Starting phenix.real_space_refine on Sat May 17 06:08:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ggm_51337/05_2025/9ggm_51337.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ggm_51337/05_2025/9ggm_51337.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ggm_51337/05_2025/9ggm_51337.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ggm_51337/05_2025/9ggm_51337.map" model { file = "/net/cci-nas-00/data/ceres_data/9ggm_51337/05_2025/9ggm_51337.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ggm_51337/05_2025/9ggm_51337.cif" } resolution = 2.71 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4632 atoms to isotropic. 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 Zn 2 6.06 5 S 82 5.16 5 C 7346 2.51 5 N 1962 2.21 5 O 2068 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 11460 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 2953 Classifications: {'peptide': 417} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 95} Link IDs: {'PTRANS': 13, 'TRANS': 403} Chain breaks: 12 Unresolved non-hydrogen bonds: 337 Unresolved non-hydrogen angles: 427 Unresolved non-hydrogen dihedrals: 270 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 6, 'TRP:plan': 2, 'ASP:plan': 13, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 213 Chain: "D" Number of atoms: 2776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2776 Classifications: {'peptide': 367} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 16, 'TRANS': 350} Unresolved non-hydrogen bonds: 187 Unresolved non-hydrogen angles: 226 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 133 Chain: "C" Number of atoms: 2953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 2953 Classifications: {'peptide': 417} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 95} Link IDs: {'PTRANS': 13, 'TRANS': 403} Chain breaks: 12 Unresolved non-hydrogen bonds: 337 Unresolved non-hydrogen angles: 427 Unresolved non-hydrogen dihedrals: 270 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 6, 'TRP:plan': 2, 'ASP:plan': 13, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 213 Chain: "B" Number of atoms: 2776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2776 Classifications: {'peptide': 367} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 16, 'TRANS': 350} Unresolved non-hydrogen bonds: 187 Unresolved non-hydrogen angles: 226 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 133 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.65, per 1000 atoms: 0.67 Number of scatterers: 11460 At special positions: 0 Unit cell: (122.304, 89.024, 113.984, 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) Zn 2 29.99 S 82 16.00 O 2068 8.00 N 1962 7.00 C 7346 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 - 3.00 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=0, symmetry=0 Time building additional restraints: 2.75 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" ND1 HIS B 179 " pdb=" ZN D 501 " pdb="ZN ZN D 501 " - pdb=" ND1 HIS D 179 " 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2912 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 22 sheets defined 37.2% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.53 Creating SS restraints... Processing helix chain 'A' and resid 41 through 57 Processing helix chain 'A' and resid 77 through 81 Processing helix chain 'A' and resid 83 through 90 Processing helix chain 'A' and resid 108 through 121 removed outlier: 3.546A pdb=" N LEU A 114 " --> pdb=" O SER A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 129 No H-bonds generated for 'chain 'A' and resid 127 through 129' Processing helix chain 'A' and resid 130 through 141 removed outlier: 3.860A pdb=" N SER A 138 " --> pdb=" O ILE A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 155 removed outlier: 3.761A pdb=" N GLU A 148 " --> pdb=" O THR A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 174 removed outlier: 3.796A pdb=" N TRP A 168 " --> pdb=" O LEU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 189 removed outlier: 3.535A pdb=" N ALA A 181 " --> pdb=" O GLU A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 214 Processing helix chain 'A' and resid 220 through 227 Processing helix chain 'D' and resid 17 through 23 removed outlier: 3.543A pdb=" N ILE D 20 " --> pdb=" O ASP D 17 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR D 23 " --> pdb=" O ILE D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 46 removed outlier: 4.245A pdb=" N LEU D 42 " --> pdb=" O MET D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 52 removed outlier: 4.186A pdb=" N LYS D 51 " --> pdb=" O GLY D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 66 Processing helix chain 'D' and resid 70 through 80 Processing helix chain 'D' and resid 90 through 95 removed outlier: 4.188A pdb=" N ARG D 94 " --> pdb=" O LYS D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 115 removed outlier: 3.605A pdb=" N LEU D 113 " --> pdb=" O GLU D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 127 removed outlier: 3.542A pdb=" N VAL D 119 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA D 120 " --> pdb=" O GLY D 116 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS D 124 " --> pdb=" O ALA D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 166 removed outlier: 3.781A pdb=" N LYS D 166 " --> pdb=" O LEU D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 188 Processing helix chain 'D' and resid 217 through 221 Processing helix chain 'D' and resid 234 through 254 Proline residue: D 244 - end of helix Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 278 through 292 removed outlier: 3.568A pdb=" N CYS D 285 " --> pdb=" O GLY D 281 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL D 286 " --> pdb=" O HIS D 282 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE D 292 " --> pdb=" O VAL D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 322 Processing helix chain 'D' and resid 334 through 339 Processing helix chain 'D' and resid 356 through 372 Processing helix chain 'C' and resid 41 through 57 Processing