Starting phenix.real_space_refine on Wed Mar 12 07:16:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x1u_32950/03_2025/7x1u_32950.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x1u_32950/03_2025/7x1u_32950.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7x1u_32950/03_2025/7x1u_32950.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x1u_32950/03_2025/7x1u_32950.map" model { file = "/net/cci-nas-00/data/ceres_data/7x1u_32950/03_2025/7x1u_32950.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x1u_32950/03_2025/7x1u_32950.cif" } resolution = 3.19 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= 0.080 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: 4 Type Number sf(0) Gaussians S 41 5.16 5 C 4782 2.51 5 N 1276 2.21 5 O 1384 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7483 Number of models: 1 Model: "" Number of chains: 7 Chain: "F" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 302 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 4, 'TRANS': 44} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 42 Chain: "A" Number of atoms: 1918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1918 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 8, 'TRANS': 262} Chain breaks: 1 Unresolved non-hydrogen bonds: 275 Unresolved non-hydrogen angles: 352 Unresolved non-hydrogen dihedrals: 246 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 3, 'TRP:plan': 3, 'ASP:plan': 3, 'PHE:plan': 5, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 150 Chain: "B" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1612 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 5, 'TRANS': 215} Chain breaks: 3 Unresolved non-hydrogen bonds: 200 Unresolved non-hydrogen angles: 241 Unresolved non-hydrogen dihedrals: 166 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 9, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 137 Chain: "C" Number of atoms: 2269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2269 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 5, 'TRANS': 324} Unresolved non-hydrogen bonds: 267 Unresolved non-hydrogen angles: 326 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 9, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 193 Chain: "D" Number of atoms: 1356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1356 Classifications: {'peptide': 208} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 10, 'TRANS': 197} Chain breaks: 7 Unresolved non-hydrogen bonds: 253 Unresolved non-hydrogen angles: 319 Unresolved non-hydrogen dihedrals: 212 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 8, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 157 Chain: "E" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 25 Classifications: {'peptide': 3} Link IDs: {'PCIS': 1, 'TRANS': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PCA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.24, per 1000 atoms: 0.70 Number of scatterers: 7483 At special positions: 0 Unit cell: (85.6, 113.42, 125.19, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 41 16.00 O 1384 8.00 N 1276 7.00 C 4782 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 98 " - pdb=" SG CYS A 179 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.06 Conformation dependent library (CDL) restraints added in 1.3 seconds 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB PRO E 3 " Number of C-beta restraints generated: 2022 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 16 sheets defined 29.0% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'F' and resid 12 through 17 removed outlier: 3.574A pdb=" N GLU F 17 " --> pdb=" O ARG F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 37 Processing helix chain 'F' and resid 38 through 41 Processing helix chain 'A' and resid 28 through 51 removed outlier: 3.752A pdb=" N VAL A 32 " --> pdb=" O THR A 28 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU A 33 " --> pdb=" O ILE A 29 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLY A 37 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY A 39 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE A 40 " --> pdb=" O CYS A 36 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL A 49 " --> pdb=" O MET A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 64 removed outlier: 3.525A pdb=" N TYR A 63 " --> pdb=" O PRO A 59 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU A 64 " --> pdb=" O THR A 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 59 through 64' Processing helix chain 'A' and resid 67 through 76 removed outlier: 4.083A pdb=" N VAL A 74 " --> pdb=" O ALA A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 88 removed outlier: 3.570A pdb=" N SER A 86 " --> pdb=" O ASN A 82 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE A 87 " --> pdb=" O ILE A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 97 Processing helix chain 'A' and resid 106 through 113 removed outlier: 3.628A pdb=" N ASN