Starting phenix.real_space_refine on Fri Jul 3 10:54:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9z67_73838/07_2026/9z67_73838.cif Found real_map, /net/cci-nas-00/data/ceres_data/9z67_73838/07_2026/9z67_73838.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9z67_73838/07_2026/9z67_73838.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9z67_73838/07_2026/9z67_73838.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9z67_73838/07_2026/9z67_73838.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9z67_73838/07_2026/9z67_73838.map" } resolution = 3.32 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 138 5.16 5 C 8644 2.51 5 N 2254 2.21 5 O 2328 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13366 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2521 Classifications: {'peptide': 321} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 315} Chain breaks: 1 Chain: "B" Number of atoms: 4020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 4020 Classifications: {'peptide': 494} Link IDs: {'PTRANS': 21, 'TRANS': 472} Chain: "C" Number of atoms: 2521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2521 Classifications: {'peptide': 321} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 315} Chain breaks: 1 Chain: "D" Number of atoms: 4020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 4020 Classifications: {'peptide': 494} Link IDs: {'PTRANS': 21, 'TRANS': 472} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {'NAG': 2, 'PAM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PAM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 69 Unusual residues: {'CLR': 1, 'PCW': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "C" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {'NAG': 2, 'PAM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PAM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 69 Unusual residues: {'CLR': 1, 'PCW': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Time building chain proxies: 3.06, per 1000 atoms: 0.23 Number of scatterers: 13366 At special positions: 0 Unit cell: (161.54, 133.66, 118.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 138 16.00 P 2 15.00 O 2328 8.00 N 2254 7.00 C 8644 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=28, symmetry=0 Simple disulfide: pdb=" SG CYS A 69 " - pdb=" SG CYS A 83 " distance=2.03 Simple disulfide: pdb=" SG CYS A 104 " - pdb=" SG CYS A 115 " distance=2.03 Simple disulfide: pdb=" SG CYS A 154 " - pdb=" SG CYS A 162 " distance=2.03 Simple disulfide: pdb=" SG CYS A 164 " - pdb=" SG CYS A 182 " distance=2.03 Simple disulfide: pdb=" SG CYS A 238 " - pdb=" SG CYS A 252 " distance=2.03 Simple disulfide: pdb=" SG CYS A 240 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 309 " - pdb=" SG CYS A 340 " distance=2.03 Simple disulfide: pdb=" SG CYS A 325 " - pdb=" SG CYS A 335 " distance=2.03 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 379 " distance=2.03 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 370 " distance=2.03 Simple disulfide: pdb=" SG CYS A 357 " - pdb=" SG CYS A 367 " distance=2.02 Simple disulfide: pdb=" SG CYS A 362 " - pdb=" SG CYS A 363 " distance=2.04 Simple disulfide: pdb=" SG CYS B 50 " - pdb=" SG CYS B 71 " distance=2.03 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 179 " distance=2.03 Simple disulfide: pdb=" SG CYS C 69 " - pdb=" SG CYS C 83 " distance=2.03 Simple disulfide: pdb=" SG CYS C 104 " - pdb=" SG CYS C 115 " distance=2.03 Simple disulfide: pdb=" SG CYS C 154 " - pdb=" SG CYS C 162 " distance=2.03 Simple disulfide: pdb=" SG CYS C 164 " - pdb=" SG CYS C 182 " distance=2.03 Simple disulfide: pdb=" SG CYS C 238 " - pdb=" SG CYS C 252 " distance=2.03 Simple disulfide: pdb=" SG CYS C 240 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 309 " - pdb=" SG CYS C 340 " distance=2.03 Simple disulfide: pdb=" SG CYS C 325 " - pdb=" SG CYS C 335 " distance=2.03 Simple disulfide: pdb=" SG CYS C 339 " - pdb=" SG CYS C 379 " distance=2.03 Simple disulfide: pdb=" SG CYS C 355 " - pdb=" SG CYS C 370 " distance=2.03 Simple disulfide: pdb=" SG CYS C 357 " - pdb=" SG CYS C 367 " distance=2.02 Simple disulfide: pdb=" SG CYS C 362 " - pdb=" SG CYS C 363 " distance=2.04 Simple disulfide: pdb=" SG CYS D 50 " - pdb=" SG CYS D 71 " distance=2.03 Simple disulfide: pdb=" SG CYS D 162 " - pdb=" SG CYS D 179 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 502 " - " ASN A 312 " " NAG A 503 " - " ASN A 326 " " NAG C 502 " - " ASN C 312 " " NAG C 503 " - " ASN C 326 " " NAG E 1 " - " ASN A 114 " " NAG F 1 " - " ASN C 114 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.24 Conformation dependent library (CDL) restraints added in 594.4 milliseconds 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3020 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 14 sheets defined 50.7% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 45 through 51 Processing helix chain 'A' and resid 76 through 86 Processing helix chain 'A' and resid 86 through 108 removed outlier: 3.671A pdb=" N MET A 90 " --> pdb=" O TYR A 86 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLN A 91 " --> pdb=" O GLN A 87 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N TYR A 92 " --> pdb=" O ASP A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 130 removed outlier: 4.323A pdb=" N VAL A 127 " --> pdb=" O PHE A 124 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE A 130 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 156 Processing helix chain 'A' and resid 172 through 181 removed outlier: 3.926A pdb=" N TRP A 179 " --> pdb=" O ARG A 175 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY A 180 " --> pdb=" O ASP A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 198 Processing helix chain 'A' and resid 198 through 204 removed outlier: 4.054A pdb=" N ARG A 204 " --> pdb=" O ARG A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 234 removed outlier: 3.722A pdb=" N ALA A 234 " --> pdb=" O VAL A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 272 Processing helix chain 'A' and resid 334 through 339 Processing helix chain 'B' and resid 4 through 9 removed outlier: 3.847A pdb=" N ASN B 8 " --> pdb=" O ALA B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 35 Processing helix chain 'B' and resid 77 through 81 Processing helix chain 'B' and resid 227 through 258 Proline residue: B 243 - end of helix Processing helix chain 'B' and resid 264 through 282 Processing helix chain 'B' and resid 283 through 290 Processing helix chain 'B' and resid 295 through 321 Processing helix chain 'B' and resid 331 through 334 removed outlier: 3.532A pdb=" N GLY B 334 " --> pdb=" O HIS B 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 331 through 334' Processing helix chain 'B' and resid 335 through 361 Proline residue: B 341 - end of helix removed outlier: 4.476A pdb=" N VAL B 359 " --> pdb=" O CYS B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 370 Processing helix chain 'B' and resid 371 through 413 removed outlier: 3.613A pdb=" N SER B 412 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N SER B 413 " --> pdb=" O GLY B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 456 Processing helix chain 'B' and resid 469 through 492 