Starting phenix.real_space_refine on Sat Aug 3 10:40:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6i_37324/08_2024/8w6i_37324.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6i_37324/08_2024/8w6i_37324.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6i_37324/08_2024/8w6i_37324.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6i_37324/08_2024/8w6i_37324.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6i_37324/08_2024/8w6i_37324.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6i_37324/08_2024/8w6i_37324.cif" } resolution = 3.7 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= 0.001 sd= 0.024 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 34 5.16 5 C 4949 2.51 5 N 1349 2.21 5 O 1412 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 134": "OE1" <-> "OE2" Residue "C GLU 138": "OE1" <-> "OE2" Residue "C PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 142": "OE1" <-> "OE2" Residue "D GLU 163": "OE1" <-> "OE2" Residue "D GLU 174": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 7750 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1637 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 7, 'TRANS': 209} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 32 Chain: "C" Number of atoms: 2204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2204 Classifications: {'peptide': 292} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 9, 'TRANS': 282} Chain breaks: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "D" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1673 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 7, 'TRANS': 211} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 2174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2174 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 9, 'TRANS': 283} Chain breaks: 1 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 4, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 55 Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.66, per 1000 atoms: 0.60 Number of scatterers: 7750 At special positions: 0 Unit cell: (63.6, 81.62, 148.4, 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 34 16.00 P 6 15.00 O 1412 8.00 N 1349 7.00 C 4949 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: 2.95 Conformation dependent library (CDL) restraints added in 1.6 seconds 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1864 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 6 sheets defined 58.0% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'B' and resid 41 through 48 removed outlier: 3.850A pdb=" N ILE B 48 " --> pdb=" O LEU B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 78 Processing helix chain 'B' and resid 79 through 81 No H-bonds generated for 'chain 'B' and resid 79 through 81' Processing helix chain 'B' and resid 95 through 99 removed outlier: 3.604A pdb=" N ASP B 98 " --> pdb=" O THR B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 108 Processing helix chain 'B' and resid 110 through 112 No H-bonds generated for 'chain 'B' and resid 110 through 112' Processing helix chain 'B' and resid 113 through 124 removed outlier: 4.427A pdb=" N LYS B 124 " --> pdb=" O ALA B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 138 removed outlier: 3.584A pdb=" N GLN B 137 " --> pdb=" O PHE B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 149 removed outlier: 4.208A pdb=" N ARG B 145 " --> pdb=" O GLY B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 182 Processing helix chain 'B' and resid 183 through 186 Processing helix chain 'B' and resid 199 through 203 removed outlier: 3.530A pdb=" N ARG B 202 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG B 203 " --> pdb=" O ILE B 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 199 through 203' Processing helix chain 'C' and resid 56 through 70 removed outlier: 3.740A pdb=" N ALA C 63 " --> pdb=" O ALA C 59 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU C 64 " --> pdb=" O PHE C 60 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN C 65 " --> pdb=" O HIS C 61 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LYS C 70 " --> pdb=" O ASP C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 83 removed outlier: 4.048A pdb=" N ILE C 81 " --> pdb=" O THR C 77 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE C 83 " --> pdb=" O MET C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 102 removed outlier: 4.045A pdb=" N SER C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL C 98 " --> pdb=" O VAL C 94 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN C 100 " --> pdb=" O LYS C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 134 removed outlier: 3.594A pdb=" N VAL C 127 " --> pdb=" O ALA C 123 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA C 133 " --> pdb=" O ALA C 129 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLU C 134 " --> pdb=" O GLN C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 160 removed outlier: 3.815A pdb=" N ARG C 153 " --> pdb=" O LEU C 149 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ASN C 154 " --> pdb=" O GLY C 150 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N TRP C 155 " --> pdb=" O GLU C 151 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER C 156 " --> pdb=" O PHE C 152 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY C 157 " --> pdb=" O ARG C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 198 removed outlier: 4.117A pdb=" N ASN