helix chain 'C' and resid 77 through 81 Processing helix chain 'C' and resid 83 through 90 Processing helix chain 'C' and resid 108 through 121 removed outlier: 3.522A pdb=" N LEU C 114 " --> pdb=" O SER C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 129 No H-bonds generated for 'chain 'C' and resid 127 through 129' Processing helix chain 'C' and resid 130 through 141 removed outlier: 3.857A pdb=" N SER C 138 " --> pdb=" O ILE C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 155 removed outlier: 3.726A pdb=" N GLU C 148 " --> pdb=" O THR C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 174 removed outlier: 3.796A pdb=" N TRP C 168 " --> pdb=" O LEU C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 189 removed outlier: 3.526A pdb=" N ALA C 181 " --> pdb=" O GLU C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 214 Processing helix chain 'C' and resid 220 through 227 Processing helix chain 'B' and resid 17 through 23 removed outlier: 3.543A pdb=" N ILE B 20 " --> pdb=" O ASP B 17 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR B 23 " --> pdb=" O ILE B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 46 removed outlier: 4.244A pdb=" N LEU B 42 " --> pdb=" O MET B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 52 removed outlier: 4.186A pdb=" N LYS B 51 " --> pdb=" O GLY B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 66 Processing helix chain 'B' and resid 70 through 80 Processing helix chain 'B' and resid 90 through 95 removed outlier: 4.188A pdb=" N ARG B 94 " --> pdb=" O LYS B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 115 removed outlier: 3.604A pdb=" N LEU B 113 " --> pdb=" O GLU B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 127 removed outlier: 3.542A pdb=" N VAL B 119 " --> pdb=" O THR B 115 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS B 124 " --> pdb=" O ALA B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 166 removed outlier: 3.782A pdb=" N LYS B 166 " --> pdb=" O LEU B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 188 Processing helix chain 'B' and resid 217 through 221 Processing helix chain 'B' and resid 234 through 254 Proline residue: B 244 - end of helix Processing helix chain 'B' and resid 265 through 267 No H-bonds generated for 'chain 'B' and resid 265 through 267' Processing helix chain 'B' and resid 278 through 292 removed outlier: 3.568A pdb=" N CYS B 285 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL B 286 " --> pdb=" O HIS B 282 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N PHE B 292 " --> pdb=" O VAL B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 322 Processing helix chain 'B' and resid 334 through 339 Processing helix chain 'B' and resid 356 through 372 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 38 Processing sheet with id=AA2, first strand: chain 'A' and resid 123 through 125 Processing sheet with id=AA3, first strand: chain 'A' and resid 281 through 287 removed outlier: 3.991A pdb=" N SER A 284 " --> pdb=" O SER A 272 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N SER A 272 " --> pdb=" O SER A 284 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N GLN A 286 " --> pdb=" O ALA A 270 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ALA A 270 " --> pdb=" O GLN A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 293 through 296 Processing sheet with id=AA5, first strand: chain 'A' and resid 336 through 337 Processing sheet with id=AA6, first strand: chain 'A' and resid 340 through 344 removed outlier: 4.652A pdb=" N VAL A 366 " --> pdb=" O THR A 379 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A 375 " --> pdb=" O ARG A 370 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 390 through 394 Processing sheet with id=AA8, first strand: chain 'A' and resid 404 through 407 Processing sheet with id=AA9, first strand: chain 'A' and resid 441 through 442 Processing sheet with id=AB1, first strand: chain 'A' and resid 441 through 442 Processing sheet with id=AB2, first strand: chain 'A' and resid 486 through 489 removed outlier: 4.181A pdb=" N ILE A 494 " --> pdb=" O LEU A 511 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 53 through 55 removed outlier: 3.909A pdb=" N GLU D 53 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N CYS D 13 " --> pdb=" O VAL D 134 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ALA D 133 " --> pdb=" O MET D 298 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N GLY D 300 " --> pdb=" O ALA D 133 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ASN D 135 " --> pdb=" O GLY D 300 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LEU D 172 " --> pdb=" O VAL D 259 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N GLN D 261 " --> pdb=" O LEU D 172 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE D 174 " --> pdb=" O GLN D 261 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N GLY D 263 " --> pdb=" O ILE D 174 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ILE D 176 " --> pdb=" O GLY D 263 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N PHE D 227 " --> pdb=" O THR D 196 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N SER D 198 " --> pdb=" O PHE D 227 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N MET D 229 " --> pdb=" O SER D 198 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N HIS D 200 " --> pdb=" O MET D 229 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 281 through 287 removed outlier: 3.986A pdb=" N SER C 284 " --> pdb=" O SER C 272 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N SER C 272 " --> pdb=" O SER C 284 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N GLN C 286 " --> pdb=" O ALA C 270 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ALA C 270 " --> pdb=" O GLN C 286 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 293 through 299 Processing sheet with id=AB6, first strand: chain 'C' and resid 336 through 337 Processing sheet with id=AB7, first strand: chain 'C' and resid 340 through 344 removed outlier: 4.669A pdb=" N VAL C 366 " --> pdb=" O