Starting phenix.real_space_refine on Sat Apr 6 17:02:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6s_35205/04_2024/8i6s_35205_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6s_35205/04_2024/8i6s_35205.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6s_35205/04_2024/8i6s_35205.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6s_35205/04_2024/8i6s_35205.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6s_35205/04_2024/8i6s_35205_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6s_35205/04_2024/8i6s_35205_updated.pdb" } resolution = 4.4 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= -0.002 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 20 5.16 5 C 5581 2.51 5 N 1432 2.21 5 O 1600 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 131": "OE1" <-> "OE2" Residue "A PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 295": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 8641 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2261 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 12, 'TRANS': 288} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ARG:plan': 20, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 65 Chain: "B" Number of atoms: 1680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1680 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 10, 'TRANS': 211} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 22} Unresolved non-hydrogen planarities: 44 Chain: "C" Number of atoms: 2316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2316 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 12, 'TRANS': 290} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ARG:plan': 20} Unresolved non-hydrogen planarities: 40 Chain: "D" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1679 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 10, 'TRANS': 211} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ARG:plan': 22} Unresolved non-hydrogen planarities: 45 Chain: "E" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 641 Classifications: {'peptide': 77} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 75} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.01, per 1000 atoms: 0.58 Number of scatterers: 8641 At special positions: 0 Unit cell: (66.066, 78.936, 179.322, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 20 16.00 P 6 15.00 Mg 2 11.99 O 1600 8.00 N 1432 7.00 C 5581 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 3.36 Conformation dependent library (CDL) restraints added in 1.7 seconds 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2050 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 40 helices and 5 sheets defined 51.0% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'A' and resid 37 through 53 Processing helix chain 'A' and resid 56 through 68 removed outlier: 3.540A pdb=" N VAL A 65 " --> pdb=" O PHE A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 80 removed outlier: 3.953A pdb=" N MET A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER A 77 " --> pdb=" O PRO A 73 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 79 " --> pdb=" O GLY A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 118 removed outlier: 3.730A pdb=" N GLU A 114 " --> pdb=" O GLN A 110 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG A 118 " --> pdb=" O GLU A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 141 Processing helix chain 'A' and resid 171 through 177 removed outlier: 3.715A pdb=" N ARG A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 231 removed outlier: 3.541A pdb=" N ILE A 213 " --> pdb=" O PHE A 209 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LEU A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU A 221 " --> pdb=" O LEU A 217 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY A 224 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG A 228 " --> pdb=" O GLY A 224 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE A 231 " --> pdb=" O ILE A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 243 removed outlier: 3.794A pdb=" N GLU A 239 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE A 241 " --> pdb=" O GLU A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 292 removed outlier: 3.547A pdb=" N ARG A 253 " --> pdb=" O GLY A 249 " (cutoff:3.500A) Proline residue: A 254 - end of helix removed outlier: 3.651A pdb=" N TYR A 257 " --> pdb=" O ARG A 253 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET A 258 " --> pdb=" O PRO A 254 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR A 262 " --> pdb=" O MET A 258 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY A 263 " --> pdb=" O GLY A 259 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE A 268 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A 269 " --> pdb=" O GLY A 265 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TRP A 271 " --> pdb=" O GLY A 267 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY A 283 " --> pdb=" O ASN A 279 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N SER A 284 " --> pdb=" O TRP A 280 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL A 286 " --> pdb=" O ASN A 282 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ASN A 287 " --> pdb=" O GLY A 283 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU A 288 " --> pdb=" O SER A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 331 removed outlier: 3.508A pdb=" N THR A 310 " --> pdb=" O GLY A 306 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA A 313 " --> pdb=" O LEU A 309 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG A 327 " --> pdb=" O LEU A 323 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N HIS A 328 " --> pdb=" O ALA A 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 48 Processing helix chain 'B' and resid 71 through 79 Proline residue: B 75 - end of helix Processing helix chain 'B' and resid 96 through 102 removed outlier: 3.708A pdb=" N ILE B 100 " --> pdb=" O VAL B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 124 removed outlier: 4.034A pdb=" N ALA B 115 " --> pdb=" O PRO B 112 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS B 116 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL B 118 " --> pdb=" O ALA B 115 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA B 121 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU B 122 " --> pdb=" O ALA B 119 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLU B 123 " --> pdb=" O SER B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 137 No H-bonds generated for 'chain 'B' and resid 135 through 137' Processing helix chain 'B' and resid 140 through 152 removed outlier: 4.120A pdb=" N GLN B 144 " --> pdb=" O THR B 140 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA B 151 " --> pdb=" O GLY B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 185 removed outlier: 4.690A pdb=" N GLU B 175 " --> pdb=" O ARG B 171 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE B 180 " --> pdb=" O ILE B 176 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU B 181 " --> pdb=" O MET B 177 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASP B 182 " --> pdb=" O GLY B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 201 No H-bonds generated for 'chain 'B' and resid 199 through 201' Processing helix chain 'C' and resid 34 through 53 Processing helix chain 'C' and resid 56 through 68 removed outlier: 3.632A pdb=" N PHE C 60 " --> pdb=" O PRO C 56 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N CYS C 63 " --> pdb=" O SER C 59 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL C 65 " --> pdb=" O PHE C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 83 removed outlier: 3.833A pdb=" N MET C 74 " --> pdb=" O LEU C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 92 No H-bonds generated for 'chain 'C' and resid 90 through 92' Processing helix chain 'C' and resid 106 through 118 removed outlier: 3.565A pdb=" N ASP C 111 " --> pdb=" O ASN C 107 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU C 117 " --> pdb=" O ARG C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 137 removed outlier: 3.912A pdb=" N LEU C 137 " --> pdb=" O ALA C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 178 removed outlier: 3.961A pdb=" N LEU C 174 " --> pdb=" O LEU C 171 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG C 175 " --> pdb=" O GLU C 172 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N GLN C 176 " --> pdb=" O ALA C 173 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN C 177 " --> pdb=" O LEU C 174 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU C 178 " --> pdb=" O ARG C 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 171 through 178' Processing helix chain 'C' and resid 192 through 195 No H-bonds generated for 'chain 'C' and resid 192 through 195' Processing helix chain 'C' and resid 197 through 200 No H-bonds generated for 'chain 'C' and resid 197 through 200' Processing helix chain 'C' and resid 203 through 232 removed outlier: 3.536A pdb=" N ILE C 213 " --> pdb=" O PHE C 209 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N VAL C 216 " --> pdb=" O THR C 212 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU C 221 " --> pdb=" O LEU C 217 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL C 222 " --> pdb=" O THR C 218 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG C 228 " --> pdb=" O GLY C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 