C 189 " --> pdb=" O THR C 185 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N THR C 190 " --> pdb=" O GLU C 186 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU C 191 " --> pdb=" O SER C 187 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG C 194 " --> pdb=" O THR C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 215 Processing helix chain 'C' and resid 216 through 250 removed outlier: 3.703A pdb=" N LEU C 220 " --> pdb=" O ALA C 216 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE C 240 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLY C 241 " --> pdb=" O PHE C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 261 removed outlier: 3.993A pdb=" N ASN C 256 " --> pdb=" O ARG C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 304 removed outlier: 3.533A pdb=" N ILE C 268 " --> pdb=" O THR C 264 " (cutoff:3.500A) Proline residue: C 271 - end of helix removed outlier: 3.627A pdb=" N ILE C 293 " --> pdb=" O ILE C 289 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU C 294 " --> pdb=" O LEU C 290 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLU C 304 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 309 Processing helix chain 'C' and resid 319 through 347 removed outlier: 3.611A pdb=" N LEU C 324 " --> pdb=" O PHE C 320 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU C 325 " --> pdb=" O ASP C 321 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN C 344 " --> pdb=" O LEU C 340 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N HIS C 345 " --> pdb=" O ALA C 341 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG C 347 " --> pdb=" O VAL C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 350 No H-bonds generated for 'chain 'C' and resid 348 through 350' Processing helix chain 'D' and resid 42 through 47 Processing helix chain 'D' and resid 73 through 78 removed outlier: 3.639A pdb=" N ARG D 78 " --> pdb=" O VAL D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 100 Processing helix chain 'D' and resid 101 through 108 removed outlier: 3.616A pdb=" N ILE D 105 " --> pdb=" O ALA D 101 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ILE D 106 " --> pdb=" O ILE D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 126 removed outlier: 4.362A pdb=" N ARG D 115 " --> pdb=" O GLY D 111 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG D 116 " --> pdb=" O ASP D 112 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS D 124 " --> pdb=" O ALA D 120 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL D 125 " --> pdb=" O ALA D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 153 removed outlier: 4.067A pdb=" N ALA D 151 " --> pdb=" O GLY D 147 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL D 152 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL D 153 " --> pdb=" O ALA D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 182 removed outlier: 3.721A pdb=" N GLU D 174 " --> pdb=" O ASP D 170 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLY D 175 " --> pdb=" O ALA D 171 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE D 180 " --> pdb=" O ILE D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 186 Processing helix chain 'D' and resid 197 through 202 Processing helix chain 'A' and resid 56 through 68 Processing helix chain 'A' and resid 70 through 85 removed outlier: 3.725A pdb=" N SER A 84 " --> pdb=" O VAL A 80 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU A 85 " --> pdb=" O ILE A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 101 removed outlier: 3.684A pdb=" N SER A 89 " --> pdb=" O LEU A 85 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL A 98 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASN A 99 " --> pdb=" O TYR A 95 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLN A 100 " --> pdb=" O LYS A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 133 removed outlier: 3.784A pdb=" N ALA A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ALA A 125 " --> pdb=" O ASP A 121 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLY A 126 " --> pdb=" O ASP A 122 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ALA A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLN A 130 " --> pdb=" O GLY A 126 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A 131 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA A 133 " --> pdb=" O ALA A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 154 Processing helix chain 'A' and resid 184 through 192 removed outlier: 3.653A pdb=" N LEU A 188 " --> pdb=" O GLY A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 250 removed outlier: 3.550A pdb=" N GLY A 219 " --> pdb=" O ALA A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 261 removed outlier: 3.993A pdb=" N GLN A 258 " --> pdb=" O SER A 254 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS A 259 " --> pdb=" O ILE A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 288 removed outlier: 3.646A pdb=" N ILE A 268 " --> pdb=" O THR A 264 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU A 269 " --> pdb=" O ASP A 265 " (cutoff:3.500A) Proline residue: A 271 - end of helix removed outlier: 3.696A pdb=" N GLY A 275 " --> pdb=" O PRO A 271 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU A 285 " --> pdb=" O PHE A 281 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER A 287 " --> pdb=" O GLY A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 299 Processing helix chain 'A' and resid 