Processing helix chain 'C' and resid 45 through 51 Processing helix chain 'C' and resid 76 through 86 Processing helix chain 'C' and resid 86 through 108 removed outlier: 3.671A pdb=" N MET C 90 " --> pdb=" O TYR C 86 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLN C 91 " --> pdb=" O GLN C 87 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N TYR C 92 " --> pdb=" O ASP C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 130 removed outlier: 4.323A pdb=" N VAL C 127 " --> pdb=" O PHE C 124 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE C 130 " --> pdb=" O VAL C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 156 Processing helix chain 'C' and resid 172 through 181 removed outlier: 3.924A pdb=" N TRP C 179 " --> pdb=" O ARG C 175 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY C 180 " --> pdb=" O ASP C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 198 Processing helix chain 'C' and resid 198 through 204 removed outlier: 4.053A pdb=" N ARG C 204 " --> pdb=" O ARG C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 234 removed outlier: 3.722A pdb=" N ALA C 234 " --> pdb=" O VAL C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 272 Processing helix chain 'C' and resid 334 through 339 Processing helix chain 'D' and resid 4 through 9 removed outlier: 3.848A pdb=" N ASN D 8 " --> pdb=" O ALA D 4 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 35 Processing helix chain 'D' and resid 77 through 81 Processing helix chain 'D' and resid 227 through 258 Proline residue: D 243 - end of helix Processing helix chain 'D' and resid 264 through 282 Processing helix chain 'D' and resid 283 through 290 Processing helix chain 'D' and resid 295 through 321 Processing helix chain 'D' and resid 331 through 334 removed outlier: 3.532A pdb=" N GLY D 334 " --> pdb=" O HIS D 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 331 through 334' Processing helix chain 'D' and resid 335 through 361 Proline residue: D 341 - end of helix removed outlier: 4.476A pdb=" N VAL D 359 " --> pdb=" O CYS D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 370 Processing helix chain 'D' and resid 371 through 413 removed outlier: 3.613A pdb=" N SER D 412 " --> pdb=" O SER D 408 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N SER D 413 " --> pdb=" O GLY D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 418 through 456 Processing helix chain 'D' and resid 469 through 492 Processing sheet with id=AA1, first strand: chain 'A' and resid 235 through 241 Processing sheet with id=AA2, first strand: chain 'A' and resid 284 through 286 Processing sheet with id=AA3, first strand: chain 'A' and resid 324 through 325 removed outlier: 4.304A pdb=" N PHE A 377 " --> pdb=" O CYS A 325 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL A 374 " --> pdb=" O THR A 349 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR A 349 " --> pdb=" O VAL A 374 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 40 through 46 removed outlier: 5.658A pdb=" N ILE B 216 " --> pdb=" O ALA B 119 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ALA B 119 " --> pdb=" O ILE B 216 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP B 218 " --> pdb=" O ASP B 117 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N MET B 110 " --> pdb=" O GLU B 186 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLU B 186 " --> pdb=" O MET B 110 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N PHE B 112 " --> pdb=" O PHE B 184 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 73 through 74 removed outlier: 4.604A pdb=" N LYS B 49 " --> pdb=" O ILE B 74 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL B 132 " --> pdb=" O PRO B 157 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N MET B 134 " --> pdb=" O ARG B 155 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ARG B 155 " --> pdb=" O MET B 134 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL B 136 " --> pdb=" O HIS B 153 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N HIS B 153 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU B 138 " --> pdb=" O MET B 151 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 162 through 163 Processing sheet with id=AA7, first strand: chain 'B' and resid 459 through 462 Processing sheet with id=AA8, first strand: chain 'C' and resid 235 through 241 Processing sheet with id=AA9, first strand: chain 'C' and resid 284 through 286 Processing sheet with id=AB1, first strand: chain 'C' and resid 324 through 325 removed outlier: 4.305A pdb=" N PHE C 377 " --> pdb=" O CYS C 325 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL C 374 " --> pdb=" O THR C 349 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR C 349 " --> pdb=" O VAL C 374 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 40 through 46 removed outlier: 5.657A pdb=" N ILE D 216 " --> pdb=" O ALA D 119 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ALA D 119 " --> pdb=" O ILE D 216 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP D 218 " --> pdb=" O ASP D 117 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N MET D 110 " --> pdb=" O GLU D 186 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLU D 186 " --> pdb=" O MET D 110 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N PHE D 112 " --> pdb=" O PHE D 184 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 73 through 74 removed outlier: 4.602A pdb=" N LYS D 49 " --> pdb=" O ILE D 74 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL D 132 " --> pdb=" O PRO D 157 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N MET D 134 " --> pdb=" O ARG D 155 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ARG D 155 " --> pdb=" O MET D 134 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL D 136 " --> pdb=" O HIS D 153 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N HIS D 153 " --> pdb=" O VAL D 136 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU D 138 " --> pdb=" O MET D 151 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 162 through 163 Processing sheet with id=AB5, first strand: chain 'D' and resid 459 through 462 732 hydrogen bonds defined for protein. 2064 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.19 Time building geometry restraints manager: 1.