 (tt0) REVERT: K 90 LYS cc_start: 0.8682 (ttpp) cc_final: 0.7874 (mmpt) REVERT: L 15 GLN cc_start: 0.7051 (pt0) cc_final: 0.6739 (pp30) REVERT: L 37 ARG cc_start: 0.8325 (tmm160) cc_final: 0.7838 (tmm-80) REVERT: L 53 ARG cc_start: 0.8081 (ttp80) cc_final: 0.7804 (ptm-80) REVERT: L 67 ARG cc_start: 0.7705 (ptp90) cc_final: 0.7430 (ptp90) REVERT: L 70 ARG cc_start: 0.7930 (ttt-90) cc_final: 0.7636 (ttp-170) outliers start: 143 outliers final: 102 residues processed: 551 average time/residue: 0.1339 time to fit residues: 108.0706 Evaluate side-chains 543 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 427 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 88 GLN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 111 TYR Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 67 LYS Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 133 GLN Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 112 ILE Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain E residue 43 TYR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 88 GLN Chi-restraints excluded: chain E residue 91 ASN Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 126 ASN Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain G residue 229 GLU Chi-restraints excluded: chain G residue 232 SER Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain H residue 30 PHE Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 147 ILE Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 258 THR Chi-restraints excluded: chain H residue 262 PHE Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain I residue 35 LYS Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 56 SER Chi-restraints excluded: chain I residue 57 GLN Chi-restraints excluded: chain I residue 121 ILE Chi-restraints excluded: chain I residue 127 MET Chi-restraints excluded: chain I residue 143 ASP Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 215 ILE Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 228 THR Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain J residue 165 ILE Chi-restraints excluded: chain J residue 175 GLN Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 203 HIS Chi-restraints excluded: chain J residue 210 SER Chi-restraints excluded: chain J residue 222 ARG Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 232 LEU Chi-restraints excluded: chain K residue 29 ARG Chi-restraints excluded: chain K residue 37 ARG Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 66 ILE Chi-restraints excluded: chain K residue 83 ASP Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 52 GLU Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain L residue 83 ASP Chi-restraints excluded: chain L residue 94 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 171 optimal weight: 0.6980 chunk 64 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 chunk 129 optimal weight: 8.9990 chunk 108 optimal weight: 0.3980 chunk 45 optimal weight: 5.9990 chunk 148 optimal weight: 10.0000 chunk 81 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 chunk 80 optimal weight: 2.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 133 GLN ** G 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 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 = 0.3894 r_free = 0.3894 target = 0.132493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.100829 restraints weight = 32951.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.104370 restraints weight = 15778.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.106677 restraints weight = 10224.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.108082 restraints weight = 7917.