299 through 307 removed outlier: 4.100A pdb=" N ALA A 303 " --> pdb=" O SER A 299 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLU A 304 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 310 No H-bonds generated for 'chain 'A' and resid 308 through 310' Processing helix chain 'A' and resid 319 through 348 removed outlier: 3.638A pdb=" N LEU A 324 " --> pdb=" O PHE A 320 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU A 325 " --> pdb=" O ASP A 321 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE A 333 " --> pdb=" O VAL A 329 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLY A 334 " --> pdb=" O CYS A 330 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA A 338 " --> pdb=" O GLY A 334 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N TRP A 339 " --> pdb=" O TRP A 335 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A 343 " --> pdb=" O TRP A 339 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N HIS A 348 " --> pdb=" O GLN A 344 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 2 through 3 Processing sheet with id=AA2, first strand: chain 'B' and resid 30 through 32 removed outlier: 3.737A pdb=" N LEU B 191 " --> pdb=" O LEU B 159 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 173 through 174 removed outlier: 4.134A pdb=" N VAL C 113 " --> pdb=" O ALA C 174 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU C 203 " --> pdb=" O TYR C 114 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 2 through 3 Processing sheet with id=AA5, first strand: chain 'D' and resid 32 through 33 removed outlier: 3.570A pdb=" N GLY D 82 " --> pdb=" O VAL D 158 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU D 160 " --> pdb=" O GLY D 82 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 60 through 61 338 hydrogen bonds defined for protein. 984 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: 1.79 Time building geometry restraints manager: 3.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 2599 1.36 - 1.51: 2092 1.51 - 1.66: 3143 1.66 - 1.80: 34 1.80 - 1.95: 24 Bond restraints: 7892 Sorted by residual: bond pdb=" CA VAL B 74 " pdb=" CB VAL B 74 " ideal model delta sigma weight residual 1.534 1.551 -0.016 6.80e-03 2.16e+04 5.89e+00 bond pdb=" CA VAL B 74 " pdb=" C VAL B 74 " ideal model delta sigma weight residual 1.520 1.539 -0.019 8.80e-03 1.29e+04 4.72e+00 bond pdb=" CA ASN D 154 " pdb=" C ASN D 154 " ideal model delta sigma weight residual 1.526 1.556 -0.030 1.75e-02 3.27e+03 2.95e+00 bond pdb=" C TYR A 106 " pdb=" N PRO A 107 " ideal model delta sigma weight residual 1.334 1.373 -0.039 2.34e-02 1.83e+03 2.80e+00 bond pdb=" CB ASN D 154 " pdb=" CG ASN D 154 " ideal model delta sigma weight residual 1.516 1.557 -0.041 2.50e-02 1.60e+03 2.73e+00 ... (remaining 7887 not shown) Histogram of bond angle deviations from ideal: 98.54 - 105.74: 144 105.74 - 112.95: 4170 112.95 - 120.16: 3053 120.16 - 127.37: 3286 127.37 - 134.57: 77 Bond angle restraints: 10730 Sorted by residual: angle pdb=" CB LYS D 155 " pdb=" CG LYS D 155 " pdb=" CD LYS D 155 " ideal model delta sigma weight residual 111.30 123.84 -12.54 2.30e+00 1.89e-01 2.97e+01 angle pdb=" C ASN A 199 " pdb=" CA ASN A 199 " pdb=" CB ASN A 199 " ideal model delta sigma weight residual 117.23 110.57 6.66 1.36e+00 5.41e-01 2.40e+01 angle pdb=" CB MET D 92 " pdb=" CG MET D 92 " pdb=" SD MET D 92 " ideal model delta sigma weight residual 112.70 126.70 -14.00 3.00e+00 1.11e-01 2.18e+01 angle pdb=" C PRO D 164 " pdb=" N THR D 165 " pdb=" CA THR D 165 " ideal model delta sigma weight residual 121.54 129.65 -8.11 1.91e+00 2.74e-01 1.80e+01 angle pdb=" CA VAL B 74 " pdb=" C VAL B 74 " pdb=" N PRO B 75 " ideal model delta sigma weight residual 121.00 124.52 -3.52 8.30e-01 1.45e+00 1.79e+01 ... (remaining 10725 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.85: 4180 16.85 - 33.70: 385 33.70 - 50.55: 87 50.55 - 67.41: 10 67.41 - 84.26: 5 Dihedral angle restraints: 4667 sinusoidal: 1766 harmonic: 2901 Sorted by residual: dihedral pdb=" CA VAL D 74 " pdb=" C VAL D 74 " pdb=" N PRO D 75 " pdb=" CA PRO D 75 " ideal model delta harmonic sigma weight residual 180.00 152.95 27.05 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA GLU D 163 " pdb=" C GLU D 163 " pdb=" N PRO D 164 " pdb=" CA PRO D 164 " ideal model delta harmonic sigma weight residual 180.00 155.53 24.47 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA LEU A 260 " pdb=" C LEU A 260 " pdb=" N ILE A 261 " pdb=" CA ILE A 261 " ideal model delta harmonic sigma weight residual 180.00 159.91 20.09 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 4664 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1034 0.069 - 0.137: 208 0.137 - 0.206: 24 0.206 - 0.274: 4 0.274 - 0.343: 3 Chirality restraints: 1273 Sorted by residual: chirality pdb=" CB VAL C 302 " pdb=" CA VAL C 302 " pdb=" CG1 VAL C 302 " pdb=" CG2 VAL C 302 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" CB VAL D 74 " pdb=" CA VAL D 74 " pdb=" CG1 VAL D 74 " pdb=" CG2 VAL D 74 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" CB ILE D 59 " pdb=" CA ILE D 59 " pdb=" CG1 ILE D 59 " pdb=" CG2 ILE D 59 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.25e+00 ... (remaining 1270 not shown) Planarity restraints: 1363 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D 74 " 0.072 5.00e-02 4.00e+02 1.07e-01 1.83e+01 pdb=" N PRO D 75 " -0.185 5.00e-02 4.00e+02 pdb=" CA PRO D 75 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO D 75 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 335 " -0.019 2.00e-02 2.50e+03 2.05e-02 1.05e+01 pdb=" CG TRP C 335 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 TRP C 335 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP C 335 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 335 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 335 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 335 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 335 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 335 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP C 335 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 76 " 0.017 2.00e-02 2.50e+03 2.00e-02 7.00e+00 pdb=" CG PHE D 76 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE D 76 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE D 76 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE D 76 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE D 76 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE D 76 " 0.001 2.00e-02 2.50e+03 ... (remaining 1360 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 2340 2.83 - 3.34: 7406 3.34 - 3.86: 12699 3.86 - 4.38: 13892 4.38 - 4.90: 23306 Nonbonded interactions: 59643 Sorted by model distance: nonbonded pdb=" O ASP D 169 " pdb=" OG SER D 173 " model vdw 2.308 3.040 nonbonded pdb=" O GLN C 65 " pdb=" OG SER C 69 " model vdw 2.314 3.040 nonbonded pdb=" O THR C 86 " pdb=" OG SER C 89 " model vdw 2.328 3.040 nonbonded pdb=" OE2 GLU B 181 " pdb=" OH TYR B 205 " model vdw 2.329 3.040 nonbonded pdb=" OG SER B 110 " pdb=" OD1 ASP B 113 " model vdw 2.345 3.040 ... (remaining 59638 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 53 through 67 or (resid 68 and (name N or name CA or name \ C or name O or name CB )) or resid 69 through 78 or (resid 79 and (name N or nam \ e CA or name C or name O or name CB )) or resid 80 through 138 or (resid 139 and \ (name N or name CA or name C or name O or name CB )) or resid 140 through 154 o \ r (resid 155 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 56 through 160 or resid 168 through 185 or (resid 186 and (name N or name CA or \ name C or name O or name CB )) or resid 187 through 317 or (resid 318 and (name \ N or name CA or name C or name O or name CB )) or resid 319 through 351)) selection = (chain 'C' and (resid 53 through 64 or (resid 65 and (name N or name CA or name \ C or name O or name CB )) or resid 66 through 69 or (resid 70 and (name N or nam \ e CA or name C or name O or name CB )) or resid 71 through 95 or (resid 96 and ( \ name N or name CA or name C or name O or name CB )) or resid 97 through 121 or ( \ resid 122 through 125 and (name N or name CA or name C or name O or name CB )) o \ r resid 126 through 146 or (resid 147 through 148 and (name N or name CA or name \ C or name O or name CB )) or resid 149 through 179 or (resid 180 through 182 an \ d (name N or name CA or name C or name O or name CB )) or resid 183 through 184 \ or (resid 185 through 186 and (name N or name CA or name C or name O or name CB \ )) or resid 187 through 193 or (resid 194 and (name N or name CA or name C or na \ me O or name CB )) or resid 195 through 204 or (resid 205 and (name N or name CA \ or name C or name O or name CB )) or resid 206 through 296 or (resid 297 and (n \ ame N or name CA or name C or name O or name CB )) or resid 298 through 311 or ( \ resid 312 and (name N or name CA or name C or name O or name CB )) or resid 313 \ or (resid 314 and (name N or name CA or name C or name O or name CB )) or resid \ 315 through 347 or (resid 348 and (name N or name CA or name C or name O or name \ CB )) or resid 349 through 351)) } ncs_group { reference = (chain 'B' and (resid 1 through 11 or (resid 12 and (name N or name CA or name C \ or name O or name CB )) or resid 13 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 na \ me CA or name C or name O or name CB )) or resid 71 through 92 or (resid 93 and \ (name N or name CA or name C or name O or name CB )) or resid 94 through 217 or \ resid 301)) selection = (chain 'D' and (resid 1 through 2 or (resid 3 and (name N or name CA or name C o \ r name O or name CB )) or resid 4 through 25 or (resid 26 and (name N or name CA \ or name C or name O or name CB )) or resid 27 through 28 or (resid 29 through 3 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 32 through 7 \ 2 or (resid 73 and (name N or name CA or name C or name O or name CB )) or resid \ 74 through 78 or (resid 79 and (name N or name CA or name C or name O or name C \ B )) or resid 80 through 131 or (resid 132 and (name N or name CA or name C or n \ ame O or name CB )) or resid 133 through 154 or (resid 155 and (name N or name C \ A or name C or name O or name CB )) or resid 156 through 184 or (resid 185 and ( \ name N or name CA or name C or name O or name CB )) or resid 186 through 217 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 23.140 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 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 : 0.004 0.054 7892 Z= 0.293 Angle : 1.097 14.000 10730 Z= 0.528 Chirality : 0.056 0.343 1273 Planarity : 0.007 0.107 1363 Dihedral : 13.870 84.257 2803 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.05 % Favored : 94.65 % Rotamer: Outliers : 0.13 % Allowed : 0.63 % Favored : 99.25 % 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: -3.33 (0.23), residues: 1009 