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4172 1.34 - 1.47: 3545 1.47 - 1.59: 5787 1.59 - 1.72: 4 1.72 - 1.84: 204 Bond restraints: 13712 Sorted by residual: bond pdb=" C11 PCW B 602 " pdb=" O3 PCW B 602 " ideal model delta sigma weight residual 1.326 1.454 -0.128 2.00e-02 2.50e+03 4.08e+01 bond pdb=" C11 PCW D 602 " pdb=" O3 PCW D 602 " ideal model delta sigma weight residual 1.326 1.453 -0.127 2.00e-02 2.50e+03 4.04e+01 bond pdb=" C31 PCW D 602 " pdb=" O2 PCW D 602 " ideal model delta sigma weight residual 1.333 1.453 -0.120 2.00e-02 2.50e+03 3.61e+01 bond pdb=" C31 PCW B 602 " pdb=" O2 PCW B 602 " ideal model delta sigma weight residual 1.333 1.453 -0.120 2.00e-02 2.50e+03 3.59e+01 bond pdb=" O4P PCW D 602 " pdb=" P PCW D 602 " ideal model delta sigma weight residual 1.652 1.607 0.045 2.00e-02 2.50e+03 5.00e+00 ... (remaining 13707 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 18040 1.85 - 3.70: 377 3.70 - 5.55: 63 5.55 - 7.39: 30 7.39 - 9.24: 4 Bond angle restraints: 18514 Sorted by residual: angle pdb=" C GLN B 326 " pdb=" N HIS B 327 " pdb=" CA HIS B 327 " ideal model delta sigma weight residual 121.54 128.20 -6.66 1.91e+00 2.74e-01 1.21e+01 angle pdb=" C GLN D 326 " pdb=" N HIS D 327 " pdb=" CA HIS D 327 " ideal model delta sigma weight residual 121.54 128.19 -6.65 1.91e+00 2.74e-01 1.21e+01 angle pdb=" N HIS D 58 " pdb=" CA HIS D 58 " pdb=" C HIS D 58 " ideal model delta sigma weight residual 111.02 115.13 -4.11 1.22e+00 6.72e-01 1.13e+01 angle pdb=" N LYS B 61 " pdb=" CA LYS B 61 " pdb=" CB LYS B 61 " ideal model delta sigma weight residual 114.17 110.42 3.75 1.14e+00 7.69e-01 1.08e+01 angle pdb=" N LYS D 61 " pdb=" CA LYS D 61 " pdb=" CB LYS D 61 " ideal model delta sigma weight residual 114.17 110.45 3.72 1.14e+00 7.69e-01 1.07e+01 ... (remaining 18509 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.83: 7735 25.83 - 51.66: 527 51.66 - 77.49: 68 77.49 - 103.32: 4 103.32 - 129.15: 2 Dihedral angle restraints: 8336 sinusoidal: 3638 harmonic: 4698 Sorted by residual: dihedral pdb=" CA CYS C 362 " pdb=" C CYS C 362 " pdb=" N CYS C 363 " pdb=" CA CYS C 363 " ideal model delta harmonic sigma weight residual -180.00 -140.02 -39.98 0 5.00e+00 4.00e-02 6.39e+01 dihedral pdb=" CA CYS A 362 " pdb=" C CYS A 362 " pdb=" N CYS A 363 " pdb=" CA CYS A 363 " ideal model delta harmonic sigma weight residual -180.00 -140.04 -39.96 0 5.00e+00 4.00e-02 6.39e+01 dihedral pdb=" CB CYS A 154 " pdb=" SG CYS A 154 " pdb=" SG CYS A 162 " pdb=" CB CYS A 162 " ideal model delta sinusoidal sigma weight residual -86.00 -155.34 69.34 1 1.00e+01 1.00e-02 6.21e+01 ... (remaining 8333 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1655 0.053 - 0.107: 295 0.107 - 0.160: 38 0.160 - 0.214: 7 0.214 - 0.267: 3 Chirality restraints: 1998 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN C 114 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 114 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" C2 PCW D 602 " pdb=" C1 PCW D 602 " pdb=" C3 PCW D 602 " pdb=" O2 PCW D 602 " both_signs ideal model delta sigma weight residual False -2.32 -2.54 0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 1995 not shown) Planarity restraints: 2308 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 340 " 0.038 5.00e-02 4.00e+02 5.73e-02 5.25e+00 pdb=" N PRO B 341 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO B 341 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 341 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 340 " 0.037 5.00e-02 4.00e+02 5.71e-02 5.22e+00 pdb=" N PRO D 341 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO D 341 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 341 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 311 " -0.161 9.50e-02 1.11e+02 7.30e-02 4.41e+00 pdb=" NE ARG A 311 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG A 311 " -0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG A 311 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG A 311 " 0.000 2.00e-02 2.50e+03 ... (remaining 2305 not shown) Histogram of nonbonded interaction distances: 1.20 - 1.94: 6 1.94 - 2.68: 224 2.68 - 3.42: 18452 3.42 - 4.16: 32252 4.16 - 4.90: 58590 Nonbonded interactions: 109524 Sorted by model distance: nonbonded pdb=" OH TYR A 106 " pdb=" O GLU B 171 " model vdw 1.201 3.040 nonbonded pdb=" OH TYR C 106 " pdb=" O GLU D 171 " model vdw 1.588 3.040 nonbonded pdb=" NH2 ARG A 152 " pdb=" OD1 ASP B 218 " model vdw 1.620 3.120 nonbonded pdb=" NH2 ARG C 152 " pdb=" OD1 ASP D 218 " model vdw 1.801 3.120 nonbonded pdb=" O ASP A 271 " pdb=" O TYR C 344 " model vdw 1.809 3.040 ... (remaining 109519 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } 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: 2.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.940 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6533 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 : 0.005 0.336 13751 Z= 0.350 Angle : 0.685 9.243 18594 Z= 0.338 Chirality : 0.043 0.267 1998 Planarity : 0.005 0.073 2302 Dihedral : 15.837 129.151 5232 Min Nonbonded Distance : 1.201 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.99 % Allowed : 18.89 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.51 % 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 are not related in a simple way. whole: 1.49 (0.21), residues: 1618 helix: 2.41 (0.18), residues: 716 sheet: 0.63 (0.34), residues: 220 loop : -0.44 (0.25), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 311 TYR 0.028 0.002 TYR D 308 PHE 0.015 0.001 PHE B 314 TRP 0.020 0.001 TRP D 481 HIS 0.010 0.001 HIS B 424 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.20 (13712) covalent geometry : angle 0.67638 / 0.33 (18514) SS BOND : bond 0.00444 / 0.34 ( 28) SS BOND : angle 1.53302 / 1.11 ( 56) hydrogen bonds : bond 0.13121 / 8.52 ( 732) hydrogen bonds : angle 6.07483 / 4.40 ( 2064) Misc. bond : bond 0.19656 / 9.38 ( 3) link_BETA1-4 : bond 0.00540 / 0.27 ( 2) link_BETA1-4 : angle 0.97113 / 0.78 ( 6) link_NAG-ASN : bond 0.00232 / 0.11 ( 6) link_NAG-ASN : angle 2.57597 / 1.72 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 405 time to evaluate : 0.468 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LEU cc_start: 0.8213 (mt) cc_final: 0.7771 (tt) REVERT: A 187 ASP cc_start: 0.6122 (m-30) cc_final: 0.5909 (t0) REVERT: A 188 TYR cc_start: 0.7840 (t80) cc_final: 0.7524 (t80) REVERT: A 201 GLU cc_start: 0.7915 (mp0) cc_final: 0.7188 (mm-30) REVERT: A 296 THR cc_start: 0.8513 (p) cc_final: 0.8248 (p) REVERT: A 333 ASP cc_start: 0.8729 (p0) cc_final: 0.8384 (p0) REVERT: B 112 PHE cc_start: 0.7627 (m-80) cc_final: 0.7303 (m-80) REVERT: B 176 TYR cc_start: 0.6964 (m-10) cc_final: 0.6515 (m-80) REVERT: B 180 ASP cc_start: 0.7882 (m-30) cc_final: 0.7352 (p0) REVERT: B 246 PHE cc_start: 0.5271 (t80) cc_final: 0.4883 (t80) REVERT: B 312 LEU cc_start: 0.7661 (mt) cc_final: 0.7004 (mt) REVERT: B 316 ILE cc_start: 0.8114 (OUTLIER) cc_final: 0.7880 (tp) REVERT: B 352 PHE cc_start: 0.7603 (t80) cc_final: 0.7260 (t80) REVERT: B 436 MET cc_start: 0.8027 (ttp) cc_final: 0.7409 (mmp) REVERT: C 202 ARG cc_start: 0.8168 (mmt180) cc_final: 0.7472 (mtm110) REVERT: C 261 LYS cc_start: 0.8982 (mtmt) cc_final: 0.8662 (mtpp) REVERT: C 332 MET cc_start: 0.6388 (ttp) cc_final: 0.5759 (ttp) REVERT: C 373 ILE cc_start: 0.9015 (mt) cc_final: 0.8762 (mt) REVERT: D 164 PHE cc_start: 0.5761 (t80) cc_final: 0.5387 (t80) REVERT: D 308 TYR cc_start: 0.8775 (m-80) cc_final: 0.8546 (m-80) REVERT: D 323 MET cc_start: 0.6711 (mmt) cc_final: 0.6299 (tmm) REVERT: D 324 MET cc_start: 0.7222 (mmm) cc_final: 0.6793 (mmt) REVERT: D 484 TYR cc_start: 0.7399 (t80) cc_final: 0.6678 (t80) outliers start: 14 outliers final: 2 residues processed: 413 average time/residue: 0.1419 time to fit residues: 80.2835 Evaluate side-chains 226 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 223 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain B residue 316 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.4980 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 70 HIS B 304 GLN B 411 GLN ** C 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 HIS D 8 