THR C 379 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL C 375 " --> pdb=" O ARG C 370 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 390 through 394 Processing sheet with id=AB9, first strand: chain 'C' and resid 404 through 407 Processing sheet with id=AC1, first strand: chain 'C' and resid 441 through 442 Processing sheet with id=AC2, first strand: chain 'C' and resid 441 through 442 Processing sheet with id=AC3, first strand: chain 'C' and resid 486 through 489 removed outlier: 4.178A pdb=" N ILE C 494 " --> pdb=" O LEU C 511 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 53 through 55 removed outlier: 3.908A pdb=" N GLU B 53 " --> pdb=" O VAL B 12 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N CYS B 13 " --> pdb=" O VAL B 134 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ALA B 133 " --> pdb=" O MET B 298 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N GLY B 300 " --> pdb=" O ALA B 133 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ASN B 135 " --> pdb=" O GLY B 300 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LEU B 172 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N GLN B 261 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE B 174 " --> pdb=" O GLN B 261 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N GLY B 263 " --> pdb=" O ILE B 174 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ILE B 176 " --> pdb=" O GLY B 263 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N PHE B 227 " --> pdb=" O THR B 196 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N SER B 198 " --> pdb=" O PHE B 227 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N MET B 229 " --> pdb=" O SER B 198 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N HIS B 200 " --> pdb=" O MET B 229 " (cutoff:3.500A) 496 hydrogen bonds defined for protein. 1389 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: 3.71 Time building geometry restraints manager: 3.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1842 1.31 - 1.44: 3243 1.44 - 1.56: 6500 1.56 - 1.69: 1 1.69 - 1.81: 122 Bond restraints: 11708 Sorted by residual: bond pdb=" C ASP A 302 " pdb=" O ASP A 302 " ideal model delta sigma weight residual 1.235 1.187 0.048 1.30e-02 5.92e+03 1.35e+01 bond pdb=" CB PRO A 464 " pdb=" CG PRO A 464 " ideal model delta sigma weight residual 1.492 1.635 -0.143 5.00e-02 4.00e+02 8.16e+00 bond pdb=" N ASP A 302 " pdb=" CA ASP A 302 " ideal model delta sigma weight residual 1.454 1.485 -0.031 1.23e-02 6.61e+03 6.34e+00 bond pdb=" N ASP C 302 " pdb=" CA ASP C 302 " ideal model delta sigma weight residual 1.454 1.484 -0.030 1.23e-02 6.61e+03 6.06e+00 bond pdb=" CG PRO A 464 " pdb=" CD PRO A 464 " ideal model delta sigma weight residual 1.503 1.421 0.082 3.40e-02 8.65e+02 5.75e+00 ... (remaining 11703 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.48: 15802 3.48 - 6.95: 120 6.95 - 10.43: 7 10.43 - 13.90: 2 13.90 - 17.38: 1 Bond angle restraints: 15932 Sorted by residual: angle pdb=" CA PRO A 464 " pdb=" N PRO A 464 " pdb=" CD PRO A 464 " ideal model delta sigma weight residual 112.00 94.62 17.38 1.40e+00 5.10e-01 1.54e+02 angle pdb=" C ASN C 463 " pdb=" CA ASN C 463 " pdb=" CB ASN C 463 " ideal model delta sigma weight residual 110.65 115.53 -4.88 1.04e+00 9.25e-01 2.21e+01 angle pdb=" N PRO A 464 " pdb=" CD PRO A 464 " pdb=" CG PRO A 464 " ideal model delta sigma weight residual 103.20 96.49 6.71 1.50e+00 4.44e-01 2.00e+01 angle pdb=" C CYS C 297 " pdb=" N LYS C 298 " pdb=" CA LYS C 298 " ideal model delta sigma weight residual 123.11 117.01 6.10 1.42e+00 4.96e-01 1.84e+01 angle pdb=" CA ASN C 463 " pdb=" CB ASN C 463 " pdb=" CG ASN C 463 " ideal model delta sigma weight residual 112.60 116.85 -4.25 1.00e+00 1.00e+00 1.80e+01 ... (remaining 15927 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 6100 17.41 - 34.81: 514 34.81 - 52.22: 161 52.22 - 69.62: 31 69.62 - 87.03: 14 Dihedral angle restraints: 6820 sinusoidal: 2284 harmonic: 4536 Sorted by residual: dihedral pdb=" CA LEU C 126 " pdb=" C LEU C 126 " pdb=" N ARG C 127 " pdb=" CA ARG C 127 " ideal model delta harmonic sigma weight residual 180.00 162.60 17.40 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA LEU A 126 " pdb=" C LEU A 126 " pdb=" N ARG A 127 " pdb=" CA ARG A 127 " ideal model delta harmonic sigma weight residual 180.00 162.89 17.11 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA THR B 305 " pdb=" C THR B 305 " pdb=" N ILE B 306 " pdb=" CA ILE B 306 " ideal model delta harmonic sigma weight residual -180.00 -163.09 -16.91 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 6817 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1376 0.048 - 0.095: 316 0.095 - 0.143: 120 0.143 - 0.191: 15 0.191 - 0.238: 3 Chirality restraints: 1830 Sorted by residual: chirality pdb=" CA GLN A 359 " pdb=" N GLN A 359 " pdb=" C GLN A 359 " pdb=" CB GLN A 359 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA ASN C 463 " pdb=" N ASN C 463 " pdb=" C ASN C 463 " pdb=" CB ASN C 463 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA ASN A 463 " pdb=" N ASN A 463 " pdb=" C ASN A 463 " pdb=" CB ASN A 463 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.47e-01 ... (remaining 1827 not shown) Planarity restraints: 2036 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 463 " -0.131 5.00e-02 4.00e+02 1.81e-01 5.25e+01 pdb=" N PRO A 464 " 0.312 5.00e-02 4.00e+02 pdb=" CA PRO A 464 " -0.096 5.00e-02 4.00e+02 pdb=" CD PRO A 464 " -0.086 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS C 297 " 0.018 2.00e-02 2.50e+03 3.57e-02 1.27e+01 pdb=" C CYS C 297 " -0.062 2.00e-02 2.50e+03 pdb=" O CYS C 297 " 0.023 2.00e-02 2.50e+03 pdb=" N LYS C 298 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 369 " 0.013 2.00e-02 2.50e+03 2.59e-02 6.72e+00 pdb=" C TYR C 369 " -0.045 2.00e-02 2.50e+03 pdb=" O TYR C 369 " 0.017 2.00e-02 2.50e+03 pdb=" N ARG C 370 " 0.015 2.00e-02 2.50e+03 ... (remaining 2033 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 174 2.65 - 3.21: 10457 3.21 - 3.77: 17753 3.77 - 4.34: 24630 4.34 - 4.90: 40650 Nonbonded