helix: -2.01 (0.19), residues: 501 sheet: -1.63 (0.63), residues: 70 loop : -2.44 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP C 335 HIS 0.010 0.001 HIS B 214 PHE 0.046 0.002 PHE D 76 TYR 0.030 0.002 TYR C 106 ARG 0.016 0.001 ARG C 252 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 200 time to evaluate : 0.940 Fit side-chains REVERT: B 87 ASP cc_start: 0.8316 (p0) cc_final: 0.8058 (p0) REVERT: B 116 ARG cc_start: 0.8828 (ptt90) cc_final: 0.8567 (tmm-80) REVERT: C 61 HIS cc_start: 0.8298 (t-90) cc_final: 0.8002 (t70) REVERT: D 59 ILE cc_start: 0.5845 (tp) cc_final: 0.5644 (tp) REVERT: D 85 PHE cc_start: 0.8401 (m-10) cc_final: 0.8070 (m-10) REVERT: D 87 ASP cc_start: 0.8192 (p0) cc_final: 0.7866 (p0) REVERT: D 89 HIS cc_start: 0.6507 (m90) cc_final: 0.6193 (m90) REVERT: A 95 TYR cc_start: 0.7979 (t80) cc_final: 0.7714 (t80) REVERT: A 100 GLN cc_start: 0.9245 (mp10) cc_final: 0.9027 (mp10) REVERT: A 206 MET cc_start: 0.4213 (mmp) cc_final: 0.3591 (mmp) REVERT: A 232 MET cc_start: 0.8157 (mmm) cc_final: 0.7573 (mtt) REVERT: A 344 GLN cc_start: 0.7785 (tt0) cc_final: 0.7154 (tm-30) outliers start: 1 outliers final: 0 residues processed: 200 average time/residue: 0.1858 time to fit residues: 50.1798 Evaluate side-chains 163 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.0980 chunk 75 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 chunk 25 optimal weight: 0.3980 chunk 51 optimal weight: 7.9990 chunk 40 optimal weight: 0.6980 chunk 78 optimal weight: 20.0000 chunk 30 optimal weight: 20.0000 chunk 47 optimal weight: 4.9990 chunk 58 optimal weight: 0.3980 chunk 90 optimal weight: 0.0670 overall best weight: 0.3318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 GLN B 144 GLN D 154 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7892 Z= 0.156 Angle : 0.663 7.025 10730 Z= 0.325 Chirality : 0.042 0.189 1273 Planarity : 0.004 0.057 1363 Dihedral : 7.751 58.839 1130 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.36 % Favored : 95.34 % Rotamer: Outliers : 1.76 % Allowed : 14.47 % Favored : 83.77 % 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: -2.20 (0.25), residues: 1009 helix: -0.78 (0.22), residues: 521 sheet: -1.61 (0.68), residues: 65 loop : -2.24 (0.27), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 335 HIS 0.004 0.001 HIS C 348 PHE 0.020 0.001 PHE A 249 TYR 0.014 0.001 TYR B 11 ARG 0.008 0.001 ARG B 203 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 178 time to evaluate : 0.851 Fit side-chains REVERT: B 116 ARG cc_start: 0.8830 (ptt90) cc_final: 0.8521 (tmm-80) REVERT: C 61 HIS cc_start: 0.8277 (t-90) cc_final: 0.8009 (t70) REVERT: D 87 ASP cc_start: 0.8161 (p0) cc_final: 0.7834 (p0) REVERT: D 89 HIS cc_start: 0.6401 (m90) cc_final: 0.5752 (m90) REVERT: D 189 THR cc_start: 0.8260 (m) cc_final: 0.8045 (p) REVERT: A 95 TYR cc_start: 0.7923 (t80) cc_final: 0.7704 (t80) REVERT: A 100 GLN cc_start: 0.9149 (mp10) cc_final: 0.8896 (mp10) REVERT: A 206 MET cc_start: 0.4137 (mmp) cc_final: 0.3295 (mmp) REVERT: A 344 GLN cc_start: 0.7738 (tt0) cc_final: 0.7260 (tm-30) outliers start: 14 outliers final: 8 residues processed: 180 average time/residue: 0.1638 time to fit residues: 41.3880 Evaluate side-chains 166 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 158 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain C residue 122 ASP Chi-restraints excluded: chain C residue 348 HIS Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 296 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 7.9990 chunk 28 optimal weight: 40.0000 chunk 75 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 90 optimal weight: 0.0870 chunk 98 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 overall best weight: 1.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 24 HIS B 216 HIS ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 7892 Z= 0.251 Angle : 0.656 7.280 10730 Z= 0.331 Chirality : 0.041 0.184 1273 Planarity : 0.004 0.059 1363 Dihedral : 7.511 58.917 1130 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.76 % Favored : 94.95 % Rotamer: Outliers : 3.27 % Allowed : 18.36 % Favored : 78.36 % 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: -1.49 (0.26), residues: 1009 helix: -0.06 (0.22), residues: 530 sheet: -1.54 (0.70), residues: 62 loop : -2.11 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 335 HIS 0.005 0.001 HIS A 345 PHE 0.015 0.002 PHE B 85 TYR 0.014 0.001 TYR B 11 ARG 0.003 0.000 ARG C 252 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 156 time to evaluate : 0.874 Fit side-chains REVERT: B 116 ARG cc_start: 0.8881 (ptt90) cc_final: 0.8574 (tmm-80) REVERT: C 61 HIS cc_start: 0.8370 (t-90) cc_final: 0.8103 (t70) REVERT: C 232 MET cc_start: 0.8589 (mmp) cc_final: 0.8171 (mmp) REVERT: C 347 ARG cc_start: 0.8383 (mmp80) cc_final: 0.8035 (mmm160) REVERT: D 87 ASP cc_start: 0.8357 (p0) cc_final: 0.7700 (p0) REVERT: D 89 HIS cc_start: 0.6537 (m90) cc_final: 0.5797 (m170) REVERT: A 100 GLN cc_start: 0.9275 (mp10) cc_final: 0.8972 (mp10) REVERT: A 206 MET cc_start: 0.4652 (mmp) cc_final: 0.4108 (mmp) outliers start: 26 outliers final: 20 residues processed: 166 average time/residue: 0.1737 time to fit residues: 39.9006 Evaluate side-chains 165 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 145 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain C residue 122 ASP Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain C residue 348 