Starting phenix.real_space_refine on Thu Sep 18 08:28:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ggm_51337/09_2025/9ggm_51337.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ggm_51337/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9ggm_51337/09_2025/9ggm_51337.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ggm_51337/09_2025/9ggm_51337.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ggm_51337/09_2025/9ggm_51337.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ggm_51337/09_2025/9ggm_51337.map" } resolution = 2.71 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ARG:plan': 7, 'GLN:plan1': 7, 'GLU:plan': 13, 'ASP:plan': 13, 'PHE:plan': 1, 'TRP:plan': 2, 'ASN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 1} 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: {'ASP:plan': 7, 'GLN:plan1': 3, 'ARG:plan': 6, 'TYR:plan': 2, 'GLU:plan': 11, 'ASN:plan1': 2, 'PHE:plan': 1} 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: {'ARG:plan': 7, 'GLN:plan1': 7, 'GLU:plan': 13, 'ASP:plan': 13, 'PHE:plan': 1, 'TRP:plan': 2, 'ASN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 1} 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: {'ASP:plan': 7, 'GLN:plan1': 3, 'ARG:plan': 6, 'TYR:plan': 2, 'GLU:plan': 11, 'ASN:plan1': 2, 'PHE:plan': 1} 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: 3.03, per 1000 atoms: 0.26 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: 0.97 Conformation dependent library (CDL) restraints added in 498.9 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.53 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: 1.91 Time building geometry restraints manager: 1.28 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: 0.01 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.400 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 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:6.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.980 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.007 0.001 ARG D 372 TYR 0.028 0.002 TYR C 462 PHE 0.014 0.001 PHE A 37 TRP 0.036 0.002 TRP A 328 HIS 0.004 0.001 HIS B 345 Details of bonding type rmsd covalent geometry : bond 0.00389 (11708) covalent geometry : angle 0.78271 (15932) hydrogen bonds : bond 0.14490 ( 492) hydrogen bonds : angle 6.88142 ( 1389) metal coordination : bond 0.00062 ( 2) *********************** 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 : 0.481 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: 0.5455 time to fit residues: 112.9138 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 : 0.325 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.6980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.0270 chunk 149 optimal weight: 1.9990 overall best weight: 0.9040 ------------------------------------------------------------------------------- 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 = 0.3955 r_free = 0.3955 target = 0.134987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.121061 restraints weight = 24435.920| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 3.20 r_work: 0.3671 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11710 Z= 0.150 Angle : 0.603 8.909 15932 Z= 0.313 Chirality : 0.044 0.140 1830 Planarity : 0.004 0.089 2036 Dihedral : 5.308 50.703 1704 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 4.75 % Allowed : 20.86 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.21), residues: 1512 helix: 0.46 (0.23), residues: 526 sheet: -0.77 (0.28), residues: 334 loop : -1.53 (0.23), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 94 TYR 0.020 0.002 TYR A 462 PHE 0.018 0.001 PHE C 37 TRP 0.008 0.001 TRP C 328 HIS 0.003 0.001 HIS A 173 Details of bonding type rmsd covalent geometry : bond 0.00346 (11708) covalent geometry : angle 0.60320 (15932) hydrogen bonds : bond 0.03590 ( 492) hydrogen bonds : angle 5.27265 ( 1389) metal coordination : bond 0.00119 ( 2) *********************** 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 206 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 155 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 369 GLU cc_start: 0.8981 (mt-10) cc_final: 0.8603 (mt-10) REVERT: D 373 MET cc_start: 0.8807 (mpt) cc_final: 0.8512 (mpt) REVERT: C 175 ASP cc_start: 0.8203 (t0) cc_final: 0.7834 (t0) REVERT: B 316 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7460 (mm-30) REVERT: B 361 GLU cc_start: 0.9245 (tp30) cc_final: 0.8908 (tp30) REVERT: B 369 GLU cc_start: 0.8977 (mt-10) cc_final: 0.8608 (mt-10) REVERT: B 373 MET cc_start: 0.8858 (mpt) cc_final: 0.8546 (mpt) outliers start: 51 outliers final: 22 residues processed: 189 average time/residue: 0.5478 time to fit residues: 112.9538 Evaluate side-chains 158 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 0.541 ------------------------------------------------------------------------------- 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 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 115 THR Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 262 CYS 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 51 MET 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 C residue 449 LEU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 316 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 25 optimal weight: 0.7980 chunk 148 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 114 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 332 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.130585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.116814 restraints weight = 24810.555| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 3.18 r_work: 0.3611 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 11710 Z= 0.203 Angle : 0.617 7.901 15932 Z= 0.324 Chirality : 0.045 0.153 1830 Planarity : 0.004 0.069 2036 Dihedral : 4.747 35.498 1680 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 6.33 % Allowed : 20.67 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.08 (0.21), residues: 1512 helix: 0.45 (0.23), residues: 526 sheet: -0.85 (0.27), residues: 348 loop : -1.58 (0.23), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 94 TYR 0.018 0.002 TYR D 304 PHE 0.014 0.002 PHE C 37 TRP 0.011 0.002 TRP C 328 HIS 0.004 0.001 HIS B 168 Details of bonding type rmsd covalent geometry : bond 0.00467 (11708) covalent geometry : angle 0.61744 (15932) hydrogen bonds : bond 0.03857 ( 492) hydrogen bonds : angle 5.25607 ( 1389) metal coordination : bond 0.00283 ( 2) *********************** 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 220 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 152 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 ASP cc_start: 0.8227 (t0) cc_final: 0.7899 (t0) REVERT: A 356 LYS cc_start: 0.8645 (ttmt) cc_final: 0.8369 (ttmm) REVERT: D 252 MET cc_start: 0.8588 (mmt) cc_final: 0.8087 (mmt) REVERT: C 356 LYS cc_start: 0.8669 (ttmt) cc_final: 0.8378 (ttmm) REVERT: B 361 GLU cc_start: 0.9181 (tp30) cc_final: 0.8736 (tp30) outliers start: 68 outliers final: 33 residues processed: 196 average time/residue: 0.5277 time to fit residues: 113.1297 Evaluate side-chains 168 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 135 time to evaluate : 0.457 ------------------------------------------------------------------------------- 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 89 MET Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 274 HIS 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 39 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 154 VAL Chi-restraints excluded: chain D residue 234 ASP 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 D residue 314 THR 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 39 THR Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 314 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 83 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 45 optimal weight: 0.0770 chunk 58 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 153 optimal weight: 0.7980 chunk 152 optimal weight: 0.9990 chunk 105 optimal weight: 5.9990 chunk 24 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 332 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.133133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.119351 restraints weight = 24557.370| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 3.21 r_work: 0.3639 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.2048 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= 0.125 Angle : 0.564 7.030 15932 Z= 0.291 Chirality : 0.043 0.138 1830 Planarity : 0.003 0.031 2036 Dihedral : 4.475 30.946 1680 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 5.12 % Allowed : 22.35 % Favored : 72.