interactions: 93664 Sorted by model distance: nonbonded pdb=" OG SER D 118 " pdb=" OD2 ASP D 156 " model vdw 2.085 3.040 nonbonded pdb=" OG SER B 118 " pdb=" OD2 ASP B 156 " model vdw 2.085 3.040 nonbonded pdb=" OD2 ASP B 265 " pdb="ZN ZN B 501 " model vdw 2.127 2.230 nonbonded pdb=" OD2 ASP D 265 " pdb="ZN ZN D 501 " model vdw 2.128 2.230 nonbonded pdb=" OD2 ASP B 235 " pdb=" OG1 THR B 278 " model vdw 2.151 3.040 ... (remaining 93659 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 30.610 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 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 0.143 11710 Z= 0.178 Angle : 0.783 17.376 15932 Z= 0.425 Chirality : 0.048 0.238 1830 Planarity : 0.006 0.181 2036 Dihedral : 15.289 87.027 3908 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.51 % Allowed : 24.86 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.21), residues: 1512 helix: 0.44 (0.23), residues: 502 sheet: -0.96 (0.28), residues: 334 loop : -1.62 (0.22), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 328 HIS 0.004 0.001 HIS B 345 PHE 0.014 0.001 PHE A 37 TYR 0.028 0.002 TYR C 462 ARG 0.007 0.001 ARG D 372 Details of bonding type rmsd hydrogen bonds : bond 0.14490 ( 492) hydrogen bonds : angle 6.88142 ( 1389) metal coordination : bond 0.00062 ( 2) covalent geometry : bond 0.00389 (11708) covalent geometry : angle 0.78271 (15932) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 166 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 306 ILE cc_start: 0.7103 (pp) cc_final: 0.6845 (pp) REVERT: B 306 ILE cc_start: 0.7222 (pp) cc_final: 0.6948 (pp) outliers start: 27 outliers final: 17 residues processed: 190 average time/residue: 1.0693 time to fit residues: 221.7880 Evaluate side-chains 159 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 298 LYS Chi-restraints excluded: chain C residue 314 ARG Chi-restraints excluded: chain B residue 41 ASN Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 374 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 3.9990 chunk 116 optimal weight: 0.0980 chunk 64 optimal weight: 0.9980 chunk 39 optimal weight: 6.9990 chunk 78 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 120 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 89 optimal weight: 6.9990 chunk 139 optimal weight: 0.0050 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 45 ASN D 282 HIS D 332 ASN B 45 ASN B 282 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.137617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.123768 restraints weight = 23789.851| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 3.21 r_work: 0.3703 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11710 Z= 0.124 Angle : 0.588 9.352 15932 Z= 0.303 Chirality : 0.043 0.135 1830 Planarity : 0.004 0.090 2036 Dihedral : 5.223 56.706 1704 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.63 % Allowed : 21.79 % Favored : 74.58 % 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: -0.98 (0.21), residues: 1512 helix: 0.49 (0.22), residues: 530 sheet: -0.70 (0.28), residues: 334 loop : -1.54 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 376 HIS 0.003 0.001 HIS B 34 PHE 0.015 0.001 PHE A 37 TYR 0.022 0.001 TYR B 16 ARG 0.006 0.000 ARG D 94 Details of bonding type rmsd hydrogen bonds : bond 0.03552 ( 492) hydrogen bonds : angle 5.22437 ( 1389) metal coordination : bond 0.00128 ( 2) covalent geometry : bond 0.00283 (11708) covalent geometry : angle 0.58800 (15932) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 155 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 ASP cc_start: 0.8277 (t0) cc_final: 0.7964 (t0) REVERT: D 361 GLU cc_start: 0.9239 (tp30) cc_final: 0.8973 (tp30) REVERT: D 369 GLU cc_start: 0.8981 (mt-10) cc_final: 0.8722 (mt-10) REVERT: C 175 ASP cc_start: 0.8198 (t0) cc_final: 0.7860 (t0) REVERT: B 361 GLU cc_start: 0.9220 (tp30) cc_final: 0.8971 (tp30) REVERT: B 369 GLU cc_start: 0.9000 (mt-10) cc_final: 0.8744 (mt-10) REVERT: B 373 MET cc_start: 0.8837 (mpt) cc_final: 0.8628 (mpt) outliers start: 39 outliers final: 14 residues processed: 178 average time/residue: 1.1472 time to fit residues: 222.8905 Evaluate side-chains 149 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 292 GLN Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 292 GLN Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 241 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 40 optimal weight: 5.9990 chunk 92 optimal weight: 0.0040 chunk 45 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 26 optimal weight: 0.3980 chunk 59 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 89 optimal weight: 7.9990 chunk 116 optimal weight: 0.0270 chunk 62 optimal weight: 0.6980 chunk 83 optimal weight: 0.0770 overall best weight: 0.2408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS C 121 HIS B 332 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.139439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.125426 restraints weight = 24200.647| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 3.30 r_work: 0.3730 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11710 Z= 0.101 Angle : 0.534 7.736 15932 Z= 0.274 Chirality : 0.042 0.136 1830 Planarity : 0.003 0.062 2036 Dihedral : 4.217 30.240 1680 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 4.47 % Allowed : 21.69 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.21), residues: 1512 helix: 0.73 (0.23), residues: 530 sheet: -0.32 (0.28), residues: 350 loop : -1.44 (0.23), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 328 HIS 0.002 0.000 HIS C 429 PHE 0.014 0.001 PHE C 37 TYR 0.017 0.001 TYR B 16 ARG 0.005 0.000 ARG B 94 Details of bonding type rmsd hydrogen bonds : bond 0.03052 ( 492) hydrogen bonds : angle 4.72485 ( 1389) metal coordination : bond 0.00079 ( 2) covalent geometry : bond 0.00226 (11708) covalent geometry : angle 0.53436 (15932) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 171 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 LYS cc_start: 0.7656 (tptm) cc_final: 0.7418 (tptm) REVERT: A 356 LYS cc_start: 