HIS Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 296 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 96 optimal weight: 0.0470 chunk 86 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 80 optimal weight: 20.0000 chunk 54 optimal weight: 0.6980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 ASN D 19 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7892 Z= 0.164 Angle : 0.622 8.412 10730 Z= 0.303 Chirality : 0.041 0.174 1273 Planarity : 0.003 0.056 1363 Dihedral : 7.323 58.717 1130 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.46 % Favored : 95.24 % Rotamer: Outliers : 2.89 % Allowed : 22.39 % Favored : 74.72 % 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: -1.16 (0.27), residues: 1009 helix: 0.27 (0.23), residues: 534 sheet: -1.61 (0.65), residues: 74 loop : -2.01 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 335 HIS 0.010 0.001 HIS B 89 PHE 0.022 0.001 PHE D 76 TYR 0.015 0.001 TYR A 95 ARG 0.003 0.000 ARG C 252 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 161 time to evaluate : 0.878 Fit side-chains REVERT: B 52 GLU cc_start: 0.8161 (mp0) cc_final: 0.7899 (pm20) REVERT: B 116 ARG cc_start: 0.8855 (ptt90) cc_final: 0.8516 (tmm-80) REVERT: B 163 GLU cc_start: 0.8730 (tt0) cc_final: 0.8523 (tt0) REVERT: C 61 HIS cc_start: 0.8341 (t-90) cc_final: 0.8096 (t70) REVERT: C 232 MET cc_start: 0.8463 (mmp) cc_final: 0.8148 (mmp) REVERT: C 347 ARG cc_start: 0.8342 (mmp80) cc_final: 0.7994 (mmm160) REVERT: D 87 ASP cc_start: 0.8386 (p0) cc_final: 0.7681 (p0) REVERT: D 89 HIS cc_start: 0.6398 (m90) cc_final: 0.5698 (m170) REVERT: A 100 GLN cc_start: 0.9222 (mp10) cc_final: 0.8951 (mp10) REVERT: A 206 MET cc_start: 0.4591 (mmp) cc_final: 0.4022 (mmp) REVERT: A 344 GLN cc_start: 0.7786 (tt0) cc_final: 0.7190 (tm-30) outliers start: 23 outliers final: 14 residues processed: 175 average time/residue: 0.1661 time to fit residues: 40.6894 Evaluate side-chains 165 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 151 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain C residue 122 ASP Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 348 HIS Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 296 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.0980 chunk 71 optimal weight: 0.0570 chunk 39 optimal weight: 4.9990 chunk 82 optimal weight: 20.0000 chunk 66 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 24 optimal weight: 0.0470 chunk 32 optimal weight: 20.0000 chunk 87 optimal weight: 0.9980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 HIS ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 GLN ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7892 Z= 0.164 Angle : 0.636 8.799 10730 Z= 0.305 Chirality : 0.041 0.202 1273 Planarity : 0.003 0.054 1363 Dihedral : 7.135 55.051 1130 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.66 % Favored : 95.14 % Rotamer: Outliers : 3.14 % Allowed : 23.02 % Favored : 73.84 % 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: -0.96 (0.27), residues: 1009 helix: 0.47 (0.23), residues: 531 sheet: -1.52 (0.65), residues: 74 loop : -1.97 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 335 HIS 0.003 0.001 HIS C 348 PHE 0.020 0.001 PHE D 76 TYR 0.014 0.001 TYR C 58 ARG 0.003 0.000 ARG C 252 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 167 time to evaluate : 0.906 Fit side-chains REVERT: B 116 ARG cc_start: 0.8847 (ptt90) cc_final: 0.8488 (tmm-80) REVERT: B 163 GLU cc_start: 0.8717 (tt0) cc_final: 0.8419 (tt0) REVERT: B 189 THR cc_start: 0.8779 (m) cc_final: 0.8564 (p) REVERT: C 61 HIS cc_start: 0.8314 (t-90) cc_final: 0.8061 (t70) REVERT: C 347 ARG cc_start: 0.8308 (mmp80) cc_final: 0.8064 (mmm160) REVERT: D 87 ASP cc_start: 0.8372 (p0) cc_final: 0.7668 (p0) REVERT: D 89 HIS cc_start: 0.6342 (m90) cc_final: 0.5543 (m170) REVERT: D 182 GLU cc_start: 0.8547 (pp20) cc_final: 0.8132 (pp20) REVERT: A 100 GLN cc_start: 0.9213 (mp10) cc_final: 0.8918 (mp10) REVERT: A 206 MET cc_start: 0.4588 (mmp) cc_final: 0.4022 (mmp) REVERT: A 232 MET cc_start: 0.8102 (mmm) cc_final: 0.7901 (mmm) REVERT: A 344 GLN cc_start: 0.7868 (tt0) cc_final: 0.7201 (tm-30) outliers start: 25 outliers final: 17 residues processed: 177 average time/residue: 0.1752 time to fit residues: 43.0735 Evaluate side-chains 176 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 159 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 214 HIS Chi-restraints excluded: chain C residue 122 ASP Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 348 HIS Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 296 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 7.9990 chunk 56 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 80 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 32 optimal weight: 40.0000 chunk 50 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 ASN ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 ASN D 216 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 7892 Z= 0.454 Angle : 0.791 9.039 10730 Z= 0.399 Chirality : 0.046 0.182 1273 Planarity : 0.005 0.059 1363 Dihedral : 7.564 55.537 1130 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.25 % Favored : 94.55 % Rotamer: Outliers : 5.91 % Allowed : 20.63 % Favored : 73.46 % 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: -1.08 (0.27), residues: 1009 helix: 0.34 (0.23), residues: 543 sheet: -1.90 (0.63), residues: 74 loop : -1.96 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 