A 110 " --> pdb=" O TYR A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 129 removed outlier: 3.695A pdb=" N ILE A 121 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE A 127 " --> pdb=" O ARG A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 136 removed outlier: 3.865A pdb=" N PHE A 135 " --> pdb=" O ILE A 131 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 136 " --> pdb=" O LYS A 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 131 through 136' Processing helix chain 'A' and resid 138 through 155 removed outlier: 4.160A pdb=" N LYS A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE A 147 " --> pdb=" O LYS A 143 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR A 153 " --> pdb=" O VAL A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 163 removed outlier: 4.212A pdb=" N PHE A 162 " --> pdb=" O MET A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 197 removed outlier: 3.743A pdb=" N MET A 194 " --> pdb=" O PRO A 190 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ASP A 195 " --> pdb=" O ILE A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 219 removed outlier: 3.596A pdb=" N MET A 204 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA A 207 " --> pdb=" O PRO A 203 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR A 208 " --> pdb=" O MET A 204 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR A 211 " --> pdb=" O ALA A 207 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE A 213 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ILE A 214 " --> pdb=" O LEU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 279 removed outlier: 3.916A pdb=" N VAL A 271 " --> pdb=" O MET A 267 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE A 273 " --> pdb=" O ALA A 269 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA A 276 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N TRP A 279 " --> pdb=" O PHE A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 289 removed outlier: 3.893A pdb=" N ARG A 283 " --> pdb=" O TRP A 279 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL A 287 " --> pdb=" O ARG A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 311 removed outlier: 4.679A pdb=" N ILE A 309 " --> pdb=" O CYS A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 323 removed outlier: 3.579A pdb=" N ASN A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Proline residue: A 317 - end of helix removed outlier: 3.539A pdb=" N TYR A 320 " --> pdb=" O ASN A 316 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASN A 321 " --> pdb=" O PRO A 317 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET A 323 " --> pdb=" O ILE A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 334 removed outlier: 3.507A pdb=" N ARG A 328 " --> pdb=" O SER A 324 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU A 334 " --> pdb=" O ALA A 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 20 removed outlier: 3.753A pdb=" N ASP B 20 " --> pdb=" O SER B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 49 removed outlier: 3.901A pdb=" N ILE B 49 " --> pdb=" O LYS B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.943A pdb=" N ASN B 101 " --> pdb=" O GLN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 130 Processing helix chain 'B' and resid 145 through 148 Processing helix chain 'B' and resid 149 through 154 Processing helix chain 'B' and resid 159 through 164 removed outlier: 3.691A pdb=" N TYR B 163 " --> pdb=" O LYS B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 168 removed outlier: 4.250A pdb=" N ALA B 168 " --> pdb=" O PRO B 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 165 through 168' Processing helix chain 'B' and resid 183 through 202 removed outlier: 3.770A pdb=" N ALA B 189 " --> pdb=" O ARG B 185 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG B 194 " --> pdb=" O LYS B 190 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 236 removed outlier: 4.259A pdb=" N ASP B 230 " --> pdb=" O ARG B 226 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ASP B 233 " --> pdb=" O ASN B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 243 removed outlier: 3.549A pdb=" N TYR B 243 " --> pdb=" O ASN B 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 26 removed outlier: 3.857A pdb=" N ILE C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP C 20 " --> pdb=" O ASN C 16 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA C 24 " --> pdb=" O ASP C 20 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N CYS C 25 " --> pdb=" O ALA C 21 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA C 26 " --> pdb=" O ARG C 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.728A pdb=" N SER D 31 " --> pdb=" O ALA D 28 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 167 through 171 removed outlier: 3.971A pdb=" N ASN A 167 " --> pdb=" O SER A 178 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER A 178 " --> pdb=" O ASN A 167 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ALA