Starting phenix.real_space_refine on Sat Jul 26 05:24:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ryc_24733/07_2025/7ryc_24733.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ryc_24733/07_2025/7ryc_24733.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ryc_24733/07_2025/7ryc_24733.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ryc_24733/07_2025/7ryc_24733.map" model { file = "/net/cci-nas-00/data/ceres_data/7ryc_24733/07_2025/7ryc_24733.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ryc_24733/07_2025/7ryc_24733.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.008 sd= 0.128 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 67 atoms to isotropic. 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 Mg 1 5.21 5 S 55 5.16 5 C 5321 2.51 5 N 1409 2.21 5 O 1491 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 8277 Number of models: 1 Model: "" Number of chains: 7 Chain: "L" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 68 Classifications: {'peptide': 9} Link IDs: {'PTRANS': 1, 'TRANS': 7} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 2097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2097 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 11, 'TRANS': 273} Chain breaks: 2 Unresolved non-hydrogen bonds: 204 Unresolved non-hydrogen angles: 251 Unresolved non-hydrogen dihedrals: 169 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 133 Chain: "D" Number of atoms: 1973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 1973 Classifications: {'peptide': 263} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 8, 'TRANS': 254} Chain breaks: 4 Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 189 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 9, 'ASN:plan1': 2, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 103 Chain: "C" Number of atoms: 2442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2442 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 200 Unresolved non-hydrogen dihedrals: 126 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 8, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 108 Chain: "E" Number of atoms: 1695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1695 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 2 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.24, per 1000 atoms: 1.00 Number of scatterers: 8277 At special positions: 0 Unit cell: (89.4705, 124.407, 130.371, 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 55 16.00 Mg 1 11.99 O 1491 8.00 N 1409 7.00 C 5321 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS L 1 " - pdb=" SG CYS L 6 " distance=2.03 Simple disulfide: pdb=" SG CYS O 112 " - pdb=" SG CYS O 187 " distance=2.04 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.87 Conformation dependent library (CDL) restraints added in 2.6 seconds 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2114 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 14 sheets defined 35.8% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'O' and resid 35 through 67 removed outlier: 3.740A pdb=" N GLU O 42 " --> pdb=" O LEU O 38 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL O 43 " --> pdb=" O ALA O 39 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA O 44 " --> pdb=" O ARG O 40 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N CYS O 47 " --> pdb=" O VAL O 43 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASN O 57 " --> pdb=" O ALA O 53 " (cutoff:3.500A) Processing helix chain 'O' and resid 74 through 92 Processing helix chain 'O' and resid 93 through 102 removed outlier: 3.699A pdb=" N ASP O 100 " --> pdb=" O GLN O 96 " (cutoff:3.500A) Processing helix chain 'O' and resid 108 through 143 removed outlier: 4.071A pdb=" N CYS O 112 " --> pdb=" O PRO O 108 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N TYR O 117 " --> pdb=" O ARG O 113 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET O 123 " --> pdb=" O GLN O 119 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LEU O 130 " --> pdb=" O SER O 126 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU O 131 " --> pdb=" O THR O 127 " (cutoff:3.500A) Processing helix chain 'O' and resid 149 through 168 removed outlier: 4.632A pdb=" N VAL O 157 " --> pdb=" O ASP O 153 " (cutoff:3.500A) Processing helix chain 'O' and resid 170 through 174 Processing helix chain 'O' and resid 195 through 209 removed outlier: 3.576A pdb=" N ALA O 199 " --> pdb=" O TRP O 195 " (cutoff:3.500A) Processing helix chain 'O' and resid 209 through 235 removed outlier: 4.025A pdb=" N TYR O 220 " --> pdb=" O LEU O 216 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER O 224 " --> pdb=" O TYR O 220 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE O 225 " --> pdb=" O GLY O 221 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TRP O 228 " --> pdb=" O SER O 224 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU O 231 " --> pdb=" O ILE O 227 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG O 232 " --> pdb=" O TRP O 228 " (cutoff:3.500A) Processing helix chain 'O' and resid 273 through 299 removed outlier: 4.224A pdb=" N ILE O 279 " --> pdb=" O LYS O 275 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE O 280 " --> pdb=" O MET O 276 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE O 284 " --> pdb=" O ILE O 280 " (cutoff:3.500A) Proline residue: O 290 - end of helix Processing helix chain 'O' and resid 308 through 316 removed outlier: 3.695A pdb=" N