Starting phenix.real_space_refine on Mon Mar 11 15:05:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6j_37325/03_2024/8w6j_37325_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6j_37325/03_2024/8w6j_37325.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6j_37325/03_2024/8w6j_37325.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6j_37325/03_2024/8w6j_37325.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6j_37325/03_2024/8w6j_37325_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6j_37325/03_2024/8w6j_37325_updated.pdb" } resolution = 3.4 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= 0.000 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 36 5.16 5 C 5448 2.51 5 N 1508 2.21 5 O 1555 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 29": "OE1" <-> "OE2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "C PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 181": "OE1" <-> "OE2" Residue "E GLU 141": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8553 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1663 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 208} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 2264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2264 Classifications: {'peptide': 300} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 9, 'TRANS': 290} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "C" Number of atoms: 2259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2259 Classifications: {'peptide': 299} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 9, 'TRANS': 289} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 4, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "D" Number of atoms: 1681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1681 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 209} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 624 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'TRANS': 94} Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 162 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 7, 'GLU:plan': 8, 'ASN:plan1': 2, 'ARG:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 89 Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} 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: 4.99, per 1000 atoms: 0.58 Number of scatterers: 8553 At special positions: 0 Unit cell: (63.6, 81.62, 187.62, 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 36 16.00 P 6 15.00 O 1555 8.00 N 1508 7.00 C 5448 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=0, symmetry=0 Time building additional restraints: 3.40 Conformation dependent library (CDL) restraints added in 1.7 seconds 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2070 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 37 helices and 4 sheets defined 50.4% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.78 Creating SS restraints... Processing helix chain 'B' and resid 41 through 49 removed outlier: 3.776A pdb=" N ILE B 48 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N CYS B 49 " --> pdb=" O LEU B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 74 No H-bonds generated for 'chain 'B' and resid 71 through 74' Processing helix chain 'B' and resid 78 through 80 No H-bonds generated for 'chain 'B' and resid 78 through 80' Processing helix chain 'B' and resid 96 through 107 removed outlier: 3.590A pdb=" N ILE B 102 " --> pdb=" O ASP B 98 " (cutoff:3.500A) Proline residue: B 103 - end of helix Processing helix chain 'B' and resid 111 through 125 removed outlier: 4.096A pdb=" N ARG B 115 " --> pdb=" O GLY B 111 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ARG B 116 " --> pdb=" O ASP B 112 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS B 124 " --> pdb=" O ALA B 120 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL B 125 " --> pdb=" O ALA B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 151 removed outlier: 3.578A pdb=" N GLY B 147 " --> pdb=" O GLN B 143 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE B 148 " --> pdb=" O GLN B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 183 removed outlier: 3.797A pdb=" N GLY B 175 " --> pdb=" O ALA B 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 68 Processing helix chain 'A' and resid 71 through 98 removed outlier: 3.759A pdb=" N PHE A 75 " --> pdb=" O PRO A 71 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LEU A 76 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU A 87 " --> pdb=" O ILE A 83 " (cutoff:3.500A) Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 121 through 131 removed outlier: 3.734A pdb=" N ALA A 125 " --> pdb=" O ASP A 121 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL A 127 " --> pdb=" O ALA A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 154 removed outlier: 4.456A pdb=" N GLU A 151 " --> pdb=" O ASP A 147 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N PHE A 152 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ARG A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASN A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 195 removed outlier: 3.725A pdb=" N ARG A 194 " --> pdb=" O THR A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 259 removed outlier: 4.582A pdb=" N THR A 218 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU A 231 " --> pdb=" O MET A 227 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE A 240 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLY A 241 " --> pdb=" O PHE A 237 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ARG A 245 " --> pdb=" O GLY A 241 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N