A 174 " --> pdb=" O TYR A 171 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 71 through 76 removed outlier: 3.957A pdb=" N LEU B 38 " --> pdb=" O PHE B 84 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA B 105 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL B 109 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ILE B 106 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N PHE B 142 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N PHE B 108 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ASN B 144 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL B 110 " --> pdb=" O ASN B 144 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU B 143 " --> pdb=" O HIS B 214 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 51 through 52 Processing sheet with id=AA4, first strand: chain 'C' and resid 58 through 62 removed outlier: 3.992A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 104 through 105 removed outlier: 3.581A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 120 through 121 Processing sheet with id=AA7, first strand: chain 'C' and resid 156 through 157 removed outlier: 3.666A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 187 through 192 removed outlier: 3.903A pdb=" N SER C 189 " --> pdb=" O GLY C 202 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE C 199 " --> pdb=" O TRP C 211 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER C 201 " --> pdb=" O LYS C 209 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 229 through 234 removed outlier: 3.791A pdb=" N PHE C 241 " --> pdb=" O PHE C 253 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 273 through 278 removed outlier: 6.354A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N VAL C 276 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LEU C 286 " --> pdb=" O VAL C 276 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 319 through 320 Processing sheet with id=AB3, first strand: chain 'D' and resid 33 through 34 removed outlier: 3.950A pdb=" N SER D 99 " --> pdb=" O GLY D 33 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 45 through 49 removed outlier: 6.575A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 146 through 148 Processing sheet with id=AB6, first strand: chain 'D' and resid 162 through 163 Processing sheet with id=AB7, first strand: chain 'D' and resid 165 through 166 204 hydrogen bonds defined for protein. 549 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: 1.98 Time building geometry restraints manager: 2.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1227 1.31 - 1.43: 2053 1.43 - 1.56: 4283 1.56 - 1.69: 7 1.69 - 1.82: 53 Bond restraints: 7623 Sorted by residual: bond pdb=" C PCA E 1 " pdb=" N HIS E 2 " ideal model delta sigma weight residual 1.329 1.499 -0.170 1.40e-02 5.10e+03 1.47e+02 bond pdb=" C HIS E 2 " pdb=" N PRO E 3 " ideal model delta sigma weight residual 1.341 1.507 -0.166 1.60e-02 3.91e+03 1.08e+02 bond pdb=" CA PRO E 3 " pdb=" CB PRO E 3 " ideal model delta sigma weight residual 1.530 1.352 0.178 2.00e-02 2.50e+03 7.95e+01 bond pdb=" CA PCA E 1 " pdb=" CB PCA E 1 " ideal model delta sigma weight residual 1.530 1.369 0.161 2.00e-02 2.50e+03 6.49e+01 bond pdb=" N PCA E 1 " pdb=" CA PCA E 1 " ideal model delta sigma weight residual 1.458 1.590 -0.132 1.90e-02 2.77e+03 4.82e+01 ... (remaining 7618 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 10182 2.74 - 5.48: 218 5.48 - 8.21: 33 8.21 - 10.95: 10 10.95 - 13.69: 2 Bond angle restraints: 10445 Sorted by residual: angle pdb=" N VAL A 49 " pdb=" CA VAL A 49 " pdb=" C VAL A 49 " ideal model delta sigma weight residual 111.90 107.34 4.56 8.10e-01 1.52e+00 3.16e+01 angle pdb=" N TYR A 181 " pdb=" CA TYR A 181 " pdb=" C TYR A 181 " ideal model delta sigma weight residual 108.23 115.97 -7.74 1.38e+00 5.25e-01 3.14e+01 angle pdb=" N VAL A 264 " pdb=" CA VAL A 264 " pdb=" C VAL A 264 " ideal model delta sigma weight residual 112.83 107.32 5.51 9.90e-01 1.02e+00 3.10e+01 angle pdb=" N ILE B 227 " pdb=" CA ILE B 227 " pdb=" C ILE B 227 " ideal model delta sigma weight residual 112.96 107.47 5.49 1.00e+00 1.00e+00 3.02e+01 angle pdb=" C ASP C 195 " pdb=" N THR C 196 " pdb=" CA THR C 196 " ideal model delta sigma weight residual 121.54 132.01 -10.47 1.91e+00 2.74e-01 3.00e+01 ... (remaining 10440 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.39: 3945 16.39 - 32.78: 386 32.78 - 49.17: 68 49.17 - 65.56: 4 65.56 - 81.95: 2 Dihedral angle restraints: 4405 sinusoidal: 1282 harmonic: 3123 Sorted by residual: dihedral pdb=" C HIS E 2 " pdb=" N HIS E 2 " pdb=" CA HIS E 2 " pdb=" CB HIS E 2 " ideal model delta harmonic sigma weight residual -122.60 -137.12 14.52 0 2.50e+00 1.60e-01 3.37e+01 dihedral pdb=" CA TYR D 223 " pdb=" C TYR D 223 " pdb=" N PRO D 224 " pdb=" CA PRO D 224 " ideal model delta harmonic sigma weight residual 180.00 -153.86 -26.14 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA PHE D 108 " pdb=" C