ILE O 312 " --> pdb=" O ALA O 308 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU O 316 " --> pdb=" O ILE O 312 " (cutoff:3.500A) Processing helix chain 'O' and resid 320 through 332 removed outlier: 3.760A pdb=" N CYS O 324 " --> pdb=" O LEU O 320 " (cutoff:3.500A) Proline residue: O 326 - end of helix Processing helix chain 'O' and resid 334 through 345 removed outlier: 4.622A pdb=" N HIS O 338 " --> pdb=" O GLY O 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 24 removed outlier: 3.959A pdb=" N VAL D 16 " --> pdb=" O ALA D 12 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 34 Processing helix chain 'D' and resid 34 through 44 removed outlier: 3.556A pdb=" N ALA D 39 " --> pdb=" O ALA D 35 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR D 40 " --> pdb=" O ASP D 36 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N CYS D 41 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU D 42 " --> pdb=" O MET D 38 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA D 43 " --> pdb=" O ALA D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 48 removed outlier: 3.794A pdb=" N ASP D 48 " --> pdb=" O ALA D 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 45 through 48' Processing helix chain 'D' and resid 1006 through 1031 removed outlier: 3.849A pdb=" N ALA D1011 " --> pdb=" O ALA D1007 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N MET D1018 " --> pdb=" O GLU D1014 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ILE D1019 " --> pdb=" O ARG D1015 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASP D1020 " --> pdb=" O SER D1016 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LYS D1021 " --> pdb=" O LYS D1017 " (cutoff:3.500A) Processing helix chain 'D' and resid 1045 through 1049 removed outlier: 3.988A pdb=" N ILE D1049 " --> pdb=" O LYS D1046 " (cutoff:3.500A) Processing helix chain 'D' and resid 1095 through 1099 removed outlier: 3.706A pdb=" N GLN D1098 " --> pdb=" O LYS D1095 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N CYS D1099 " --> pdb=" O TRP D1096 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1095 through 1099' Processing helix chain 'D' and resid 1117 through 1130 Processing helix chain 'D' and resid 1145 through 1156 removed outlier: 3.957A pdb=" N LEU D1149 " --> pdb=" O LYS D1145 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA D1150 " --> pdb=" O GLN D1146 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU D1151 " --> pdb=" O ASP D1147 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLY D1156 " --> pdb=" O LYS D1152 " (cutoff:3.500A) Processing helix chain 'D' and resid 1159 through 1163 Processing helix chain 'D' and resid 1164 through 1169 removed outlier: 3.685A pdb=" N ARG D1169 " --> pdb=" O GLU D1166 " (cutoff:3.500A) Processing helix chain 'D' and resid 1184 through 1204 removed outlier: 3.858A pdb=" N PHE D1197 " --> pdb=" O ILE D1193 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE D1200 " --> pdb=" O GLU D1196 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N SER D1204 " --> pdb=" O ILE D1200 " (cutoff:3.500A) Processing helix chain 'D' and resid 1223 through 1240 removed outlier: 4.118A pdb=" N ILE D1227 " --> pdb=" O ASN D1223 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE D1228 " --> pdb=" O ALA D1224 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASP D1233 " --> pdb=" O ASN D1229 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN D1237 " --> pdb=" O ASP D1233 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU D1240 " --> pdb=" O LEU D1236 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 24 removed outlier: 4.277A pdb=" N GLU C 10 " --> pdb=" O GLN C 6 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA C 11 " --> pdb=" O LEU C 7 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU C 12 " --> pdb=" O ARG C 8 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA C 24 " --> pdb=" O ASP C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 removed outlier: 3.742A pdb=" N ILE C 33 " --> pdb=" O THR C 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.516A pdb=" N PHE E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'O' and resid 175 through 181 removed outlier: 6.768A pdb=" N VAL O 184 " --> pdb=" O VAL O 180 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 1070 through 1076 removed outlier: 7.190A pdb=" N ARG D1035 " --> pdb=" O ALA D1105 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N ILE D1107 " --> pdb=" O ARG D1035 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LEU D1037 " --> pdb=" O ILE D1107 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N VAL D1109 " --> pdb=" O LEU D1037 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE D1106 " --> pdb=" O ILE D1140 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N PHE D1142 " --> pdb=" O ILE D1106 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N PHE D1108 " --> pdb=" O PHE D1142 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ASN D1144 " --> pdb=" O PHE D1108 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL D1110 " --> pdb=" O ASN D1144 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 47 through 51 removed outlier: 6.681A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 58 through 63 removed outlier: 7.139A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.844A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 146 through 153 removed outlier: 