ASP A 253 " --> pdb=" O PHE A 249 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N SER A 254 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE A 255 " --> pdb=" O ARG A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 298 removed outlier: 4.091A pdb=" N LEU A 269 " --> pdb=" O ASP A 265 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG A 270 " --> pdb=" O GLY A 266 " (cutoff:3.500A) Proline residue: A 271 - end of helix Processing helix chain 'A' and resid 302 through 309 removed outlier: 3.528A pdb=" N GLN A 307 " --> pdb=" O ALA A 303 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL A 308 " --> pdb=" O GLU A 304 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE A 309 " --> pdb=" O VAL A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 348 removed outlier: 3.928A pdb=" N LEU A 324 " --> pdb=" O PHE A 320 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU A 325 " --> pdb=" O ASP A 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 68 No H-bonds generated for 'chain 'C' and resid 65 through 68' Processing helix chain 'C' and resid 71 through 100 removed outlier: 3.745A pdb=" N LEU C 87 " --> pdb=" O ILE C 83 " (cutoff:3.500A) Proline residue: C 88 - end of helix Processing helix chain 'C' and resid 122 through 130 removed outlier: 4.819A pdb=" N VAL C 128 " --> pdb=" O ALA C 124 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ALA C 129 " --> pdb=" O ALA C 125 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLN C 130 " --> pdb=" O GLY C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 155 removed outlier: 4.424A pdb=" N LEU C 149 " --> pdb=" O ARG C 145 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE C 152 " --> pdb=" O ALA C 148 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ARG C 153 " --> pdb=" O LEU C 149 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASN C 154 " --> pdb=" O GLY C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 196 Processing helix chain 'C' and resid 210 through 243 removed outlier: 4.986A pdb=" N GLY C 219 " --> pdb=" O ALA C 215 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL C 230 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU C 231 " --> pdb=" O MET C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 250 Processing helix chain 'C' and resid 252 through 260 Processing helix chain 'C' and resid 265 through 297 removed outlier: 4.020A pdb=" N LEU C 269 " --> pdb=" O ASP C 265 " (cutoff:3.500A) Proline residue: C 271 - end of helix removed outlier: 3.960A pdb=" N TYR C 274 " --> pdb=" O ARG C 270 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLY C 275 " --> pdb=" O PRO C 271 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU C 292 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ILE C 293 " --> pdb=" O ILE C 289 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU C 294 " --> pdb=" O LEU C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 309 removed outlier: 3.730A pdb=" N GLN C 307 " --> pdb=" O ALA C 303 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL C 308 " --> pdb=" O GLU C 304 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE C 309 " --> pdb=" O VAL C 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 303 through 309' Processing helix chain 'C' and resid 320 through 340 Processing helix chain 'C' and resid 343 through 349 removed outlier: 3.725A pdb=" N ARG C 347 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N HIS C 348 " --> pdb=" O GLN C 344 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N PHE C 349 " --> pdb=" O HIS C 345 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 343 through 349' Processing helix chain 'D' and resid 42 through 49 Processing helix chain 'D' and resid 71 through 77 Proline residue: D 75 - end of helix No H-bonds generated for 'chain 'D' and resid 71 through 77' Processing helix chain 'D' and resid 96 through 107 Proline residue: D 103 - end of helix Processing helix chain 'D' and resid 113 through 125 removed outlier: 3.689A pdb=" N ALA D 120 " --> pdb=" O ARG D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 151 removed outlier: 3.621A pdb=" N VAL D 146 " --> pdb=" O GLU D 142 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY D 147 " --> pdb=" O GLN D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 177 removed outlier: 4.001A pdb=" N GLU D 174 " --> pdb=" O ASP D 170 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY D 175 " --> pdb=" O ALA D 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 126 removed outlier: 3.580A pdb=" N ARG E 126 " --> pdb=" O ASP E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 168 removed outlier: 4.062A pdb=" N GLN E 157 " --> pdb=" O GLY E 153 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN E 160 " --> pdb=" O ASN E 156 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU E 161 " --> pdb=" O GLN E 157 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU E 166 " --> pdb=" O THR E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 184 Processing sheet with id= A, first strand: chain 'B' and resid 2 through 4 Processing sheet with id= B, first strand: chain 'B' and resid 81 through 84 removed outlier: 7.846A pdb=" N VAL B 158 " --> pdb=" O GLY B 82 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N ILE B 84 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LEU B 160 " --> pdb=" O ILE B 84 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N THR B 189 " --> pdb=" O LEU B 159 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ALA B 161 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N LEU B 191 " --> pdb=" O ALA B 161 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'D' and resid 2 through 4 Processing sheet with id= D, first strand: chain 'D' and resid 81 through 84 removed outlier: 7.576A pdb=" N VAL D 158 " --> pdb=" O GLY D 82 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ILE D 84 " --> pdb=" O VAL D 158 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU D 160 " --> pdb=" O ILE D 84 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N THR D 189 " --> pdb=" O LEU D 159 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ALA D 161 " --> pdb=" O THR D 189 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N LEU D 191 " --> pdb=" O ALA D 161 " (cutoff:3.500A) No H-bonds generated for sheet with id= D 337 hydrogen bonds defined for protein. 