0.8462 (ttmt) cc_final: 0.8170 (ttmm) REVERT: A 463 ASN cc_start: 0.7374 (p0) cc_final: 0.7149 (p0) REVERT: D 88 TYR cc_start: 0.7887 (m-80) cc_final: 0.7523 (m-80) REVERT: D 205 TYR cc_start: 0.8415 (OUTLIER) cc_final: 0.8196 (t80) REVERT: D 211 ASP cc_start: 0.8585 (t0) cc_final: 0.8359 (t0) REVERT: D 221 LYS cc_start: 0.9129 (tttp) cc_final: 0.8833 (tptm) REVERT: D 373 MET cc_start: 0.8843 (mpt) cc_final: 0.8603 (mpt) REVERT: C 318 LYS cc_start: 0.7702 (tptm) cc_final: 0.7468 (tptm) REVERT: C 356 LYS cc_start: 0.8492 (ttmt) cc_final: 0.8203 (ttmm) REVERT: B 31 MET cc_start: 0.6853 (OUTLIER) cc_final: 0.6269 (tmm) REVERT: B 88 TYR cc_start: 0.7873 (m-80) cc_final: 0.7464 (m-80) REVERT: B 132 MET cc_start: 0.7666 (mmm) cc_final: 0.7454 (mmm) REVERT: B 221 LYS cc_start: 0.9118 (tttp) cc_final: 0.8850 (tptm) REVERT: B 333 ASP cc_start: 0.8442 (t0) cc_final: 0.8136 (m-30) REVERT: B 361 GLU cc_start: 0.9101 (tp30) cc_final: 0.8703 (tp30) outliers start: 48 outliers final: 19 residues processed: 203 average time/residue: 1.1797 time to fit residues: 260.4531 Evaluate side-chains 163 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 234 ASP Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 89 MET Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 292 GLN Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain B residue 31 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 79 optimal weight: 7.9990 chunk 107 optimal weight: 0.9980 chunk 128 optimal weight: 0.9990 chunk 15 optimal weight: 0.2980 chunk 49 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 136 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 355 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 = 0.3950 r_free = 0.3950 target = 0.134276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.120373 restraints weight = 24403.051| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 3.21 r_work: 0.3651 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11710 Z= 0.153 Angle : 0.569 7.216 15932 Z= 0.296 Chirality : 0.043 0.133 1830 Planarity : 0.003 0.056 2036 Dihedral : 4.194 29.009 1678 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.47 % Allowed : 22.16 % Favored : 73.37 % 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: -0.75 (0.21), residues: 1512 helix: 0.68 (0.23), residues: 532 sheet: -0.55 (0.27), residues: 358 loop : -1.45 (0.24), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 376 HIS 0.004 0.001 HIS A 173 PHE 0.011 0.001 PHE D 108 TYR 0.019 0.002 TYR B 304 ARG 0.003 0.000 ARG D 94 Details of bonding type rmsd hydrogen bonds : bond 0.03307 ( 492) hydrogen bonds : angle 4.79399 ( 1389) metal coordination : bond 0.00132 ( 2) covalent geometry : bond 0.00352 (11708) covalent geometry : angle 0.56883 (15932) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 147 time to evaluate : 1.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ASP cc_start: 0.6175 (OUTLIER) cc_final: 0.5897 (m-30) REVERT: A 292 GLN cc_start: 0.7465 (OUTLIER) cc_final: 0.7197 (mt0) REVERT: A 356 LYS cc_start: 0.8559 (ttmt) cc_final: 0.8274 (ttmm) REVERT: A 425 THR cc_start: 0.8863 (OUTLIER) cc_final: 0.8621 (p) REVERT: D 31 MET cc_start: 0.6899 (OUTLIER) cc_final: 0.6360 (tmm) REVERT: D 88 TYR cc_start: 0.7962 (m-80) cc_final: 0.7398 (m-80) REVERT: D 92 MET cc_start: 0.6905 (mmm) cc_final: 0.6688 (mmm) REVERT: D 221 LYS cc_start: 0.9169 (tttp) cc_final: 0.8874 (tptm) REVERT: D 252 MET cc_start: 0.8549 (mmt) cc_final: 0.8086 (mmt) REVERT: D 361 GLU cc_start: 0.9320 (tp30) cc_final: 0.8874 (tp30) REVERT: D 373 MET cc_start: 0.8784 (mpt) cc_final: 0.8412 (mpt) REVERT: C 356 LYS cc_start: 0.8580 (ttmt) cc_final: 0.8288 (ttmm) REVERT: B 38 MET cc_start: 0.7120 (ptp) cc_final: 0.6821 (ptp) REVERT: B 132 MET cc_start: 0.7661 (mmm) cc_final: 0.7385 (mmm) REVERT: B 221 LYS cc_start: 0.9166 (tttp) cc_final: 0.8886 (tptm) REVERT: B 361 GLU cc_start: 0.9113 (tp30) cc_final: 0.8698 (tp30) outliers start: 48 outliers final: 23 residues processed: 179 average time/residue: 1.1182 time to fit residues: 218.1377 Evaluate side-chains 165 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 138 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 292 GLN Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain D residue 31 MET Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 262 CYS Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 292 GLN Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain B residue 54 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 97 optimal weight: 0.0980 chunk 28 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 58 optimal weight: 3.9990 chunk 35 optimal weight: 0.0020 chunk 12 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 chunk 139 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 332 ASN B 41 ASN B 332 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.136115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.122212 restraints weight = 24222.703| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 3.24 r_work: 0.3683 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11710 Z= 0.112 Angle : 0.533 6.930 15932 Z= 0.273 Chirality : 0.042 0.141 1830 Planarity : 0.003 0.029 2036 Dihedral : 4.022 29.884 1678 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 4.84 % Allowed : 22.35 % Favored : 72.81 % 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: -0.64 (0.21), residues: 1512 helix: 0.80 (0.23), residues: 532 sheet: -0.44 (0.27), residues: 358 loop : -1.44 (0.23), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 376 HIS 0.002 0.001 HIS A 173 PHE 0.008 0.001 PHE A 37 TYR 0.013 0.001 TYR B 16 ARG 0.003 0.000 ARG D 213 Details of bonding type rmsd hydrogen bonds : bond 0.02931 ( 492) hydrogen bonds : angle 4.57111 ( 1389) metal coordination : bond 0.00091 ( 2) covalent geometry : bond 0.00252 (11708) covalent geometry : angle 0.53323 (15932) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 160 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ASP cc_start: 0.6104 (OUTLIER) cc_final: 0.5796 (m-30) REVERT: A 175 ASP cc_start: 