6.850A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.781A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE C 199 " --> pdb=" O TRP C 211 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA C 203 " --> pdb=" O SER C 207 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N SER C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.725A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N CYS C 250 " --> pdb=" O TYR C 264 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.902A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N CYS C 294 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N VAL C 307 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N VAL C 296 " --> pdb=" O ALA C 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.151A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU E 117 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ALA E 92 " --> pdb=" O LEU E 117 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL E 37 " --> pdb=" O TYR E 95 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER E 99 " --> pdb=" O GLY E 33 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 146 through 148 removed outlier: 5.914A pdb=" N VAL E 147 " --> pdb=" O GLU E 246 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 194 through 195 removed outlier: 5.858A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ILE E 189 " --> pdb=" O TRP E 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 205 through 207 removed outlier: 3.954A pdb=" N THR E 213 " --> pdb=" O SER E 206 " (cutoff:3.500A) 337 hydrogen bonds defined for protein. 957 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.07 Time building geometry restraints manager: 5.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1849 1.33 - 1.45: 1916 1.45 - 1.58: 4613 1.58 - 1.70: 0 1.70 - 1.82: 76 Bond restraints: 8454 Sorted by residual: bond pdb=" C TRP O 203 " pdb=" N ILE O 204 " ideal model delta sigma weight residual 1.335 1.257 0.077 1.26e-02 6.30e+03 3.77e+01 bond pdb=" C LEU O 139 " pdb=" N ALA O 140 " ideal model delta sigma weight residual 1.334 1.423 -0.088 1.49e-02 4.50e+03 3.52e+01 bond pdb=" C VAL O 157 " pdb=" N LEU O 158 " ideal model delta sigma weight residual 1.335 1.256 0.079 1.36e-02 5.41e+03 3.35e+01 bond pdb=" C ARG D1117 " pdb=" N LEU D1118 " ideal model delta sigma weight residual 1.335 1.259 0.076 1.36e-02 5.41e+03 3.13e+01 bond pdb=" C LYS O 270 " pdb=" N ILE O 271 " ideal model delta sigma weight residual 1.332 1.257 0.075 1.36e-02 5.41e+03 3.01e+01 ... (remaining 8449 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 10863 1.71 - 3.42: 551 3.42 - 5.13: 98 5.13 - 6.84: 15 6.84 - 8.55: 4 Bond angle restraints: 11531 Sorted by residual: angle pdb=" N ILE O 101 " pdb=" CA ILE O 101 " pdb=" C ILE O 101 " ideal model delta sigma weight residual 110.42 105.48 4.94 9.60e-01 1.09e+00 2.65e+01 angle pdb=" O VAL O 157 " pdb=" C VAL O 157 " pdb=" N LEU O 158 " ideal model delta sigma weight residual 121.87 117.12 4.75 9.70e-01 1.06e+00 2.40e+01 angle pdb=" N CYS O 138 " pdb=" CA CYS O 138 " pdb=" C CYS O 138 " ideal model delta sigma weight residual 111.28 116.47 -5.19 1.09e+00 8.42e-01 2.26e+01 angle pdb=" O TRP O 203 " pdb=" C TRP O 203 " pdb=" N ILE O 204 " ideal model delta sigma weight residual 122.07 117.40 4.67 1.03e+00 9.43e-01 2.05e+01 angle pdb=" N ARG O 73 " pdb=" CA ARG O 73 " pdb=" C ARG O 73 " ideal model delta sigma weight residual 112.97 108.37 4.60 1.06e+00 8.90e-01 1.88e+01 ... (remaining 11526 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.92: 4411 15.92 - 31.83: 388 31.83 - 47.75: 103 47.75 - 63.66: 23 63.66 - 79.58: 6 Dihedral angle restraints: 4931 sinusoidal: 1668 harmonic: 3263 Sorted by residual: dihedral pdb=" CB CYS O 112 " pdb=" SG CYS O 112 " pdb=" SG CYS O 187 " pdb=" CB CYS O 187 " ideal model delta sinusoidal sigma weight residual 93.00 161.54 -68.54 1 1.00e+01 1.00e-02 6.09e+01 dihedral pdb=" CA ARG D1032 " pdb=" C ARG D1032 " pdb=" N THR D1033 " pdb=" CA THR D1033 " ideal model delta harmonic sigma weight residual -180.00 -154.44 -25.56 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA ARG D1031 " pdb=" C ARG D1031 " pdb=" N ARG D1032 " pdb=" CA ARG D1032 " ideal model delta harmonic sigma weight residual -180.00 -155.50 -24.50 0 5.00e+00 4.00e-02 2.40e+01 ... (remaining 4928 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1014 0.052 - 0.104: 248 0.104 - 0.156: 73 0.156 - 0.208: 16 0.208 - 0.260: 6 Chirality restraints: 1357 Sorted by residual: chirality pdb=" CA ILE O 101 " pdb=" N ILE O 101 " pdb=" C ILE O 101 " pdb=" CB ILE O 101 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA LEU C 210 " pdb=" N LEU C 210 " pdb=" C LEU C 210 " pdb=" CB LEU C 210 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA ILE E 216 " pdb=" N ILE E 216 " pdb=" C ILE E 216 " pdb=" CB ILE E 216 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 1354 not shown) Planarity restraints: 1454 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS O 270 " -0.013 2.00e-02 2.50e+03 2.45e-02 6.00e+00 pdb=" C LYS O 270 " 0.042 2.00e-02 2.50e+03 pdb=" O LYS O 270 " -0.015 2.00e-02 2.50e+03 pdb=" N ILE O 271 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU O 139 " -0.010 2.00e-02 2.50e+03 2.01e-02 4.02e+00 pdb=" C LEU O 139 " 0.035 2.00e-02 2.50e+03 pdb=" O LEU O 139 " -0.013 2.00e-02 2.50e+03 pdb=" N ALA O 140 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL O 294 " -0.009 2.00e-02 2.50e+03 1.77e-02 3.14e+00 pdb=" C VAL O 294 " 0.031 2.00e-02 2.50e+03 pdb=" O VAL O 294 " -0.011 2.00e-02 2.50e+03 pdb=" N GLN O 295 " -0.010 2.00e-02 2.50e+03 ... (remaining 1451 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 659 2.74 - 3.28: 7570 3.28 - 3.82: 11897 3.82 - 4.36: 14432 4.36 - 4.90: 25748 Nonbonded interactions: 60306 Sorted by model distance: nonbonded pdb=" O ASP D1233 " pdb=" OD1 ASP D1233 " model vdw 2.198 3.040 nonbonded pdb=" O ASP C 333 " pdb=" OG SER C 334 " model vdw 2.278 3.040 nonbonded pdb=" OD1 ASP O 100 " pdb="MG MG O 401 " model vdw 2.281 2.170 nonbonded pdb=" O SER E 52 " pdb=" NH1 ARG E 72 " model vdw 2.296 3.120 nonbonded pdb=" O GLN D1119 " pdb=" ND2 ASN D1123 " model vdw 2.312 3.120 ... (remaining 60301 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 416.