242 removed outlier: 3.591A pdb=" N ILE C 238 " --> pdb=" O ARG C 235 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU C 239 " --> pdb=" O ASN C 236 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL C 240 " --> pdb=" O GLU C 237 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS C 242 " --> pdb=" O GLU C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 280 Proline residue: C 254 - end of helix removed outlier: 3.684A pdb=" N TYR C 257 " --> pdb=" O ARG C 253 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N MET C 258 " --> pdb=" O PRO C 254 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR C 262 " --> pdb=" O MET C 258 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE C 268 " --> pdb=" O LEU C 264 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU C 273 " --> pdb=" O LEU C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 291 Processing helix chain 'C' and resid 304 through 331 removed outlier: 3.869A pdb=" N ALA C 326 " --> pdb=" O TRP C 322 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ARG C 327 " --> pdb=" O LEU C 323 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N HIS C 328 " --> pdb=" O ALA C 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 49 removed outlier: 3.661A pdb=" N ILE D 48 " --> pdb=" O LEU D 44 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU D 49 " --> pdb=" O LEU D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 79 Proline residue: D 75 - end of helix Processing helix chain 'D' and resid 97 through 107 Proline residue: D 103 - end of helix removed outlier: 4.062A pdb=" N ILE D 106 " --> pdb=" O LEU D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 121 removed outlier: 4.595A pdb=" N ALA D 115 " --> pdb=" O PRO D 112 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYS D 116 " --> pdb=" O GLU D 113 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG D 117 " --> pdb=" O ILE D 114 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA D 119 " --> pdb=" O LYS D 116 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER D 120 " --> pdb=" O ARG D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 152 Processing helix chain 'D' and resid 170 through 182 removed outlier: 3.957A pdb=" N SER D 174 " --> pdb=" O PRO D 170 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLU D 175 " --> pdb=" O ARG D 171 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE D 176 " --> pdb=" O LEU D 172 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLU D 181 " --> pdb=" O MET D 177 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP D 182 " --> pdb=" O GLY D 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 115 removed outlier: 4.263A pdb=" N ALA E 98 " --> pdb=" O LYS E 94 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN E 115 " --> pdb=" O ARG E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 162 removed outlier: 3.507A pdb=" N ARG E 148 " --> pdb=" O ILE E 144 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU E 149 " --> pdb=" O ASN E 145 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLU E 150 " --> pdb=" O LYS E 146 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN E 151 " --> pdb=" O ALA E 147 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR E 158 " --> pdb=" O SER E 154 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG E 160 " --> pdb=" O ASN E 156 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLN E 161 " --> pdb=" O GLU E 157 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 124 through 127 Processing sheet with id= B, first strand: chain 'B' and resid 2 through 4 removed outlier: 3.773A pdb=" N PHE B 4 " --> pdb=" O PHE B 23 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 59 through 61 removed outlier: 4.468A pdb=" N LEU B 59 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU B 61 " --> pdb=" O GLN B 64 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLN B 64 " --> pdb=" O LEU B 61 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 96 through 99 removed outlier: 3.610A pdb=" N VAL C 161 " --> pdb=" O ILE C 96 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU C 98 " --> pdb=" O ILE C 159 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ILE C 159 " --> pdb=" O LEU C 98 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL C 158 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE C 128 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLN C 126 " --> pdb=" O SER C 160 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 190 through 193 removed outlier: 3.882A pdb=" N VAL D 33 " --> pdb=" O ILE D 192 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LEU D 208 " --> pdb=" O THR D 34 " (cutoff:3.500A) 321 hydrogen bonds defined for protein. 