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.90 (0.21), residues: 1512 helix: 0.59 (0.23), residues: 534 sheet: -0.70 (0.27), residues: 362 loop : -1.52 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 94 TYR 0.012 0.001 TYR B 304 PHE 0.008 0.001 PHE A 37 TRP 0.017 0.001 TRP C 328 HIS 0.002 0.001 HIS A 173 Details of bonding type rmsd covalent geometry : bond 0.00286 (11708) covalent geometry : angle 0.56422 (15932) hydrogen bonds : bond 0.03169 ( 492) hydrogen bonds : angle 4.87646 ( 1389) metal coordination : bond 0.00132 ( 2) *********************** 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 214 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 159 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 ASP cc_start: 0.8348 (t0) cc_final: 0.7962 (t0) REVERT: A 356 LYS cc_start: 0.8584 (ttmt) cc_final: 0.8292 (ttmm) REVERT: A 425 THR cc_start: 0.8772 (OUTLIER) cc_final: 0.8476 (p) REVERT: D 221 LYS cc_start: 0.9137 (tptm) cc_final: 0.8899 (tptm) REVERT: D 361 GLU cc_start: 0.9361 (tp30) cc_final: 0.8852 (tp30) REVERT: C 318 LYS cc_start: 0.7701 (tptm) cc_final: 0.7418 (tptm) REVERT: C 356 LYS cc_start: 0.8591 (ttmt) cc_final: 0.8311 (ttmm) REVERT: C 425 THR cc_start: 0.8790 (OUTLIER) cc_final: 0.8544 (p) REVERT: B 92 MET cc_start: 0.7134 (mmm) cc_final: 0.6934 (mmm) REVERT: B 132 MET cc_start: 0.7681 (mmm) cc_final: 0.7437 (mmm) REVERT: B 361 GLU cc_start: 0.9197 (tp30) cc_final: 0.8726 (tp30) REVERT: B 373 MET cc_start: 0.8844 (mpt) cc_final: 0.8394 (mpt) outliers start: 55 outliers final: 28 residues processed: 193 average time/residue: 0.5714 time to fit residues: 120.0391 Evaluate side-chains 165 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 135 time to evaluate : 0.462 ------------------------------------------------------------------------------- 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 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 234 ASP Chi-restraints excluded: chain D residue 262 CYS Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 89 MET Chi-restraints excluded: chain C residue 130 GLU 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 425 THR 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 115 THR Chi-restraints excluded: chain B residue 234 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 146 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 133 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 97 optimal weight: 0.5980 chunk 126 optimal weight: 4.9990 chunk 131 optimal weight: 0.7980 chunk 132 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 89 optimal weight: 7.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS D 141 HIS D 142 HIS C 121 HIS B 332 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.130849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.117056 restraints weight = 24610.503| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 3.17 r_work: 0.3617 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11710 Z= 0.178 Angle : 0.585 7.076 15932 Z= 0.304 Chirality : 0.044 0.134 1830 Planarity : 0.004 0.037 2036 Dihedral : 4.525 30.296 1680 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 5.87 % Allowed : 23.18 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.21), residues: 1512 helix: 0.53 (0.23), residues: 532 sheet: -0.89 (0.27), residues: 346 loop : -1.49 (0.23), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 152 TYR 0.019 0.002 TYR D 304 PHE 0.011 0.001 PHE A 469 TRP 0.007 0.001 TRP A 328 HIS 0.004 0.001 HIS D 168 Details of bonding type rmsd covalent geometry : bond 0.00405 (11708) covalent geometry : angle 0.58525 (15932) hydrogen bonds : bond 0.03410 ( 492) hydrogen bonds : angle 4.94956 ( 1389) metal coordination : bond 0.00234 ( 2) *********************** 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 208 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 145 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 ASP cc_start: 0.8388 (t0) cc_final: 0.7979 (t0) REVERT: A 356 LYS cc_start: 0.8628 (ttmt) cc_final: 0.8353 (ttmm) REVERT: D 92 MET cc_start: 0.6882 (mmm) cc_final: 0.6648 (mmm) REVERT: D 132 MET cc_start: 0.7695 (mmm) cc_final: 0.7459 (mmm) REVERT: D 221 LYS cc_start: 0.9175 (tptm) cc_final: 0.8963 (tptm) REVERT: D 252 MET cc_start: 0.8605 (mmt) cc_final: 0.8113 (mmt) REVERT: D 361 GLU cc_start: 0.9327 (tp30) cc_final: 0.8802 (tp30) REVERT: C 316 MET cc_start: 0.7498 (OUTLIER) cc_final: 0.6958 (ttt) REVERT: C 356 LYS cc_start: 0.8652 (ttmt) cc_final: 0.8374 (ttmm) REVERT: B 361 GLU cc_start: 0.9192 (tp30) cc_final: 0.8708 (tp30) outliers start: 63 outliers final: 37 residues processed: 189 average time/residue: 0.5320 time to fit residues: 110.1551 Evaluate side-chains 175 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 137 time to evaluate : 0.447 ------------------------------------------------------------------------------- 