335 HIS 0.007 0.002 HIS D 88 PHE 0.032 0.003 PHE D 183 TYR 0.012 0.002 TYR B 11 ARG 0.004 0.001 ARG D 203 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 153 time to evaluate : 0.884 Fit side-chains REVERT: B 189 THR cc_start: 0.8859 (m) cc_final: 0.8618 (p) REVERT: C 61 HIS cc_start: 0.8399 (t-90) cc_final: 0.8176 (t70) REVERT: C 232 MET cc_start: 0.8738 (mmp) cc_final: 0.8492 (mmm) REVERT: C 347 ARG cc_start: 0.8464 (mmp80) cc_final: 0.8232 (mmm160) REVERT: D 25 MET cc_start: 0.8921 (tpt) cc_final: 0.8635 (tpt) REVERT: A 100 GLN cc_start: 0.9427 (mp10) cc_final: 0.9114 (mp10) REVERT: A 206 MET cc_start: 0.5203 (mmp) cc_final: 0.4898 (mmt) REVERT: A 231 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7658 (pp) outliers start: 47 outliers final: 32 residues processed: 176 average time/residue: 0.1827 time to fit residues: 44.0614 Evaluate side-chains 169 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 136 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 312 LYS Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain C residue 348 HIS Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 216 HIS Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 296 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 81 optimal weight: 30.0000 chunk 96 optimal weight: 9.9990 chunk 60 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 HIS ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 19 GLN D 89 HIS D 154 ASN A 258 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 7892 Z= 0.209 Angle : 0.694 9.387 10730 Z= 0.332 Chirality : 0.044 0.214 1273 Planarity : 0.004 0.062 1363 Dihedral : 7.383 55.175 1130 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.86 % Favored : 95.04 % Rotamer: Outliers : 4.28 % Allowed : 22.64 % Favored : 73.08 % 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: -0.88 (0.27), residues: 1009 helix: 0.52 (0.23), residues: 536 sheet: -1.70 (0.65), residues: 74 loop : -1.87 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 335 HIS 0.015 0.001 HIS D 216 PHE 0.012 0.001 PHE B 4 TYR 0.017 0.001 TYR A 95 ARG 0.003 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 158 time to evaluate : 0.924 Fit side-chains REVERT: C 61 HIS cc_start: 0.8350 (t-90) cc_final: 0.8081 (t70) REVERT: C 232 MET cc_start: 0.8610 (mmp) cc_final: 0.8325 (mmm) REVERT: C 347 ARG cc_start: 0.8263 (mmp80) cc_final: 0.7900 (ttp-170) REVERT: D 87 ASP cc_start: 0.8641 (p0) cc_final: 0.7938 (p0) REVERT: D 89 HIS cc_start: 0.7596 (OUTLIER) cc_final: 0.6818 (m170) REVERT: A 100 GLN cc_start: 0.9295 (mp10) cc_final: 0.8952 (mp10) REVERT: A 206 MET cc_start: 0.5050 (mmp) cc_final: 0.4749 (mmt) outliers start: 34 outliers final: 23 residues processed: 174 average time/residue: 0.1776 time to fit residues: 42.5119 Evaluate side-chains 173 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 149 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 214 HIS Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 312 LYS Chi-restraints excluded: chain C residue 348 HIS Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 89 HIS Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 258 GLN Chi-restraints excluded: chain A residue 296 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 0.0980 chunk 18 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 HIS ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 GLN ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 HIS D 154 ASN A 258 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7892 Z= 0.207 Angle : 0.705 15.189 10730 Z= 0.333 Chirality : 0.044 0.312 1273 Planarity : 0.004 0.054 1363 Dihedral : 7.269 56.562 1130 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.86 % Favored : 95.04 % Rotamer: Outliers : 4.28 % Allowed : 22.64 % Favored : 73.08 % 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: -0.79 (0.27), residues: 1009 helix: 0.61 (0.23), residues: 538 sheet: -1.65 (0.67), residues: 74 loop : -1.88 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 335 HIS 0.008 0.001 HIS D 216 PHE 0.014 0.001 PHE B 4 TYR 0.016 0.001 TYR A 95 ARG 0.004 0.000 ARG D 78 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 165 time to evaluate : 0.875 Fit side-chains REVERT: B 163 GLU cc_start: 0.8740 (tt0) cc_final: 0.8449 (tt0) REVERT: C 61 HIS cc_start: 0.8395 (t-90) cc_final: 0.8136 (t70) REVERT: C 70 LYS cc_start: 0.8379 (tptp) cc_final: 0.8161 (tptp) REVERT: C 232 MET cc_start: 0.8545 (mmp) cc_final: 0.8247 (mmm) REVERT: C 347 ARG cc_start: 0.8245 (mmp80) cc_final: 0.7907 (ttp-170) REVERT: D 89 HIS cc_start: 0.7445 (m90) cc_final: 0.7076 (m-70) REVERT: D 142 GLU cc_start: 0.8652 (pm20) cc_final: 0.8348 (pm20) REVERT: A 100 GLN cc_start: 0.9287 (mp10) cc_final: 0.8936 (mp10) REVERT: A 206 MET cc_start: 0.5068 (mmp) cc_final: 0.4769 (mmt) outliers start: 34 outliers final: 26 residues processed: 179 average time/residue: 0.1861 time to fit residues: 45.4889 Evaluate side-chains 178 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 152 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 214 HIS Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 312 LYS Chi-restraints excluded: chain C residue 348 HIS Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 336 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 39 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 27 optimal weight: 20.0000 chunk 81 optimal weight: 20.0000 chunk 84 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 