PHE D 108 " pdb=" N ASP D 109 " pdb=" CA ASP D 109 " ideal model delta harmonic sigma weight residual 180.00 -154.19 -25.81 0 5.00e+00 4.00e-02 2.66e+01 ... (remaining 4402 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.076: 1283 1.076 - 2.151: 0 2.151 - 3.226: 0 3.226 - 4.302: 0 4.302 - 5.377: 1 Chirality restraints: 1284 Sorted by residual: chirality pdb=" CA PRO E 3 " pdb=" N PRO E 3 " pdb=" C PRO E 3 " pdb=" CB PRO E 3 " both_signs ideal model delta sigma weight residual False 2.72 -2.66 5.38 2.00e-01 2.50e+01 7.23e+02 chirality pdb=" CA HIS E 2 " pdb=" N HIS E 2 " pdb=" C HIS E 2 " pdb=" CB HIS E 2 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.45e+00 chirality pdb=" CA PCA E 1 " pdb=" N PCA E 1 " pdb=" C PCA E 1 " pdb=" CB PCA E 1 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 1281 not shown) Planarity restraints: 1331 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 316 " 0.058 5.00e-02 4.00e+02 8.74e-02 1.22e+01 pdb=" N PRO A 317 " -0.151 5.00e-02 4.00e+02 pdb=" CA PRO A 317 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 317 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 187 " -0.057 5.00e-02 4.00e+02 8.70e-02 1.21e+01 pdb=" N PRO D 188 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO D 188 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO D 188 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR D 223 " -0.052 5.00e-02 4.00e+02 7.70e-02 9.48e+00 pdb=" N PRO D 224 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO D 224 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO D 224 " -0.036 5.00e-02 4.00e+02 ... (remaining 1328 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.16: 1 2.16 - 2.85: 2708 2.85 - 3.53: 9528 3.53 - 4.22: 17568 4.22 - 4.90: 29060 Nonbonded interactions: 58865 Sorted by model distance: nonbonded pdb=" C PRO E 3 " pdb=" N NH2 E 4 " model vdw 1.476 3.350 nonbonded pdb=" NH2 ARG A 306 " pdb=" N NH2 E 4 " model vdw 2.166 2.560 nonbonded pdb=" O ILE C 58 " pdb=" OG SER C 316 " model vdw 2.190 3.040 nonbonded pdb=" NE ARG A 306 " pdb=" N NH2 E 4 " model vdw 2.273 2.560 nonbonded pdb=" OG SER C 227 " pdb=" OD1 ASP C 228 " model vdw 2.281 3.040 ... (remaining 58860 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.660 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.140 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6740 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 : 0.008 0.178 7623 Z= 0.574 Angle : 1.029 13.689 10445 Z= 0.574 Chirality : 0.161 5.377 1284 Planarity : 0.007 0.087 1331 Dihedral : 13.418 81.955 2380 Min Nonbonded Distance : 1.476 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.74 % Favored : 92.17 % Rotamer: Outliers : 0.46 % Allowed : 10.09 % Favored : 89.45 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 3.03 % 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: -5.61 (0.19), residues: 1047 helix: -4.86 (0.12), residues: 294 sheet: -3.25 (0.31), residues: 214 loop : -3.23 (0.22), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP D 36 HIS 0.010 0.002 HIS B 82 PHE 0.024 0.003 PHE D 27 TYR 0.023 0.002 TYR C 59 ARG 0.004 0.001 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 174 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 49 ARG cc_start: 0.7806 (mpt90) cc_final: 0.7289 (mpp-170) REVERT: D 110 PHE cc_start: 0.7172 (t80) cc_final: 0.6694 (t80) outliers start: 3 outliers final: 2 residues processed: 177 average time/residue: 0.2098 time to fit residues: 49.1010 Evaluate side-chains 136 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 134 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain C residue 315 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 8.9990 chunk 80 optimal weight: 0.7980 chunk 44 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 chunk 83 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 61 optimal weight: 0.0030 chunk 96 optimal weight: 0.9980 overall best weight: 1.2992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN A 105 GLN B 98 GLN B 237 GLN C 62 HIS C 88 ASN D 174 GLN D 220 HIS E 2 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.194480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.161031 restraints weight = 10590.650| |-----------------------------------------------------------------------------| r_work (start): 0.4151 rms_B_bonded: 2.96 r_work: 0.3987 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 7623 Z= 0.244 Angle : 0.705 16.250 10445 Z= 0.360 Chirality : 0.046 0.194 1284 Planarity : 0.006 0.072 1331 Dihedral : 6.505 29.566 1135 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.31 % Favored : 91.60 % Rotamer: Outliers : 3.21 % Allowed : 17.43 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -4.96 (0.21), residues: 1047 helix: -4.01 (0.17), residues: 307 sheet: -3.01 (0.29), residues: 241 loop : -2.84 (0.25), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP D 47 HIS 0.006 0.001 HIS C 225 PHE 0.023 0.002 PHE A 148 TYR 0.016 0.002 