924 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: 2.13 Time building geometry restraints manager: 3.57 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: 2048 1.33 - 1.46: 1723 1.46 - 1.58: 4967 1.58 - 1.70: 10 1.70 - 1.83: 38 Bond restraints: 8786 Sorted by residual: bond pdb=" C6 ATP D 301 " pdb=" N6 ATP D 301 " ideal model delta sigma weight residual 1.337 1.449 -0.112 1.10e-02 8.26e+03 1.04e+02 bond pdb=" C6 ATP B 302 " pdb=" N6 ATP B 302 " ideal model delta sigma weight residual 1.337 1.449 -0.112 1.10e-02 8.26e+03 1.03e+02 bond pdb=" C5 ATP B 302 " pdb=" N7 ATP B 302 " ideal model delta sigma weight residual 1.387 1.469 -0.082 1.00e-02 1.00e+04 6.69e+01 bond pdb=" C5 ATP D 301 " pdb=" N7 ATP D 301 " ideal model delta sigma weight residual 1.387 1.468 -0.081 1.00e-02 1.00e+04 6.57e+01 bond pdb=" O5' ATP D 301 " pdb=" PA ATP D 301 " ideal model delta sigma weight residual 1.579 1.650 -0.071 1.10e-02 8.26e+03 4.14e+01 ... (remaining 8781 not shown) Histogram of bond angle deviations from ideal: 97.81 - 105.50: 182 105.50 - 113.18: 4802 113.18 - 120.87: 4183 120.87 - 128.56: 2637 128.56 - 136.24: 82 Bond angle restraints: 11886 Sorted by residual: angle pdb=" PB ATP B 302 " pdb=" O3B ATP B 302 " pdb=" PG ATP B 302 " ideal model delta sigma weight residual 139.87 116.52 23.35 1.00e+00 1.00e+00 5.45e+02 angle pdb=" PB ATP D 301 " pdb=" O3B ATP D 301 " pdb=" PG ATP D 301 " ideal model delta sigma weight residual 139.87 125.37 14.50 1.00e+00 1.00e+00 2.10e+02 angle pdb=" PA ATP B 302 " pdb=" O3A ATP B 302 " pdb=" PB ATP B 302 " ideal model delta sigma weight residual 136.83 122.76 14.07 1.00e+00 1.00e+00 1.98e+02 angle pdb=" O3A ATP B 302 " pdb=" PB ATP B 302 " pdb=" O3B ATP B 302 " ideal model delta sigma weight residual 101.57 116.72 -15.15 1.54e+00 4.24e-01 9.73e+01 angle pdb=" PA ATP D 301 " pdb=" O3A ATP D 301 " pdb=" PB ATP D 301 " ideal model delta sigma weight residual 136.83 127.43 9.40 1.00e+00 1.00e+00 8.84e+01 ... (remaining 11881 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 4659 17.97 - 35.95: 550 35.95 - 53.92: 125 53.92 - 71.89: 23 71.89 - 89.86: 9 Dihedral angle restraints: 5366 sinusoidal: 2178 harmonic: 3188 Sorted by residual: dihedral pdb=" CA VAL A 192 " pdb=" C VAL A 192 " pdb=" N TRP A 193 " pdb=" CA TRP A 193 " ideal model delta harmonic sigma weight residual 180.00 137.38 42.62 0 5.00e+00 4.00e-02 7.27e+01 dihedral pdb=" CA ASP C 190 " pdb=" C ASP C 190 " pdb=" N LEU C 191 " pdb=" CA LEU C 191 " ideal model delta harmonic sigma weight residual -180.00 -157.62 -22.38 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA LEU A 229 " pdb=" C LEU A 229 " pdb=" N HIS A 230 " pdb=" CA HIS A 230 " ideal model delta harmonic sigma weight residual 180.00 157.90 22.10 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 5363 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1133 0.073 - 0.146: 224 0.146 - 0.219: 46 0.219 - 0.292: 5 0.292 - 0.365: 3 Chirality restraints: 1411 Sorted by residual: chirality pdb=" CB ILE B 215 " pdb=" CA ILE B 215 " pdb=" CG1 ILE B 215 " pdb=" CG2 ILE B 215 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" CB ILE D 2 " pdb=" CA ILE D 2 " pdb=" CG1 ILE D 2 " pdb=" CG2 ILE D 2 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CB VAL B 125 " pdb=" CA VAL B 125 " pdb=" CG1 VAL B 125 " pdb=" CG2 VAL B 125 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.18e+00 ... (remaining 1408 not shown) Planarity restraints: 1476 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS B 195 " -0.045 2.00e-02 2.50e+03 6.17e-02 5.71e+01 pdb=" CG HIS B 195 " 0.107 2.00e-02 2.50e+03 pdb=" ND1 HIS B 195 " -0.056 2.00e-02 2.50e+03 pdb=" CD2 HIS B 195 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 HIS B 195 " 0.050 2.00e-02 2.50e+03 pdb=" NE2 HIS B 195 " -0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 192 " -0.025 2.00e-02 2.50e+03 4.92e-02 2.42e+01 pdb=" C VAL A 192 " 0.085 2.00e-02 2.50e+03 pdb=" O VAL A 192 " -0.032 2.00e-02 2.50e+03 pdb=" N TRP A 193 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 280 " -0.013 2.00e-02 2.50e+03 1.55e-02 6.01e+00 pdb=" CG TRP C 280 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP C 280 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP C 280 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 280 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 280 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 280 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 280 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 280 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 280 " 0.001 2.00e-02 2.50e+03 ... (remaining 1473 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 