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.108698 restraints weight = 6823.421| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 16171 Z= 0.202 Angle : 0.729 11.797 21890 Z= 0.367 Chirality : 0.046 0.273 2689 Planarity : 0.004 0.047 2753 Dihedral : 9.269 59.322 2507 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Rotamer: Outliers : 8.49 % Allowed : 35.03 % Favored : 56.49 % 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: -2.06 (0.18), residues: 2100 helix: 0.09 (0.18), residues: 902 sheet: -1.92 (0.30), residues: 278 loop : -2.73 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 239 TYR 0.023 0.002 TYR B 40 PHE 0.051 0.002 PHE C 13 TRP 0.011 0.001 TRP G 219 HIS 0.004 0.001 HIS I 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.20 (16171) covalent geometry : angle 0.72868 / 0.37 (21890) hydrogen bonds : bond 0.03435 / 2.33 ( 722) hydrogen bonds : angle 5.12870 / 3.56 ( 2100) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 431 time to evaluate : 0.651 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 52 VAL cc_start: 0.9210 (t) cc_final: 0.8893 (p) REVERT: A 84 MET cc_start: 0.8712 (pmm) cc_final: 0.8408 (pmm) REVERT: A 106 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8738 (tt) REVERT: A 124 LYS cc_start: 0.6807 (ttpp) cc_final: 0.6455 (mtpp) REVERT: B 7 GLU cc_start: 0.6850 (tt0) cc_final: 0.6449 (tm-30) REVERT: B 47 ASP cc_start: 0.8551 (t0) cc_final: 0.8256 (t0) REVERT: B 60 LEU cc_start: 0.9016 (tp) cc_final: 0.8590 (tp) REVERT: B 67 LYS cc_start: 0.8801 (tttt) cc_final: 0.8421 (ttmt) REVERT: B 85 GLU cc_start: 0.7745 (tp30) cc_final: 0.7205 (tp30) REVERT: B 139 GLU cc_start: 0.8461 (mm-30) cc_final: 0.7877 (tp30) REVERT: C 55 ARG cc_start: 0.7721 (ttt90) cc_final: 0.7091 (ttt90) REVERT: C 133 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7793 (mp10) REVERT: D 100 SER cc_start: 0.8937 (t) cc_final: 0.8627 (p) REVERT: D 131 ASP cc_start: 0.8149 (p0) cc_final: 0.7740 (p0) REVERT: D 140 ASP cc_start: 0.7991 (m-30) cc_final: 0.7706 (m-30) REVERT: D 144 LYS cc_start: 0.8516 (ptmm) cc_final: 0.8223 (ptmm) REVERT: E 7 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7218 (mt-10) REVERT: E 13 PHE cc_start: 0.6650 (m-10) cc_final: 0.6423 (m-10) REVERT: G 19 ASP cc_start: 0.8461 (t0) cc_final: 0.8184 (t0) REVERT: G 36 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8976 (pp) REVERT: G 50 LYS cc_start: 0.8991 (tptp) cc_final: 0.8774 (tptm) REVERT: G 80 ASN cc_start: 0.8885 (t0) cc_final: 0.8582 (t0) REVERT: G 89 GLN cc_start: 0.8641 (mp10) cc_final: 0.8435 (mp10) REVERT: G 148 VAL cc_start: 0.8713 (OUTLIER) cc_final: 0.8439 (p) REVERT: G 165 ILE cc_start: 0.8471 (mt) cc_final: 0.8083 (mp) REVERT: G 176 MET cc_start: 0.8467 (tmm) cc_final: 0.7934 (tmm) REVERT: G 227 ASP cc_start: 0.7723 (t70) cc_final: 0.7322 (t0) REVERT: H 9 ARG cc_start: 0.6569 (tpp80) cc_final: 0.5682 (ptm-80) REVERT: H 198 GLN cc_start: 0.7523 (mm-40) cc_final: 0.7109 (tp-100) REVERT: H 227 ASP cc_start: 0.8149 (t0) cc_final: 0.7552 (t0) REVERT: H 262 PHE cc_start: 0.6952 (OUTLIER) cc_final: 0.5427 (m-80) REVERT: I 35 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.7921 (mptt) REVERT: I 40 MET cc_start: 0.7636 (mtp) cc_final: 0.7278 (mtp) REVERT: I 57 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.7266 (tm-30) REVERT: I 144 GLU cc_start: 0.8719 (mt-10) cc_final: 0.8293 (mt-10) REVERT: J 62 LYS cc_start: 0.8910 (pttp) cc_final: 0.8492 (tppt) REVERT: J 83 MET cc_start: 0.8632 (tpp) cc_final: 0.7990 (tpp) REVERT: J 172 PHE cc_start: 0.8973 (OUTLIER) cc_final: 0.8615 (p90) REVERT: J 175 GLN cc_start: 0.6220 (OUTLIER) cc_final: 0.5550 (pm20) REVERT: J 222 ARG cc_start: 0.7733 (OUTLIER) cc_final: 0.7388 (ttp-110) REVERT: J 232 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7563 (mp) REVERT: K 8 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7510 (tm-30) REVERT: K 29 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7845 (tmm-80) REVERT: K 52 GLU cc_start: 0.8441 (pt0) cc_final: 0.8005 (tt0) REVERT: K 90 LYS cc_start: 0.8715 (ttpp) cc_final: 0.7915 (mmtt) REVERT: L 15 GLN cc_start: 0.7128 (pt0) cc_final: 0.6779 (mp10) REVERT: L 37 ARG