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.116929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.102159 restraints weight = 50091.530| |-----------------------------------------------------------------------------| r_work (start): 0.4274 rms_B_bonded: 5.32 r_work (final): 0.4274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 13751 Z= 0.161 Angle : 0.716 11.170 18594 Z= 0.366 Chirality : 0.043 0.160 1998 Planarity : 0.005 0.058 2302 Dihedral : 8.925 104.525 2163 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 4.12 % Allowed : 17.90 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.38 % 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 are not related in a simple way. whole: 1.54 (0.22), residues: 1618 helix: 2.33 (0.18), residues: 732 sheet: 0.46 (0.33), residues: 240 loop : -0.27 (0.27), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 220 TYR 0.022 0.002 TYR D 308 PHE 0.019 0.001 PHE D 314 TRP 0.018 0.001 TRP B 481 HIS 0.017 0.001 HIS D 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (13712) covalent geometry : angle 0.70369 / 0.36 (18514) SS BOND : bond 0.00533 / 0.37 ( 28) SS BOND : angle 2.33413 / 1.43 ( 56) hydrogen bonds : bond 0.04279 / 2.83 ( 732) hydrogen bonds : angle 4.51381 / 3.26 ( 2064) Misc. bond : bond 0.00224 / 0.11 ( 3) link_BETA1-4 : bond 0.00309 / 0.16 ( 2) link_BETA1-4 : angle 1.51894 / 1.28 ( 6) link_NAG-ASN : bond 0.00233 / 0.12 ( 6) link_NAG-ASN : angle 1.57598 / 1.03 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 240 time to evaluate : 0.456 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.6085 (OUTLIER) cc_final: 0.5844 (mtp) REVERT: A 155 ARG cc_start: 0.7569 (mtt90) cc_final: 0.7010 (mpt-90) REVERT: A 159 LEU cc_start: 0.8311 (mt) cc_final: 0.8001 (tt) REVERT: A 176 ASP cc_start: 0.7723 (OUTLIER) cc_final: 0.7507 (t70) REVERT: A 332 MET cc_start: 0.6305 (OUTLIER) cc_final: 0.6037 (ttt) REVERT: A 333 ASP cc_start: 0.8451 (p0) cc_final: 0.8180 (p0) REVERT: A 338 MET cc_start: 0.6439 (tpt) cc_final: 0.5935 (tpt) REVERT: B 22 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8240 (pp) REVERT: B 26 ILE cc_start: 0.8680 (OUTLIER) cc_final: 0.8401 (tp) REVERT: B 246 PHE cc_start: 0.5338 (t80) cc_final: 0.4821 (t80) REVERT: B 331 HIS cc_start: 0.5804 (OUTLIER) cc_final: 0.5500 (t-90) REVERT: B 436 MET cc_start: 0.7957 (ttp) cc_final: 0.7450 (mmp) REVERT: B 445 MET cc_start: 0.7966 (mmp) cc_final: 0.7463 (mtp) REVERT: D 75 ARG cc_start: 0.7292 (mpp80) cc_final: 0.7004 (mpp80) REVERT: D 178 GLU cc_start: 0.7382 (tm-30) cc_final: 0.7102 (tm-30) REVERT: D 308 TYR cc_start: 0.8761 (m-80) cc_final: 0.8510 (m-80) outliers start: 58 outliers final: 23 residues processed: 281 average time/residue: 0.1195 time to fit residues: 47.9754 Evaluate side-chains 232 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 203 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 304 GLN Chi-restraints excluded: chain B residue 331 HIS Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain B residue 405 ARG Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 277 ARG Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 208 LYS Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 331 HIS Chi-restraints excluded: chain D residue 410 LYS Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 488 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 86 optimal weight: 20.0000 chunk 6 optimal weight: 0.9980 chunk 126 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 48 optimal weight: 0.0870 chunk 19 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 149 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 107 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 overall best weight: 1.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 ASN ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN B 411 GLN ** C 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 HIS ** D 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.112934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.099053 restraints weight = 55919.507| |-----------------------------------------------------------------------------| r_work (start): 0.4146 rms_B_bonded: 5.08 r_work (final): 0.4146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.4489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 13751 Z= 0.169 Angle : 0.683 13.037 18594 Z= 0.349 Chirality : 0.043 0.239 1998 Planarity : 0.005 0.051 2302 Dihedral : 8.402 102.310 2158 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.48 % Allowed : 19.39 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.38 % 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 are not related in a simple way. whole: 1.35 (0.21), residues: 1618 helix: 2.31 (0.19), residues: 732 sheet: 0.31 (0.33), residues: 236 loop : -0.52 (0.26), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 220 TYR 0.032 0.002 TYR A 188 PHE 0.020 0.002 PHE C 377 TRP 0.020 0.001 TRP B 481 HIS 0.020 0.001 HIS D 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 (13712) covalent geometry : angle 0.66991 / 0.34 (18514) SS BOND : bond 0.00503 / 0.37 ( 28) SS BOND : angle 2.37350 / 1.50 ( 56) hydrogen bonds : bond 0.04033 / 2.69 ( 732) hydrogen bonds : angle 4.26589 / 3.07 ( 2064) Misc. bond : bond 0.00445 / 0.21 ( 3) link_BETA1-4 : bond 0.00288 / 0.14 ( 2) link_BETA1-4 : angle 1.43246 / 1.15 ( 6) link_NAG-ASN : bond 0.00242 / 0.12 ( 6) link_NAG-ASN : angle 1.60248 / 1.05 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 218 time to evaluate : 0.525 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 51 MET cc_start: 0.6309 (OUTLIER) cc_final: 0.6084 (mtp) REVERT: A 155 ARG cc_start: 0.7956 (mtt90) cc_final: 0.7563 (mpt-90) REVERT: A 159 LEU cc_start: 0.8500 (mt) cc_final: 0.8229 (tt) REVERT: A 176 ASP cc_start: 0.7707 (OUTLIER) cc_final: 0.7363 (t0) REVERT: A 332 MET cc_start: 0.6324 (OUTLIER) cc_final: 0.6094 (ttp) REVERT: A 333 ASP cc_start: 0.8484 (p0) cc_final: 0.8187 (p0) REVERT: A 338 MET cc_start: 0.6706 (tpt) cc_final: 0.6234 (tpt) REVERT: B 22 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8380 (pp) REVERT: B 331 HIS cc_start: 0.5902 (OUTLIER) cc_final: 0.5581 (t-90) REVERT: B 376 GLU cc_start: 0.7989 (pt0) cc_final: 0.7755 (tp30) REVERT: B 399 MET cc_start: 0.7077 (ttm) cc_final: 0.6805 (mtt) REVERT: B 436 MET cc_start: 0.7859 (ttp) cc_final: 0.7542 (mmp) REVERT: C 150 MET cc_start: 0.7610 (mmm) cc_final: 0.6987 (mmt) REVERT: C 202 ARG cc_start: 0.8153 (mmt180) cc_final: 0.7459 (mtm-85) REVERT: D 178 GLU cc_start: 0.7489 (tm-30) cc_final: 0.7090 (tm-30) REVERT: D 308 TYR cc_start: 0.8702 (m-80) cc_final: 0.8329 (m-80) REVERT: D 436 MET cc_start: 0.7100 (mmm) cc_final: 0.6839 (mmm) outliers start: 49 outliers final: 26 residues processed: 251 average time/residue: 0.1119 time to fit residues: 41.4588 Evaluate side-chains 225 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 194 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 331 HIS Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain C residue 91 GLN Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 277 ARG Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 362 CYS Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 208 LYS Chi-restraints excluded: chain D residue 225 