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 36.580 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:32.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 486.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 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 : 0.006 0.112 8458 Z= 0.436 Angle : 0.865 8.554 11537 Z= 0.576 Chirality : 0.053 0.260 1357 Planarity : 0.004 0.044 1454 Dihedral : 13.762 79.578 2808 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.38 % Allowed : 13.50 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.22), residues: 1099 helix: -1.76 (0.25), residues: 346 sheet: -1.30 (0.31), residues: 247 loop : -2.44 (0.22), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 36 HIS 0.006 0.001 HIS E 35 PHE 0.018 0.002 PHE C 235 TYR 0.018 0.002 TYR L 2 ARG 0.002 0.000 ARG O 104 Details of bonding type rmsd hydrogen bonds : bond 0.20038 ( 337) hydrogen bonds : angle 6.82837 ( 957) SS BOND : bond 0.00719 ( 3) SS BOND : angle 2.13985 ( 6) covalent geometry : bond 0.00629 ( 8454) covalent geometry : angle 0.86374 (11531) Misc. bond : bond 0.11249 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 140 time to evaluate : 0.845 Fit side-chains revert: symmetry clash REVERT: D 29 LYS cc_start: 0.5538 (mttt) cc_final: 0.5282 (tmmt) REVERT: D 1018 MET cc_start: 0.6654 (mtp) cc_final: 0.6424 (mtt) REVERT: C 154 ASP cc_start: 0.7708 (m-30) cc_final: 0.7445 (m-30) REVERT: C 188 MET cc_start: 0.8859 (mmp) cc_final: 0.8581 (mmm) REVERT: C 258 ASP cc_start: 0.7636 (t0) cc_final: 0.7231 (t0) outliers start: 3 outliers final: 2 residues processed: 143 average time/residue: 1.2930 time to fit residues: 195.9411 Evaluate side-chains 96 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 94 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 6 CYS Chi-restraints excluded: chain O residue 296 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.2980 chunk 84 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 chunk 28 optimal weight: 0.7980 chunk 56 optimal weight: 9.9990 chunk 44 optimal weight: 0.0040 chunk 87 optimal weight: 4.9990 chunk 33 optimal weight: 0.4980 chunk 52 optimal weight: 4.9990 chunk 64 optimal weight: 0.4980 chunk 100 optimal weight: 5.9990 overall best weight: 0.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 171 GLN D 59 ASN C 176 GLN E 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.133094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.109952 restraints weight = 14133.016| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 3.04 r_work: 0.3332 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8458 Z= 0.121 Angle : 0.578 9.035 11537 Z= 0.303 Chirality : 0.042 0.153 1357 Planarity : 0.004 0.033 1454 Dihedral : 4.763 51.546 1198 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.38 % Allowed : 18.38 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.24), residues: 1099 helix: -0.29 (0.28), residues: 341 sheet: -0.68 (0.30), residues: 278 loop : -2.21 (0.24), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP O 300 HIS 0.005 0.001 HIS E 35 PHE 0.009 0.001 PHE C 151 TYR 0.014 0.001 TYR E 190 ARG 0.003 0.000 ARG C 49 Details of bonding type rmsd hydrogen bonds : bond 0.05609 ( 337) hydrogen bonds : angle 4.57724 ( 957) SS BOND : bond 0.00380 ( 3) SS BOND : angle 1.30541 ( 6) covalent geometry : bond 0.00241 ( 8454) covalent geometry : angle 0.57699 (11531) Misc. bond : bond 0.00002 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 0.904 Fit side-chains revert: symmetry clash REVERT: O 123 MET cc_start: 0.6671 (ttm) cc_final: 0.6376 (mtp) REVERT: D 29 LYS cc_start: 0.5249 (mttt) cc_final: 0.4908 (tmmt) REVERT: D 1018 MET cc_start: 0.6318 (mtp) cc_final: 0.6096 (mtt) REVERT: C 154 ASP cc_start: 0.7638 (m-30) cc_final: 0.7381 (m-30) REVERT: C 258 ASP cc_start: 0.7685 (t0) cc_final: 0.7122 (t0) REVERT: E 69 THR cc_start: 0.6185 (OUTLIER) cc_final: 0.5854 (m) outliers start: 11 outliers final: 3 residues processed: 113 average time/residue: 1.4219 time to fit residues: 170.3743 Evaluate side-chains 112 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 108 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 6 CYS Chi-restraints excluded: chain O residue 315 MET Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain E residue 69 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 54 optimal weight: 0.0020 chunk 14 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 295 GLN D 59 ASN C 183 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.129796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.106482 restraints weight = 14433.431| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 3.05 r_work: 0.3271 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8458 