1005 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: 2.08 Time building geometry restraints manager: 3.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1405 1.32 - 1.45: 2253 1.45 - 1.57: 4971 1.57 - 1.70: 10 1.70 - 1.83: 64 Bond restraints: 8703 Sorted by residual: bond pdb=" CA ARG E 126 " pdb=" C ARG E 126 " ideal model delta sigma weight residual 1.524 1.415 0.108 1.27e-02 6.20e+03 7.27e+01 bond pdb=" N ALA E 123 " pdb=" CA ALA E 123 " ideal model delta sigma weight residual 1.459 1.380 0.079 1.24e-02 6.50e+03 4.06e+01 bond pdb=" N ARG E 126 " pdb=" CA ARG E 126 " ideal model delta sigma weight residual 1.459 1.385 0.074 1.19e-02 7.06e+03 3.87e+01 bond pdb=" CA ASP E 122 " pdb=" C ASP E 122 " ideal model delta sigma weight residual 1.522 1.438 0.084 1.39e-02 5.18e+03 3.62e+01 bond pdb=" CA TYR A 106 " pdb=" CB TYR A 106 " ideal model delta sigma weight residual 1.530 1.454 0.076 1.58e-02 4.01e+03 2.31e+01 ... (remaining 8698 not shown) Histogram of bond angle deviations from ideal: 94.11 - 103.25: 66 103.25 - 112.38: 4356 112.38 - 121.52: 5333 121.52 - 130.65: 2005 130.65 - 139.79: 55 Bond angle restraints: 11815 Sorted by residual: angle pdb=" N ARG E 126 " pdb=" CA ARG E 126 " pdb=" C ARG E 126 " ideal model delta sigma weight residual 111.07 94.12 16.95 1.07e+00 8.73e-01 2.51e+02 angle pdb=" N ALA E 123 " pdb=" CA ALA E 123 " pdb=" C ALA E 123 " ideal model delta sigma weight residual 111.40 125.08 -13.68 1.22e+00 6.72e-01 1.26e+02 angle pdb=" N ASP E 122 " pdb=" CA ASP E 122 " pdb=" C ASP E 122 " ideal model delta sigma weight residual 111.75 98.58 13.17 1.28e+00 6.10e-01 1.06e+02 angle pdb=" N ALA A 215 " pdb=" CA ALA A 215 " pdb=" C ALA A 215 " ideal model delta sigma weight residual 110.80 94.11 16.69 2.13e+00 2.20e-01 6.14e+01 angle pdb=" C ASP E 122 " pdb=" N ALA E 123 " pdb=" CA ALA E 123 " ideal model delta sigma weight residual 120.71 108.03 12.68 1.67e+00 3.59e-01 5.77e+01 ... (remaining 11810 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.84: 4637 16.84 - 33.68: 443 33.68 - 50.51: 95 50.51 - 67.35: 28 67.35 - 84.19: 8 Dihedral angle restraints: 5211 sinusoidal: 1996 harmonic: 3215 Sorted by residual: dihedral pdb=" C GLN E 127 " pdb=" N GLN E 127 " pdb=" CA GLN E 127 " pdb=" CB GLN E 127 " ideal model delta harmonic sigma weight residual -122.60 -136.60 14.00 0 2.50e+00 1.60e-01 3.14e+01 dihedral pdb=" CA GLN B 163 " pdb=" C GLN B 163 " pdb=" N PRO B 164 " pdb=" CA PRO B 164 " ideal model delta harmonic sigma weight residual 180.00 152.48 27.52 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA ASN B 184 " pdb=" C ASN B 184 " pdb=" N ARG B 185 " pdb=" CA ARG B 185 " ideal model delta harmonic sigma weight residual 180.00 152.87 27.13 0 5.00e+00 4.00e-02 2.94e+01 ... (remaining 5208 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.149: 1355 0.149 - 0.297: 30 0.297 - 0.446: 2 0.446 - 0.594: 2 0.594 - 0.743: 1 Chirality restraints: 1390 Sorted by residual: chirality pdb=" CA ALA E 123 " pdb=" N ALA E 123 " pdb=" C ALA E 123 " pdb=" CB ALA E 123 " both_signs ideal model delta sigma weight residual False 2.48 1.74 0.74 2.00e-01 2.50e+01 1.38e+01 chirality pdb=" CA PHE E 125 " pdb=" N PHE E 125 " pdb=" C PHE E 125 " pdb=" CB PHE E 125 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.62e+00 chirality pdb=" CA GLN E 127 " pdb=" N GLN E 127 " pdb=" C GLN E 127 " pdb=" CB GLN E 127 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.12e+00 ... (remaining 1387 not shown) Planarity restraints: 1505 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU E 121 " -0.024 2.00e-02 2.50e+03 5.12e-02 2.62e+01 pdb=" C LEU E 121 " 0.088 2.00e-02 2.50e+03 pdb=" O LEU E 121 " -0.035 2.00e-02 2.50e+03 pdb=" N ASP E 122 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 213 " 0.019 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C ARG A 213 " -0.067 2.00e-02 2.50e+03 pdb=" O ARG A 213 " 0.025 2.00e-02 2.50e+03 pdb=" N LEU A 214 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 123 " 0.015 2.00e-02 2.50e+03 3.20e-02 1.02e+01 pdb=" C ALA E 123 " -0.055 2.00e-02 2.50e+03 pdb=" O ALA E 123 " 0.021 2.00e-02 2.50e+03 pdb=" N ALA E 124 " 0.019 2.00e-02 2.50e+03 ... (remaining 1502 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2531 2.82 - 3.34: 8111 3.34 - 3.86: 13980 3.86 - 4.38: 15113 4.38 - 4.90: 26184 Nonbonded interactions: 65919 Sorted by model distance: nonbonded pdb=" O ALA C 82 " pdb=" OG1 THR C 86 " model vdw 2.303 2.440 nonbonded pdb=" O SER B 8 " pdb=" OG SER B 55 " model vdw 2.307 2.440 nonbonded pdb=" NE2 GLN B 86 " pdb=" O1B ATP B 301 " model vdw 2.307 2.520 nonbonded pdb=" N ARG E 126 " pdb=" N GLN E 127 " model vdw 2.316 2.560 nonbonded pdb=" OG SER D 173 " pdb=" OE1 GLU D 174 " model vdw 2.324 2.440 ... (remaining 65914 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' and (resid 53 