cc_start: 0.8340 (tmm160) cc_final: 0.7841 (tmm-80) REVERT: L 53 ARG cc_start: 0.8057 (ttp80) cc_final: 0.7785 (ptm-80) REVERT: L 67 ARG cc_start: 0.7733 (ptp90) cc_final: 0.7453 (ptp90) REVERT: L 70 ARG cc_start: 0.7953 (ttt-90) cc_final: 0.7709 (ttp-170) outliers start: 142 outliers final: 111 residues processed: 535 average time/residue: 0.1370 time to fit residues: 107.6331 Evaluate side-chains 544 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 421 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 111 TYR Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 67 LYS Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 133 GLN Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 112 ILE Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain E residue 43 TYR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 88 GLN Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 126 ASN Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain G residue 218 THR Chi-restraints excluded: chain G residue 229 GLU Chi-restraints excluded: chain G residue 232 SER Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain H residue 30 PHE Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 258 THR Chi-restraints excluded: chain H residue 262 PHE Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain I residue 35 LYS Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 56 SER Chi-restraints excluded: chain I residue 57 GLN Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 121 ILE Chi-restraints excluded: chain I residue 127 MET Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 215 ILE Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 228 THR Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain J residue 165 ILE Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 175 GLN Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 203 HIS Chi-restraints excluded: chain J residue 210 SER Chi-restraints excluded: chain J residue 215 ILE Chi-restraints excluded: chain J residue 222 ARG Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 232 LEU Chi-restraints excluded: chain J residue 262 ARG Chi-restraints excluded: chain K residue 29 ARG Chi-restraints excluded: chain K residue 37 ARG Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 66 ILE Chi-restraints excluded: chain K residue 83 ASP Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 52 GLU Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain L residue 83 ASP Chi-restraints excluded: chain L residue 94 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 126 optimal weight: 0.8980 chunk 153 optimal weight: 5.9990 chunk 145 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 131 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 192 optimal weight: 0.9990 chunk 163 optimal weight: 0.1980 chunk 105 optimal weight: 0.7980 chunk 202 optimal weight: 0.9990 chunk 172 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 133 GLN ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 GLN E 91 ASN E 133 GLN ** G 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.135173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.103650 restraints weight = 32463.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.107362 restraints weight = 15318.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.109735 restraints weight = 9810.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.111203 restraints weight = 7572.