Z= 0.178 Angle : 0.629 9.279 11537 Z= 0.329 Chirality : 0.043 0.151 1357 Planarity : 0.004 0.045 1454 Dihedral : 4.700 47.822 1195 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.38 % Allowed : 17.62 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.24), residues: 1099 helix: -0.10 (0.27), residues: 350 sheet: -0.74 (0.30), residues: 290 loop : -1.95 (0.26), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 82 HIS 0.005 0.001 HIS E 35 PHE 0.016 0.002 PHE O 76 TYR 0.018 0.002 TYR L 2 ARG 0.006 0.000 ARG C 137 Details of bonding type rmsd hydrogen bonds : bond 0.06389 ( 337) hydrogen bonds : angle 4.61323 ( 957) SS BOND : bond 0.00953 ( 3) SS BOND : angle 1.72839 ( 6) covalent geometry : bond 0.00411 ( 8454) covalent geometry : angle 0.62793 (11531) Misc. bond : bond 0.00022 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 0.869 Fit side-chains revert: symmetry clash REVERT: D 29 LYS cc_start: 0.5296 (mttt) cc_final: 0.4899 (ttmt) REVERT: D 1229 ASN cc_start: 0.7609 (t0) cc_final: 0.7291 (t0) REVERT: D 1244 ASN cc_start: 0.8718 (t0) cc_final: 0.8453 (t0) REVERT: C 154 ASP cc_start: 0.7651 (m-30) cc_final: 0.7412 (m-30) REVERT: C 188 MET cc_start: 0.8879 (mmp) cc_final: 0.8647 (mmm) REVERT: C 226 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7170 (mp0) REVERT: C 258 ASP cc_start: 0.7720 (t0) cc_final: 0.7166 (t0) REVERT: E 69 THR cc_start: 0.6261 (OUTLIER) cc_final: 0.5936 (m) REVERT: E 158 SER cc_start: 0.7751 (t) cc_final: 0.7479 (m) outliers start: 27 outliers final: 11 residues processed: 128 average time/residue: 1.1520 time to fit residues: 157.6149 Evaluate side-chains 118 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 1 CYS Chi-restraints excluded: chain L residue 6 CYS Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 299 VAL Chi-restraints excluded: chain O residue 315 MET Chi-restraints excluded: chain D residue 1082 HIS Chi-restraints excluded: chain D residue 1201 SER Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 260 GLU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 192 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 89 optimal weight: 1.9990 chunk 17 optimal weight: 0.1980 chunk 75 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 37 optimal weight: 0.0050 chunk 81 optimal weight: 0.2980 chunk 56 optimal weight: 8.9990 chunk 106 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 74 optimal weight: 0.1980 chunk 43 optimal weight: 0.9990 overall best weight: 0.2594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 59 ASN D1080 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.133853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.110801 restraints weight = 14356.372| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 3.14 r_work: 0.3347 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8458 Z= 0.099 Angle : 0.512 7.787 11537 Z= 0.265 Chirality : 0.040 0.138 1357 Planarity : 0.003 0.033 1454 Dihedral : 4.238 45.881 1195 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.75 % Allowed : 19.75 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.25), residues: 1099 helix: 0.57 (0.28), residues: 348 sheet: -0.39 (0.30), residues: 291 loop : -1.75 (0.26), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 36 HIS 0.004 0.001 HIS E 35 PHE 0.009 0.001 PHE D1074 TYR 0.016 0.001 TYR L 2 ARG 0.006 0.000 ARG C 137 Details of bonding type rmsd hydrogen bonds : bond 0.04234 ( 337) hydrogen bonds : angle 4.06624 ( 957) SS BOND : bond 0.00579 ( 3) SS BOND : angle 1.26455 ( 6) covalent geometry : bond 0.00197 ( 8454) covalent geometry : angle 0.51118 (11531) Misc. bond : bond 0.00015 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 0.838 Fit side-chains revert: symmetry clash REVERT: D 29 LYS cc_start: 0.5212 (mttt) cc_final: 0.4868 (ttmt) REVERT: D 1018 MET cc_start: 0.6444 (mtp) cc_final: 0.6218 (mtt) REVERT: D 1024 ARG cc_start: 0.7225 (ttp-110) cc_final: 0.6999 (ttp80) REVERT: D 1229 ASN cc_start: 0.7541 (t0) cc_final: 0.7249 (t0) REVERT: C 154 ASP cc_start: 0.7595 (m-30) cc_final: 0.7382 (m-30) REVERT: C 226 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7137 (mp0) REVERT: C 258 ASP cc_start: 0.7629 (t0) cc_final: 0.7047 (t0) REVERT: E 69 THR cc_start: 0.5995 (OUTLIER) cc_final: 0.5736 (m) REVERT: E 158 SER cc_start: 0.7588 (t) cc_final: 0.7384 (m) outliers start: 22 outliers final: 5 residues processed: 136 average time/residue: 1.7799 time to fit residues: 256.9664 Evaluate side-chains 114 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 107 time to evaluate : 2.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 1 CYS Chi-restraints excluded: chain L residue 6 CYS Chi-restraints excluded: chain O residue 315 MET Chi-restraints excluded: chain D residue 1082 HIS Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain E residue 69 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1131 ASN C 75 GLN C 176 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.131401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.107973 restraints weight = 14217.380| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.99 r_work: 0.3304 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8458 Z= 0.138 Angle : 0.574 9.923 11537 Z= 0.297 Chirality : 0.042 0.138 1357 Planarity : 0.003 0.039 1454 Dihedral : 4.322 45.988 1195 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.12 % Allowed : 19.50 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.25), residues: 