Starting phenix.real_space_refine on Fri Jul 3 18:28:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9csb_45890/07_2026/9csb_45890.cif Found real_map, /net/cci-nas-00/data/ceres_data/9csb_45890/07_2026/9csb_45890.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9csb_45890/07_2026/9csb_45890.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9csb_45890/07_2026/9csb_45890.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9csb_45890/07_2026/9csb_45890.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9csb_45890/07_2026/9csb_45890.map" } resolution = 3.34 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= 0.003 sd= 0.034 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 7 5.49 5 S 89 5.16 5 C 10063 2.51 5 N 2494 2.21 5 O 2872 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: 15525 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2716 Classifications: {'peptide': 331} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 316} Chain breaks: 1 Chain: "B" Number of atoms: 2702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2702 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 319} Chain breaks: 1 Chain: "C" Number of atoms: 2696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2696 Classifications: {'peptide': 329} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 314} Chain breaks: 1 Chain: "D" Number of atoms: 2678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2678 Classifications: {'peptide': 332} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 317} Chain breaks: 1 Chain: "E" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2675 Classifications: {'peptide': 326} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 312} Chain breaks: 1 Chain: "I" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 802 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 99} Chain: "J" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 907 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" 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: "B" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 99 Unusual residues: {'PIO': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.68, per 1000 atoms: 0.17 Number of scatterers: 15525 At special positions: 0 Unit cell: (122.485, 115.005, 133.705, 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 89 16.00 P 7 15.00 O 2872 8.00 N 2494 7.00 C 10063 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS A 150 " distance=2.03 Simple disulfide: pdb=" SG CYS B 139 " - pdb=" SG CYS B 153 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 150 " distance=2.03 Simple disulfide: pdb=" SG CYS D 138 " - pdb=" SG CYS D 152 " distance=2.03 Simple disulfide: pdb=" SG CYS E 151 " - pdb=" SG CYS E 165 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " 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 Atom "HETATM15188 O5 NAG F 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN G 4 " - " MAN G 5 " ALPHA1-3 " BMA G 3 " - " MAN G 4 " " MAN G 6 " - " MAN G 7 " ALPHA1-6 " BMA G 3 " - " MAN G 6 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG E 501 " - " ASN E 208 " " NAG F 1 " - " ASN A 149 " " NAG G 1 " - " ASN B 111 " " NAG H 1 " - " ASN C 149 " " NAG O 1 " - " ASN A 80 " Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 433.7 milliseconds 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3554 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 27 sheets defined 35.3% alpha, 33.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 7 through 20 removed outlier: 3.933A pdb=" N VAL A 16 " --> pdb=" O VAL A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 90 removed outlier: 3.672A pdb=" N ALA A 88 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP A 89 " --> pdb=" O ARG A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 173 Processing helix chain 'A' and resid 218 through 225 Processing helix chain 'A' and resid 225 through 237 removed outlier: 3.780A pdb=" N THR A 233 " --> pdb=" O SER A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 242 removed outlier: 4.097A pdb=" N TRP A 241 " --> pdb=" O TRP A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 269 removed outlier: 3.519A pdb=" N ARG A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 307 Processing helix chain 'A' and resid 421 through 447 Proline residue: A 432 - end of helix Processing helix chain 'B' and resid 13 through 24 Processing helix chain 'B' and resid 88 through 93 removed outlier: 3.908A pdb=" N SER B 92 " --> pdb=" O ASN B 88 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS B 93 " --> pdb=" O LEU B 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 88 through 93' Processing helix chain 'B' and resid 142 through 146 removed outlier: 4.564A pdb=" N ASP B 145 " --> pdb=" O HIS B 142 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE B 146 " --> pdb=" O LEU B 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 142 through 146' Processing helix chain 'B' and resid 174 through 177 Processing helix chain 'B' and resid 225 through 230 Processing helix chain 'B' and resid 230 through 243 