TYR D 50 ARG 0.004 0.001 ARG D 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 216 ARG cc_start: 0.8106 (tmm-80) cc_final: 0.7641 (ttt180) REVERT: A 310 TYR cc_start: 0.7757 (m-10) cc_final: 0.6756 (m-10) REVERT: A 318 VAL cc_start: 0.8991 (OUTLIER) cc_final: 0.8738 (m) REVERT: B 25 GLU cc_start: 0.7867 (pt0) cc_final: 0.7523 (pt0) REVERT: D 108 PHE cc_start: 0.5604 (m-80) cc_final: 0.5404 (m-80) outliers start: 21 outliers final: 9 residues processed: 156 average time/residue: 0.1802 time to fit residues: 39.0686 Evaluate side-chains 142 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 132 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain D residue 80 PHE Chi-restraints excluded: chain D residue 214 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 5.9990 chunk 60 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 chunk 21 optimal weight: 0.3980 chunk 25 optimal weight: 0.9980 chunk 82 optimal weight: 0.0770 chunk 7 optimal weight: 0.0870 chunk 69 optimal weight: 0.0000 chunk 23 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 overall best weight: 0.2920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 HIS B 98 GLN C 88 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.200508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.165154 restraints weight = 10632.954| |-----------------------------------------------------------------------------| r_work (start): 0.4203 rms_B_bonded: 3.22 r_work: 0.4046 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.4046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6782 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 7623 Z= 0.163 Angle : 0.624 13.947 10445 Z= 0.315 Chirality : 0.043 0.227 1284 Planarity : 0.005 0.061 1331 Dihedral : 5.597 27.819 1134 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.87 % Favored : 95.03 % Rotamer: Outliers : 2.91 % Allowed : 19.27 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -4.19 (0.23), residues: 1047 helix: -3.19 (0.22), residues: 303 sheet: -2.64 (0.31), residues: 239 loop : -2.48 (0.26), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 47 HIS 0.006 0.001 HIS B 82 PHE 0.026 0.001 PHE B 228 TYR 0.012 0.001 TYR D 102 ARG 0.005 0.001 ARG C 137 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 153 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 TYR cc_start: 0.8200 (m-80) cc_final: 0.7972 (m-80) REVERT: A 123 ARG cc_start: 0.7886 (mtt180) cc_final: 0.7640 (mtt180) REVERT: A 310 TYR cc_start: 0.7757 (m-10) cc_final: 0.7148 (m-10) REVERT: A 318 VAL cc_start: 0.8807 (OUTLIER) cc_final: 0.8604 (m) REVERT: C 49 ARG cc_start: 0.8198 (mpt90) cc_final: 0.7525 (mpp-170) REVERT: C 234 PHE cc_start: 0.7491 (OUTLIER) cc_final: 0.6834 (t80) REVERT: C 323 ASP cc_start: 0.7407 (p0) cc_final: 0.6639 (p0) REVERT: D 110 PHE cc_start: 0.6995 (t80) cc_final: 0.6708 (t80) outliers start: 19 outliers final: 13 residues processed: 163 average time/residue: 0.1732 time to fit residues: 39.3969 Evaluate side-chains 147 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain D residue 80 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 103 optimal weight: 0.0870 chunk 53 optimal weight: 20.0000 chunk 10 optimal weight: 7.9990 chunk 11 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 overall best weight: 1.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 HIS D 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.196753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.163567 restraints weight = 10680.049| |-----------------------------------------------------------------------------| r_work (start): 0.4180 rms_B_bonded: 2.93 r_work: 0.4015 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6805 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7623 Z= 0.218 Angle : 0.646 13.942 10445 Z= 0.321 Chirality : 0.045 0.229 1284 Planarity : 0.005 0.057 1331 Dihedral : 5.512 29.159 1134 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.11 % Favored : 93.79 % Rotamer: Outliers : 3.82 % Allowed : 20.80 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -3.89 (0.23), residues: 1047 helix: -2.80 (0.24), residues: 310 sheet: -2.48 (0.31), residues: 246 loop : -2.37 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 47 HIS 0.003 0.001 HIS C 225 PHE 0.023 0.002 PHE A 148 TYR 0.025 0.002 TYR A 200 ARG 0.003 0.000 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 141 time to evaluate : 0.762 Fit side-chains revert: symmetry clash REVERT: A 166 LEU cc_start: 0.6898 (OUTLIER) cc_final: 0.6400 (mm) REVERT: A 310 TYR cc_start: 0.7764 (m-10) cc_final: 0.7061 (m-10) REVERT: A 318 VAL cc_start: 0.8835 (OUTLIER) cc_final: 0.8606 (m) REVERT: B 21 LYS cc_start: 0.6857 (tptm) cc_final: 0.5458 (pttt) REVERT: B 25 GLU cc_start: 0.7849 (pt0) cc_final: 0.7477 (pt0) REVERT: C 49 ARG cc_start: 0.8229 (mpt90) cc_final: 0.7528 (mpp-170) REVERT: C 234 PHE cc_start: 0.7621 (OUTLIER) cc_final: 0.6926 (t80) REVERT: C 323 ASP cc_start: 0.7489 (p0) cc_final: 