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 130 GLU 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 115 THR Chi-restraints excluded: chain D residue 234 ASP Chi-restraints excluded: chain D residue 262 CYS Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 130 GLU 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 316 MET Chi-restraints excluded: chain C residue 425 THR 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 115 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 84 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 140 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 ** D 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 = 0.3925 r_free = 0.3925 target = 0.132269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.118524 restraints weight = 24530.996| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 3.19 r_work: 0.3639 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11710 Z= 0.132 Angle : 0.549 6.063 15932 Z= 0.283 Chirality : 0.043 0.133 1830 Planarity : 0.003 0.041 2036 Dihedral : 4.364 31.909 1680 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 5.68 % Allowed : 23.74 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.21), residues: 1512 helix: 0.72 (0.23), residues: 530 sheet: -0.85 (0.27), residues: 350 loop : -1.44 (0.23), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 152 TYR 0.013 0.001 TYR B 304 PHE 0.008 0.001 PHE A 469 TRP 0.006 0.001 TRP A 317 HIS 0.003 0.001 HIS A 173 Details of bonding type rmsd covalent geometry : bond 0.00303 (11708) covalent geometry : angle 0.54853 (15932) hydrogen bonds : bond 0.03118 ( 492) hydrogen bonds : angle 4.78815 ( 1389) metal coordination : bond 0.00128 ( 2) *********************** 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 218 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 157 time to evaluate : 0.320 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: 0.8376 (t0) cc_final: 0.7947 (t0) REVERT: A 356 LYS cc_start: 0.8600 (ttmt) cc_final: 0.8307 (ttmm) REVERT: D 221 LYS cc_start: 0.9138 (tptm) cc_final: 0.8873 (tptm) REVERT: D 252 MET cc_start: 0.8615 (mmt) cc_final: 0.8166 (mmt) REVERT: D 361 GLU cc_start: 0.9323 (tp30) cc_final: 0.8842 (tp30) REVERT: C 316 MET cc_start: 0.7314 (OUTLIER) cc_final: 0.6773 (ttt) REVERT: C 356 LYS cc_start: 0.8586 (ttmt) cc_final: 0.8313 (ttmm) REVERT: B 361 GLU cc_start: 0.9182 (tp30) cc_final: 0.8692 (tp30) outliers start: 61 outliers final: 38 residues processed: 201 average time/residue: 0.5043 time to fit residues: 110.9568 Evaluate side-chains 181 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 142 time to evaluate : 0.429 ------------------------------------------------------------------------------- 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 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 115 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 234 ASP Chi-restraints excluded: chain D residue 262 CYS Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain C residue 130 GLU 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 316 MET Chi-restraints excluded: chain C residue 425 THR 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 115 THR Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 314 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 39 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 91 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 45 ASN B 141 HIS B 142 HIS B 332 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.127279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.114167 restraints weight = 25056.704| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 3.07 r_work: 0.3560 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 11710 Z= 0.328 Angle : 0.717 7.087 15932 Z= 0.377 Chirality : 0.049 0.201 1830 Planarity : 0.004 0.044 2036 Dihedral : 5.086 29.333 1680 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 7.17 % Allowed : 24.58 % Favored : 68.