1099 helix: 0.56 (0.28), residues: 358 sheet: -0.31 (0.31), residues: 290 loop : -1.68 (0.26), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 82 HIS 0.005 0.001 HIS E 35 PHE 0.014 0.002 PHE O 76 TYR 0.014 0.001 TYR L 2 ARG 0.006 0.000 ARG C 137 Details of bonding type rmsd hydrogen bonds : bond 0.05258 ( 337) hydrogen bonds : angle 4.16000 ( 957) SS BOND : bond 0.00469 ( 3) SS BOND : angle 2.12207 ( 6) covalent geometry : bond 0.00313 ( 8454) covalent geometry : angle 0.57222 (11531) Misc. bond : bond 0.00007 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 116 time to evaluate : 1.272 Fit side-chains revert: symmetry clash REVERT: D 29 LYS cc_start: 0.5186 (mttt) cc_final: 0.4923 (ttpt) REVERT: D 1018 MET cc_start: 0.6625 (mtp) cc_final: 0.6193 (mtt) REVERT: D 1229 ASN cc_start: 0.7540 (t0) cc_final: 0.7246 (t0) REVERT: C 154 ASP cc_start: 0.7622 (m-30) cc_final: 0.7413 (m-30) REVERT: C 226 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7136 (mp0) REVERT: C 258 ASP cc_start: 0.7719 (t0) cc_final: 0.7219 (t0) REVERT: E 69 THR cc_start: 0.6224 (OUTLIER) cc_final: 0.5978 (m) outliers start: 33 outliers final: 13 residues processed: 135 average time/residue: 1.7071 time to fit residues: 246.9633 Evaluate side-chains 124 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 1 CYS Chi-restraints excluded: chain L residue 6 CYS Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 299 VAL Chi-restraints excluded: chain O residue 313 ILE Chi-restraints excluded: chain O residue 315 MET Chi-restraints excluded: chain D residue 1082 HIS Chi-restraints excluded: chain D residue 1201 SER Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 186 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 80 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 19 optimal weight: 0.0010 chunk 37 optimal weight: 1.9990 chunk 104 optimal weight: 0.0970 chunk 7 optimal weight: 0.5980 chunk 48 optimal weight: 6.9990 chunk 105 optimal weight: 0.2980 overall best weight: 0.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.133418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.110241 restraints weight = 14224.020| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 3.08 r_work: 0.3337 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8458 Z= 0.101 Angle : 0.522 8.238 11537 Z= 0.270 Chirality : 0.040 0.132 1357 Planarity : 0.003 0.035 1454 Dihedral : 4.130 44.437 1195 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.38 % Allowed : 22.12 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.25), residues: 1099 helix: 0.89 (0.28), residues: 354 sheet: -0.01 (0.32), residues: 279 loop : -1.55 (0.26), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 36 HIS 0.004 0.001 HIS E 35 PHE 0.009 0.001 PHE O 76 TYR 0.014 0.001 TYR L 2 ARG 0.007 0.000 ARG C 137 Details of bonding type rmsd hydrogen bonds : bond 0.04342 ( 337) hydrogen bonds : angle 3.97295 ( 957) SS BOND : bond 0.00716 ( 3) SS BOND : angle 1.59027 ( 6) covalent geometry : bond 0.00210 ( 8454) covalent geometry : angle 0.52046 (11531) Misc. bond : bond 0.00007 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 1.180 Fit side-chains revert: symmetry clash REVERT: D 29 LYS cc_start: 0.5143 (mttt) cc_final: 0.4919 (ttpt) REVERT: D 36 ASP cc_start: 0.7984 (t70) cc_final: 0.7602 (t0) REVERT: D 1018 MET cc_start: 0.6452 (mtp) cc_final: 0.6169 (mtt) REVERT: D 1024 ARG cc_start: 0.7114 (ttp-110) cc_final: 0.6837 (ttp80) REVERT: C 78 LYS cc_start: 0.9070 (mmtp) cc_final: 0.8832 (mmtt) REVERT: C 226 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7148 (mp0) REVERT: C 258 ASP cc_start: 0.7613 (t0) cc_final: 0.7152 (t0) REVERT: E 69 THR cc_start: 0.6115 (OUTLIER) cc_final: 0.5867 (m) outliers start: 19 outliers final: 8 residues processed: 120 average time/residue: 1.5287 time to fit residues: 194.8639 Evaluate side-chains 119 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 1 CYS Chi-restraints excluded: chain L residue 6 CYS Chi-restraints excluded: chain O residue 315 MET Chi-restraints excluded: chain D residue 1082 HIS Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain E residue 69 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 89 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 106 optimal weight: 0.5980 chunk 82 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 91 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 73 optimal weight: 4.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 59 ASN C 75 GLN C 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.131683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.108172 restraints weight = 14353.750| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 3.02 r_work: 0.3308 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8458 Z= 0.132 Angle : 0.568 10.103 11537 Z= 0.294 Chirality : 0.042 0.135 1357 Planarity : 0.003 0.040 1454 Dihedral : 4.244 43.175 1195 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.88 % Allowed : 22.12 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.25), residues: 1099 helix: 0.79 (0.28), residues: 359 sheet: -0.24 (0.31), residues: 299 loop : -1.43 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 332 HIS 0.004 0.001 HIS E 35 PHE 0.015 0.002 PHE E 68 TYR 0.014 0.001 TYR L 2 ARG 0.007 0.000 ARG C 137 Details of bonding type rmsd hydrogen bonds : bond 0.05084 ( 337) hydrogen bonds : angle 4.09217 ( 957) SS BOND : bond 0.00505 ( 3) SS BOND : angle 1.61075 ( 6) covalent geometry : bond 0.00297 ( 8454) covalent geometry : angle 0.56681 (11531) Misc. bond : bond 0.00002 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.914 Fit side-chains revert: symmetry clash REVERT: D 29 LYS cc_start: 0.5216 (mttt) cc_final: 0.4965 (ttpt) REVERT: D 36 ASP cc_start: 0.7973 (t70) cc_final: 0.7602 (t0) REVERT: D 1018 MET cc_start: 0.6550 (mtp) cc_final: 0.6139 (mtt) REVERT: D 1229 ASN cc_start: 0.7556 (t0) cc_final: 0.7281 (t0) REVERT: C 78 LYS cc_start: 0.9108 (mmtp) cc_final: 0.8833 (mmtt) REVERT: C 226 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7172 (mp0) REVERT: C 258 ASP cc_start: 0.7602 (t0) cc_final: 0.7255 (t0) REVERT: E 69 THR cc_start: 0.6290 (OUTLIER) cc_final: 0.6027 (m) REVERT: E 87 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.7850 (mtp180) outliers start: 23 outliers final: 11 residues processed: 123 average time/residue: 1.3561 time to fit residues: 178.2189 Evaluate side-chains 120 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 1 CYS Chi-restraints excluded: chain L residue 6 CYS Chi-restraints excluded: chain O residue 278 PHE Chi-restraints excluded: chain O residue 299 VAL Chi-restraints excluded: chain O residue 315 MET Chi-restraints excluded: chain D residue 1082 HIS Chi-restraints excluded: chain D residue 1118 LEU Chi-restraints excluded: chain D residue 1198 VAL Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 87 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 7 optimal weight: 0.5980 chunk 98 optimal weight: 0.6980 chunk 102 optimal weight: 0.8980 chunk 25 optimal weight: 0.0570 chunk 31 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 55 optimal weight: 10.0000 chunk 87 optimal weight: 8.9990 chunk 21 optimal weight: 0.3980 chunk 33 optimal weight: 1.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 59 ASN D1244 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.130110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.106891 restraints weight = 14422.635| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.98 r_work: 0.3341 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8458 Z= 0.107 Angle : 0.528 9.374 11537 Z= 0.273 Chirality : 0.041 0.132 1357 Planarity : 0.003 0.035 1454 Dihedral : 4.064 39.167 1195 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.25 % Allowed : 23.00 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.25), residues: 1099 helix: 1.10 (0.28), residues: 356 sheet: 0.02 (0.32), residues: 283 loop : -1.43 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 36 HIS 0.004 0.001 HIS E 35 PHE 0.013 0.001 PHE E 68 TYR 0.013 0.001 TYR L 2 ARG 0.006 0.000 ARG C 137 Details of bonding type rmsd hydrogen bonds : bond 0.04394 ( 337) hydrogen bonds : angle 3.93839 ( 957) SS BOND : bond 0.00404 ( 3) SS BOND : angle 1.16165 ( 6) covalent geometry : bond 0.00230 ( 8454) covalent geometry : angle 0.52705 (11531) Misc. bond : bond 0.00006 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.905 Fit side-chains REVERT: D 29 LYS cc_start: 0.5254 (mttt) cc_final: 0.5038 (ttpt) REVERT: D 36 ASP cc_start: 0.8099 (t70) cc_final: 0.7694 (t0) REVERT: D 1018 MET cc_start: 0.6555 (mtp) cc_final: 0.6231 (mtt) REVERT: D 1024 ARG cc_start: 0.7219 (ttp-110) cc_final: 0.6957 (ttp80) REVERT: D 1229 ASN cc_start: 0.7578 (t0) cc_final: 0.7296 (t0) REVERT: C 78 LYS cc_start: 0.9105 (mmtp) cc_final: 0.8855 (mmtt) REVERT: C 226 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7191 (mp0) REVERT: C 258 ASP cc_start: 0.7650 (t0) cc_final: 0.7273 (t0) REVERT: E 69 THR cc_start: 0.6197 (OUTLIER) cc_final: 0.5939 (m) REVERT: E 87 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.8191 (mtp180) REVERT: E 158 SER cc_start: 0.7588 (t) cc_final: 0.7261 (m) outliers start: 18 outliers final: 10 residues processed: 124 average time/residue: 1.5134 time to fit residues: 200.7360 Evaluate side-chains 123 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 ASN Chi-restraints excluded: chain L residue 6 CYS Chi-restraints excluded: chain O residue 299 VAL Chi-restraints excluded: chain O residue 315 MET Chi-restraints excluded: chain D residue 1082 HIS Chi-restraints excluded: chain D residue 1118 LEU Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 87 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 91 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 101 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 27 optimal weight: 0.0370 chunk 57 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 59 ASN D1244 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.131985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.108692 restraints weight = 14349.552| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 3.02 r_work: 0.3317 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8458 Z= 0.128 Angle : 0.561 9.071 11537 Z= 0.291 Chirality : 0.041 0.137 1357 Planarity : 0.003 0.039 1454 Dihedral : 4.111 36.675 1195 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.00 % Allowed : 23.25 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.25), residues: 1099 helix: 1.09 (0.28), residues: 357 sheet: 0.04 (0.32), residues: 282 loop : -1.42 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 332 HIS 0.004 0.001 HIS E 35 PHE 0.014 0.002 PHE E 68 TYR 0.016 0.001 TYR L 2 ARG 0.007 0.000 ARG C 137 Details of bonding type rmsd hydrogen bonds : bond 0.04909 ( 337) hydrogen bonds : angle 4.01514 ( 957) SS BOND : bond 0.00470 ( 3) SS BOND : angle 1.35615 ( 6) covalent geometry : bond 