through 60 or (resid 61 and (name N or name CA or name \ C or name O or name CB )) or resid 62 through 119 or (resid 120 and (name N or n \ ame CA or name C or name O or name CB )) or resid 121 through 162 or (resid 163 \ and (name N or name CA or name C or name O or name CB )) or resid 164 through 17 \ 9 or (resid 180 through 181 and (name N or name CA or name C or name O or name C \ B )) or resid 182 through 196 or (resid 197 and (name N or name CA or name C or \ name O or name CB )) or resid 198 or (resid 199 and (name N or name CA or name C \ or name O or name CB )) or resid 200 through 351)) selection = (chain 'C' and ((resid 53 through 55 and (name N or name CA or name C or name O \ or name CB )) or resid 56 through 64 or (resid 65 and (name N or name CA or name \ C or name O or name CB )) or resid 66 through 105 or (resid 106 and (name N or \ name CA or name C or name O or name CB )) or resid 107 through 118 or (resid 119 \ through 120 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 21 through 320 or (resid 321 and (name N or name CA or name C or name O or name \ CB )) or resid 322 through 351)) } ncs_group { reference = (chain 'B' and (resid 1 through 92 or (resid 93 and (name N or name CA or name C \ or name O or name CB )) or resid 94 through 216 or resid 301)) selection = (chain 'D' and (resid 1 through 67 or (resid 68 and (name N or name CA or name C \ or name O or name CB )) or resid 69 or (resid 70 and (name N or name CA or name \ C or name O or name CB )) or resid 71 through 173 or (resid 174 and (name N or \ name CA or name C or name O or name CB )) or resid 175 through 197 or (resid 198 \ and (name N or name CA or name C or name O or name CB )) or resid 199 through 2 \ 16 or resid 301)) } 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: 0.710 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: 3.970 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 26.660 Find NCS groups from input model: 0.500 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:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 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 0.108 8703 Z= 0.388 Angle : 1.248 16.952 11815 Z= 0.649 Chirality : 0.064 0.743 1390 Planarity : 0.006 0.053 1505 Dihedral : 14.811 84.191 3141 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.45 % Allowed : 7.97 % Favored : 91.58 % Rotamer: Outliers : 0.46 % Allowed : 1.16 % Favored : 98.38 % Cbeta Deviations : 0.39 % 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: -2.91 (0.22), residues: 1117 helix: -1.63 (0.18), residues: 570 sheet: -0.81 (0.74), residues: 52 loop : -2.34 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A 210 HIS 0.014 0.001 HIS C 348 PHE 0.029 0.002 PHE A 72 TYR 0.019 0.002 TYR A 95 ARG 0.012 0.001 ARG B 178 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 198 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 MET cc_start: 0.2337 (tpp) cc_final: 0.1902 (tpt) REVERT: A 208 ASP cc_start: 0.7719 (t0) cc_final: 0.7508 (t0) REVERT: C 164 MET cc_start: 0.3143 (ppp) cc_final: 0.2592 (ppp) REVERT: C 206 MET cc_start: 0.3030 (mmm) cc_final: 0.1874 (mmm) REVERT: E 146 GLN cc_start: 0.7178 (mm110) cc_final: 0.6243 (mt0) outliers start: 4 outliers final: 2 residues processed: 201 average time/residue: 0.2016 time to fit residues: 55.2490 Evaluate side-chains 163 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 161 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 126 ARG Chi-restraints excluded: chain E residue 129 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 46 optimal weight: 0.0050 chunk 28 optimal weight: 8.9990 chunk 56 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 overall best weight: 2.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 24 HIS A 110 GLN A 348 HIS ** C 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 HIS ** D 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 GLN ** D 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 GLN ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 GLN E 160 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 8703 Z= 0.364 Angle : 0.740 9.006 11815 Z= 0.369 Chirality : 0.044 0.163 1390 Planarity : 0.004 0.052 1505 Dihedral : 8.905 74.602 1284 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.89 % Favored : 92.66 % Rotamer: Outliers : 2.90 % Allowed : 15.18 % Favored : 81.92 % 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: -1.76 (0.24), residues: 1117 helix: -0.36 (0.21), residues: 593 sheet: -1.36 (0.72), residues: 53 loop : -2.17 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP B 60 HIS 0.005 0.001 HIS B 64 PHE 0.025 0.002 PHE D 4 TYR 0.014 0.001 TYR A 95 ARG 0.008 0.001 ARG A 251 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 176 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 58 LYS cc_start: 0.8852 (ttmm) cc_final: 0.8583 (ttmm) REVERT: C 164 MET cc_start: 0.3328 (ppp) cc_final: 0.2964 (ppp) REVERT: C 227 MET cc_start: 0.8287 (tmm) cc_final: 0.7885 (ttm) REVERT: D 1 MET cc_start: 0.6952 (mmm) cc_final: 0.6580 (mmm) REVERT: D 132 LYS cc_start: 0.8174 (mmtt) cc_final: 0.7957 (mtpp) REVERT: D 155 LYS cc_start: 0.7600 (mmtt) cc_final: 0.7087 (pptt) REVERT: D 162 ASP cc_start: 0.8302 (t0) cc_final: 0.7906 (t70) REVERT: E 129 GLU cc_start: 0.6221 (OUTLIER) cc_final: 0.4718 (tm-30) outliers start: 25 outliers final: 17 residues processed: 191 average time/residue: 0.2049 time to fit residues: 54.3343 Evaluate side-chains 177 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 159 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain E residue 129 