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.38 (0.21), residues: 1512 helix: 0.16 (0.22), residues: 514 sheet: -1.03 (0.27), residues: 348 loop : -1.65 (0.22), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 152 TYR 0.037 0.003 TYR D 304 PHE 0.016 0.002 PHE A 469 TRP 0.007 0.002 TRP B 313 HIS 0.007 0.002 HIS D 168 Details of bonding type rmsd covalent geometry : bond 0.00745 (11708) covalent geometry : angle 0.71676 (15932) hydrogen bonds : bond 0.04360 ( 492) hydrogen bonds : angle 5.54236 ( 1389) metal coordination : bond 0.00463 ( 2) *********************** 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 222 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 145 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 ASP cc_start: 0.8397 (t0) cc_final: 0.7950 (t0) REVERT: A 356 LYS cc_start: 0.8634 (ttmt) cc_final: 0.8354 (ttmm) REVERT: A 532 GLN cc_start: 0.8275 (tt0) cc_final: 0.8021 (tt0) REVERT: D 91 GLN cc_start: 0.8088 (mp10) cc_final: 0.7854 (mp10) REVERT: D 205 TYR cc_start: 0.9096 (OUTLIER) cc_final: 0.8457 (t80) REVERT: D 221 LYS cc_start: 0.9219 (tptm) cc_final: 0.8995 (tptm) REVERT: D 361 GLU cc_start: 0.9335 (tp30) cc_final: 0.8791 (tp30) REVERT: C 167 MET cc_start: 0.5564 (mmt) cc_final: 0.5320 (mmt) REVERT: C 175 ASP cc_start: 0.8394 (t0) cc_final: 0.7884 (t0) REVERT: C 356 LYS cc_start: 0.8631 (ttmt) cc_final: 0.8342 (ttmm) REVERT: C 532 GLN cc_start: 0.8292 (tt0) cc_final: 0.8013 (tt0) REVERT: B 91 GLN cc_start: 0.8034 (mp10) cc_final: 0.7787 (mp10) REVERT: B 205 TYR cc_start: 0.9113 (OUTLIER) cc_final: 0.8593 (t80) REVERT: B 361 GLU cc_start: 0.9227 (tp30) cc_final: 0.8723 (tp30) outliers start: 77 outliers final: 44 residues processed: 200 average time/residue: 0.4980 time to fit residues: 109.0976 Evaluate side-chains 183 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 137 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 292 GLN Chi-restraints excluded: chain A residue 306 VAL 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 465 LEU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain D residue 42 LEU 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 154 VAL 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 314 THR Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 130 GLU Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 292 GLN Chi-restraints excluded: chain C residue 297 CYS Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 529 THR 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 115 THR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 205 TYR Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 262 CYS Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 374 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 53 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 115 optimal weight: 0.6980 chunk 14 optimal weight: 9.9990 chunk 50 optimal weight: 0.7980 chunk 150 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 46 optimal weight: 8.9990 chunk 56 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 ASN D 332 ASN ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 320 ASN B 45 ASN B 141 HIS B 282 HIS ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.131397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.117764 restraints weight = 24489.504| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 3.18 r_work: 0.3625 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11710 Z= 0.136 Angle : 0.572 6.634 15932 Z= 0.296 Chirality : 0.043 0.144 1830 Planarity : 0.004 0.051 2036 Dihedral : 4.497 31.632 1678 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 4.66 % Allowed : 26.44 % Favored : 68.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.21), residues: 1512 helix: 0.61 (0.23), residues: 516 sheet: -0.85 (0.27), residues: 350 loop : -1.46 (0.23), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 152 TYR 0.013 0.001 TYR A 369 PHE 0.007 0.001 PHE A 469 TRP 0.021 0.002 TRP A 328 HIS 0.003 0.001 HIS A 173 Details of bonding type rmsd covalent geometry : bond 0.00310 (11708) covalent geometry : angle 0.57160 (15932) hydrogen bonds : bond 0.03259 ( 492) hydrogen bonds : angle 4.93737 ( 1389) metal coordination : bond 0.00174 ( 2) *********************** 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 203 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 153 time to evaluate : 0.434 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: 0.8417 (t0) cc_final: 0.7973 (t0) REVERT: A 356 LYS cc_start: 0.8599 (ttmt) cc_final: 0.8319 (ttmm) REVERT: D 221 LYS cc_start: 0.9167 (tptm) cc_final: 0.8891 (tptm) REVERT: D 361 GLU cc_start: 0.9319 (tp30) cc_final: 0.8789 (tp30) REVERT: D 373 MET cc_start: 0.8849 (mpt) cc_final: 0.8493 (mpt) REVERT: C 167 MET cc_start: 0.5516 (mmt) cc_final: 0.5277 (mmt) REVERT: C 356 LYS cc_start: 0.8588 (ttmt) cc_final: 0.8310 (ttmm) REVERT: B 91 GLN cc_start: 0.8111 (mp10) cc_final: 0.7909 (mp10) REVERT: B 205 TYR cc_start: 0.9018 (OUTLIER) cc_final: 0.8638 (t80) REVERT: B 252 MET cc_start: 0.8552 (mmt) cc_final: 0.8127 (mmt) REVERT: B 361 GLU cc_start: 0.9193 (tp30) cc_final: 0.8704 (tp30) outliers start: 50 outliers final: 36 residues processed: 192 average time/residue: 0.5492 time to fit residues: 114.8341 Evaluate side-chains 179 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 142 time to evaluate : 0.394 ------------------------------------------------------------------------------- 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 306 VAL Chi-restraints excluded: chain A residue 310 ILE 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 460 VAL 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 157 ILE Chi-restraints excluded: chain D residue 234 ASP Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 130 GLU 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 425 THR Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 471 ARG Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 529 THR 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 115 THR Chi-restraints excluded: chain B residue 205 TYR Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 374 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 28 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 152 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 120 optimal weight: 0.0870 chunk 0 optimal weight: 5.9990 chunk 51 optimal weight: 0.0000 chunk 29 optimal weight: 0.6980 chunk 70 optimal weight: 4.9990 chunk 31 optimal weight: 0.0980 chunk 118 optimal weight: 2.9990 overall best weight: 0.3762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 141 HIS ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 HIS B 282 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.133866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.120206 restraints weight = 23979.747| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 3.19 r_work: 0.3666 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11710 Z= 0.114 Angle : 0.579 7.644 15932 Z= 0.296 Chirality : 0.042 0.142 1830 Planarity : 0.004 0.048 2036 Dihedral : 4.230 32.594 1678 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.10 % Allowed : 27.28 % Favored : 68.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.21), residues: 1512 helix: 0.76 (0.23), residues: 520 sheet: -0.70 (0.27), residues: 348 loop : -1.36 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 94 TYR 0.014 0.001 TYR B 359 PHE 0.008 0.001 PHE A 37 TRP 0.011 0.001 TRP A 317 HIS 0.003 0.001 HIS D 180 Details of bonding type rmsd covalent geometry : bond 0.00261 (11708) covalent geometry : angle 0.57854 (15932) hydrogen bonds : bond 0.02974 ( 492) hydrogen bonds : angle 4.70436 ( 1389) metal coordination : bond 0.00084 ( 2) *********************** 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 201 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 157 time to evaluate : 0.488 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: 0.8463 (t0) cc_final: 0.8085 (t0) REVERT: A 356 LYS cc_start: 0.8527 (ttmt) cc_final: 0.8297 (ttmm) REVERT: D 221 LYS cc_start: 0.9163 (tptm) cc_final: 0.8867 (tptm) REVERT: D 361 GLU cc_start: 0.9252 (tp30) cc_final: 0.8769 (tp30) REVERT: D 373 MET cc_start: 0.8754 (mpt) cc_final: 0.8553 (mpt) REVERT: C 356 LYS cc_start: 0.8551 (ttmt) cc_final: 0.8262 (ttmm) REVERT: B 252 MET cc_start: 0.8529 (mmt) cc_final: 0.8108 (mmt) REVERT: B 361 GLU cc_start: 0.9116 (tp30) cc_final: 0.8632 (tp30) REVERT: B 373 MET cc_start: 0.8770 (mpt) cc_final: 0.8548 (mpt) outliers start: 44 outliers final: 34 residues processed: 193 average time/residue: 0.5621 time to fit residues: 118.0601 Evaluate side-chains 178 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 144 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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 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 460 VAL 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 157 ILE Chi-restraints excluded: chain D residue 234 ASP Chi-restraints excluded: chain D residue 286 VAL 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 130 GLU Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 297 CYS Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 471 ARG 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 115 THR Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 374 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 17 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 91 optimal weight: 5.9990 chunk 52 optimal weight: 0.5980 chunk 97 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 148 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 HIS ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.133695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.120404 restraints weight = 24578.359| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 3.15 r_work: 0.3648 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11710 Z= 0.139 Angle : 0.608 10.268 15932 Z= 0.309 Chirality : 0.043 0.141 1830 Planarity : 0.004 0.047 2036 Dihedral : 4.286 32.291 1678 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.54 % Allowed : 27.93 % Favored : 68.