Starting phenix.real_space_refine on Fri Jul 19 12:27:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6i_37324/07_2024/8w6i_37324.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6i_37324/07_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_37324/07_2024/8w6i_37324.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6i_37324/07_2024/8w6i_37324.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6i_37324/07_2024/8w6i_37324.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6i_37324/07_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-5388/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: 4.76, per 1000 atoms: 0.61 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: 2.96 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: 0.78 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: 2.00 Time building geometry restraints manager: 3.26 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 2.440 nonbonded pdb=" O GLN C 65 " pdb=" OG SER C 69 " model vdw 2.314 2.440 nonbonded pdb=" O THR C 86 " pdb=" OG SER C 89 " model vdw 2.328 2.440 nonbonded pdb=" OE2 GLU B 181 " pdb=" OH TYR B 205 " model vdw 2.329 2.440 nonbonded pdb=" OG SER B 110 " pdb=" OD1 ASP B 113 " model vdw 2.345 2.440 ... (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 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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 23.800 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.360 ------------------------------------------------------------------------------- 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 : 0.920 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: 0.1968 time to fit residues: 53.4303 Evaluate side-chains 163 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 0.851 ------------------------------------------------------------------------------- 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: 6.9990 chunk 75 optimal weight: 8.9990 chunk 42 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 51 optimal weight: 6.9990 chunk 40 optimal weight: 0.8980 chunk 78 optimal weight: 30.0000 chunk 30 optimal weight: 20.0000 chunk 47 optimal weight: 4.9990 chunk 58 optimal weight: 0.0050 chunk 90 optimal weight: 0.0770 overall best weight: 1.1354 ------------------------------------------------------------------------------- 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 154 ASN D 154 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7892 Z= 0.194 Angle : 0.650 6.732 10730 Z= 0.322 Chirality : 0.041 0.195 1273 Planarity : 0.004 0.058 1363 Dihedral : 7.478 57.714 1130 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.36 % Favored : 95.34 % Rotamer: Outliers : 2.64 % Allowed : 14.21 % Favored : 83.14 % 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: -2.14 (0.25), residues: 1009 helix: -0.72 (0.22), residues: 523 sheet: -1.40 (0.70), residues: 62 loop : -2.28 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 335 HIS 0.004 0.001 HIS A 345 PHE 0.019 0.001 PHE A 249 TYR 0.017 0.001 TYR B 11 ARG 0.005 0.000 ARG C 252 *********************** 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 189 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 168 time to evaluate : 0.928 Fit side-chains REVERT: B 116 ARG cc_start: 0.8862 (ptt90) cc_final: 0.8567 (tmm-80) REVERT: C 61 HIS cc_start: 0.8300 (t-90) cc_final: 0.8009 (t70) REVERT: C 290 LEU cc_start: 0.9554 (tt) cc_final: 0.9339 (tt) REVERT: D 87 ASP cc_start: 0.8279 (p0) cc_final: 0.7936 (p0) REVERT: D 89 HIS cc_start: 0.6725 (m90) cc_final: 0.5961 (m90) REVERT: A 95 TYR cc_start: 0.7931 (t80) cc_final: 0.7720 (t80) REVERT: A 100 GLN cc_start: 0.9183 (mp10) cc_final: 0.8906 (mp10) REVERT: A 206 MET cc_start: 0.4306 (mmp) cc_final: 0.3440 (mmp) outliers start: 21 outliers final: 16 residues processed: 172 average time/residue: 0.1639 time to fit residues: 39.6716 Evaluate side-chains 171 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 155 time to evaluate : 0.864 ------------------------------------------------------------------------------- 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 112 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 179 LEU 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 348 HIS Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain A residue 84 SER 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: 5.9990 chunk 28 optimal weight: 40.0000 chunk 75 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 25 optimal weight: 0.3980 chunk 90 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 81 optimal weight: 7.9990 chunk 31 optimal weight: 8.9990 chunk 72 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 24 HIS B 216 HIS ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 ASN D 19 GLN D 154 ASN A 99 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7892 Z= 0.221 Angle : 0.619 6.529 10730 Z= 0.307 Chirality : 0.040 0.182 1273 Planarity : 