86 2.64 - 3.20: 7084 3.20 - 3.77: 13855 3.77 - 4.33: 17647 4.33 - 4.90: 27274 Nonbonded interactions: 65946 Sorted by model distance: nonbonded pdb=" OG1 THR B 140 " pdb="MG MG B 301 " model vdw 2.073 2.170 nonbonded pdb="MG MG B 301 " pdb=" O3A ATP D 301 " model vdw 2.077 2.170 nonbonded pdb=" O1A ATP B 302 " pdb="MG MG B 303 " model vdw 2.133 2.170 nonbonded pdb="MG MG B 301 " pdb=" O2B ATP D 301 " model vdw 2.135 2.170 nonbonded pdb=" O1B ATP B 302 " pdb="MG MG B 303 " model vdw 2.253 2.170 ... (remaining 65941 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'C' and (resid 35 through 88 or (resid 89 and (name N or name CA or name \ C or name O or name CB )) or resid 90 or (resid 91 through 95 and (name N or nam \ e CA or name C or name O or name CB )) or resid 96 through 122 or (resid 123 and \ (name N or name CA or name C or name O or name CB )) or resid 124 through 164 o \ r (resid 165 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 66 or (resid 167 through 169 and (name N or name CA or name C or name O or name \ CB )) or resid 170 or (resid 171 and (name N or name CA or name C or name O or n \ ame CB )) or resid 172 through 194 or (resid 195 and (name N or name CA or name \ C or name O or name CB )) or resid 196 or (resid 197 through 199 and (name N or \ name CA or name C or name O or name CB )) or resid 200 through 335)) } ncs_group { reference = (chain 'B' and (resid 1 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 \ or name CZ )) or resid 12 through 222)) selection = (chain 'D' and resid 1 through 222) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 25.780 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 26.010 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6010 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 8786 Z= 0.419 Angle : 1.394 23.352 11886 Z= 0.763 Chirality : 0.063 0.365 1411 Planarity : 0.007 0.062 1476 Dihedral : 16.404 89.863 3316 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.13 % Favored : 95.70 % Rotamer: Outliers : 0.97 % Allowed : 2.48 % Favored : 96.54 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -5.18 (0.17), residues: 1115 helix: -4.23 (0.09), residues: 575 sheet: -0.91 (0.68), residues: 55 loop : -2.52 (0.22), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP C 280 HIS 0.080 0.004 HIS B 195 PHE 0.039 0.001 PHE D 180 TYR 0.040 0.002 TYR A 250 ARG 0.004 0.000 ARG E 118 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 120 time to evaluate : 1.100 Fit side-chains revert: symmetry clash REVERT: A 74 MET cc_start: 0.6692 (mmp) cc_final: 0.6455 (mmp) REVERT: A 215 LEU cc_start: 0.6983 (mm) cc_final: 0.5502 (tp) REVERT: B 162 ASP cc_start: 0.7197 (p0) cc_final: 0.6967 (p0) REVERT: C 66 MET cc_start: 0.4364 (tpt) cc_final: 0.3997 (tpt) REVERT: D 154 HIS cc_start: 0.6844 (p-80) cc_final: 0.5443 (t-90) outliers start: 9 outliers final: 9 residues processed: 126 average time/residue: 0.1623 time to fit residues: 30.3392 Evaluate side-chains 85 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 76 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 46 optimal weight: 0.1980 chunk 28 optimal weight: 0.5980 chunk 56 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 87 optimal weight: 9.9990 chunk 33 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 64 optimal weight: 0.0170 chunk 100 optimal weight: 0.8980 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 HIS A 230 HIS C 82 ASN ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6027 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8786 Z= 0.149 Angle : 0.623 7.134 11886 Z= 0.312 Chirality : 0.040 0.181 1411 Planarity : 0.004 0.034 1476 Dihedral : 8.556 76.322 1213 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.14 % Favored : 96.68 % Rotamer: Outliers : 0.97 % Allowed : 5.40 % Favored : 93.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.80 (0.21), residues: 1115 helix: -1.73 (0.18), residues: 570 sheet: -0.76 (0.72), residues: 53 loop : -2.03 (0.24), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 271 HIS 0.024 0.001 HIS B 195 PHE 0.013 0.001 PHE C 207 TYR 0.007 0.001 TYR A 250 ARG 0.001 0.000 ARG E 104 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 103 time to evaluate : 1.027 Fit side-chains revert: symmetry clash REVERT: B 51 MET cc_start: 0.2115 (ppp) cc_final: 0.1196 (ptt) REVERT: B 86 GLN cc_start: 0.7810 (mm-40) cc_final: 0.7318 (mm-40) REVERT: B 109 MET cc_start: 0.5702 (ptp) cc_final: 0.5437 (ptp) REVERT: B 162 ASP cc_start: 0.7382 (p0) cc_final: 0.6782 (p0) outliers start: 9 outliers final: 9 residues processed: 110 average time/residue: 0.1632 time to fit residues: 27.1113 Evaluate side-chains 81 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 