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.21), residues: 1512 helix: 0.84 (0.23), residues: 518 sheet: -0.71 (0.27), residues: 348 loop : -1.37 (0.23), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 94 TYR 0.015 0.001 TYR D 16 PHE 0.008 0.001 PHE C 469 TRP 0.009 0.001 TRP A 317 HIS 0.004 0.001 HIS D 345 Details of bonding type rmsd covalent geometry : bond 0.00326 (11708) covalent geometry : angle 0.60784 (15932) hydrogen bonds : bond 0.03135 ( 492) hydrogen bonds : angle 4.72030 ( 1389) metal coordination : bond 0.00158 ( 2) ********************** 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 183 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 145 time to evaluate : 0.485 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: 0.8461 (t0) cc_final: 0.8024 (t0) REVERT: A 356 LYS cc_start: 0.8575 (ttmt) cc_final: 0.8369 (ttmm) REVERT: D 221 LYS cc_start: 0.9197 (tptm) cc_final: 0.8938 (tptm) REVERT: D 361 GLU cc_start: 0.9256 (tp30) cc_final: 0.8701 (tp30) REVERT: C 356 LYS cc_start: 0.8604 (ttmt) cc_final: 0.8335 (ttmm) REVERT: B 252 MET cc_start: 0.8544 (mmt) cc_final: 0.8160 (mmt) REVERT: B 361 GLU cc_start: 0.9095 (tp30) cc_final: 0.8660 (tp30) REVERT: B 373 MET cc_start: 0.8789 (mpt) cc_final: 0.8544 (mpt) outliers start: 38 outliers final: 35 residues processed: 180 average time/residue: 0.6240 time to fit residues: 121.3722 Evaluate side-chains 168 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 133 time to evaluate : 0.470 ------------------------------------------------------------------------------- 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 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 460 VAL 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 234 ASP Chi-restraints excluded: chain D residue 306 ILE 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 130 GLU Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 297 CYS Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 471 ARG Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 529 THR 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 115 THR Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 374 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 21 optimal weight: 0.5980 chunk 89 optimal weight: 10.0000 chunk 149 optimal weight: 0.0370 chunk 45 optimal weight: 0.1980 chunk 82 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 39 optimal weight: 0.0040 chunk 99 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 120 optimal weight: 0.9980 chunk 108 optimal weight: 0.8980 overall best weight: 0.3270 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 332 ASN ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 HIS B 282 HIS ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.136162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.122636 restraints weight = 24281.986| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 3.20 r_work: 0.3694 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.3098 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= 0.108 Angle : 0.580 9.413 15932 Z= 0.293 Chirality : 0.042 0.143 1830 Planarity : 0.004 0.047 2036 Dihedral : 4.082 33.125 1678 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.98 % Allowed : 28.49 % Favored : 68.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.21), residues: 1512 helix: 0.85 (0.23), residues: 530 sheet: -0.67 (0.27), residues: 352 loop : -1.34 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 94 TYR 0.015 0.001 TYR D 16 PHE 0.008 0.001 PHE A 37 TRP 0.012 0.001 TRP A 317 HIS 0.003 0.001 HIS D 180 Details of bonding type rmsd covalent geometry : bond 0.00251 (11708) covalent geometry : angle 0.57964 (15932) hydrogen bonds : bond 0.02799 ( 492) hydrogen bonds : angle 4.47916 ( 1389) metal coordination : bond 0.00072 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3607.97 seconds wall clock time: 62 minutes 26.52 seconds (3746.52 seconds total)