0.6713 (p0) REVERT: D 110 PHE cc_start: 0.7291 (t80) cc_final: 0.6933 (t80) outliers start: 25 outliers final: 17 residues processed: 156 average time/residue: 0.1728 time to fit residues: 37.5067 Evaluate side-chains 155 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain D residue 80 PHE Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 214 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 28 optimal weight: 0.5980 chunk 90 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 0 optimal weight: 50.0000 chunk 38 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.192819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.160174 restraints weight = 10700.948| |-----------------------------------------------------------------------------| r_work (start): 0.4146 rms_B_bonded: 2.86 r_work: 0.3965 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6877 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7623 Z= 0.287 Angle : 0.680 14.157 10445 Z= 0.340 Chirality : 0.046 0.226 1284 Planarity : 0.005 0.052 1331 Dihedral : 5.666 29.969 1134 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.26 % Favored : 92.65 % Rotamer: Outliers : 4.43 % Allowed : 21.56 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -3.71 (0.24), residues: 1047 helix: -2.61 (0.24), residues: 311 sheet: -2.35 (0.33), residues: 229 loop : -2.32 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP D 47 HIS 0.006 0.001 HIS C 225 PHE 0.021 0.002 PHE A 148 TYR 0.024 0.002 TYR A 156 ARG 0.003 0.000 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 142 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 LEU cc_start: 0.6892 (OUTLIER) cc_final: 0.6397 (mm) REVERT: A 310 TYR cc_start: 0.7784 (m-10) cc_final: 0.6988 (m-10) REVERT: B 25 GLU cc_start: 0.7930 (pt0) cc_final: 0.7534 (pt0) REVERT: B 142 PHE cc_start: 0.7643 (OUTLIER) cc_final: 0.7378 (t80) REVERT: C 49 ARG cc_start: 0.8291 (mpt90) cc_final: 0.7584 (mpp-170) REVERT: C 234 PHE cc_start: 0.7828 (OUTLIER) cc_final: 0.7048 (t80) REVERT: C 323 ASP cc_start: 0.7557 (p0) cc_final: 0.6793 (p0) REVERT: D 110 PHE cc_start: 0.7349 (t80) cc_final: 0.7058 (t80) outliers start: 29 outliers final: 23 residues processed: 159 average time/residue: 0.1646 time to fit residues: 36.6068 Evaluate side-chains 162 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain D residue 80 PHE Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 214 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 12 optimal weight: 0.9980 chunk 53 optimal weight: 40.0000 chunk 61 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 70 optimal weight: 0.0980 chunk 101 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 3 optimal weight: 0.4980 chunk 87 optimal weight: 10.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.197675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.164155 restraints weight = 10636.238| |-----------------------------------------------------------------------------| r_work (start): 0.4202 rms_B_bonded: 3.12 r_work: 0.4023 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 7623 Z= 0.168 Angle : 0.612 12.597 10445 Z= 0.304 Chirality : 0.043 0.224 1284 Planarity : 0.004 0.052 1331 Dihedral : 5.185 31.405 1134 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.68 % Favored : 95.22 % Rotamer: Outliers : 3.98 % Allowed : 23.55 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -3.30 (0.24), residues: 1047 helix: -2.11 (0.27), residues: 308 sheet: -2.15 (0.34), residues: 225 loop : -2.17 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP D 47 HIS 0.004 0.001 HIS C 225 PHE 0.019 0.001 PHE A 148 TYR 0.026 0.001 TYR A 156 ARG 0.003 0.000 ARG D 72 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 146 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 166 LEU cc_start: 0.6938 (OUTLIER) cc_final: 0.6477 (mm) REVERT: A 310 TYR cc_start: 0.7723 (m-10) cc_final: 0.6982 (m-10) REVERT: B 21 LYS cc_start: 0.6773 (tptm) cc_final: 0.5383 (pttt) REVERT: B 25 GLU cc_start: 0.7859 (pt0) cc_final: 0.7472 (pt0) REVERT: B 142 PHE cc_start: 0.7351 (OUTLIER) cc_final: 0.7022 (t80) REVERT: B 229 ASN cc_start: 0.7696 (p0) cc_final: 0.7386 (p0) REVERT: C 49 ARG cc_start: 0.8238 (mpt90) cc_final: 0.7544 (mpp-170) REVERT: C 234 PHE cc_start: 0.7510 (OUTLIER) cc_final: 0.6980 (t80) REVERT: C 323 ASP cc_start: 0.7390 (p0) cc_final: 0.6698 (p0) REVERT: D 110 PHE cc_start: 0.7091 (t80) cc_final: 0.6679 (t80) outliers start: 26 outliers final: 21 residues processed: 164 average time/residue: 0.1653 time to fit residues: 38.4671 Evaluate side-chains 157 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain D residue 80 PHE Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 214 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 70 optimal weight: 7.9990 chunk 86 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 2 optimal weight: 20.0000 chunk 25 optimal weight: 0.0060 chunk 9 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 chunk 8 