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.111912 restraints weight = 6513.153| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 16171 Z= 0.136 Angle : 0.724 12.591 21890 Z= 0.360 Chirality : 0.045 0.276 2689 Planarity : 0.004 0.050 2753 Dihedral : 9.006 58.264 2507 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 7.65 % Allowed : 36.28 % Favored : 56.07 % 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: -1.90 (0.18), residues: 2100 helix: 0.23 (0.18), residues: 894 sheet: -1.75 (0.30), residues: 279 loop : -2.65 (0.18), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 239 TYR 0.030 0.001 TYR H 79 PHE 0.056 0.002 PHE C 13 TRP 0.014 0.001 TRP J 66 HIS 0.003 0.001 HIS I 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (16171) covalent geometry : angle 0.72360 / 0.36 (21890) hydrogen bonds : bond 0.03277 / 2.22 ( 722) hydrogen bonds : angle 5.01982 / 3.49 ( 2100) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 443 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8615 (pmm) cc_final: 0.8346 (pmm) REVERT: A 124 LYS cc_start: 0.6752 (ttpp) cc_final: 0.6462 (mtpp) REVERT: B 7 GLU cc_start: 0.6839 (tt0) cc_final: 0.6466 (tm-30) REVERT: B 47 ASP cc_start: 0.8491 (t0) cc_final: 0.8202 (t0) REVERT: B 60 LEU cc_start: 0.9000 (tp) cc_final: 0.8609 (tp) REVERT: B 67 LYS cc_start: 0.8775 (tttt) cc_final: 0.8388 (ttmt) REVERT: B 85 GLU cc_start: 0.7687 (tp30) cc_final: 0.7328 (tp30) REVERT: B 139 GLU cc_start: 0.8315 (mm-30) cc_final: 0.7759 (tp30) REVERT: C 133 GLN cc_start: 0.8008 (OUTLIER) cc_final: 0.7686 (mp10) REVERT: D 43 TYR cc_start: 0.8670 (m-80) cc_final: 0.8440 (m-80) REVERT: D 98 THR cc_start: 0.8319 (OUTLIER) cc_final: 0.7715 (t) REVERT: D 100 SER cc_start: 0.8931 (t) cc_final: 0.8608 (p) REVERT: D 131 ASP cc_start: 0.8056 (p0) cc_final: 0.7683 (p0) REVERT: D 140 ASP cc_start: 0.7870 (m-30) cc_final: 0.7591 (m-30) REVERT: E 7 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7177 (mt-10) REVERT: E 13 PHE cc_start: 0.6557 (m-10) cc_final: 0.6335 (m-10) REVERT: F 39 THR cc_start: 0.7577 (t) cc_final: 0.6972 (t) REVERT: F 85 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7383 (mm-30) REVERT: G 19 ASP cc_start: 0.8453 (t0) cc_final: 0.8181 (t0) REVERT: G 36 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8863 (pp) REVERT: G 50 LYS cc_start: 0.8960 (tptp) cc_final: 0.8738 (tptm) REVERT: G 165 ILE cc_start: 0.8411 (mt) cc_final: 0.8012 (mp) REVERT: G 176 MET cc_start: 0.8429 (tmm) cc_final: 0.8114 (tmm) REVERT: G 227 ASP cc_start: 0.7582 (t70) cc_final: 0.7253 (t0) REVERT: H 8 GLU cc_start: 0.7728 (tt0) cc_final: 0.7396 (pt0) REVERT: H 9 ARG cc_start: 0.6605 (tpp80) cc_final: 0.5610 (ptm-80) REVERT: H 132 GLN cc_start: 0.8428 (tt0) cc_final: 0.8048 (tt0) REVERT: H 198 GLN cc_start: 0.7377 (mm-40) cc_final: 0.6985 (tp-100) REVERT: H 227 ASP cc_start: 0.8199 (t0) cc_final: 0.7571 (t0) REVERT: H 262 PHE cc_start: 0.6904 (OUTLIER) cc_final: 0.5495 (m-80) REVERT: I 35 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.8023 (mptt) REVERT: I 57 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.7155 (tm-30) REVERT: I 83 MET cc_start: 0.8260 (tpp) cc_final: 0.8003 (tpp) REVERT: I 144 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8502 (mt-10) REVERT: I 149 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.8296 (ttm) REVERT: J 62 LYS cc_start: 0.8910 (pttp) cc_final: 0.8467 (tppt) REVERT: J 83 MET cc_start: 0.8620 (tpp) cc_final: 0.8113 (tpp) REVERT: J 175 GLN cc_start: 0.6014 (OUTLIER) cc_final: 0.5334 (pm20) REVERT: J 222 ARG cc_start: 0.7694 (OUTLIER) cc_final: 0.7425 (ttp-110) REVERT: J 232 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7472 (mp) REVERT: J 243 PHE cc_start: 0.8555 (t80) cc_final: 0.8335 (t80) REVERT: K 8 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7503 (tm-30) REVERT: K 29 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7826 (tmt170) REVERT: K 34 ARG cc_start: 0.6232 (OUTLIER) cc_final: 0.5930 (mmm160) REVERT: K 52 GLU cc_start: 0.8441 (pt0) cc_final: 0.7997 (tt0) REVERT: K 65 PHE cc_start: 0.8987 (m-10) cc_final: 0.8709 (m-10) REVERT: K 90 LYS cc_start: 0.8708 (ttpp) cc_final: 0.7879 (mmtt) REVERT: L 15 GLN cc_start: 0.7005 (pt0) cc_final: 0.6640 (mp10) REVERT: L 37 ARG cc_start: 0.8346 (tmm160) cc_final: 0.7850 (tmm-80) REVERT: L 53 ARG cc_start: 0.8075 (ttp80) cc_final: 0.7837 (ptm-80) REVERT: L 70 