Starting phenix.real_space_refine on Tue Sep 24 15:41:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryc_24733/09_2024/7ryc_24733.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryc_24733/09_2024/7ryc_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryc_24733/09_2024/7ryc_24733.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryc_24733/09_2024/7ryc_24733.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryc_24733/09_2024/7ryc_24733.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryc_24733/09_2024/7ryc_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 5.61, per 1000 atoms: 0.68 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: 2.04 Conformation dependent library (CDL) restraints added in 1.2 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: 0.97 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: 2.34 Time building geometry restraints manager: 2.37 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: 5.430 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.040 Process input model: 22.290 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 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:11.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.800 ------------------------------------------------------------------------------- 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 0.088 8454 Z= 0.408 Angle : 0.864 8.554 11531 Z= 0.575 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 *********************** 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 fitting. rotamer outliers: 3 poor density : 140 time to evaluate : 0.898 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: 1.3025 time to fit residues: 197.1070 Evaluate side-chains 96 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 94 time to evaluate : 0.905 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 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 8454 Z= 0.158 Angle : 0.577 9.035 11531 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 *********************** 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 fitting. rotamer outliers: 11 poor density : 107 time to evaluate : 0.897 Fit side-chains revert: symmetry clash REVERT: D 29 LYS cc_start: 0.5559 (mttt) cc_final: 0.5223 (tmmt) REVERT: C 154 ASP cc_start: 0.7666 (m-30) cc_final: 0.7417 (m-30) REVERT: C 258 ASP cc_start: 0.7568 (t0) cc_final: 0.7099 (t0) outliers start: 11 outliers final: 3 residues processed: 113 average time/residue: 1.3156 time to fit residues: 157.5203 Evaluate side-chains 112 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 109 time to evaluate : 0.846 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 100 optimal weight: 5.9990 chunk 109 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 99 optimal weight: 0.0980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8454 Z= 0.222 Angle : 0.594 9.613 11531 Z= 0.309 Chirality : 0.042 0.151 1357 Planarity : 0.004 0.042 1454 Dihedral : 4.554 47.222 1195 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.00 % Allowed : 18.25 % Favored : 78.75 % 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: -1.48 (0.24), residues: 1099 helix: 0.03 (0.28), residues: 350 sheet: -0.73 (0.30), residues: 295 loop : -1.91 (0.26), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 82 HIS 0.004 0.001 HIS E 35 PHE 0.014 0.002 PHE O 76 TYR 0.018 0.002 TYR L 2 ARG 0.006 0.000 ARG C 137 *********************** 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 138 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 114 time to evaluate : 0.911 Fit side-chains revert: symmetry clash REVERT: D 29 LYS cc_start: 0.5632 (mttt) cc_final: 0.5215 (ttmt) REVERT: C 154 ASP cc_start: 0.7683 (m-30) cc_final: 0.7434 (m-30) REVERT: C 188 MET cc_start: 0.8848 (mmp) cc_final: 0.8628 (mmm) REVERT: C 226 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.6948 (mp0) REVERT: C 258 ASP cc_start: 0.7557 (t0) cc_final: 0.7100 (t0) REVERT: E 158 SER cc_start: 0.7614 (t) cc_final: 0.7361 (m) outliers start: 24 outliers final: 11 residues processed: 126 average time/residue: 1.1994 time to fit residues: 161.2027 Evaluate side-chains 116 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 104 time to evaluate : 0.930 ------------------------------------------------------------------------------- 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 192 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 67 optimal weight: 0.5980 chunk 101 optimal weight: 0.0050 chunk 107 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 89 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 59 ASN D1080 ASN C 176 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8454 Z= 0.164 Angle : 0.543 7.782 11531 Z= 0.284 Chirality : 0.041 0.141 1357 Planarity : 0.003 0.039 1454 Dihedral : 4.373 46.887 1195 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.88 % Allowed : 19.75 % Favored : 77.38 % 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: -1.07 (0.24), residues: 1099 helix: 0.44 (0.28), residues: 352 sheet: -0.46 (0.30), residues: 292 loop : -1.76 (0.26), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 36 HIS 0.005 0.001 HIS C 225 PHE 0.011 0.001 PHE O 76 TYR 0.018 0.001 TYR L 2 ARG 0.006 0.000 ARG C 137 *********************** 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 141 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 118 time to evaluate : 0.920 Fit side-chains revert: symmetry clash REVERT: D 22 GLU cc_start: 0.6214 (tt0) cc_final: 0.5994 (tt0) REVERT: D 29 LYS cc_start: 0.5521 (mttt) cc_final: 0.5084 (ttmt) REVERT: D 1024 ARG cc_start: 0.7308 (ttp-110) cc_final: 0.7072 (ttp80) REVERT: D 1229 ASN cc_start: 0.7617 (t0) cc_final: 0.7310 (t0) REVERT: C 154 ASP cc_start: 0.7636 (m-30) cc_final: 0.7430 (m-30) REVERT: C 226 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.6908 (mp0) REVERT: C 258 ASP cc_start: 0.7531 (t0) cc_final: 0.7065 (t0) REVERT: E 87 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7616 (mtp180) REVERT: E 158 SER cc_start: 0.7541 (t) cc_final: 0.7336 (m) outliers start: 23 outliers final: 8 residues processed: 129 average time/residue: 1.2765 time to fit residues: 174.8309 Evaluate side-chains 119 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 109 time to evaluate : 0.950 ------------------------------------------------------------------------------- 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 315 MET Chi-restraints excluded: chain D residue 1082 HIS 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 E residue 87 ARG Chi-restraints excluded: chain E residue 186 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 4.9990 chunk 79 optimal weight: 8.9990 chunk 44 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 27 optimal weight: 0.0870 chunk 36 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 59 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8454 Z= 0.202 Angle : 0.562 7.054 11531 Z= 0.295 Chirality : 0.042 0.136 1357 Planarity : 0.003 0.042 1454 Dihedral : 4.367 46.583 1195 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.88 % Allowed : 19.88 % Favored : 76.25 % 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: -0.95 (0.25), residues: 1099 helix: 0.48 (0.28), residues: 356 sheet: -0.40 (0.30), residues: 295 loop : -1.66 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 36 HIS 0.005 0.001 HIS E 35 PHE 0.013 0.002 PHE O 76 TYR 0.015 0.001 TYR L 2 ARG 0.006 0.000 ARG C 137 *********************** 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 144 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 113 time to evaluate : 0.913 Fit side-chains revert: symmetry clash REVERT: D 22 GLU cc_start: 0.6226 (tt0) cc_final: 0.5964 (tt0) REVERT: D 29 LYS cc_start: 0.5544 (mttt) cc_final: 0.5255 (ttpt) REVERT: D 1229 ASN cc_start: 0.7619 (t0) cc_final: 0.7314 (t0) REVERT: C 226 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.6957 (mp0) REVERT: C 258 ASP cc_start: 0.7555 (t0) cc_final: 0.7181 (t0) REVERT: E 87 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.8035 (mtp180) outliers start: 31 outliers final: 13 residues processed: 130 average time/residue: 1.1768 time to fit residues: 162.8926 Evaluate side-chains 124 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 109 time to evaluate : 0.903 ------------------------------------------------------------------------------- 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 52 LEU 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 105 TYR Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain E residue 87 ARG 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 62 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 0.0170 chunk 35 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 103 optimal weight: 0.0870 chunk 12 optimal weight: 0.8980 chunk 61 optimal weight: 0.0970 overall best weight: 0.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 59 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8454 Z= 0.137 Angle : 0.521 10.192 11531 Z= 0.268 Chirality : 0.040 0.133 1357 Planarity : 0.003 0.035 1454 Dihedral : 4.132 44.705 1195 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.62 % Allowed : 21.50 % Favored : 75.88 % 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: -0.59 (0.25), residues: 1099 helix: 0.82 (0.28), residues: 354 sheet: -0.17 (0.31), residues: 292 loop : -1.50 (0.27), residues: 453 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 0.009 0.001 PHE O 76 TYR 0.014 0.001 TYR L 2 ARG 0.007 0.000 ARG C 137 *********************** 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 140 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 119 time to evaluate : 0.982 Fit side-chains revert: symmetry clash REVERT: D 22 GLU cc_start: 0.6198 (tt0) cc_final: 0.5968 (tt0) REVERT: D 29 LYS cc_start: 0.5506 (mttt) cc_final: 0.5240 (ttpt) REVERT: D 1024 ARG cc_start: 0.7258 (ttp-110) cc_final: 0.6990 (ttp80) REVERT: D 1229 ASN cc_start: 0.7567 (t0) cc_final: 0.7273 (t0) REVERT: C 78 LYS cc_start: 0.9066 (mmtp) cc_final: 0.8823 (mmtt) REVERT: C 226 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.6943 (mp0) REVERT: C 258 ASP cc_start: 0.7414 (t0) cc_final: 0.7118 (t0) outliers start: 21 outliers final: 9 residues processed: 131 average time/residue: 1.2139 time to fit residues: 169.8265 Evaluate side-chains 121 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 111 time to evaluate : 0.890 ------------------------------------------------------------------------------- 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 1246 VAL Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 255 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.3980 chunk 60 optimal weight: 0.9990 chunk 90 optimal weight: 0.0970 chunk 59 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 59 ASN D1244 ASN C 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8454 Z= 0.173 Angle : 0.545 8.732 11531 Z= 0.283 Chirality : 0.041 0.132 1357 Planarity : 0.003 0.036 1454 Dihedral : 4.153 43.997 1195 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.88 % Allowed : 22.00 % Favored : 76.12 % 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: -0.51 (0.25), residues: 1099 helix: 0.89 (0.28), residues: 355 sheet: -0.20 (0.31), residues: 296 loop : -1.40 (0.27), residues: 448 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 0.012 0.001 PHE O 76 TYR 0.013 0.001 TYR L 2 ARG 0.007 0.000 ARG C 137 *********************** 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 126 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 111 time to evaluate : 0.968 Fit side-chains revert: symmetry clash REVERT: D 22 GLU cc_start: 0.6180 (tt0) cc_final: 0.5964 (tt0) REVERT: D 29 LYS cc_start: 0.5510 (mttt) cc_final: 0.5239 (ttpt) REVERT: D 1229 ASN cc_start: 0.7578 (t0) cc_final: 0.7292 (t0) REVERT: C 226 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.6934 (mp0) REVERT: C 258 ASP cc_start: 0.7456 (t0) cc_final: 0.7245 (t0) outliers start: 15 outliers final: 10 residues processed: 120 average time/residue: 1.2699 time to fit residues: 161.5781 Evaluate side-chains 115 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 104 time to evaluate : 0.865 ------------------------------------------------------------------------------- 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 139 LEU 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 1246 VAL Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 255 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 99 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8454 Z= 0.219 Angle : 0.585 8.419 11531 Z= 0.304 Chirality : 0.042 0.135 1357 Planarity : 0.003 0.040 1454 Dihedral : 4.274 41.170 1195 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.12 % Allowed : 22.25 % Favored : 75.62 % 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: -0.60 (0.25), residues: 1099 helix: 0.82 (0.28), residues: 358 sheet: -0.24 (0.31), residues: 300 loop : -1.48 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 332 HIS 0.005 0.001 HIS C 225 PHE 0.014 0.002 PHE O 76 TYR 0.015 0.001 TYR L 2 ARG 0.007 0.000 ARG C 137 *********************** 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 131 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 114 time to evaluate : 0.837 Fit side-chains REVERT: D 22 GLU cc_start: 0.6204 (tt0) cc_final: 0.5977 (tt0) REVERT: D 29 LYS cc_start: 0.5579 (mttt) cc_final: 0.5198 (mptt) REVERT: D 36 ASP cc_start: 0.7919 (t70) cc_final: 0.7367 (t0) REVERT: D 1024 ARG cc_start: 0.7361 (ttp-110) cc_final: 0.7110 (ttp80) REVERT: D 1229 ASN cc_start: 0.7589 (t0) cc_final: 0.7303 (t0) REVERT: C 226 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.6946 (mp0) REVERT: C 258 ASP cc_start: 0.7564 (t0) cc_final: 0.7311 (t0) outliers start: 17 outliers final: 10 residues processed: 123 average time/residue: 1.2443 time to fit residues: 162.4479 Evaluate side-chains 115 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 104 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 6 CYS Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 139 LEU 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 1246 VAL 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 186 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 90 optimal weight: 0.6980 chunk 94 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 105 optimal weight: 0.2980 chunk 64 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8454 Z= 0.180 Angle : 0.557 8.214 11531 Z= 0.289 Chirality : 0.041 0.133 1357 Planarity : 0.003 0.039 1454 Dihedral : 4.188 