0.004 0.057 1363 Dihedral : 7.160 56.078 1130 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.76 % Favored : 94.95 % Rotamer: Outliers : 3.52 % Allowed : 18.11 % 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: -1.41 (0.26), residues: 1009 helix: 0.03 (0.23), residues: 523 sheet: -1.46 (0.69), residues: 62 loop : -2.09 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 335 HIS 0.005 0.001 HIS B 89 PHE 0.016 0.001 PHE B 85 TYR 0.013 0.001 TYR B 11 ARG 0.004 0.000 ARG C 347 *********************** 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 190 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 162 time to evaluate : 0.787 Fit side-chains REVERT: B 83 MET cc_start: 0.7719 (mmm) cc_final: 0.7383 (tpt) REVERT: B 116 ARG cc_start: 0.8917 (ptt90) cc_final: 0.8598 (tmm-80) REVERT: C 61 HIS cc_start: 0.8356 (t-90) cc_final: 0.8118 (t70) REVERT: C 232 MET cc_start: 0.8566 (mmp) cc_final: 0.8152 (mmp) REVERT: D 87 ASP cc_start: 0.8493 (p0) cc_final: 0.7925 (p0) REVERT: D 89 HIS cc_start: 0.6827 (m90) cc_final: 0.5983 (m170) REVERT: A 100 GLN cc_start: 0.9263 (mp10) cc_final: 0.8951 (mp10) REVERT: A 206 MET cc_start: 0.4777 (mmp) cc_final: 0.3915 (mmp) REVERT: A 232 MET cc_start: 0.8369 (mmm) cc_final: 0.8143 (mmm) outliers start: 28 outliers final: 18 residues processed: 172 average time/residue: 0.1668 time to fit residues: 39.9732 Evaluate side-chains 166 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 148 time to evaluate : 0.834 ------------------------------------------------------------------------------- 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 170 ASP 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 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 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: 0.0370 chunk 47 optimal weight: 2.9990 chunk 10 optimal weight: 0.0040 chunk 43 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 overall best weight: 1.2074 ------------------------------------------------------------------------------- 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 89 HIS B 143 GLN ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 19 GLN D 154 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7892 Z= 0.199 Angle : 0.629 7.294 10730 Z= 0.304 Chirality : 0.041 0.202 1273 Planarity : 0.004 0.055 1363 Dihedral : 7.040 58.970 1130 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.96 % Favored : 94.75 % Rotamer: Outliers : 3.90 % Allowed : 21.13 % Favored : 74.97 % 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: -1.10 (0.26), residues: 1009 helix: 0.36 (0.23), residues: 534 sheet: -1.43 (0.70), residues: 62 loop : -2.09 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 335 HIS 0.010 0.001 HIS B 89 PHE 0.012 0.001 PHE A 249 TYR 0.016 0.001 TYR C 58 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 192 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 161 time to evaluate : 0.904 Fit side-chains REVERT: B 52 GLU cc_start: 0.8272 (mp0) cc_final: 0.8002 (pm20) REVERT: B 116 ARG cc_start: 0.8921 (ptt90) cc_final: 0.8595 (tmm-80) REVERT: C 61 HIS cc_start: 0.8310 (t-90) cc_final: 0.8076 (t70) REVERT: C 85 LEU cc_start: 0.9249 (mm) cc_final: 0.9031 (mm) REVERT: C 232 MET cc_start: 0.8529 (mmp) cc_final: 0.8161 (mmp) REVERT: D 87 ASP cc_start: 0.8476 (p0) cc_final: 0.7845 (p0) REVERT: D 89 HIS cc_start: 0.6778 (m90) cc_final: 0.5894 (m170) REVERT: A 100 GLN cc_start: 0.9250 (mp10) cc_final: 0.8785 (mp10) REVERT: A 206 MET cc_start: 0.4903 (mmp) cc_final: 0.4351 (mmp) REVERT: A 240 ILE cc_start: 0.8767 (tt) cc_final: 0.8334 (pt) REVERT: A 344 GLN cc_start: 0.7797 (tt0) cc_final: 0.7254 (tm-30) outliers start: 31 outliers final: 21 residues processed: 173 average time/residue: 0.1681 time to fit residues: 40.5809 Evaluate side-chains 175 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 154 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 158 VAL Chi-restraints excluded: chain B residue 170 ASP 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 209 THR 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 348 HIS Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 285 LEU 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: 1.9990 chunk 71 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 chunk 82 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 49 optimal weight: 0.4980 chunk 86 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- 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 ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 19 GLN D 154 ASN D 216 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7892 Z= 0.274 Angle : 0.672 10.917 10730 Z= 0.330 Chirality : 0.042 0.180 1273 Planarity : 0.004 0.055 1363 Dihedral : 6.957 55.303 1130 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.66 % Favored : 95.14 % Rotamer: Outliers : 4.53 % Allowed : 22.01 % 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: -0.91 (0.27), residues: 1009 helix: 0.50 (0.23), residues: 543 sheet: -1.40 (0.71), residues: 62 loop : -2.02 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 335 HIS 0.004 0.001 HIS B 89 PHE 0.022 0.002 PHE D 76 TYR 0.013 0.001 TYR A 95 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 193 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 157 time to evaluate : 0.864 Fit side-chains REVERT: B 189 THR cc_start: 0.8778 (m) cc_final: 0.8504 (p) REVERT: C 61 HIS cc_start: 0.8344 (t-90) cc_final: 0.8097 (t70) REVERT: C 85 LEU cc_start: 0.9265 (mm) cc_final: 0.9034 (mm) REVERT: C 232 MET cc_start: 0.8624 (mmp) cc_final: 0.8359 (mmp) REVERT: A 100 GLN cc_start: 0.9352 (mp10) cc_final: 0.8892 (mp10) REVERT: A 206 MET cc_start: 0.4851 (mmp) cc_final: 0.4642 (mmt) outliers start: 36 outliers final: 26 residues processed: 172 average time/residue: 0.1689 time to fit residues: 40.5315 Evaluate side-chains 169 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 143 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 64 HIS 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 170 ASP 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 331 SER Chi-restraints excluded: chain C residue 348 HIS Chi-restraints excluded: chain D residue 30 MET 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 93 MET Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 285 LEU 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: 5.9990 chunk 56 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 96 optimal weight: 8.9990 chunk 80 optimal weight: 10.0000 chunk 44 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 32 optimal weight: 20.0000 chunk 50 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 overall best weight: 2.5386 ------------------------------------------------------------------------------- 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 99 ASN ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 19 GLN ** D 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 HIS D 154 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 7892 Z= 0.336 Angle : 0.710 9.001 10730 Z= 0.349 Chirality : 0.043 0.184 1273 Planarity : 0.004 0.060 1363 Dihedral : 6.954 57.934 1130 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 19.42 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.35 % Favored : 94.45 % Rotamer: Outliers : 5.16 % Allowed : 22.01 % Favored : 72.83 % 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: -0.93 (0.27), residues: 1009 helix: 0.49 (0.23), residues: 544 sheet: -1.39 (0.68), residues: 67 loop : -2.03 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 335 HIS 0.020 0.002 HIS D 216 PHE 0.018 0.002 PHE D 76 TYR 0.013 0.002 TYR B 11 ARG 0.005 0.000 ARG D 78 *********************** 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 194 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 153 time to evaluate : 0.896 Fit side-chains REVERT: B 89 HIS cc_start: 0.7909 (m-70) cc_final: 0.7603 (m-70) REVERT: B 189 THR cc_start: 0.8718 (m) cc_final: 0.8495 (p) REVERT: C 61 HIS cc_start: 0.8371 (t-90) cc_final: 0.8087 (t-90) REVERT: C 85 LEU cc_start: 0.9278 (mm) cc_final: 0.9054 (mm) REVERT: D 89 HIS cc_start: 0.7498 (OUTLIER) cc_final: 0.6987 (m170) REVERT: A 100 GLN cc_start: 0.9435 (mp10) cc_final: 0.8989 (mp10) REVERT: A 206 MET cc_start: 0.5175 (mmp) cc_final: 0.4834 (mmt) REVERT: A 289 ILE cc_start: 0.9410 (pt) cc_final: 0.9205 (mm) outliers start: 41 outliers final: 31 residues processed: 172 average time/residue: 0.1837 time to fit residues: 42.8711 Evaluate side-chains 171 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 139 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 64 HIS 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 170 ASP 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 209 THR Chi-restraints excluded: chain B residue 214 HIS Chi-restraints excluded: chain C residue 221 VAL 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 331 SER Chi-restraints excluded: chain C residue 348 HIS Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 89 HIS Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 336 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 0.9980 chunk 70 optimal weight: 5.9990 chunk 54 optimal weight: 0.2980 chunk 81 optimal weight: 30.0000 chunk 96 optimal weight: 9.9990 chunk 60 optimal weight: 0.8980 chunk 58 optimal weight: 0.0670 chunk 44 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 overall best weight: 0.5718 ------------------------------------------------------------------------------- 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 99 ASN ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 HIS A 258 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7892 Z= 0.185 Angle : 0.667 10.664 10730 Z= 0.317 Chirality : 0.042 0.219 1273 Planarity : 0.004 0.049 1363 Dihedral : 6.869 58.256 1130 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.76 % Favored : 95.04 % Rotamer: Outliers : 4.28 % Allowed : 23.52 % Favored : 72.20 % 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: -0.69 (0.27), residues: 1009 helix: 0.67 (0.23), residues: 538 sheet: -1.18 (0.70), residues: 67 loop : -1.90 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 335 HIS 0.007 0.001 HIS D 89 PHE 0.022 0.001 PHE D 76 TYR 0.012 0.001 TYR A 95 ARG 0.004 0.000 ARG D 78 *********************** 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 196 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 162 time to evaluate : 0.939 Fit side-chains REVERT: B 189 THR cc_start: 0.8663 (m) cc_final: 0.8459 (p) REVERT: C 61 HIS cc_start: 0.8349 (t-90) cc_final: 0.8076 (t70) REVERT: D 160 LEU cc_start: 0.9091 (mt) cc_final: 0.8810 (mt) REVERT: A 100 GLN cc_start: 0.9314 (mp10) cc_final: 0.8938 (mp10) REVERT: A 206 MET cc_start: 0.5172 (mmp) cc_final: 0.4851 (mmt) outliers start: 34 outliers final: 23 residues processed: 179 average time/residue: 0.1761 time to fit residues: 43.5302 Evaluate side-chains 173 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 150 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 64 HIS 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 170 ASP Chi-restraints excluded: chain B residue 179 LEU 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 308 VAL Chi-restraints excluded: chain C residue 348 HIS Chi-restraints excluded: chain D residue 30 MET 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 6.9990 chunk 18 optimal weight: 0.0980 chunk 61 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 89 optimal weight: 0.6980 overall best weight: 0.9586 ------------------------------------------------------------------------------- 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 99 ASN ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7892 Z= 0.206 Angle : 0.693 14.096 10730 Z= 0.325 Chirality : 0.042 0.195 1273 Planarity : 0.004 0.050 1363 Dihedral : 6.764 59.853 1130 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.15 % Favored : 94.65 % Rotamer: Outliers : 4.78 % Allowed : 23.40 % Favored : 71.82 % 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 (0.27), residues: 1009 helix: 0.78 (0.23), residues: 540 sheet: -1.32 (0.72), residues: 65 loop : -1.89 (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 B 214 PHE 0.017 0.001 PHE B 4 TYR 0.011 0.001 TYR B 11 ARG 0.007 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 194 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 156 time to evaluate : 0.868 Fit side-chains revert: symmetry clash REVERT: B 89 HIS cc_start: 0.7884 (m-70) cc_final: 0.7624 (m-70) REVERT: B 189 THR cc_start: 0.8673 (m) cc_final: 0.8424 (p) REVERT: C 61 HIS cc_start: 0.8324 (t-90) cc_final: 0.8078 (t70) REVERT: C 232 MET cc_start: 0.8527 (mmm) cc_final: 0.8299 (mmm) REVERT: A 100 GLN cc_start: 0.9316 (mp10) cc_final: 0.8944 (mp10) REVERT: A 206 MET cc_start: 0.5000 (mmp) cc_final: 0.4374 (mmp) REVERT: A 232 MET cc_start: 0.8093 (mmm) cc_final: 0.7375 (mtt) outliers start: 38 outliers final: 29 residues processed: 173 average time/residue: 0.1761 time to fit residues: 42.0388 Evaluate side-chains 182 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 153 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 64 HIS 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 170 ASP Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 214 HIS Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 286 LEU 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 30 MET 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 D residue 170 ASP Chi-restraints excluded: chain D residue 191 LEU 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 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: 0.9980 chunk 39 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 81 optimal weight: 9.9990 chunk 84 optimal weight: 0.2980 chunk 89 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 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 0.041 7892 Z= 0.222 Angle : 0.696 11.992 10730 Z= 0.328 Chirality : 0.042 0.175 1273 Planarity : 0.004 0.051 1363 Dihedral : 6.698 58.124 1130 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 18.19 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.86 % Favored : 94.95 % Rotamer: Outliers : 4.15 % Allowed : 24.15 % Favored : 71.70 % 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: -0.54 (0.28), residues: 1009 helix: 0.85 (0.24), residues: 540 sheet: -1.33 (0.72), residues: 65 loop : -1.89 (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 0.016 0.001 PHE B 4 TYR 0.012 0.001 TYR B 11 ARG 0.007 0.000 ARG D 78 *********************** 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 187 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 154 time to evaluate : 0.930 Fit side-chains REVERT: B 89 HIS cc_start: 0.7901 (m-70) cc_final: 0.7626 (m-70) REVERT: B 189 THR cc_start: 0.8640 (m) cc_final: 