ARG cc_start: 0.7952 (ttt-90) cc_final: 0.7618 (ttp-170) outliers start: 128 outliers final: 95 residues processed: 539 average time/residue: 0.1318 time to fit residues: 103.9447 Evaluate side-chains 533 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 426 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 111 TYR Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 67 LYS Chi-restraints excluded: chain C residue 91 ASN Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 133 GLN Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 112 ILE Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain E residue 43 TYR Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 88 GLN Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 126 ASN Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain H residue 30 PHE Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 258 THR Chi-restraints excluded: chain H residue 262 PHE Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain I residue 35 LYS Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 56 SER Chi-restraints excluded: chain I residue 57 GLN Chi-restraints excluded: chain I residue 121 ILE Chi-restraints excluded: chain I residue 149 MET Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 215 ILE Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 228 THR Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain J residue 175 GLN Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 203 HIS Chi-restraints excluded: chain J residue 210 SER Chi-restraints excluded: chain J residue 222 ARG Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 232 LEU Chi-restraints excluded: chain J residue 262 ARG Chi-restraints excluded: chain K residue 29 ARG Chi-restraints excluded: chain K residue 34 ARG Chi-restraints excluded: chain K residue 37 ARG Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 66 ILE Chi-restraints excluded: chain K residue 83 ASP Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 52 GLU Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 81 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 168 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 125 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 chunk 101 optimal weight: 0.6980 chunk 187 optimal weight: 0.0270 chunk 26 optimal weight: 6.9990 chunk 161 optimal weight: 5.9990 chunk 183 optimal weight: 5.9990 chunk 198 optimal weight: 1.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 ASN C 35 ASN ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 133 GLN ** G 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 198 GLN H 93 GLN ** H 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 191 ASN ** L 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.135855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.104520 restraints weight = 32321.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.108235 restraints weight = 15207.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.110618 restraints weight = 9729.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.112131 restraints weight = 7481.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.112894 restraints weight = 6410.345| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.4300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 16171 Z= 0.137 Angle : 0.730 12.684 21890 Z= 0.364 Chirality : 0.045 0.287 2689 Planarity : 0.004 0.047 2753 Dihedral : 8.817 57.034 2504 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 6.46 % Allowed : 37.60 % Favored : 55.95 % 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: -1.79 (0.18), residues: 2100 helix: 0.34 (0.18), residues: 885 sheet: -1.74 (0.30), residues: 283 loop : -2.58 (0.18), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 55 TYR 0.025 0.001 TYR H 79 PHE 0.055 0.002 PHE C 13 TRP 0.017 0.001 TRP J 66 HIS 0.003 0.000 HIS I 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (16171) covalent