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 39 optimal weight: 0.0980 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN C 125 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.197394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.164753 restraints weight = 10635.829| |-----------------------------------------------------------------------------| r_work (start): 0.4205 rms_B_bonded: 2.90 r_work: 0.4028 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6828 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7623 Z= 0.181 Angle : 0.617 12.722 10445 Z= 0.305 Chirality : 0.043 0.183 1284 Planarity : 0.004 0.051 1331 Dihedral : 5.068 31.205 1134 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.06 % Favored : 94.84 % Rotamer: Outliers : 4.59 % Allowed : 24.77 % Favored : 70.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -3.09 (0.25), residues: 1047 helix: -1.87 (0.27), residues: 310 sheet: -2.05 (0.34), residues: 225 loop : -2.08 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP D 47 HIS 0.004 0.001 HIS C 225 PHE 0.027 0.002 PHE B 228 TYR 0.027 0.001 TYR A 156 ARG 0.010 0.000 ARG C 52 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 138 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 166 LEU cc_start: 0.6902 (OUTLIER) cc_final: 0.6436 (mm) REVERT: A 310 TYR cc_start: 0.7653 (m-10) cc_final: 0.6891 (m-10) REVERT: B 21 LYS cc_start: 0.6931 (tptm) cc_final: 0.5851 (pttt) REVERT: B 142 PHE cc_start: 0.7377 (OUTLIER) cc_final: 0.7020 (t80) REVERT: B 229 ASN cc_start: 0.7685 (p0) cc_final: 0.7392 (p0) REVERT: C 49 ARG cc_start: 0.7967 (mpt90) cc_final: 0.7389 (mpp-170) REVERT: C 52 ARG cc_start: 0.7750 (ptp90) cc_final: 0.7347 (mtt90) REVERT: C 234 PHE cc_start: 0.7413 (OUTLIER) cc_final: 0.6900 (t80) REVERT: D 110 PHE cc_start: 0.6984 (t80) cc_final: 0.6757 (t80) outliers start: 30 outliers final: 22 residues processed: 157 average time/residue: 0.1610 time to fit residues: 36.0924 Evaluate side-chains 156 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain D residue 80 PHE Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 214 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 99 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 chunk 59 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.197867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.165052 restraints weight = 10763.571| |-----------------------------------------------------------------------------| r_work (start): 0.4209 rms_B_bonded: 2.92 r_work: 0.4034 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6818 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7623 Z= 0.179 Angle : 0.618 12.623 10445 Z= 0.306 Chirality : 0.043 0.208 1284 Planarity : 0.004 0.052 1331 Dihedral : 5.000 31.695 1134 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.35 % Favored : 94.56 % Rotamer: Outliers : 4.59 % Allowed : 24.92 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.25), residues: 1047 helix: -1.66 (0.28), residues: 312 sheet: -1.94 (0.36), residues: 217 loop : -2.03 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP D 47 HIS 0.004 0.001 HIS C 225 PHE 0.024 0.002 PHE A 148 TYR 0.027 0.001 TYR A 156 ARG 0.007 0.000 ARG C 52 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 136 time to evaluate : 0.807 Fit side-chains revert: symmetry clash REVERT: A 166 LEU cc_start: 0.7062 (OUTLIER) cc_final: 0.6605 (mm) REVERT: A 310 TYR cc_start: 0.7613 (m-10) cc_final: 0.6941 (m-10) REVERT: B 21 LYS cc_start: 0.6934 (tptm) cc_final: 0.5853 (pttt) REVERT: B 142 PHE cc_start: 0.7359 (OUTLIER) cc_final: 0.7016 (t80) REVERT: B 229 ASN cc_start: 0.7668 (p0) cc_final: 0.7394 (p0) REVERT: C 49 ARG cc_start: 0.7972 (mpt90) cc_final: 0.7422 (mpp-170) REVERT: C 52 ARG cc_start: 0.7765 (ptp90) cc_final: 0.7320 (mtt90) REVERT: C 234 PHE cc_start: 0.7391 (OUTLIER) cc_final: 0.6901 (t80) REVERT: D 110 PHE cc_start: 0.7156 (t80) cc_final: 0.6817 (t80) outliers start: 30 outliers final: 23 residues processed: 156 average time/residue: 0.1635 time to fit residues: 36.3248 Evaluate side-chains 160 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 93 TYR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain D residue 80 PHE Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 214 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 55 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 0 optimal weight: 50.0000 chunk 18 optimal weight: 7.9990 chunk 79 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.192631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.158786 restraints weight = 10876.817| |-----------------------------------------------------------------------------| r_work (start): 0.4134 rms_B_bonded: 3.15 r_work: 0.3942 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7623 Z= 0.300 Angle : 0.684 13.371 10445 Z= 0.341 Chirality : 0.046 0.209 1284 Planarity : 0.005 0.053 1331 Dihedral : 5.411 31.227 1134 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.07 % Favored : 92.84 % Rotamer: Outliers : 4.43 % Allowed : 25.08 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -2.96 (0.25), residues: 1047 helix: -1.74 (0.27), residues: 307 sheet: -2.05 (0.34), residues: 219 loop : -1.98 (0.27), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP D 47 HIS 0.006 0.001 HIS C 225 PHE 0.025 0.002 PHE A 148 TYR 0.028 0.002 TYR A 156 ARG 0.006 0.001 ARG C 52 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 137 time to evaluate : 0.756 Fit side-chains revert: symmetry clash REVERT: A 166 LEU cc_start: 0.7000 (OUTLIER) cc_final: 0.6453 (mm) REVERT: A 310 TYR cc_start: 0.7749 (m-10) cc_final: 0.7065 (m-10) REVERT: B 25 GLU cc_start: 0.7954 (pt0) cc_final: 0.7612 (pt0) REVERT: B 229 ASN cc_start: 0.7848 (p0) cc_final: 0.7556 (p0) REVERT: C 49 ARG cc_start: 0.7993 (mpt90) cc_final: 0.7374 (mpp-170) REVERT: C 234 PHE cc_start: 0.7740 (OUTLIER) cc_final: 0.6946 (t80) REVERT: C 323 ASP cc_start: 0.7330 (p0) cc_final: 0.6602 (p0) REVERT: D 110 PHE cc_start: 0.7430 (t80) cc_final: 0.7134 (t80) outliers start: 29 outliers final: 23 residues processed: 155 average time/residue: 0.1532 time to fit residues: 33.6046 Evaluate side-chains 160 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 93 TYR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain D residue 80 PHE Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 214 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.0670 chunk 50 optimal weight: 0.7980 chunk 67 optimal weight: 0.0870 chunk 32 optimal weight: 0.2980 chunk 72 optimal weight: 6.9990 chunk 44 optimal weight: 8.9990 chunk 92 optimal weight: 0.4980 chunk 99 optimal weight: 9.9990 chunk 55 optimal weight: 20.0000 chunk 60 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 overall best weight: 0.3496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.199802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.164300 restraints weight = 10693.018| |-----------------------------------------------------------------------------| r_work (start): 0.4199 rms_B_bonded: 3.26 r_work: 0.4040 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.4040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6755 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7623 Z= 0.149 Angle : 0.615 12.147 10445 Z= 0.302 Chirality : 0.043 0.206 1284 Planarity : 0.004 0.052 1331 Dihedral : 4.949 32.353 1134 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 3.98 % Allowed : 25.84 % Favored : 70.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -2.72 (0.25), residues: 1047 helix: -1.39 (0.29), residues: 311 sheet: -2.00 (0.35), residues: 221 loop : -1.90 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP D 47 HIS 0.004 0.001 HIS C 225 PHE 0.025 0.001 PHE A 148 TYR 0.026 0.001 TYR A 156 ARG 0.007 0.000 ARG C 52 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 LEU cc_start: 0.7064 (OUTLIER) cc_final: 0.6555 (mm) REVERT: B 21 LYS cc_start: 0.6767 (tptm) cc_final: 0.5629 (pttt) REVERT: C 52 ARG cc_start: 0.7803 (ptp90) cc_final: 0.7438 (mtt90) REVERT: C 234 PHE cc_start: 0.7424 (OUTLIER) cc_final: 0.7012 (t80) REVERT: D 110 PHE cc_start: 0.7220 (t80) cc_final: 0.6845 (t80) outliers start: 26 outliers final: 20 residues processed: 159 average time/residue: 0.1591 time to fit residues: 35.5745 Evaluate side-chains 157 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 93 TYR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain D residue 80 PHE Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 214 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 16 optimal weight: 2.9990 chunk 64 optimal weight: 0.2980 chunk 14 optimal weight: 2.9990 chunk 10 optimal weight: 0.2980 chunk 92 optimal weight: 5.9990 chunk 69 optimal weight: 0.5980 chunk 87 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 55 optimal weight: 20.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.198775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.163713 restraints weight = 10680.113| |-----------------------------------------------------------------------------| r_work (start): 0.4196 rms_B_bonded: 3.21 r_work: 0.4029 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6786 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7623 Z= 0.174 Angle : 0.616 12.335 10445 Z= 0.303 Chirality : 0.043 0.207 1284 Planarity : 0.004 0.053 1331 Dihedral : 4.873 32.349 1134 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.78 % Favored : 95.13 % Rotamer: Outliers : 3.98 % Allowed : 25.08 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -2.58 (0.26), residues: 1047 helix: -1.20 (0.29), residues: 307 sheet: -1.97 (0.35), residues: 221 loop : -1.84 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP D 47 HIS 0.004 0.001 HIS C 225 PHE 0.025 0.001 PHE A 148 TYR 0.029 0.001 TYR A 156 ARG 0.009 0.001 ARG C 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4857.43 seconds wall clock time: 83 minutes 27.60 seconds (5007.60 seconds total)