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 chunk 83 optimal weight: 4.9990 chunk 68 optimal weight: 0.5980 chunk 27 optimal weight: 9.9990 chunk 100 optimal weight: 2.9990 chunk 108 optimal weight: 7.9990 chunk 89 optimal weight: 0.5980 chunk 99 optimal weight: 0.7980 chunk 34 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 ASN C 345 HIS D 16 GLN ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 GLN ** D 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 HIS E 134 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 8703 Z= 0.301 Angle : 0.680 8.206 11815 Z= 0.337 Chirality : 0.043 0.259 1390 Planarity : 0.004 0.048 1505 Dihedral : 8.599 89.193 1280 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.98 % Favored : 92.57 % Rotamer: Outliers : 4.52 % Allowed : 17.84 % Favored : 77.64 % 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: -1.25 (0.25), residues: 1117 helix: 0.19 (0.22), residues: 601 sheet: -1.33 (0.70), residues: 57 loop : -2.15 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 335 HIS 0.003 0.001 HIS E 130 PHE 0.016 0.001 PHE D 4 TYR 0.012 0.001 TYR A 95 ARG 0.006 0.000 ARG E 159 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 162 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 58 LYS cc_start: 0.8877 (ttmm) cc_final: 0.8603 (ttmm) REVERT: B 104 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8761 (mm) REVERT: B 163 GLN cc_start: 0.7629 (mp10) cc_final: 0.7377 (mp10) REVERT: A 286 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7849 (tt) REVERT: C 155 TRP cc_start: 0.6936 (m-90) cc_final: 0.6568 (m-90) REVERT: C 164 MET cc_start: 0.3520 (ppp) cc_final: 0.3181 (ppp) REVERT: C 227 MET cc_start: 0.8374 (tmm) cc_final: 0.8003 (ttm) REVERT: C 345 HIS cc_start: 0.8731 (OUTLIER) cc_final: 0.7825 (t-90) REVERT: D 162 ASP cc_start: 0.8296 (t0) cc_final: 0.7879 (t70) REVERT: D 212 ASP cc_start: 0.7420 (t0) cc_final: 0.7192 (t0) outliers start: 39 outliers final: 24 residues processed: 187 average time/residue: 0.1902 time to fit residues: 49.3617 Evaluate side-chains 179 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 152 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 345 HIS Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 49 CYS Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 210 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 10.0000 chunk 52 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 chunk 28 optimal weight: 10.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 GLN ** B 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 HIS D 137 GLN ** D 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 8703 Z= 0.380 Angle : 0.721 7.545 11815 Z= 0.361 Chirality : 0.044 0.206 1390 Planarity : 0.004 0.044 1505 Dihedral : 8.416 89.115 1277 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.45 % Allowed : 7.61 % Favored : 91.94 % Rotamer: Outliers : 4.98 % Allowed : 20.28 % Favored : 74.74 % 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: -1.18 (0.25), residues: 1117 helix: 0.28 (0.22), residues: 604 sheet: -1.62 (0.69), residues: 57 loop : -2.13 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 335 HIS 0.018 0.001 HIS C 345 PHE 0.019 0.002 PHE D 4 TYR 0.022 0.001 TYR D 11 ARG 0.006 0.000 ARG A 251 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 165 time to evaluate : 1.028 Fit side-chains REVERT: B 26 GLN cc_start: 0.8073 (mm-40) cc_final: 0.7758 (mm110) REVERT: B 58 LYS cc_start: 0.8875 (ttmm) cc_final: 0.8550 (ttmm) REVERT: B 76 PHE cc_start: 0.8496 (m-80) cc_final: 0.8181 (m-10) REVERT: A 206 MET cc_start: 0.3285 (OUTLIER) cc_final: 0.2610 (tpp) REVERT: A 286 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7834 (tt) REVERT: C 164 MET cc_start: 0.3903 (ppp) cc_final: 0.3611 (ppp) REVERT: C 227 MET cc_start: 0.8467 (tmm) cc_final: 0.8152 (ttm) REVERT: C 345 HIS cc_start: 0.8821 (OUTLIER) cc_final: 0.8032 (t70) REVERT: D 162 ASP cc_start: 0.8392 (t0) cc_final: 0.7981 (t70) REVERT: D 212 ASP cc_start: 0.7582 (t0) cc_final: 0.7359 (t0) REVERT: E 126 ARG cc_start: 0.8157 (tpt-90) cc_final: 0.7431 (mtt90) outliers start: 43 outliers final: 26 residues processed: 192 average time/residue: 0.2088 time to fit residues: 55.0311 Evaluate side-chains 189 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 160 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 345 HIS Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 49 CYS Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain E residue 117 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.9980 chunk 60 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 90 optimal weight: 0.3980 chunk 73 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 54 optimal weight: 0.3980 chunk 95 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 GLN ** D 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8703 Z= 0.194 Angle : 0.646 8.650 11815 Z= 0.319 Chirality : 0.040 0.169 1390 Planarity : 0.003 0.044 1505 Dihedral : 8.020 87.253 1277 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.54 % Allowed : 6.18 % Favored : 93.29 % Rotamer: Outliers : 4.17 % Allowed : 23.06 % Favored : 72.77 % 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: -0.90 (0.26), residues: 1117 helix: 0.57 (0.22), residues: 605 sheet: -1.56 (0.71), residues: 57 loop : -2.10 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 335 HIS 0.004 0.001 HIS D 216 PHE 0.010 0.001 PHE A 72 TYR 0.027 0.001 TYR D 11 ARG 0.003 0.000 ARG A 251 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 175 time to evaluate : 0.969 Fit side-chains revert: symmetry clash REVERT: B 26 GLN cc_start: 