geometry : angle 0.73010 / 0.36 (21890) hydrogen bonds : bond 0.03239 / 2.20 ( 722) hydrogen bonds : angle 4.95449 / 3.44 ( 2100) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 442 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8630 (pmm) cc_final: 0.8386 (pmm) REVERT: A 86 ILE cc_start: 0.9272 (mm) cc_final: 0.8951 (mm) REVERT: A 124 LYS cc_start: 0.6771 (ttpp) cc_final: 0.6477 (mtpp) REVERT: B 7 GLU cc_start: 0.6929 (tt0) cc_final: 0.6524 (tm-30) REVERT: B 47 ASP cc_start: 0.8486 (t0) cc_final: 0.8181 (t0) REVERT: B 60 LEU cc_start: 0.8973 (tp) cc_final: 0.8564 (tp) REVERT: B 67 LYS cc_start: 0.8744 (tttt) cc_final: 0.8406 (tptt) REVERT: B 85 GLU cc_start: 0.7639 (tp30) cc_final: 0.7297 (tp30) REVERT: B 139 GLU cc_start: 0.8311 (mm-30) cc_final: 0.7777 (tp30) REVERT: C 133 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.7628 (mp10) REVERT: D 27 ARG cc_start: 0.8292 (mtt180) cc_final: 0.7064 (mtp180) REVERT: D 100 SER cc_start: 0.9033 (t) cc_final: 0.8763 (p) REVERT: D 131 ASP cc_start: 0.7969 (p0) cc_final: 0.7589 (p0) REVERT: D 140 ASP cc_start: 0.7797 (m-30) cc_final: 0.7521 (m-30) REVERT: E 7 GLU cc_start: 0.7645 (mt-10) cc_final: 0.7134 (mt-10) REVERT: E 13 PHE cc_start: 0.6536 (m-10) cc_final: 0.6321 (m-10) REVERT: F 39 THR cc_start: 0.7577 (t) cc_final: 0.7018 (t) REVERT: F 43 TYR cc_start: 0.8891 (m-10) cc_final: 0.8319 (m-80) REVERT: F 85 GLU cc_start: 0.7609 (mm-30) cc_final: 0.7350 (mm-30) REVERT: G 19 ASP cc_start: 0.8442 (t0) cc_final: 0.8223 (t0) REVERT: G 36 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8802 (pp) REVERT: G 50 LYS cc_start: 0.8958 (tptp) cc_final: 0.8745 (tptm) REVERT: G 165 ILE cc_start: 0.8419 (mt) cc_final: 0.8015 (mp) REVERT: G 176 MET cc_start: 0.8426 (tmm) cc_final: 0.8110 (tmm) REVERT: G 193 MET cc_start: 0.7796 (ttp) cc_final: 0.7410 (ttm) REVERT: G 201 GLU cc_start: 0.8181 (tp30) cc_final: 0.7728 (tp30) REVERT: G 227 ASP cc_start: 0.7505 (t70) cc_final: 0.7218 (t0) REVERT: H 8 GLU cc_start: 0.7675 (tt0) cc_final: 0.7402 (pt0) REVERT: H 9 ARG cc_start: 0.6631 (tpp80) cc_final: 0.5621 (ptm-80) REVERT: H 132 GLN cc_start: 0.8468 (tt0) cc_final: 0.8133 (tt0) REVERT: H 198 GLN cc_start: 0.7398 (mm-40) cc_final: 0.6954 (tp-100) REVERT: H 227 ASP cc_start: 0.8174 (t0) cc_final: 0.7544 (t0) REVERT: H 262 PHE cc_start: 0.6885 (OUTLIER) cc_final: 0.5475 (m-80) REVERT: I 35 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.7882 (mptt) REVERT: I 40 MET cc_start: 0.7579 (mmm) cc_final: 0.7195 (mmm) REVERT: I 57 GLN cc_start: 0.8612 (OUTLIER) cc_final: 0.7121 (tm-30) REVERT: I 83 MET cc_start: 0.8230 (tpp) cc_final: 0.7972 (tpp) REVERT: I 144 GLU cc_start: 0.8740 (mt-10) cc_final: 0.8540 (mt-10) REVERT: J 62 LYS cc_start: 0.8940 (pttp) cc_final: 0.8461 (tppt) REVERT: J 83 MET cc_start: 0.8609 (tpp) cc_final: 0.8013 (tpp) REVERT: J 175 GLN cc_start: 0.5941 (OUTLIER) cc_final: 0.5671 (pm20) REVERT: J 222 ARG cc_start: 0.7678 (OUTLIER) cc_final: 0.7426 (ttp-110) REVERT: J 232 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7468 (mp) REVERT: K 7 ARG cc_start: 0.7641 (ppt170) cc_final: 0.7417 (ppt170) REVERT: K 8 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7463 (tm-30) REVERT: K 29 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7778 (tmt170) REVERT: K 52 GLU cc_start: 0.8368 (pt0) cc_final: 0.7871 (tt0) REVERT: K 65 PHE cc_start: 0.9008 (m-10) cc_final: 0.8749 (m-10) REVERT: K 90 LYS cc_start: 0.8739 (ttpp) cc_final: 0.7925 (mmtt) REVERT: L 15 GLN cc_start: 0.7002 (pt0) cc_final: 0.6669 (mp10) REVERT: L 37 ARG cc_start: 0.8359 (tmm160) cc_final: 0.7882 (tmm-80) REVERT: L 53 ARG cc_start: 0.8073 (ttp80) cc_final: 0.7819 (ptm-80) REVERT: L 70 ARG cc_start: 0.8014 (ttt-90) cc_final: 0.7681 (ttp-170) outliers start: 108 outliers final: 93 residues processed: 522 average time/residue: 0.1299 time to fit residues: 99.8188 Evaluate side-chains 