72 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 83 optimal weight: 0.2980 chunk 68 optimal weight: 0.0070 chunk 27 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 109 optimal weight: 0.5980 chunk 89 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 81 optimal weight: 9.9990 chunk 99 optimal weight: 0.8980 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 HIS ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 ASN E 102 GLN ** E 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6042 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 8786 Z= 0.136 Angle : 0.589 6.721 11886 Z= 0.287 Chirality : 0.040 0.145 1411 Planarity : 0.003 0.034 1476 Dihedral : 8.064 66.653 1213 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.41 % Favored : 96.41 % Rotamer: Outliers : 1.08 % Allowed : 5.94 % Favored : 92.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.46 (0.24), residues: 1115 helix: -0.31 (0.21), residues: 585 sheet: -0.83 (0.70), residues: 53 loop : -1.77 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 271 HIS 0.014 0.001 HIS B 195 PHE 0.029 0.001 PHE D 180 TYR 0.007 0.001 TYR E 141 ARG 0.001 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 102 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 215 LEU cc_start: 0.7446 (mm) cc_final: 0.5862 (tp) REVERT: B 86 GLN cc_start: 0.7931 (mm-40) cc_final: 0.7462 (mm-40) REVERT: B 109 MET cc_start: 0.5564 (ptp) cc_final: 0.5314 (ptp) REVERT: B 162 ASP cc_start: 0.7397 (p0) cc_final: 0.6739 (p0) outliers start: 10 outliers final: 9 residues processed: 109 average time/residue: 0.1582 time to fit residues: 26.3385 Evaluate side-chains 80 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 71 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 11 optimal weight: 0.0970 chunk 48 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 89 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 HIS ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 ASN C 138 GLN ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6102 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8786 Z= 0.147 Angle : 0.595 7.338 11886 Z= 0.288 Chirality : 0.040 0.159 1411 Planarity : 0.003 0.036 1476 Dihedral : 7.875 66.841 1213 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.23 % Favored : 96.59 % Rotamer: Outliers : 0.97 % Allowed : 6.80 % Favored : 92.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.01 (0.25), residues: 1115 helix: 0.11 (0.22), residues: 594 sheet: -0.77 (0.72), residues: 53 loop : -1.63 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 318 HIS 0.017 0.001 HIS B 195 PHE 0.007 0.001 PHE C 207 TYR 0.008 0.001 TYR C 37 ARG 0.001 0.000 ARG E 148 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 99 time to evaluate : 1.008 Fit side-chains revert: symmetry clash REVERT: A 100 LEU cc_start: 0.6846 (mm) cc_final: 0.6640 (mm) REVERT: B 51 MET cc_start: 0.2044 (ppp) cc_final: 0.1573 (ptt) REVERT: B 86 GLN cc_start: 0.8094 (mm-40) cc_final: 0.7527 (mm-40) REVERT: B 162 ASP cc_start: 0.7479 (p0) cc_final: 0.6740 (p0) REVERT: D 180 PHE cc_start: 0.8882 (m-10) cc_final: 0.8632 (m-80) outliers start: 9 outliers final: 9 residues processed: 105 average time/residue: 0.1563 time to fit residues: 25.3214 Evaluate side-chains 82 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 73 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 chunk 74 optimal weight: 0.1980 chunk 0 optimal weight: 7.9990 chunk 54 optimal weight: 0.0970 chunk 96 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 HIS ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 ASN C 230 HIS ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6082 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8786 Z= 0.131 Angle : 0.581 6.609 11886 Z= 0.279 Chirality : 0.040 0.157 1411 Planarity : 0.003 0.037 1476 Dihedral : 7.563 64.505 1213 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.32 % Favored : 96.50 % Rotamer: Outliers : 0.97 % Allowed : 4.00 % Favored : 95.