0.8026 (mm-40) cc_final: 0.7694 (mm110) REVERT: B 58 LYS cc_start: 0.8850 (ttmm) cc_final: 0.8541 (ttmm) REVERT: B 76 PHE cc_start: 0.8409 (m-80) cc_final: 0.8099 (m-10) REVERT: B 192 MET cc_start: 0.8102 (OUTLIER) cc_final: 0.7427 (tpt) REVERT: A 114 TYR cc_start: 0.4755 (t80) cc_final: 0.4228 (t80) REVERT: A 208 ASP cc_start: 0.7421 (t0) cc_final: 0.7164 (t0) REVERT: A 256 ASN cc_start: 0.9027 (t0) cc_final: 0.8797 (t0) REVERT: C 155 TRP cc_start: 0.7018 (m-90) cc_final: 0.6619 (m-90) REVERT: C 164 MET cc_start: 0.4138 (ppp) cc_final: 0.3848 (ppp) REVERT: C 227 MET cc_start: 0.8315 (tmm) cc_final: 0.7996 (ttm) REVERT: C 335 TRP cc_start: 0.8407 (t-100) cc_final: 0.8090 (t-100) REVERT: C 345 HIS cc_start: 0.8711 (OUTLIER) cc_final: 0.8055 (t-170) REVERT: D 1 MET cc_start: 0.6946 (mmm) cc_final: 0.6712 (mmm) REVERT: D 98 ASP cc_start: 0.8132 (p0) cc_final: 0.7756 (p0) REVERT: D 162 ASP cc_start: 0.8243 (t0) cc_final: 0.7835 (t70) REVERT: D 212 ASP cc_start: 0.7428 (t0) cc_final: 0.7139 (t0) REVERT: E 126 ARG cc_start: 0.8157 (tpt-90) cc_final: 0.7245 (mtt90) REVERT: E 146 GLN cc_start: 0.7175 (mm-40) cc_final: 0.6213 (mt0) outliers start: 36 outliers final: 22 residues processed: 191 average time/residue: 0.1933 time to fit residues: 51.2822 Evaluate side-chains 187 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 163 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 24 HIS Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 71 ASN Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 345 HIS Chi-restraints excluded: chain D residue 49 CYS Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 76 PHE Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain E residue 117 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 106 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 102 optimal weight: 30.0000 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 HIS D 137 GLN D 163 GLN ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8703 Z= 0.326 Angle : 0.708 8.677 11815 Z= 0.350 Chirality : 0.043 0.184 1390 Planarity : 0.004 0.043 1505 Dihedral : 8.089 83.930 1277 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.63 % Allowed : 7.52 % Favored : 91.85 % Rotamer: Outliers : 5.68 % Allowed : 23.29 % Favored : 71.03 % 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: -0.85 (0.26), residues: 1117 helix: 0.61 (0.22), residues: 598 sheet: -1.77 (0.69), residues: 57 loop : -2.01 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 335 HIS 0.008 0.001 HIS C 348 PHE 0.016 0.001 PHE D 4 TYR 0.043 0.002 TYR D 11 ARG 0.004 0.000 ARG A 251 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 165 time to evaluate : 1.003 Fit side-chains revert: symmetry clash REVERT: B 26 GLN cc_start: 0.8066 (mm-40) cc_final: 0.7749 (mm110) REVERT: B 58 LYS cc_start: 0.8835 (ttmm) cc_final: 0.8529 (ttmm) REVERT: B 76 PHE cc_start: 0.8551 (m-80) cc_final: 0.8341 (m-10) REVERT: B 83 MET cc_start: 0.7377 (OUTLIER) cc_final: 0.6910 (ttt) REVERT: B 192 MET cc_start: 0.8184 (OUTLIER) cc_final: 0.7443 (tpt) REVERT: A 114 TYR cc_start: 0.4852 (t80) cc_final: 0.4368 (t80) REVERT: A 206 MET cc_start: 0.3026 (tpp) cc_final: 0.1961 (tpp) REVERT: A 208 ASP cc_start: 0.7461 (t0) cc_final: 0.7212 (t0) REVERT: A 256 ASN cc_start: 0.9094 (t0) cc_final: 0.8829 (t0) REVERT: C 134 GLU cc_start: 0.5689 (pp20) cc_final: 0.5383 (tm-30) REVERT: C 155 TRP cc_start: 0.7094 (m-90) cc_final: 0.6672 (m-90) REVERT: C 227 MET cc_start: 0.8416 (tmm) cc_final: 0.8135 (ttm) REVERT: C 248 ILE cc_start: 0.8998 (OUTLIER) cc_final: 0.8778 (mp) REVERT: C 335 TRP cc_start: 0.8485 (t-100) cc_final: 0.8140 (t-100) REVERT: C 345 HIS cc_start: 0.8722 (OUTLIER) cc_final: 0.8011 (t70) REVERT: D 98 ASP cc_start: 0.8284 (p0) cc_final: 0.7898 (p0) REVERT: D 162 ASP cc_start: 0.8401 (t0) cc_final: 0.7914 (t70) REVERT: D 212 ASP cc_start: 0.7562 (t0) cc_final: 0.7277 (t0) REVERT: E 126 ARG cc_start: 0.8134 (tpt-90) cc_final: 0.7129 (mtt90) outliers start: 49 outliers final: 34 residues processed: 194 average time/residue: 0.1972 time to fit residues: 52.7174 Evaluate side-chains 205 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 167 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 24 HIS Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 345 HIS Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 49 CYS Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain E residue 117 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.7980 chunk 60 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 89 optimal weight: 0.4980 chunk 59 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 42 optimal weight: 0.4980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 HIS D 137 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8703 Z= 0.252 Angle : 0.695 10.637 11815 Z= 0.344 Chirality : 0.042 0.199 1390 Planarity : 0.004 0.044 1505 Dihedral : 7.976 88.856 1277 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.54 % Allowed : 6.71 % Favored : 92.75 % Rotamer: Outliers : 4.98 % Allowed : 24.91 % Favored : 70.10 % 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: -0.78 (0.26), residues: 1117 helix: 0.70 (0.22), residues: 605 sheet: -1.76 (0.70), residues: 57 loop : -2.05 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 335 HIS 0.004 0.001 HIS D 216 PHE 0.018 0.001 PHE C 182 TYR 0.040 0.002 TYR D 11 ARG 0.004 0.000 ARG A 251 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 165 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 26 GLN cc_start: 0.8039 (mm-40) cc_final: 0.7755 (mm110) REVERT: B 53 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.7586 (mmp80) REVERT: B 58 LYS cc_start: 0.8811 (ttmm) cc_final: 0.8521 (ttmm) REVERT: B 83 MET cc_start: 0.7389 (OUTLIER) cc_final: 0.6880 (ttt) REVERT: B 192 MET cc_start: 0.8092 (OUTLIER) cc_final: 0.7339 (tpt) REVERT: A 114 TYR cc_start: 0.4834 (t80) cc_final: 0.4285 (t80) REVERT: A 206 MET cc_start: 0.3104 (tpp) cc_final: 0.2236 (tpp) REVERT: A 256 ASN cc_start: 0.9184 (t0) cc_final: 0.8945 (t0) REVERT: C 155 TRP cc_start: 0.7115 (m-90) cc_final: 0.6684 (m-90) REVERT: C 227 MET cc_start: 0.8307 (tmm) cc_final: 0.8013 (ttm) REVERT: C 248 ILE cc_start: 0.8993 (OUTLIER) cc_final: 0.8762 (mp) REVERT: C 335 TRP cc_start: 0.8462 (t-100) cc_final: 0.8129 (t-100) REVERT: C 345 HIS cc_start: 0.8693 (OUTLIER) cc_final: 0.7619 (t-90) REVERT: D 162 ASP cc_start: 0.8293 (t0) cc_final: 0.7846 (t70) REVERT: D 212 ASP cc_start: 0.7556 (t0) cc_final: 0.7249 (t0) REVERT: E 126 ARG cc_start: 0.8121 (tpt-90) cc_final: 0.7125 (mtt90) REVERT: E 146 GLN cc_start: 0.7187 (mm-40) cc_final: 0.6258 (mt0) outliers start: 43 outliers final: 32 residues processed: 192 average time/residue: 0.1975 time to fit residues: 52.0225 Evaluate side-chains 198 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 161 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 24 HIS Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 53 ARG Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 345 HIS Chi-restraints excluded: chain D residue 49 CYS Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain E residue 117 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 chunk 20 optimal weight: 0.4980 chunk 67 optimal weight: 4.9990 chunk 72 optimal weight: 0.0050 chunk 52 optimal weight: 0.1980 chunk 9 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 96 optimal weight: 0.0970 chunk 101 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 ASN ** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 HIS D 137 GLN ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8703 Z= 0.199 Angle : 0.669 8.609 11815 Z= 0.332 Chirality : 0.041 0.208 1390 Planarity : 0.003 0.040 1505 Dihedral : 7.670 80.298 1277 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.45 % Allowed : 7.52 % Favored : 92.03 % Rotamer: Outliers : 4.75 % Allowed : 25.14 % Favored : 70.10 % 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: -0.65 (0.26), residues: 1117 helix: 0.82 (0.22), residues: 604 sheet: -1.72 (0.71), residues: 57 loop : -2.02 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 335 HIS 0.011 0.001 HIS C 345 PHE 0.010 0.001 PHE A 152 TYR 0.011 0.001 TYR E 151 ARG 0.005 0.000 ARG E 115 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 173 time to evaluate : 1.036 Fit side-chains revert: symmetry clash REVERT: B 26 GLN cc_start: 0.7862 (mm-40) cc_final: 0.7553 (mm110) REVERT: B 53 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.7567 (mmp80) REVERT: B 58 LYS cc_start: 0.8852 (ttmm) cc_final: 0.8518 (ttmm) REVERT: B 83 MET cc_start: 0.7267 (OUTLIER) cc_final: 0.6766 (ttt) REVERT: B 184 ASN cc_start: 0.8161 (t0) cc_final: 0.7839 (t0) REVERT: B 192 MET cc_start: 0.8011 (OUTLIER) cc_final: 0.7281 (tpt) REVERT: A 114 TYR cc_start: 0.5438 (t80) cc_final: 0.4751 (t80) REVERT: A 206 MET cc_start: 0.2978 (tpp) cc_final: 0.2250 (tpp) REVERT: A 256 ASN cc_start: 0.9123 (t0) cc_final: 0.8884 (t0) REVERT: C 155 TRP cc_start: 0.7182 (m-90) cc_final: 0.6725 (m-90) REVERT: C 227 MET cc_start: 0.8252 (tmm) cc_final: 0.8007 (ttm) REVERT: C 248 ILE cc_start: 0.8995 (OUTLIER) cc_final: 0.8768 (mp) REVERT: C 335 TRP cc_start: 0.8439 (t-100) cc_final: 0.8160 (t-100) REVERT: C 345 HIS cc_start: 0.8480 (OUTLIER) cc_final: 0.7721 (t-90) REVERT: D 60 TRP cc_start: 0.6983 (m-10) cc_final: 0.6770 (m-10) REVERT: D 162 ASP cc_start: 0.8310 (t0) cc_final: 0.7829 (t70) REVERT: D 212 ASP cc_start: 0.7511 (t0) cc_final: 0.7197 (t0) REVERT: E 126 ARG cc_start: 0.8123 (tpt-90) cc_final: 0.7098 (mtt90) REVERT: E 146 GLN cc_start: 0.7206 (mm-40) cc_final: 0.6320 (mt0) outliers start: 41 outliers final: 30 residues processed: 199 average time/residue: 0.2210 time to fit residues: 60.0163 Evaluate side-chains 199 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 164 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 24 HIS Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 53 ARG Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 345 HIS Chi-restraints excluded: chain D residue 49 CYS Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain E residue 117 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 1.9990 chunk 101 optimal weight: 50.0000 chunk 59 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 89 optimal weight: 0.9990 chunk 93 optimal weight: 0.4980 chunk 64 optimal weight: 8.9990 chunk 104 optimal weight: 0.0570 chunk 63 optimal weight: 9.9990 overall best weight: 1.1104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 HIS C 348 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 8703 Z= 0.258 Angle : 0.696 9.514 11815 Z= 0.347 Chirality : 0.042 0.202 1390 Planarity : 0.003 0.038 1505 Dihedral : 7.570 77.458 1277 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.89 % Favored : 92.66 % Rotamer: Outliers : 4.63 % Allowed : 25.26 % Favored : 70.10 % 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: -0.58 (0.26), residues: 1117 helix: 0.88 (0.22), residues: 604 sheet: -1.78 (0.71), residues: 57 loop : -1.97 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 335 HIS 0.009 0.001 HIS C 345 PHE 0.011 0.001 PHE D 180 TYR 0.012 0.001 TYR C 105 ARG 0.007 0.000 ARG B 178 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 162 time