533 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 431 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 111 TYR Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 35 ASN Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 67 LYS Chi-restraints excluded: chain C residue 91 ASN Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 133 GLN Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 112 ILE Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain E residue 43 TYR Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 87 ASN Chi-restraints excluded: chain E residue 88 GLN Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 126 ASN Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain H residue 194 GLN Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 258 THR Chi-restraints excluded: chain H residue 262 PHE Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain I residue 35 LYS Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 56 SER Chi-restraints excluded: chain I residue 57 GLN Chi-restraints excluded: chain I residue 121 ILE Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 215 ILE Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 228 THR Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain J residue 175 GLN Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 203 HIS Chi-restraints excluded: chain J residue 210 SER Chi-restraints excluded: chain J residue 222 ARG Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 232 LEU Chi-restraints excluded: chain J residue 262 ARG Chi-restraints excluded: chain K residue 29 ARG Chi-restraints excluded: chain K residue 37 ARG Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 66 ILE Chi-restraints excluded: chain K residue 83 ASP Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 81 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 41 optimal weight: 8.9990 chunk 76 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 183 optimal weight: 3.9990 chunk 162 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 84 optimal weight: 6.9990 chunk 111 optimal weight: 6.9990 chunk 173 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 72 optimal weight: 7.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 ASN ** B 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 35 ASN ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 133 GLN ** G 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.135730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.104229 restraints weight = 32264.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.107907 restraints weight = 15290.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.110297 restraints weight = 9821.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.111768 restraints weight = 7575.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.112630 restraints weight = 6514.427| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.130 16171 Z= 0.199 Angle : 0.900 59.199 21890 Z= 0.490 Chirality : 0.045 0.276 2689 Planarity : 0.004 0.059 2753 Dihedral : 8.846 57.062 2504 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.48 % Favored : 91.48 % Rotamer: Outliers : 6.58 % Allowed : 37.72 % Favored : 55.71 % Cbeta Deviations : 0.05 % 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: -1.79 (0.18), residues: 2100 helix: 0.31 (0.18), residues: 891 sheet: -1.73 (0.30), residues: 279 loop : -2.56 (0.18), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.088 0.001 ARG F 75 TYR 0.040 0.001 TYR F 43 PHE 0.051 0.002 PHE C 13 TRP 0.014 0.001 TRP J 66 HIS 0.002 0.000 HIS I 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.20 (16171) covalent geometry : angle 0.89969 / 0.49 (21890) hydrogen bonds : bond 0.03242 / 2.20 ( 722) hydrogen bonds : angle 4.95735 / 3.44 ( 2100) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3540.41 seconds wall clock time: 61 minutes 43.96 seconds (3703.96 seconds total)