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.62 (0.26), residues: 1115 helix: 0.52 (0.23), residues: 586 sheet: -0.79 (0.70), residues: 60 loop : -1.55 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 271 HIS 0.011 0.001 HIS B 195 PHE 0.006 0.001 PHE C 207 TYR 0.009 0.001 TYR C 37 ARG 0.001 0.000 ARG E 148 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 102 time to evaluate : 0.968 Fit side-chains revert: symmetry clash REVERT: B 51 MET cc_start: 0.2024 (ppp) cc_final: 0.1675 (ptt) REVERT: B 109 MET cc_start: 0.5691 (ptp) cc_final: 0.5471 (ptp) REVERT: B 162 ASP cc_start: 0.7376 (p0) cc_final: 0.7008 (p0) REVERT: D 180 PHE cc_start: 0.8897 (m-10) cc_final: 0.8657 (m-80) outliers start: 9 outliers final: 9 residues processed: 108 average time/residue: 0.1666 time to fit residues: 27.1621 Evaluate side-chains 84 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 75 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.3980 chunk 26 optimal weight: 0.0670 chunk 107 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 35 optimal weight: 9.9990 chunk 56 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 HIS ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 ASN ** C 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6106 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8786 Z= 0.136 Angle : 0.590 6.657 11886 Z= 0.282 Chirality : 0.040 0.154 1411 Planarity : 0.003 0.037 1476 Dihedral : 6.991 69.804 1213 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.50 % Favored : 96.41 % Rotamer: Outliers : 1.08 % Allowed : 4.75 % Favored : 94.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.43 (0.26), residues: 1115 helix: 0.68 (0.23), residues: 585 sheet: -0.98 (0.64), residues: 70 loop : -1.42 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 271 HIS 0.027 0.001 HIS B 195 PHE 0.006 0.001 PHE A 99 TYR 0.009 0.001 TYR C 37 ARG 0.001 0.000 ARG E 148 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 101 time to evaluate : 1.060 Fit side-chains revert: symmetry clash REVERT: B 162 ASP cc_start: 0.7416 (p0) cc_final: 0.7188 (p0) REVERT: D 51 MET cc_start: 0.1645 (pmm) cc_final: 0.1246 (pmm) REVERT: D 180 PHE cc_start: 0.8941 (m-10) cc_final: 0.8692 (m-80) outliers start: 10 outliers final: 10 residues processed: 108 average time/residue: 0.1621 time to fit residues: 26.7996 Evaluate side-chains 86 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 76 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.0000 chunk 60 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 106 optimal weight: 7.9990 chunk 66 optimal weight: 0.9990 chunk 65 optimal weight: 0.0970 chunk 49 optimal weight: 0.1980 chunk 42 optimal weight: 0.9980 chunk 63 optimal weight: 0.0670 chunk 32 optimal weight: 5.9990 overall best weight: 0.2720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 HIS ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 ASN C 82 ASN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6058 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8786 Z= 0.125 Angle : 0.598 8.131 11886 Z= 0.281 Chirality : 0.040 0.162 1411 Planarity : 0.003 0.038 1476 Dihedral : 6.825 71.263 1213 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.32 % Favored : 96.59 % Rotamer: Outliers : 1.08 % Allowed : 4.43 % Favored : 94.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.32 (0.26), residues: 1115 helix: 0.80 (0.23), residues: 584 sheet: -0.92 (0.64), residues: 70 loop : -1.41 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 271 HIS 0.016 0.001 HIS B 195 PHE 0.022 0.001 PHE C 53 TYR 0.009 0.001 TYR C 37 ARG 0.001 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 99 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 162 ASP cc_start: 0.7304 (p0) cc_final: 0.7051 (p0) REVERT: D 51 MET cc_start: 0.1615 (pmm) cc_final: 0.1194 (pmm) REVERT: D 180 PHE cc_start: 0.8914 (m-10) cc_final: 0.8667 (m-80) outliers start: 10 outliers final: 10 residues processed: 106 average time/residue: 0.1549 time to fit residues: 25.3615 Evaluate side-chains 82 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 72 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 97 optimal weight: 0.0470 chunk 102 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 99 optimal weight: 5.9990 overall best weight: 0.9482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 ASN ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 ASN C 82 ASN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6170 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8786 Z= 0.164 Angle : 0.623 8.119 11886 Z= 0.297 Chirality : 0.042 0.162 1411 Planarity : 0.003 0.037 1476 Dihedral : 6.873 75.796 1213 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.22 % Favored : 95.70 % Rotamer: Outliers : 1.08 % Allowed : 3.13 % Favored : 95.