0.8360 (t0) cc_final: 0.7911 (t0) REVERT: A 310 ILE cc_start: 0.8195 (pp) cc_final: 0.7977 (mm) REVERT: A 356 LYS cc_start: 0.8495 (ttmt) cc_final: 0.8229 (ttmm) REVERT: A 425 THR cc_start: 0.8908 (OUTLIER) cc_final: 0.8703 (p) REVERT: A 512 ASP cc_start: 0.7260 (t0) cc_final: 0.5894 (p0) REVERT: D 31 MET cc_start: 0.6920 (OUTLIER) cc_final: 0.6314 (tmm) REVERT: D 92 MET cc_start: 0.6921 (mmm) cc_final: 0.6625 (mmm) REVERT: D 221 LYS cc_start: 0.9133 (tttp) cc_final: 0.8909 (tptm) REVERT: D 252 MET cc_start: 0.8551 (mmt) cc_final: 0.8035 (mmt) REVERT: D 361 GLU cc_start: 0.9281 (tp30) cc_final: 0.8843 (tp30) REVERT: C 356 LYS cc_start: 0.8547 (ttmt) cc_final: 0.8262 (ttmm) REVERT: C 512 ASP cc_start: 0.7286 (t0) cc_final: 0.5873 (p0) REVERT: B 31 MET cc_start: 0.6890 (OUTLIER) cc_final: 0.6378 (tmm) REVERT: B 221 LYS cc_start: 0.9140 (tttp) cc_final: 0.8881 (tptm) REVERT: B 361 GLU cc_start: 0.9084 (tp30) cc_final: 0.8676 (tp30) REVERT: B 373 MET cc_start: 0.8840 (mpt) cc_final: 0.8492 (mpt) outliers start: 52 outliers final: 24 residues processed: 195 average time/residue: 1.0829 time to fit residues: 230.4175 Evaluate side-chains 173 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 145 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 292 GLN Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain D residue 31 MET Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 234 ASP Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 89 MET Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 103 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 13 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 145 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 140 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 chunk 82 optimal weight: 0.8980 chunk 136 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 chunk 133 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 141 HIS D 142 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.134610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.120711 restraints weight = 24470.420| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 3.23 r_work: 0.3656 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11710 Z= 0.130 Angle : 0.552 6.765 15932 Z= 0.283 Chirality : 0.042 0.135 1830 Planarity : 0.003 0.032 2036 Dihedral : 4.034 29.639 1678 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 4.56 % Allowed : 24.86 % Favored : 70.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.21), residues: 1512 helix: 0.83 (0.23), residues: 534 sheet: -0.45 (0.27), residues: 358 loop : -1.44 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 376 HIS 0.003 0.001 HIS C 173 PHE 0.009 0.001 PHE A 469 TYR 0.021 0.001 TYR B 16 ARG 0.003 0.000 ARG B 37 Details of bonding type rmsd hydrogen bonds : bond 0.03036 ( 492) hydrogen bonds : angle 4.56817 ( 1389) metal coordination : bond 0.00088 ( 2) covalent geometry : bond 0.00299 (11708) covalent geometry : angle 0.55160 (15932) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 155 time to evaluate : 1.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ASP cc_start: 0.6116 (OUTLIER) cc_final: 0.5826 (m-30) REVERT: A 167 MET cc_start: 0.5162 (mmt) cc_final: 0.4798 (mmt) REVERT: A 175 ASP cc_start: 0.8372 (t0) cc_final: 0.7897 (t0) REVERT: A 356 LYS cc_start: 0.8501 (ttmt) cc_final: 0.8201 (ttmm) REVERT: A 425 THR cc_start: 0.8907 (OUTLIER) cc_final: 0.8645 (p) REVERT: A 512 ASP cc_start: 0.7286 (t0) cc_final: 0.5864 (p0) REVERT: D 92 MET cc_start: 0.6935 (mmm) cc_final: 0.6698 (mmm) REVERT: D 221 LYS cc_start: 0.9188 (tttp) cc_final: 0.8908 (tptm) REVERT: D 361 GLU cc_start: 0.9277 (tp30) cc_final: 0.8789 (tp30) REVERT: C 356 LYS cc_start: 0.8559 (ttmt) cc_final: 0.8278 (ttmm) REVERT: B 221 LYS cc_start: 0.9157 (tttp) cc_final: 0.8913 (tptm) REVERT: B 361 GLU cc_start: 0.9137 (tp30) cc_final: 0.8709 (tp30) outliers start: 49 outliers final: 29 residues processed: 191 average time/residue: 1.1336 time to fit residues: 235.9748 Evaluate side-chains 175 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 144 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 292 GLN Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 234 ASP Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain C residue 89 MET Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 292 GLN Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 346 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 40 optimal weight: 0.3980 chunk 129 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 79 optimal weight: 7.9990 chunk 74 optimal weight: 0.2980 chunk 139 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 141 HIS D 332 ASN B 41 ASN B 332 ASN ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.135527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.121651 restraints weight = 24617.207| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 3.25 r_work: 0.3677 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11710 Z= 0.114 Angle : 0.539 6.341 15932 Z= 0.276 Chirality : 0.042 0.130 1830 Planarity : 0.003 0.035 2036 Dihedral : 3.935 30.023 1678 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 5.12 % Allowed : 24.21 % Favored : 70.67 % 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: -0.52 (0.21), residues: 1512 helix: 1.01 (0.23), residues: 530 sheet: -0.40 (0.27), residues: 358 loop : -1.47 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 376 HIS 0.002 0.001 HIS A 173 PHE 0.008 0.001 PHE C 469 TYR 0.022 0.001 TYR B 16 ARG 0.002 0.000 ARG B 94 Details of bonding type rmsd hydrogen bonds : bond 0.02922 ( 492) hydrogen bonds : angle 4.49204 ( 1389) metal coordination : bond 0.00084 ( 2) covalent geometry : bond 0.00263 (11708) covalent geometry : angle 0.53931 (15932) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 157 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ASP cc_start: 0.6138 (OUTLIER) cc_final: 0.5829 (m-30) REVERT: A 167 MET cc_start: 0.5116 (mmt) cc_final: 0.4878 (mmt) REVERT: A 175 ASP cc_start: 0.8410 (t0) cc_final: 0.7927 (t0) REVERT: A 356 LYS cc_start: 0.8485 (ttmt) cc_final: 0.8210 (ttmm) REVERT: A 425 THR cc_start: 0.8918 (OUTLIER) cc_final: 0.8660 (p) REVERT: A 512 ASP cc_start: 0.7299 (t0) cc_final: 0.5840 (p0) REVERT: D 31 MET cc_start: 0.6839 (OUTLIER) cc_final: 0.6279 (tmm) REVERT: D 92 MET cc_start: 0.6884 (mmm) cc_final: 0.6589 (mmm) REVERT: D 221 LYS cc_start: 0.9180 (tttp) cc_final: 0.8944 (tptm) REVERT: D 361 GLU cc_start: 0.9245 (tp30) cc_final: 0.8773 (tp30) REVERT: D 373 MET cc_start: 0.8826 (mpt) cc_final: 0.8424 (mpt) REVERT: C 318 LYS cc_start: 0.7716 (tptm) cc_final: 0.7392 (tptm) REVERT: C 356 LYS cc_start: 0.8523 (ttmt) cc_final: 0.8243 (ttmm) REVERT: B 31 MET cc_start: 0.7011 (OUTLIER) cc_final: 0.6468 (tmm) REVERT: B 91 GLN cc_start: 0.7750 (mp10) cc_final: 0.7539 (mp10) REVERT: B 221 LYS cc_start: 0.9127 (tttp) cc_final: 0.8901 (tptm) REVERT: B 361 GLU cc_start: 0.9126 (tp30) cc_final: 0.8686 (tp30) outliers start: 55 outliers final: 29 residues processed: 196 average time/residue: 1.0125 time to fit residues: 217.9131 Evaluate side-chains 180 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 147 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain D residue 31 MET Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 234 ASP Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 292 GLN Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 346 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 91 optimal weight: 0.0970 chunk 12 optimal weight: 9.9990 chunk 121 optimal weight: 1.9990 chunk 40 optimal weight: 0.1980 chunk 59 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 120 optimal weight: 0.7980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 141 HIS B 41 ASN ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.135631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.121746 restraints weight = 24491.615| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 3.25 r_work: 0.3673 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11710 Z= 0.113 Angle : 0.547 8.478 15932 Z= 0.277 Chirality : 0.042 0.131 1830 Planarity : 0.003 0.039 2036 Dihedral : 3.887 30.108 1678 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 4.38 % Allowed : 24.95 % Favored : 70.67 % 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: -0.46 (0.21), residues: 1512 helix: 1.06 (0.23), residues: 530 sheet: -0.35 (0.27), residues: 358 loop : -1.44 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 376 HIS 0.002 0.001 HIS A 173 PHE 0.008 0.001 PHE C 469 TYR 0.019 0.001 TYR B 16 ARG 0.002 0.000 ARG D 94 Details of bonding type rmsd hydrogen bonds : bond 0.02868 ( 492) hydrogen bonds : angle 4.44465 ( 1389) metal coordination : bond 0.00072 ( 2) covalent geometry : bond 0.00260 (11708) covalent geometry : angle 0.54707 (15932) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 155 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ASP cc_start: 0.6128 (OUTLIER) cc_final: 0.5825 (m-30) REVERT: A 167 MET cc_start: 0.5189 (mmt) cc_final: 0.4913 (mmt) REVERT: A 175 ASP cc_start: 0.8451 (t0) cc_final: 0.7970 (t0) REVERT: A 356 LYS cc_start: 0.8485 (ttmt) cc_final: 0.8183 (ttmm) REVERT: A 394 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8323 (mm) REVERT: A 425 THR cc_start: 0.8942 (OUTLIER) cc_final: 0.8718 (p) REVERT: A 512 ASP cc_start: 0.7311 (t0) cc_final: 0.5812 (p0) REVERT: D 92 MET cc_start: 0.6882 (mmm) cc_final: 0.6587 (mmm) REVERT: D 221 LYS cc_start: 0.9183 (tttp) cc_final: 0.8943 (tptm) REVERT: D 361 GLU cc_start: 0.9208 (tp30) cc_final: 0.8693 (tp30) REVERT: C 318 LYS cc_start: 0.7744 (tptm) cc_final: 0.7411 (tptm) REVERT: C 356 LYS cc_start: 0.8498 (ttmt) cc_final: 0.8205 (ttmm) REVERT: C 394 LEU cc_start: 0.8833 (mm) cc_final: 0.8348 (mm) REVERT: B 31 MET cc_start: 0.6969 (OUTLIER) cc_final: 0.6459 (tmm) REVERT: B 91 GLN cc_start: 0.7701 (mp10) cc_final: 0.7472 (mp10) REVERT: B 221 LYS cc_start: 0.9155 (tttp) cc_final: 0.8942 (tptm) REVERT: B 361 GLU cc_start: 0.9130 (tp30) cc_final: 0.8703 (tp30) outliers start: 47 outliers final: 31 residues processed: 190 average time/residue: 1.0987 time to fit residues: 227.8229 Evaluate side-chains 181 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 146 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 234 ASP Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 292 GLN Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 346 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 62 optimal weight: 0.8980 chunk 133 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 14 optimal weight: 8.9990 chunk 146 optimal weight: 0.7980 chunk 138 optimal weight: 0.6980 chunk 132 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 141 HIS D 282 HIS ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 ASN B 332 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.135407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.122059 restraints weight = 24887.360| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 3.17 r_work: 0.3667 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11710 Z= 0.132 Angle : 0.566 8.241 15932 Z= 0.288 Chirality : 0.043 0.136 1830 Planarity : 0.003 0.042 2036 Dihedral : 3.964 29.870 1678 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 4.47 % Allowed : 24.95 % Favored : 70.