to evaluate : 0.981 Fit side-chains revert: symmetry clash REVERT: B 26 GLN cc_start: 0.7870 (mm-40) cc_final: 0.7597 (mm110) REVERT: B 53 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.7606 (mmp80) REVERT: B 58 LYS cc_start: 0.8858 (ttmm) cc_final: 0.8508 (ttmm) REVERT: B 83 MET cc_start: 0.7272 (OUTLIER) cc_final: 0.6799 (ttt) REVERT: B 184 ASN cc_start: 0.8153 (t0) cc_final: 0.7834 (t0) REVERT: B 192 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7335 (tpt) REVERT: A 114 TYR cc_start: 0.5489 (t80) cc_final: 0.5241 (t80) REVERT: A 256 ASN cc_start: 0.9112 (t0) cc_final: 0.8870 (t0) REVERT: C 134 GLU cc_start: 0.7357 (tm-30) cc_final: 0.6788 (tm-30) REVERT: C 155 TRP cc_start: 0.7178 (m-90) cc_final: 0.6708 (m-90) REVERT: C 227 MET cc_start: 0.8261 (tmm) cc_final: 0.7992 (ttm) REVERT: C 248 ILE cc_start: 0.9000 (OUTLIER) cc_final: 0.8770 (mp) REVERT: C 335 TRP cc_start: 0.8463 (t-100) cc_final: 0.8192 (t-100) REVERT: C 345 HIS cc_start: 0.8419 (OUTLIER) cc_final: 0.7760 (t-90) REVERT: D 162 ASP cc_start: 0.8276 (t0) cc_final: 0.7794 (t70) REVERT: D 212 ASP cc_start: 0.7536 (t0) cc_final: 0.7236 (t0) REVERT: E 126 ARG cc_start: 0.8104 (tpt-90) cc_final: 0.7064 (mtt90) REVERT: E 146 GLN cc_start: 0.7295 (mm-40) cc_final: 0.6421 (mt0) outliers start: 40 outliers final: 30 residues processed: 187 average time/residue: 0.2030 time to fit residues: 52.2764 Evaluate side-chains 194 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 159 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 24 HIS Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 53 ARG Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 345 HIS Chi-restraints excluded: chain D residue 49 CYS Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain E residue 117 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.6980 chunk 72 optimal weight: 0.5980 chunk 109 optimal weight: 50.0000 chunk 100 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 26 optimal weight: 9.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 HIS C 348 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8703 Z= 0.246 Angle : 0.697 9.693 11815 Z= 0.345 Chirality : 0.042 0.206 1390 Planarity : 0.003 0.037 1505 Dihedral : 7.479 77.668 1277 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.45 % Allowed : 7.25 % Favored : 92.30 % Rotamer: Outliers : 4.63 % Allowed : 25.72 % Favored : 69.64 % 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: -0.60 (0.26), residues: 1117 helix: 0.88 (0.22), residues: 604 sheet: -2.55 (0.77), residues: 45 loop : -1.93 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 335 HIS 0.007 0.001 HIS C 348 PHE 0.010 0.001 PHE D 4 TYR 0.014 0.001 TYR C 106 ARG 0.007 0.000 ARG B 178 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 162 time to evaluate : 0.972 Fit side-chains revert: symmetry clash REVERT: B 26 GLN cc_start: 0.7833 (mm-40) cc_final: 0.7565 (mm110) REVERT: B 58 LYS cc_start: 0.8855 (ttmm) cc_final: 0.8501 (ttmm) REVERT: B 83 MET cc_start: 0.7232 (OUTLIER) cc_final: 0.6702 (ttt) REVERT: B 184 ASN cc_start: 0.8123 (t0) cc_final: 0.7819 (t0) REVERT: B 192 MET cc_start: 0.8040 (OUTLIER) cc_final: 0.7279 (tpt) REVERT: A 114 TYR cc_start: 0.5569 (t80) cc_final: 0.5340 (t80) REVERT: A 256 ASN cc_start: 0.9111 (t0) cc_final: 0.8874 (t0) REVERT: C 155 TRP cc_start: 0.7171 (m-90) cc_final: 0.6668 (m-90) REVERT: C 227 MET cc_start: 0.8248 (tmm) cc_final: 0.7990 (ttm) REVERT: C 248 ILE cc_start: 0.9003 (OUTLIER) cc_final: 0.8766 (mp) REVERT: C 335 TRP cc_start: 0.8460 (t-100) cc_final: 0.8179 (t-100) REVERT: D 162 ASP cc_start: 0.8347 (t0) cc_final: 0.7848 (t70) REVERT: D 212 ASP cc_start: 0.7536 (t0) cc_final: 0.7220 (t0) REVERT: E 126 ARG cc_start: 0.8112 (tpt-90) cc_final: 0.7087 (mtt90) REVERT: E 146 GLN cc_start: 0.7392 (mm-40) cc_final: 0.6516 (mt0) outliers start: 40 outliers final: 35 residues processed: 185 average time/residue: 0.1890 time to fit residues: 48.8362 Evaluate side-chains 197 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 159 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 24 HIS Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 345 HIS Chi-restraints excluded: chain D residue 49 CYS Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain E residue 117 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 36 optimal weight: 7.9990 chunk 89 optimal weight: 0.3980 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.2980 chunk 76 optimal weight: 0.0470 chunk 4 optimal weight: 0.5980 chunk 63 optimal weight: 5.9990 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 HIS C 348 HIS ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.156563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.115130 restraints weight = 14612.486| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.78 r_work: 0.3390 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8703 Z= 0.194 Angle : 0.682 9.478 11815 Z= 0.337 Chirality : 0.041 0.211 1390 Planarity : 0.003 0.037 1505 Dihedral : 7.313 80.347 1277 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.80 % Favored : 92.75 % Rotamer: Outliers : 4.06 % Allowed : 26.07 % Favored : 69.87 % 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: -0.48 (0.26), residues: 1117 helix: 0.99 (0.22), residues: 601 sheet: -2.55 (0.78), residues: 45 loop : -1.86 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 335 HIS 0.007 0.001 HIS C 348 PHE 0.008 0.001 PHE B 85 TYR 0.014 0.001 TYR C 106 ARG 0.007 0.000 ARG B 178 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2071.70 seconds wall clock time: 38 minutes 9.86 seconds (2289.86 seconds total)