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.32 (0.26), residues: 1115 helix: 0.80 (0.23), residues: 584 sheet: -0.95 (0.64), residues: 70 loop : -1.40 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 271 HIS 0.014 0.001 HIS B 195 PHE 0.020 0.001 PHE C 53 TYR 0.009 0.001 TYR C 37 ARG 0.002 0.000 ARG E 148 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 96 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 TRP cc_start: 0.6078 (t60) cc_final: 0.5865 (t60) REVERT: D 180 PHE cc_start: 0.9015 (m-10) cc_final: 0.8748 (m-80) outliers start: 10 outliers final: 10 residues processed: 104 average time/residue: 0.1636 time to fit residues: 25.6570 Evaluate side-chains 86 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 76 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 0.0070 chunk 60 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 94 optimal weight: 0.5980 chunk 99 optimal weight: 2.9990 chunk 65 optimal weight: 20.0000 chunk 105 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 ASN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6148 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8786 Z= 0.145 Angle : 0.618 7.580 11886 Z= 0.294 Chirality : 0.041 0.151 1411 Planarity : 0.003 0.039 1476 Dihedral : 7.017 80.889 1213 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.59 % Favored : 96.32 % Rotamer: Outliers : 1.08 % Allowed : 2.81 % Favored : 96.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.23 (0.26), residues: 1115 helix: 0.85 (0.23), residues: 588 sheet: -1.15 (0.66), residues: 65 loop : -1.29 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 271 HIS 0.035 0.002 HIS B 195 PHE 0.019 0.001 PHE C 53 TYR 0.009 0.001 TYR C 37 ARG 0.001 0.000 ARG E 148 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 94 time to evaluate : 1.106 Fit side-chains revert: symmetry clash REVERT: B 51 MET cc_start: 0.1846 (ppp) cc_final: 0.1528 (ptt) REVERT: D 180 PHE cc_start: 0.9003 (m-10) cc_final: 0.8735 (m-80) outliers start: 10 outliers final: 10 residues processed: 102 average time/residue: 0.1703 time to fit residues: 26.8585 Evaluate side-chains 86 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 76 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 10.0000 chunk 73 optimal weight: 0.2980 chunk 110 optimal weight: 0.6980 chunk 101 optimal weight: 10.0000 chunk 88 optimal weight: 0.0570 chunk 9 optimal weight: 0.9990 chunk 68 optimal weight: 0.0010 chunk 53 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 HIS C 82 ASN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6119 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8786 Z= 0.135 Angle : 0.617 7.687 11886 Z= 0.290 Chirality : 0.041 0.153 1411 Planarity : 0.003 0.038 1476 Dihedral : 6.817 77.660 1213 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.95 % Favored : 95.96 % Rotamer: Outliers : 1.08 % Allowed : 2.05 % Favored : 96.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.16 (0.26), residues: 1115 helix: 0.91 (0.23), residues: 582 sheet: -1.10 (0.66), residues: 65 loop : -1.24 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 271 HIS 0.029 0.001 HIS B 195 PHE 0.019 0.001 PHE C 53 TYR 0.009 0.001 TYR C 37 ARG 0.001 0.000 ARG E 118 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 97 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 51 MET cc_start: 0.1788 (ppp) cc_final: 0.1485 (ptt) REVERT: D 180 PHE cc_start: 0.8950 (m-10) cc_final: 0.8718 (m-80) outliers start: 10 outliers final: 10 residues processed: 105 average time/residue: 0.1494 time to fit residues: 24.4547 Evaluate side-chains 83 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 73 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 24 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 36 optimal weight: 0.0040 chunk 90 optimal weight: 5.9990 chunk 11 optimal weight: 0.0370 chunk 16 optimal weight: 0.9980 chunk 77 optimal weight: 0.0570 chunk 5 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 overall best weight: 0.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 ASN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.095402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.078578 restraints weight = 52981.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.080269 restraints weight = 37642.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.081554 restraints weight = 29548.761| |-----------------------------------------------------------------------------| r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6251 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8786 Z= 0.131 Angle : 0.607 8.732 11886 Z= 0.286 Chirality : 0.041 0.152 1411 Planarity : 0.003 0.038 1476 Dihedral : 6.607 76.673 1213 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.68 % Favored : 96.23 % Rotamer: Outliers : 1.08 % Allowed : 2.05 % Favored : 96.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.07 (0.26), residues: 1115 helix: 0.98 (0.23), residues: 584 sheet: -1.08 (0.66), residues: 65 loop : -1.21 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 271 HIS 0.024 0.001 HIS B 195 PHE 0.018 0.001 PHE C 53 TYR 0.009 0.001 TYR C 37 ARG 0.001 0.000 ARG E 148 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2074.55 seconds wall clock time: 39 minutes 1.79 seconds (2341.79 seconds total)