0.00287 ( 8454) covalent geometry : angle 0.55988 (11531) Misc. bond : bond 0.00009 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.993 Fit side-chains REVERT: D 29 LYS cc_start: 0.5247 (mttt) cc_final: 0.4905 (mptt) REVERT: D 36 ASP cc_start: 0.8029 (t70) cc_final: 0.7641 (t0) REVERT: D 1018 MET cc_start: 0.6586 (mtp) cc_final: 0.6197 (mtt) REVERT: D 1229 ASN cc_start: 0.7584 (t0) cc_final: 0.7295 (t0) REVERT: C 226 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7249 (mp0) REVERT: C 258 ASP cc_start: 0.7754 (t0) cc_final: 0.7461 (t0) REVERT: E 69 THR cc_start: 0.6218 (OUTLIER) cc_final: 0.5973 (m) REVERT: E 87 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.7882 (mtp180) REVERT: E 158 SER cc_start: 0.7696 (t) cc_final: 0.7363 (m) REVERT: E 192 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.8306 (ptm) outliers start: 16 outliers final: 9 residues processed: 119 average time/residue: 1.2887 time to fit residues: 162.8075 Evaluate side-chains 117 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 6 CYS Chi-restraints excluded: chain O residue 206 LEU Chi-restraints excluded: chain O residue 315 MET Chi-restraints excluded: chain D residue 1082 HIS Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 192 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 74 optimal weight: 0.0060 chunk 73 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 53 optimal weight: 0.0070 chunk 9 optimal weight: 0.6980 chunk 46 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 overall best weight: 0.4614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1244 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.130261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.107003 restraints weight = 14219.830| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.85 r_work: 0.3349 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8458 Z= 0.107 Angle : 0.529 8.944 11537 Z= 0.274 Chirality : 0.041 0.136 1357 Planarity : 0.003 0.036 1454 Dihedral : 3.996 35.639 1195 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.50 % Allowed : 23.62 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.25), residues: 1099 helix: 1.26 (0.28), residues: 357 sheet: 0.08 (0.32), residues: 283 loop : -1.33 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 332 HIS 0.004 0.001 HIS E 35 PHE 0.013 0.001 PHE E 68 TYR 0.021 0.001 TYR L 2 ARG 0.007 0.000 ARG C 137 Details of bonding type rmsd hydrogen bonds : bond 0.04358 ( 337) hydrogen bonds : angle 3.90119 ( 957) SS BOND : bond 0.00400 ( 3) SS BOND : angle 1.11072 ( 6) covalent geometry : bond 0.00229 ( 8454) covalent geometry : angle 0.52856 (11531) Misc. bond : bond 0.00006 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.897 Fit side-chains REVERT: D 29 LYS cc_start: 0.5263 (mttt) cc_final: 0.4929 (mptt) REVERT: D 36 ASP cc_start: 0.8069 (t70) cc_final: 0.7697 (t0) REVERT: D 1018 MET cc_start: 0.6554 (mtp) cc_final: 0.6348 (mtt) REVERT: D 1024 ARG cc_start: 0.7238 (ttp-110) cc_final: 0.6993 (ttp80) REVERT: D 1114 ASP cc_start: 0.6936 (t0) cc_final: 0.6188 (p0) REVERT: D 1229 ASN cc_start: 0.7582 (t0) cc_final: 0.7289 (t0) REVERT: C 226 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7270 (mp0) REVERT: C 258 ASP cc_start: 0.7660 (t0) cc_final: 0.7293 (t0) REVERT: E 69 THR cc_start: 0.6169 (OUTLIER) cc_final: 0.5928 (m) REVERT: E 87 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.7831 (mtp180) REVERT: E 158 SER cc_start: 0.7635 (t) cc_final: 0.7338 (m) outliers start: 12 outliers final: 7 residues processed: 117 average time/residue: 1.5312 time to fit residues: 190.6609 Evaluate side-chains 116 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 278 PHE Chi-restraints excluded: chain O residue 315 MET Chi-restraints excluded: chain D residue 1082 HIS Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 87 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 103 optimal weight: 1.9990 chunk 84 optimal weight: 0.4980 chunk 13 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 104 optimal weight: 0.0470 chunk 55 optimal weight: 8.9990 chunk 67 optimal weight: 0.1980 chunk 17 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 overall best weight: 0.7482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1244 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.131863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.108499 restraints weight = 14410.021| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 3.01 r_work: 0.3315 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8458 Z= 0.132 Angle : 0.566 8.764 11537 Z= 0.294 Chirality : 0.042 0.142 1357 Planarity : 0.003 0.039 1454 Dihedral : 3.960 20.502 1194 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.88 % Allowed : 23.38 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.25), residues: 1099 helix: 1.21 (0.28), residues: 357 sheet: 0.02 (0.32), residues: 286 loop : -1.30 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 332 HIS 0.004 0.001 HIS E 35 PHE 0.014 0.002 PHE E 68 TYR 0.021 0.001 TYR L 2 ARG 0.007 0.000 ARG C 137 Details of bonding type rmsd hydrogen bonds : bond 0.04976 ( 337) hydrogen bonds : angle 4.02128 ( 957) SS BOND : bond 0.00494 ( 3) SS BOND : angle 1.43621 ( 6) covalent geometry : bond 0.00298 ( 8454) covalent geometry : angle 0.56531 (11531) Misc. bond : bond 0.00004 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8687.70 seconds wall clock time: 157 minutes 34.29 seconds (9454.29 seconds total)