HIS Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 331 HIS Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 410 LYS Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 485 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 121 optimal weight: 7.9990 chunk 33 optimal weight: 10.0000 chunk 153 optimal weight: 0.8980 chunk 23 optimal weight: 0.3980 chunk 152 optimal weight: 8.9990 chunk 98 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 71 optimal weight: 9.9990 chunk 92 optimal weight: 0.3980 chunk 48 optimal weight: 0.1980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.108526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.094269 restraints weight = 51611.118| |-----------------------------------------------------------------------------| r_work (start): 0.4111 rms_B_bonded: 5.02 r_work (final): 0.4111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.4994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 13751 Z= 0.139 Angle : 0.647 9.980 18594 Z= 0.330 Chirality : 0.042 0.191 1998 Planarity : 0.004 0.052 2302 Dihedral : 7.993 92.507 2158 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.56 % Allowed : 21.24 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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 are not related in a simple way. whole: 1.42 (0.21), residues: 1618 helix: 2.37 (0.19), residues: 732 sheet: 0.47 (0.35), residues: 220 loop : -0.53 (0.25), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 220 TYR 0.019 0.002 TYR D 484 PHE 0.019 0.001 PHE A 124 TRP 0.014 0.001 TRP B 481 HIS 0.011 0.001 HIS D 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (13712) covalent geometry : angle 0.63393 / 0.32 (18514) SS BOND : bond 0.00452 / 0.34 ( 28) SS BOND : angle 2.37270 / 1.53 ( 56) hydrogen bonds : bond 0.03752 / 2.50 ( 732) hydrogen bonds : angle 4.15940 / 3.00 ( 2064) Misc. bond : bond 0.00097 / 0.05 ( 3) link_BETA1-4 : bond 0.00689 / 0.36 ( 2) link_BETA1-4 : angle 0.99236 / 0.72 ( 6) link_NAG-ASN : bond 0.00315 / 0.16 ( 6) link_NAG-ASN : angle 1.34603 / 0.90 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 212 time to evaluate : 0.544 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 155 ARG cc_start: 0.7880 (mtt90) cc_final: 0.7542 (mpt-90) REVERT: A 159 LEU cc_start: 0.8514 (mt) cc_final: 0.8156 (tt) REVERT: A 176 ASP cc_start: 0.7714 (OUTLIER) cc_final: 0.7310 (t0) REVERT: A 178 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8321 (mm) REVERT: A 276 MET cc_start: 0.6457 (mmp) cc_final: 0.6173 (mmp) REVERT: A 333 ASP cc_start: 0.8534 (p0) cc_final: 0.8251 (p0) REVERT: A 338 MET cc_start: 0.6585 (tpt) cc_final: 0.6003 (ttp) REVERT: B 26 ILE cc_start: 0.8680 (OUTLIER) cc_final: 0.8328 (tp) REVERT: B 103 MET cc_start: 0.7722 (mmm) cc_final: 0.7346 (mtp) REVERT: B 331 HIS cc_start: 0.5952 (OUTLIER) cc_final: 0.5629 (t-90) REVERT: B 436 MET cc_start: 0.7927 (ttp) cc_final: 0.7568 (mmp) REVERT: B 445 MET cc_start: 0.8035 (mmp) cc_final: 0.7495 (mtp) REVERT: C 95 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8260 (mp0) REVERT: C 99 THR cc_start: 0.9025 (m) cc_final: 0.8764 (t) REVERT: D 51 VAL cc_start: 0.7267 (t) cc_final: 0.7037 (p) REVERT: D 178 GLU cc_start: 0.7490 (tm-30) cc_final: 0.7033 (tm-30) REVERT: D 308 TYR cc_start: 0.8808 (m-80) cc_final: 0.8330 (m-80) REVERT: D 324 MET cc_start: 0.7976 (mmm) cc_final: 0.7564 (mmm) REVERT: D 401 PHE cc_start: 0.7592 (m-10) cc_final: 0.7235 (m-80) outliers start: 36 outliers final: 17 residues processed: 238 average time/residue: 0.1150 time to fit residues: 40.3787 Evaluate side-chains 213 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 191 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 331 HIS Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 459 HIS Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 362 CYS Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 208 LYS Chi-restraints excluded: chain D residue 410 LYS Chi-restraints excluded: chain D residue 435 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 35 optimal weight: 10.0000 chunk 40 optimal weight: 0.7980 chunk 63 optimal weight: 8.9990 chunk 150 optimal weight: 9.9990 chunk 118 optimal weight: 3.9990 chunk 84 optimal weight: 0.5980 chunk 90 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 125 optimal weight: 0.2980 chunk 136 optimal weight: 0.5980 chunk 101 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 304 GLN ** C 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.108440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.094283 restraints weight = 51483.652| |-----------------------------------------------------------------------------| r_work (start): 0.4106 rms_B_bonded: 5.03 r_work (final): 0.4106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.5408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 13751 Z= 0.119 Angle : 0.619 9.832 18594 Z= 0.315 Chirality : 0.041 0.169 1998 Planarity : 0.004 0.053 2302 Dihedral : 7.519 81.439 2158 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.84 % Allowed : 20.67 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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 are not related in a simple way. whole: 1.51 (0.22), residues: 1618 helix: 2.56 (0.19), residues: 718 sheet: 0.46 (0.35), residues: 216 loop : -0.54 (0.25), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 422 TYR 0.016 0.001 TYR D 484 PHE 0.027 0.001 PHE B 398 TRP 0.011 0.001 TRP B 62 HIS 0.010 0.001 HIS D 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (13712) covalent geometry : angle 0.60884 / 0.31 (18514) SS BOND : bond 0.00432 / 0.33 ( 28) SS BOND : angle 2.03229 / 1.35 ( 56) hydrogen bonds : bond 0.03566 / 2.39 ( 732) hydrogen bonds : angle 4.01374 / 2.88 ( 2064) Misc. bond : bond 0.00357 / 0.17 ( 3) link_BETA1-4 : bond 0.00104 / 0.05 ( 2) link_BETA1-4 : angle 0.97706 / 0.78 ( 6) link_NAG-ASN : bond 0.00091 / 0.05 ( 6) link_NAG-ASN : angle 1.16856 / 0.76 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 200 time to evaluate : 0.523 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 159 LEU cc_start: 0.8476 (mt) cc_final: 0.8177 (tt) REVERT: A 176 ASP cc_start: 0.7782 (OUTLIER) cc_final: 0.7364 (t0) REVERT: A 178 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8261 (mm) REVERT: A 338 MET cc_start: 0.6617 (tpt) cc_final: 0.6090 (ttp) REVERT: B 331 HIS cc_start: 0.5982 (OUTLIER) cc_final: 0.5662 (t-90) REVERT: B 354 MET cc_start: 0.7924 (mmm) cc_final: 0.7714 (ptm) REVERT: B 399 MET cc_start: 0.7071 (ttm) cc_final: 0.6865 (mtt) REVERT: B 436 MET cc_start: 0.7961 (ttp) cc_final: 0.7589 (mmp) REVERT: B 445 MET cc_start: 0.7995 (mmp) cc_final: 0.7467 (mtp) REVERT: C 95 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8296 (mp0) REVERT: C 99 THR cc_start: 0.8995 (m) cc_final: 0.8765 (t) REVERT: C 150 MET cc_start: 0.7701 (mmm) cc_final: 0.7063 (mmt) REVERT: D 178 GLU cc_start: 0.7535 (tm-30) cc_final: 0.7022 (tm-30) REVERT: D 308 TYR cc_start: 0.8788 (m-80) cc_final: 0.8338 (m-80) outliers start: 40 outliers final: 26 residues processed: 231 average time/residue: 0.1168 time to fit residues: 39.6812 Evaluate side-chains 216 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 186 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 