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.21), residues: 1512 helix: 1.03 (0.23), residues: 530 sheet: -0.40 (0.27), residues: 358 loop : -1.42 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 376 HIS 0.003 0.001 HIS A 173 PHE 0.009 0.001 PHE C 469 TYR 0.018 0.001 TYR B 16 ARG 0.005 0.000 ARG B 213 Details of bonding type rmsd hydrogen bonds : bond 0.03055 ( 492) hydrogen bonds : angle 4.52071 ( 1389) metal coordination : bond 0.00129 ( 2) covalent geometry : bond 0.00307 (11708) covalent geometry : angle 0.56568 (15932) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 155 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ASP cc_start: 0.6228 (OUTLIER) cc_final: 0.5935 (m-30) REVERT: A 175 ASP cc_start: 0.8435 (t0) cc_final: 0.7958 (t0) REVERT: A 356 LYS cc_start: 0.8518 (ttmt) cc_final: 0.8303 (ttmm) REVERT: A 394 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8349 (mm) REVERT: A 425 THR cc_start: 0.8936 (OUTLIER) cc_final: 0.8661 (p) REVERT: D 31 MET cc_start: 0.6892 (OUTLIER) cc_final: 0.6335 (tmm) REVERT: D 92 MET cc_start: 0.6931 (mmm) cc_final: 0.6708 (mmm) REVERT: D 221 LYS cc_start: 0.9201 (tttp) cc_final: 0.8952 (tptm) REVERT: D 361 GLU cc_start: 0.9204 (tp30) cc_final: 0.8687 (tp30) REVERT: D 373 MET cc_start: 0.8807 (mpt) cc_final: 0.8529 (mpt) REVERT: C 318 LYS cc_start: 0.7756 (tptm) cc_final: 0.7423 (tptm) REVERT: C 356 LYS cc_start: 0.8546 (ttmt) cc_final: 0.8267 (ttmm) REVERT: C 394 LEU cc_start: 0.8836 (mm) cc_final: 0.8346 (mm) REVERT: B 31 MET cc_start: 0.6951 (OUTLIER) cc_final: 0.6416 (tmm) REVERT: B 91 GLN cc_start: 0.7807 (mp10) cc_final: 0.7542 (mp10) REVERT: B 221 LYS cc_start: 0.9179 (tttp) cc_final: 0.8946 (tptm) REVERT: B 361 GLU cc_start: 0.9110 (tp30) cc_final: 0.8629 (tp30) outliers start: 48 outliers final: 32 residues processed: 191 average time/residue: 1.1212 time to fit residues: 233.5236 Evaluate side-chains 184 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 147 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain D residue 31 MET Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 234 ASP Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 292 GLN Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 346 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 54 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 141 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 117 optimal weight: 0.0770 chunk 100 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 102 optimal weight: 0.0570 chunk 10 optimal weight: 0.0570 chunk 66 optimal weight: 0.4980 overall best weight: 0.3174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 141 HIS D 282 HIS ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 320 ASN B 41 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.137005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.123219 restraints weight = 24456.978| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 3.29 r_work: 0.3695 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11710 Z= 0.103 Angle : 0.547 9.396 15932 Z= 0.277 Chirality : 0.042 0.144 1830 Planarity : 0.003 0.045 2036 Dihedral : 3.806 30.689 1678 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.35 % Allowed : 26.26 % Favored : 70.39 % 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: -0.41 (0.22), residues: 1512 helix: 1.11 (0.23), residues: 532 sheet: -0.45 (0.27), residues: 370 loop : -1.35 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 376 HIS 0.002 0.001 HIS D 34 PHE 0.007 0.001 PHE C 469 TYR 0.016 0.001 TYR B 16 ARG 0.002 0.000 ARG B 94 Details of bonding type rmsd hydrogen bonds : bond 0.02762 ( 492) hydrogen bonds : angle 4.32588 ( 1389) metal coordination : bond 0.00070 ( 2) covalent geometry : bond 0.00238 (11708) covalent geometry : angle 0.54744 (15932) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 163 time to evaluate : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ASP cc_start: 0.5984 (OUTLIER) cc_final: 0.5661 (m-30) REVERT: A 175 ASP cc_start: 0.8465 (t0) cc_final: 0.7984 (t0) REVERT: A 356 LYS cc_start: 0.8415 (ttmt) cc_final: 0.8183 (ttmm) REVERT: A 394 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8308 (mm) REVERT: A 425 THR cc_start: 0.8902 (OUTLIER) cc_final: 0.8688 (p) REVERT: D 92 MET cc_start: 0.6939 (mmm) cc_final: 0.6683 (mmm) REVERT: D 205 TYR cc_start: 0.8698 (OUTLIER) cc_final: 0.8282 (t80) REVERT: D 221 LYS cc_start: 0.9153 (tttp) cc_final: 0.8876 (tptm) REVERT: D 361 GLU cc_start: 0.9159 (tp30) cc_final: 0.8693 (tp30) REVERT: C 318 LYS cc_start: 0.7715 (tptm) cc_final: 0.7408 (tptm) REVERT: C 335 ASP cc_start: 0.8017 (m-30) cc_final: 0.7707 (p0) REVERT: C 356 LYS cc_start: 0.8421 (ttmt) cc_final: 0.8146 (ttmm) REVERT: B 31 MET cc_start: 0.6840 (OUTLIER) cc_final: 0.6431 (tmm) REVERT: B 221 LYS cc_start: 0.9163 (tttp) cc_final: 0.8938 (tptm) REVERT: B 361 GLU cc_start: 0.9076 (tp30) cc_final: 0.8628 (tp30) outliers start: 36 outliers final: 26 residues processed: 190 average time/residue: 1.1971 time to fit residues: 247.0056 Evaluate side-chains 184 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 153 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 234 ASP Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 91 GLN Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 314 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 1 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 25 optimal weight: 8.9990 chunk 109 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 120 optimal weight: 0.2980 chunk 144 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 141 HIS D 282 HIS ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 ASN B 332 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.134647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.120736 restraints weight = 24745.818| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 3.27 r_work: 0.3656 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11710 Z= 0.132 Angle : 0.592 9.837 15932 Z= 0.299 Chirality : 0.043 0.239 1830 Planarity : 0.003 0.043 2036 Dihedral : 3.935 30.419 1677 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.63 % Allowed : 26.82 % Favored : 69.55 % 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: -0.41 (0.22), residues: 1512 helix: 1.04 (0.23), residues: 532 sheet: -0.35 (0.27), residues: 358 loop : -1.34 (0.24), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 376 HIS 0.003 0.001 HIS A 173 PHE 0.009 0.001 PHE C 469 TYR 0.025 0.001 TYR B 16 ARG 0.003 0.000 ARG C 314 Details of bonding type rmsd hydrogen bonds : bond 0.03049 ( 492) hydrogen bonds : angle 4.37945 ( 1389) metal coordination : bond 0.00124 ( 2) covalent geometry : bond 0.00308 (11708) covalent geometry : angle 0.59217 (15932) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7020.37 seconds wall clock time: 122 minutes 18.34 seconds (7338.34 seconds total)