0.8423 (p) REVERT: C 61 HIS cc_start: 0.8316 (t-90) cc_final: 0.8018 (t-90) REVERT: D 46 LYS cc_start: 0.9435 (mtpp) cc_final: 0.8973 (mtpp) REVERT: A 100 GLN cc_start: 0.9325 (mp10) cc_final: 0.8951 (mp10) REVERT: A 206 MET cc_start: 0.5107 (mmp) cc_final: 0.4506 (mmp) REVERT: A 232 MET cc_start: 0.8091 (mmm) cc_final: 0.7526 (mtt) outliers start: 33 outliers final: 29 residues processed: 169 average time/residue: 0.1720 time to fit residues: 40.0246 Evaluate side-chains 178 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 149 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 64 HIS 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 170 ASP Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 214 HIS Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain C residue 348 HIS Chi-restraints excluded: chain D residue 30 MET 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 170 ASP Chi-restraints excluded: chain D residue 191 LEU 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 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: 0.9990 chunk 91 optimal weight: 0.9980 chunk 79 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 84 optimal weight: 0.0370 chunk 24 optimal weight: 0.7980 overall best weight: 0.6258 ------------------------------------------------------------------------------- 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: 0.8022 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7892 Z= 0.185 Angle : 0.705 11.552 10730 Z= 0.326 Chirality : 0.041 0.177 1273 Planarity : 0.003 0.050 1363 Dihedral : 6.589 54.408 1130 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.96 % Favored : 94.85 % Rotamer: Outliers : 2.89 % Allowed : 25.53 % Favored : 71.57 % 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: -0.50 (0.28), residues: 1009 helix: 0.92 (0.24), residues: 539 sheet: -1.35 (0.75), residues: 61 loop : -1.91 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 335 HIS 0.003 0.001 HIS C 61 PHE 0.016 0.001 PHE B 4 TYR 0.011 0.001 TYR B 11 ARG 0.007 0.000 ARG D 78 ********************** 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 184 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 161 time to evaluate : 0.849 Fit side-chains REVERT: B 32 PHE cc_start: 0.8392 (m-80) cc_final: 0.8169 (t80) REVERT: C 61 HIS cc_start: 0.8295 (t-90) cc_final: 0.8038 (t-90) REVERT: C 70 LYS cc_start: 0.8366 (tptp) cc_final: 0.8149 (tptp) REVERT: C 332 MET cc_start: 0.8144 (tpp) cc_final: 0.7762 (tpp) REVERT: D 46 LYS cc_start: 0.9384 (mtpp) cc_final: 0.8972 (mtpp) REVERT: D 142 GLU cc_start: 0.8601 (pm20) cc_final: 0.8371 (pm20) REVERT: A 100 GLN cc_start: 0.9286 (mp10) cc_final: 0.8906 (mp10) REVERT: A 206 MET cc_start: 0.5109 (mmp) cc_final: 0.4527 (mmp) REVERT: A 232 MET cc_start: 0.8161 (mmm) cc_final: 0.7662 (mtt) outliers start: 23 outliers final: 21 residues processed: 173 average time/residue: 0.1990 time to fit residues: 46.1334 Evaluate side-chains 173 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 152 time to evaluate : 0.918 ------------------------------------------------------------------------------- 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 170 ASP Chi-restraints excluded: chain B residue 179 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 308 VAL Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 348 HIS Chi-restraints excluded: chain D residue 30 MET Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 170 ASP 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 22 optimal weight: 0.0980 chunk 79 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 81 optimal weight: 9.9990 chunk 10 optimal weight: 0.0970 chunk 14 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 57 optimal weight: 0.9980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 143 GLN D 24 HIS D 154 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.114056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.085197 restraints weight = 24477.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.087323 restraints weight = 14269.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.088786 restraints weight = 9644.807| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7892 Z= 0.177 Angle : 0.691 11.294 10730 Z= 0.320 Chirality : 0.041 0.255 1273 Planarity : 0.004 0.050 1363 Dihedral : 6.482 54.959 1130 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.96 % Favored : 94.85 % Rotamer: Outliers : 2.77 % Allowed : 26.04 % Favored : 71.19 % 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: -0.42 (0.28), residues: 1009 helix: 0.98 (0.24), residues: 541 sheet: -1.40 (0.76), residues: 59 loop : -1.86 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 335 HIS 0.003 0.001 HIS C 61 PHE 0.014 0.001 PHE B 4 TYR 0.011 0.001 TYR A 95 ARG 0.007 0.000 ARG D 78 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1698.28 seconds wall clock time: 31 minutes 16.04 seconds (1876.04 seconds total)