356 HIS Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 331 HIS Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 459 HIS Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 362 CYS Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 208 LYS Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 410 LYS Chi-restraints excluded: chain D residue 435 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 68 optimal weight: 0.0270 chunk 111 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 82 optimal weight: 20.0000 chunk 72 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 104 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 129 optimal weight: 8.9990 chunk 78 optimal weight: 20.0000 chunk 109 optimal weight: 9.9990 overall best weight: 2.3844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 ASN ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 ASN B 454 GLN D 8 ASN D 25 GLN ** D 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.101031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.086958 restraints weight = 51081.158| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 4.81 r_work (final): 0.3989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.6504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 13751 Z= 0.189 Angle : 0.699 11.380 18594 Z= 0.355 Chirality : 0.044 0.199 1998 Planarity : 0.005 0.052 2302 Dihedral : 7.447 59.637 2158 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.69 % Allowed : 20.95 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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 are not related in a simple way. whole: 1.27 (0.21), residues: 1618 helix: 2.40 (0.19), residues: 706 sheet: 0.17 (0.33), residues: 234 loop : -0.59 (0.25), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 422 TYR 0.019 0.002 TYR D 484 PHE 0.019 0.002 PHE A 124 TRP 0.023 0.002 TRP B 481 HIS 0.009 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.19 (13712) covalent geometry : angle 0.68915 / 0.35 (18514) SS BOND : bond 0.00477 / 0.35 ( 28) SS BOND : angle 2.07956 / 1.41 ( 56) hydrogen bonds : bond 0.04102 / 2.76 ( 732) hydrogen bonds : angle 4.21561 / 3.04 ( 2064) Misc. bond : bond 0.00340 / 0.16 ( 3) link_BETA1-4 : bond 0.00356 / 0.19 ( 2) link_BETA1-4 : angle 1.73647 / 1.46 ( 6) link_NAG-ASN : bond 0.00407 / 0.21 ( 6) link_NAG-ASN : angle 1.57241 / 1.09 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 202 time to evaluate : 0.581 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: symmetry clash REVERT: A 155 ARG cc_start: 0.7819 (mtt90) cc_final: 0.7588 (mpt-90) REVERT: A 159 LEU cc_start: 0.8671 (mt) cc_final: 0.8461 (tt) REVERT: A 176 ASP cc_start: 0.7958 (OUTLIER) cc_final: 0.7569 (t0) REVERT: A 288 ASN cc_start: 0.8587 (t0) cc_final: 0.7919 (p0) REVERT: B 331 HIS cc_start: 0.6365 (OUTLIER) cc_final: 0.6004 (t-90) REVERT: B 436 MET cc_start: 0.8084 (ttp) cc_final: 0.7778 (mmp) REVERT: B 440 LEU cc_start: 0.8460 (mp) cc_final: 0.8059 (pp) REVERT: B 449 PHE cc_start: 0.8473 (m-10) cc_final: 0.8264 (m-10) REVERT: C 337 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7437 (mt) REVERT: D 9 MET cc_start: 0.8247 (tpp) cc_final: 0.8030 (ttp) REVERT: D 178 GLU cc_start: 0.7625 (tm-30) cc_final: 0.7105 (tm-30) REVERT: D 203 VAL cc_start: 0.7221 (t) cc_final: 0.6616 (p) REVERT: D 259 MET cc_start: 0.5734 (mmp) cc_final: 0.5367 (mmt) REVERT: D 308 TYR cc_start: 0.8687 (m-80) cc_final: 0.8264 (m-80) REVERT: D 401 PHE cc_start: 0.7744 (m-10) cc_final: 0.7254 (m-80) outliers start: 52 outliers final: 35 residues processed: 242 average time/residue: 0.1114 time to fit residues: 40.1470 Evaluate side-chains 228 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 190 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 331 HIS Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 459 HIS Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 355 CYS Chi-restraints excluded: chain C residue 362 CYS Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain D residue 101 MET Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 208 LYS Chi-restraints excluded: chain D residue 225 HIS Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain D residue 410 LYS Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 488 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 157 optimal weight: 1.9990 chunk 136 optimal weight: 8.9990 chunk 39 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 50 optimal weight: 7.9990 chunk 95 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 89 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 120 optimal weight: 0.0470 chunk 145 optimal weight: 20.0000 overall best weight: 2.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 ASN D 454 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.101533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.087503 restraints weight = 55075.999| |-----------------------------------------------------------------------------| r_work (start): 0.3949 rms_B_bonded: 4.90 r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.7081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 13751 Z= 0.187 Angle : 0.691 9.596 18594 Z= 0.349 Chirality : 0.043 0.183 1998 Planarity : 0.004 0.052 2302 Dihedral : 7.413 58.984 2158 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.41 % Allowed : 22.16 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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 are not related in a simple way. whole: 1.17 (0.21), residues: 1618 helix: 2.26 (0.19), residues: 720 sheet: 0.22 (0.34), residues: 218 loop : -0.67 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 277 TYR 0.018 0.002 TYR D 140 PHE 0.025 0.002 PHE B 240 TRP 0.021 0.001 TRP B 481 HIS 0.006 0.001 HIS D 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.19 (13712) covalent geometry : angle 0.68185 / 0.34 (18514) SS BOND : bond 0.00489 / 0.36 ( 28) SS BOND : angle 2.03329 / 1.36 ( 56) hydrogen bonds : bond 0.03870 / 2.60 ( 732) hydrogen bonds : angle 4.19667 / 3.01 ( 2064) Misc. bond : bond 0.00125 / 0.06 ( 3) link_BETA1-4 : bond 0.00264 / 0.14 ( 2) link_BETA1-4 : angle 1.29669 / 1.04 ( 6) link_NAG-ASN : bond 0.00231 / 0.12 ( 6) link_NAG-ASN : angle 1.36323 / 0.88 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 191 time to evaluate : 0.452 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: symmetry clash REVERT: A 176 ASP cc_start: 0.7926 (OUTLIER) cc_final: 0.7528 (t0) REVERT: A 261 LYS cc_start: 0.8903 (mtmt) cc_final: 0.8682 (mptt) REVERT: B 26 ILE cc_start: 0.8725 (OUTLIER) cc_final: 0.8369 (tt) REVERT: B 103 MET cc_start: 0.7538 (mtp) cc_final: 0.7317 (mtp) REVERT: B 110 MET cc_start: 0.7265 (ttm) cc_final: 0.6889 (mtt) REVERT: B 151 MET cc_start: 0.7513 (ptp) cc_final: 0.7189 (ptm) REVERT: B 331 HIS cc_start: 0.6536 (OUTLIER) cc_final: 0.6170 (t-90) REVERT: B 376 GLU cc_start: 0.7811 (mp0) cc_final: 0.7606 (mm-30) REVERT: B 395 PHE cc_start: 0.7555 (m-10) cc_final: 0.7285 (m-10) REVERT: B 445 MET cc_start: 0.8120 (mmp) cc_final: 0.7423 (mtp) REVERT: B 449 PHE cc_start: 0.8485 (m-10) cc_final: 0.8230 (m-10) REVERT: B 483 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8542 (mp) REVERT: C 337 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7484 (mt) REVERT: D 178 GLU cc_start: 0.7614 (tm-30) cc_final: 0.7104 (tm-30) REVERT: D 203 VAL cc_start: 0.7401 (t) cc_final: 0.6834 (p) REVERT: D 379 MET cc_start: 0.8479 (tpp) cc_final: 0.8029 (tpp) REVERT: D 401 PHE cc_start: 0.7887 (m-10) cc_final: 0.7372 (m-80) outliers start: 48 outliers final: 34 residues processed: 228 average time/residue: 0.1051 time to fit residues: 35.9721 Evaluate side-chains 217 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 178 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 331 HIS Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 459 HIS Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 355 CYS Chi-restraints excluded: chain C residue 362 CYS Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 208 LYS Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 331 HIS Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain D residue 435 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 148 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 106 optimal weight: 4.9990 chunk 35 optimal weight: 0.0970 chunk 131 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 222 ASN ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 322 HIS ** D 327 HIS ** 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 = 0.4214 r_free = 0.4214 target = 0.098415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.084615 restraints weight = 50538.339| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 4.73 r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.7458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 13751 Z= 0.161 Angle : 0.698 13.417 18594 Z= 0.350 Chirality : 0.042 0.193 1998 Planarity : 0.004 0.054 2302 Dihedral : 7.274 58.886 2158 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.34 % Allowed : 23.22 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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 are not related in a simple way. whole: 1.25 (0.22), residues: 1618 helix: 2.46 (0.19), residues: 704 sheet: 0.05 (0.33), residues: 232 loop : -0.64 (0.25), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 277 TYR 0.020 0.002 TYR D 140 PHE 0.018 0.001 PHE D 307 TRP 0.020 0.001 TRP B 481 HIS 0.009 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (13712) covalent geometry : angle 0.68978 / 0.35 (18514) SS BOND : bond 0.00439 / 0.33 ( 28) SS BOND : angle 1.96393 / 1.31 ( 56) hydrogen bonds : bond 0.03819 / 2.57 ( 732) hydrogen bonds : angle 4.18239 / 3.00 ( 2064) Misc. bond : bond 0.00103 / 0.05 ( 3) link_BETA1-4 : bond 0.00068 / 0.04 ( 2) link_BETA1-4 : angle 1.30153 / 1.07 ( 6) link_NAG-ASN : bond 0.00229 / 0.11 ( 6) link_NAG-ASN : angle 1.24342 / 0.80 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 191 time to evaluate : 0.529 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: symmetry clash revert: symmetry clash REVERT: A 176 ASP cc_start: 0.7897 (OUTLIER) cc_final: 0.7524 (t0) REVERT: A 276 MET cc_start: 0.6130 (mmp) cc_final: 0.5813 (mmt) REVERT: A 288 ASN cc_start: 0.8629 (t0) cc_final: 0.7763 (p0) REVERT: B 26 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8150 (tt) REVERT: B 103 MET cc_start: 0.7684 (mtp) cc_final: 0.7263 (mtp) REVERT: B 110 MET cc_start: 0.7614 (ttm) cc_final: 0.7109 (mtt) REVERT: B 151 MET cc_start: 0.7687 (ptp) cc_final: 0.7400 (ptm) REVERT: B 331 HIS cc_start: 0.6625 (OUTLIER) cc_final: 0.6241 (t-90) REVERT: B 395 PHE cc_start: 0.7690 (m-10) cc_final: 0.7351 (m-10) REVERT: B 445 MET cc_start: 0.8040 (mmp) cc_final: 0.7310 (mtm) REVERT: B 449 PHE cc_start: 0.8477 (m-10) cc_final: 0.8228 (m-10) REVERT: C 337 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7367 (mt) REVERT: D 21 LEU cc_start: 0.8911 (mt) cc_final: 0.8584 (pp) REVERT: D 101 MET cc_start: 0.7657 (OUTLIER) cc_final: 0.7382 (mtm) REVERT: D 134 MET cc_start: 0.8304 (mpp) cc_final: 0.7818 (mtt) REVERT: D 178 GLU cc_start: 0.7622 (tm-30) cc_final: 0.7063 (tm-30) REVERT: D 401 PHE cc_start: 0.7972 (m-10) cc_final: 0.7477 (m-80) outliers start: 47 outliers final: 32 residues processed: 226 average time/residue: 0.1097 time to fit residues: 37.4927 Evaluate side-chains 220 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 183 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 237 MET Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 331 HIS Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 459 HIS Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 355 CYS Chi-restraints excluded: chain C residue 362 CYS Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 101 MET Chi-restraints excluded: chain D residue 225 HIS Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 331 HIS Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 488 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 50 optimal weight: 4.9990 chunk 71 optimal weight: 9.9990 chunk 149 optimal weight: 2.9990 chunk 111 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 chunk 121 optimal weight: 8.9990 chunk 94 optimal weight: 3.9990 chunk 6 optimal weight: 0.4980 chunk 129 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.097103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.083228 restraints weight = 51233.017| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 4.75 r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.7861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 13751 Z= 0.176 Angle : 0.712 11.266 18594 Z= 0.357 Chirality : 0.043 0.181 1998 Planarity : 0.004 0.053 2302 Dihedral : 7.264 59.609 2158 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.98 % Allowed : 23.30 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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 are not related in a simple way. whole: 1.14 (0.22), residues: 1618 helix: 2.34 (0.19), residues: 706 sheet: -0.03 (0.33), residues: 232 loop : -0.66 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 126 TYR 0.042 0.002 TYR D 308 PHE 0.018 0.002 PHE A 124 TRP 0.018 0.001 TRP B 481 HIS 0.009 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.18 (13712) covalent geometry : angle 0.70320 / 0.35 (18514) SS BOND : bond 0.00455 / 0.33 ( 28) SS BOND : angle 1.99467 / 1.34 ( 56) hydrogen bonds : bond 0.03855 / 2.60 ( 732) hydrogen bonds : angle 4.20263 / 3.02 ( 2064) Misc. bond : bond 0.00358 / 0.17 ( 3) link_BETA1-4 : bond 0.00411 / 0.20 ( 2) link_BETA1-4 : angle 1.29786 / 1.11 ( 6) link_NAG-ASN : bond 0.00233 / 0.12 ( 6) link_NAG-ASN : angle 1.29882 / 0.82 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 198 time to evaluate : 0.530 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: symmetry clash revert: symmetry clash REVERT: A 261 LYS cc_start: 0.8979 (mtmt) cc_final: 0.8729 (mptt) REVERT: A 288 ASN cc_start: 0.8560 (t0) cc_final: 0.7935 (p0) REVERT: A 338 MET cc_start: 0.7820 (tpp) cc_final: 0.7204 (ttm) REVERT: A 370 CYS cc_start: 0.6240 (OUTLIER) cc_final: 0.5919 (p) REVERT: B 22 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8747 (pp) REVERT: B 26 ILE cc_start: 0.8482 (tp) cc_final: 0.8129 (tt) REVERT: B 103 MET cc_start: 0.7616 (mtp) cc_final: 0.7218 (mtp) REVERT: B 110 MET cc_start: 0.7571 (ttm) cc_final: 0.7114 (mtt) REVERT: B 151 MET cc_start: 0.7736 (ptp) cc_final: 0.7484 (ptm) REVERT: B 331 HIS cc_start: 0.6746 (OUTLIER) cc_final: 0.6354 (t-90) REVERT: B 483 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8494 (mp) REVERT: C 276 MET cc_start: 0.7898 (tpp) cc_final: 0.7680 (tpp) REVERT: C 337 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7502 (mt) REVERT: D 21 LEU cc_start: 0.8870 (mt) cc_final: 0.8631 (pp) REVERT: D 101 MET cc_start: 0.7702 (OUTLIER) cc_final: 0.7475 (mtm) REVERT: D 178 GLU cc_start: 0.7600 (tm-30) cc_final: 0.7089 (tm-30) REVERT: D 417 MET cc_start: 0.3757 (pmm) cc_final: 0.3410 (pmm) outliers start: 42 outliers final: 30 residues processed: 230 average time/residue: 0.1159 time to fit residues: 39.5087 Evaluate side-chains 226 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 190 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 370 CYS Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 237 MET Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 331 HIS Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 459 HIS Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 355 CYS Chi-restraints excluded: chain C residue 362 CYS Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 101 MET Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 225 HIS Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 331 HIS Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain D residue 435 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 159 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 chunk 22 optimal weight: 9.9990 chunk 121 optimal weight: 6.9990 chunk 86 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 118 optimal weight: 8.9990 chunk 71 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.098280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.084611 restraints weight = 50688.006| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 4.73 r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.8039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 13751 Z= 0.137 Angle : 0.712 12.421 18594 Z= 0.353 Chirality : 0.042 0.166 1998 Planarity : 0.004 0.055 2302 Dihedral : 7.067 59.776 2158 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.49 % Allowed : 23.93 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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 are not related in a simple way. whole: 1.27 (0.22), residues: 1618 helix: 2.49 (0.19), residues: 704 sheet: 0.02 (0.33), residues: 234 loop : -0.63 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 83 TYR 0.045 0.002 TYR D 308 PHE 0.014 0.001 PHE D 352 TRP 0.016 0.001 TRP D 234 HIS 0.008 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (13712) covalent geometry : angle 0.70413 / 0.35 (18514) SS BOND : bond 0.00411 / 0.31 ( 28) SS BOND : angle 1.94027 / 1.30 ( 56) hydrogen bonds : bond 0.03613 / 2.45 ( 732) hydrogen bonds : angle 4.11710 / 2.96 ( 2064) Misc. bond : bond 0.00276 / 0.13 ( 3) link_BETA1-4 : bond 0.00134 / 0.07 ( 2) link_BETA1-4 : angle 1.16888 / 0.92 ( 6) link_NAG-ASN : bond 0.00147 / 0.07 ( 6) link_NAG-ASN : angle 1.05857 / 0.63 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 196 time to evaluate : 0.537 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 LYS cc_start: 0.8962 (mtmt) cc_final: 0.8729 (mptt) REVERT: A 288 ASN cc_start: 0.8529 (t0) cc_final: 0.7924 (p0) REVERT: A 370 CYS cc_start: 0.6124 (OUTLIER) cc_final: 0.5805 (p) REVERT: B 22 LEU cc_start: 0.8974 (tt) cc_final: 0.8701 (pp) REVERT: B 103 MET cc_start: 0.7642 (mtp) cc_final: 0.7309 (mtp) REVERT: B 110 MET cc_start: 0.7510 (ttm) cc_final: 0.7176 (mtt) REVERT: B 151 MET cc_start: 0.7605 (ptp) cc_final: 0.7296 (ptm) REVERT: B 331 HIS cc_start: 0.6795 (OUTLIER) cc_final: 0.6391 (t-90) REVERT: B 395 PHE cc_start: 0.7847 (m-80) cc_final: 0.7271 (m-10) REVERT: B 445 MET cc_start: 0.7981 (mmp) cc_final: 0.7395 (mtm) REVERT: B 483 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8496 (mp) REVERT: C 159 LEU cc_start: 0.8677 (mt) cc_final: 0.8461 (mt) REVERT: C 276 MET cc_start: 0.7796 (tpp) cc_final: 0.7577 (tpp) REVERT: C 337 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7498 (mt) REVERT: D 21 LEU cc_start: 0.8880 (mt) cc_final: 0.8569 (pp) REVERT: D 101 MET cc_start: 0.7596 (OUTLIER) cc_final: 0.7343 (mtm) REVERT: D 178 GLU cc_start: 0.7581 (tm-30) cc_final: 0.7066 (tm-30) REVERT: D 206 LYS cc_start: 0.8177 (pptt) cc_final: 0.7957 (ptpp) REVERT: D 347 PHE cc_start: 0.8320 (t80) cc_final: 0.8047 (t80) REVERT: D 401 PHE cc_start: 0.8033 (m-10) cc_final: 0.7546 (m-80) outliers start: 35 outliers final: 25 residues processed: 222 average time/residue: 0.1112 time to fit residues: 37.2023 Evaluate side-chains 216 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 186 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 370 CYS Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain B residue 237 MET Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 331 HIS Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 459 HIS Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 355 CYS Chi-restraints excluded: chain C residue 362 CYS Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 101 MET Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain D residue 435 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 104 optimal weight: 0.0970 chunk 143 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 118 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 chunk 138 optimal weight: 10.0000 chunk 23 optimal weight: 0.0030 chunk 24 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 41 optimal weight: 0.0470 overall best weight: 0.3686 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 ASN D 129 ASN ** D 327 HIS ** 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 = 0.4247 r_free = 0.4247 target = 0.099785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.086161 restraints weight = 50978.752| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 4.71 r_work (final): 0.3983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.8114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 13751 Z= 0.129 Angle : 0.717 11.471 18594 Z= 0.356 Chirality : 0.041 0.162 1998 Planarity : 0.004 0.056 2302 Dihedral : 6.863 56.961 2158 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.92 % Allowed : 24.15 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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 are not related in a simple way. whole: 1.52 (0.22), residues: 1618 helix: 2.60 (0.19), residues: 704 sheet: 0.60 (0.35), residues: 214 loop : -0.54 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 83 TYR 0.046 0.002 TYR D 308 PHE 0.019 0.001 PHE C 192 TRP 0.025 0.001 TRP A 177 HIS 0.008 0.001 HIS C 356 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (13712) covalent geometry : angle 0.70235 / 0.35 (18514) SS BOND : bond 0.00561 / 0.40 ( 28) SS BOND : angle 2.65613 / 1.83 ( 56) hydrogen bonds : bond 0.03403 / 2.29 ( 732) hydrogen bonds : angle 4.02914 / 2.89 ( 2064) Misc. bond : bond 0.00240 / 0.11 ( 3) link_BETA1-4 : bond 0.00252 / 0.12 ( 2) link_BETA1-4 : angle 1.15433 / 0.92 ( 6) link_NAG-ASN : bond 0.00157 / 0.08 ( 6) link_NAG-ASN : angle 0.98745 / 0.59 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3492.97 seconds wall clock time: 60 minutes 46.51 seconds (3646.51 seconds total)