38.829 1195 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.00 % Allowed : 23.00 % 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: -0.44 (0.25), residues: 1099 helix: 0.96 (0.28), residues: 357 sheet: -0.18 (0.31), residues: 300 loop : -1.37 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 36 HIS 0.005 0.001 HIS E 35 PHE 0.012 0.001 PHE O 76 TYR 0.017 0.001 TYR L 2 ARG 0.007 0.000 ARG C 137 *********************** 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 130 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 114 time to evaluate : 0.946 Fit side-chains REVERT: D 22 GLU cc_start: 0.6199 (tt0) cc_final: 0.5969 (tt0) REVERT: D 29 LYS cc_start: 0.5580 (mttt) cc_final: 0.5177 (mptt) REVERT: D 36 ASP cc_start: 0.7943 (t70) cc_final: 0.7541 (t0) REVERT: D 1024 ARG cc_start: 0.7342 (ttp-110) cc_final: 0.7079 (ttp80) REVERT: D 1112 SER cc_start: 0.8526 (m) cc_final: 0.8256 (p) REVERT: D 1229 ASN cc_start: 0.7601 (t0) cc_final: 0.7324 (t0) REVERT: C 226 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.6932 (mp0) REVERT: C 258 ASP cc_start: 0.7587 (t0) cc_final: 0.7327 (t0) outliers start: 16 outliers final: 10 residues processed: 122 average time/residue: 1.2901 time to fit residues: 167.1429 Evaluate side-chains 118 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 107 time to evaluate : 0.904 ------------------------------------------------------------------------------- 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 139 LEU 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 1246 VAL Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 255 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.5980 chunk 73 optimal weight: 4.9990 chunk 110 optimal weight: 0.8980 chunk 101 optimal weight: 20.0000 chunk 88 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 68 optimal weight: 0.1980 chunk 53 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 93 optimal weight: 0.0770 chunk 26 optimal weight: 0.8980 overall best weight: 0.5138 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8454 Z= 0.158 Angle : 0.538 8.129 11531 Z= 0.279 Chirality : 0.041 0.134 1357 Planarity : 0.003 0.037 1454 Dihedral : 4.039 35.341 1195 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.25 % Allowed : 23.75 % 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: -0.27 (0.25), residues: 1099 helix: 1.14 (0.28), residues: 357 sheet: -0.09 (0.31), residues: 294 loop : -1.30 (0.28), residues: 448 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 0.010 0.001 PHE O 76 TYR 0.023 0.001 TYR L 2 ARG 0.007 0.000 ARG C 137 ********************** 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 125 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 115 time to evaluate : 0.878 Fit side-chains REVERT: D 22 GLU cc_start: 0.6175 (tt0) cc_final: 0.5950 (tt0) REVERT: D 29 LYS cc_start: 0.5551 (mttt) cc_final: 0.5157 (mptt) REVERT: D 36 ASP cc_start: 0.7982 (t70) cc_final: 0.7770 (t0) REVERT: D 1024 ARG cc_start: 0.7306 (ttp-110) cc_final: 0.7060 (ttp80) REVERT: D 1112 SER cc_start: 0.8539 (m) cc_final: 0.8305 (p) REVERT: D 1229 ASN cc_start: 0.7599 (t0) cc_final: 0.7319 (t0) REVERT: C 226 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.6934 (mp0) REVERT: C 258 ASP cc_start: 0.7526 (t0) cc_final: 0.7285 (t0) REVERT: E 192 MET cc_start: 0.7988 (ptm) cc_final: 0.7765 (ptm) outliers start: 10 outliers final: 7 residues processed: 121 average time/residue: 1.2327 time to fit residues: 158.2989 Evaluate side-chains 115 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 107 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 139 LEU Chi-restraints excluded: chain O residue 204 ILE 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 98 SER Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 255 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 36 optimal weight: 0.1980 chunk 90 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.3879 r_free = 0.3879 target = 0.130922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.101938 restraints weight = 14220.906| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.41 r_work: 0.3332 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8454 Z= 0.228 Angle : 0.590 10.526 11531 Z= 0.306 Chirality : 0.042 0.140 1357 Planarity : 0.003 0.041 1454 Dihedral : 4.064 19.268 1194 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.62 % Allowed : 23.62 % 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: -0.39 (0.25), residues: 1099 helix: 1.02 (0.28), residues: 357 sheet: -0.21 (0.31), residues: 300 loop : -1.30 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 332 HIS 0.005 0.001 HIS E 35 PHE 0.014 0.002 PHE O 76 TYR 0.020 0.002 TYR L 2 ARG 0.007 0.000 ARG C 137 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3473.32 seconds wall clock time: 61 minutes 2.69 seconds (3662.69 seconds total)