58 optimal weight: 5.9990 chunk 94 optimal weight: 0.3980 chunk 57 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 HIS ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 GLN ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 ASN D 216 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7892 Z= 0.221 Angle : 0.706 8.301 10730 Z= 0.337 Chirality : 0.043 0.150 1273 Planarity : 0.004 0.053 1363 Dihedral : 7.248 58.470 1130 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.05 % Favored : 94.85 % Rotamer: Outliers : 4.03 % Allowed : 23.02 % Favored : 72.96 % 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: -0.70 (0.27), residues: 1009 helix: 0.70 (0.23), residues: 537 sheet: -1.39 (0.74), residues: 62 loop : -1.90 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 335 HIS 0.008 0.001 HIS D 216 PHE 0.014 0.001 PHE B 4 TYR 0.016 0.001 TYR A 95 ARG 0.007 0.000 ARG D 150 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 152 time to evaluate : 0.922 Fit side-chains REVERT: B 163 GLU cc_start: 0.8757 (tt0) cc_final: 0.8435 (tt0) REVERT: B 189 THR cc_start: 0.8699 (m) cc_final: 0.8431 (p) REVERT: C 61 HIS cc_start: 0.8360 (t-90) cc_final: 0.8097 (t70) REVERT: C 70 LYS cc_start: 0.8424 (tptp) cc_final: 0.8172 (tptp) REVERT: C 232 MET cc_start: 0.8568 (mmp) cc_final: 0.8211 (mmm) REVERT: C 347 ARG cc_start: 0.8263 (mmp80) cc_final: 0.7944 (ttp-170) REVERT: A 100 GLN cc_start: 0.9287 (mp10) cc_final: 0.8926 (mp10) REVERT: A 206 MET cc_start: 0.4975 (mmp) cc_final: 0.4681 (mmt) outliers start: 32 outliers final: 26 residues processed: 167 average time/residue: 0.1770 time to fit residues: 40.9861 Evaluate side-chains 172 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 146 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 312 LYS Chi-restraints excluded: chain C residue 348 HIS Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 336 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 7.9990 chunk 66 optimal weight: 0.6980 chunk 99 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 79 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 chunk 61 optimal weight: 0.0770 chunk 48 optimal weight: 4.9990 chunk 63 optimal weight: 0.5980 chunk 84 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 143 GLN C 65 GLN ** D 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7892 Z= 0.187 Angle : 0.710 11.594 10730 Z= 0.334 Chirality : 0.042 0.151 1273 Planarity : 0.004 0.053 1363 Dihedral : 7.043 55.884 1130 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.56 % Favored : 95.34 % Rotamer: Outliers : 3.27 % Allowed : 24.03 % Favored : 72.70 % 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: -0.66 (0.27), residues: 1009 helix: 0.77 (0.23), residues: 534 sheet: -1.30 (0.71), residues: 71 loop : -1.94 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 335 HIS 0.004 0.001 HIS B 214 PHE 0.027 0.001 PHE D 76 TYR 0.015 0.001 TYR A 95 ARG 0.006 0.000 ARG D 150 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 166 time to evaluate : 0.840 Fit side-chains REVERT: B 92 MET cc_start: 0.8558 (mmt) cc_final: 0.8201 (mmm) REVERT: B 163 GLU cc_start: 0.8727 (tt0) cc_final: 0.8292 (tt0) REVERT: B 189 THR cc_start: 0.8606 (m) cc_final: 0.8403 (p) REVERT: C 61 HIS cc_start: 0.8370 (t-90) cc_final: 0.8141 (t70) REVERT: C 70 LYS cc_start: 0.8398 (tptp) cc_final: 0.8135 (tptp) REVERT: C 232 MET cc_start: 0.8641 (mmp) cc_final: 0.8290 (mmm) REVERT: C 347 ARG cc_start: 0.8223 (mmp80) cc_final: 0.7916 (ttp-170) REVERT: A 100 GLN cc_start: 0.9251 (mp10) cc_final: 0.8884 (mp10) REVERT: A 206 MET cc_start: 0.4945 (mmp) cc_final: 0.4361 (mmp) outliers start: 26 outliers final: 24 residues processed: 178 average time/residue: 0.1689 time to fit residues: 41.7212 Evaluate side-chains 182 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 158 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 348 HIS Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 336 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 79 optimal weight: 7.9990 chunk 33 optimal weight: 8.9990 chunk 81 optimal weight: 30.0000 chunk 10 optimal weight: 0.0870 chunk 14 optimal weight: 3.9990 chunk 69 optimal weight: 0.0010 chunk 4 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.5166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 71 ASN B 89 HIS B 143 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.113594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.084840 restraints weight = 23957.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.086972 restraints weight = 13686.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.088485 restraints weight = 9188.794| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7892 Z= 0.193 Angle : 0.724 13.620 10730 Z= 0.340 Chirality : 0.043 0.148 1273 Planarity : 0.004 0.053 1363 Dihedral : 7.002 55.091 1130 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.66 % Favored : 95.24 % Rotamer: Outliers : 2.77 % Allowed : 25.16 % Favored : 72.08 % 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: -0.54 (0.28), residues: 1009 helix: 0.84 (0.24), residues: 535 sheet: -1.33 (0.75), residues: 62 loop : -1.82 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 335 HIS 0.004 0.001 HIS B 214 PHE 0.027 0.001 PHE D 76 TYR 0.016 0.001 TYR A 95 ARG 0.010 0.000 ARG D 78 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1674.77 seconds wall clock time: 30 minutes 27.30 seconds (1827.30 seconds total)