Processing helix chain 'B' and resid 244 through 247 removed outlier: 3.639A pdb=" N LEU B 247 " --> pdb=" O SER B 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 244 through 247' Processing helix chain 'B' and resid 251 through 277 removed outlier: 3.651A pdb=" N ILE B 271 " --> pdb=" O THR B 267 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER B 272 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA B 273 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG B 274 " --> pdb=" O SER B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 310 removed outlier: 4.336A pdb=" N ALA B 300 " --> pdb=" O PHE B 296 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU B 301 " --> pdb=" O VAL B 297 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE B 302 " --> pdb=" O PHE B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 417 removed outlier: 4.085A pdb=" N ILE B 398 " --> pdb=" O ARG B 394 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N PHE B 400 " --> pdb=" O SER B 396 " (cutoff:3.500A) Proline residue: B 401 - end of helix removed outlier: 3.815A pdb=" N ALA B 413 " --> pdb=" O LEU B 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 20 Processing helix chain 'C' and resid 70 through 73 removed outlier: 3.701A pdb=" N SER C 73 " --> pdb=" O LYS C 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 70 through 73' Processing helix chain 'C' and resid 86 through 90 removed outlier: 4.003A pdb=" N ASP C 89 " --> pdb=" O ARG C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 174 removed outlier: 3.596A pdb=" N ALA C 174 " --> pdb=" O ASP C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 225 Processing helix chain 'C' and resid 225 through 237 removed outlier: 3.605A pdb=" N SER C 236 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TRP C 237 " --> pdb=" O THR C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 241 Processing helix chain 'C' and resid 246 through 268 removed outlier: 3.583A pdb=" N ARG C 250 " --> pdb=" O ALA C 246 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR C 257 " --> pdb=" O LEU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 308 removed outlier: 3.541A pdb=" N PHE C 291 " --> pdb=" O GLY C 287 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR C 304 " --> pdb=" O ALA C 300 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE C 307 " --> pdb=" O ASN C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 487 removed outlier: 3.652A pdb=" N ILE C 469 " --> pdb=" O ARG C 465 " (cutoff:3.500A) Proline residue: C 472 - end of helix Processing helix chain 'D' and resid 10 through 23 Processing helix chain 'D' and resid 72 through 75 removed outlier: 3.678A pdb=" N LYS D 75 " --> pdb=" O GLU D 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 72 through 75' Processing helix chain 'D' and resid 88 through 92 Processing helix chain 'D' and resid 222 through 229 removed outlier: 3.685A pdb=" N ILE D 227 " --> pdb=" O GLY D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 241 removed outlier: 3.578A pdb=" N THR D 236 " --> pdb=" O PRO D 232 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL D 237 " --> pdb=" O CYS D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 246 removed outlier: 3.779A pdb=" N LEU D 246 " --> pdb=" O SER D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 275 removed outlier: 3.745A pdb=" N LEU D 263 " --> pdb=" O VAL D 259 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER D 271 " --> pdb=" O THR D 267 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA D 272 " --> pdb=" O LEU D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 310 removed outlier: 4.153A pdb=" N VAL D 291 " --> pdb=" O TRP D 287 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU D 300 " --> pdb=" O VAL D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 412 removed outlier: 4.103A pdb=" N ILE D 395 " --> pdb=" O ARG D 391 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE D 397 " --> pdb=" O SER D 393 " (cutoff:3.500A) Proline residue: D 398 - end of helix removed outlier: 3.675A pdb=" N TYR D 412 " --> pdb=" O TYR D 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 36 removed outlier: 3.646A pdb=" N VAL E 29 " --> pdb=" O GLY E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 106 removed outlier: 3.583A pdb=" N MET E 102 " --> pdb=" O ASN E 99 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N GLY E 104 " --> pdb=" O ASN E 101 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS E 105 " --> pdb=" O MET E 102 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE E 106 " --> pdb=" O VAL E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 235 through 240 Processing helix chain 'E' and resid 240 through 252 removed outlier: 3.537A pdb=" N TRP E 252 " --> pdb=" O VAL E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 257 Processing helix chain 'E' and resid 261 through 286 removed outlier: 3.684A pdb=" N LYS E 285 " --> pdb=" O THR E 281 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N SER E 286 " --> pdb=" O ILE E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 322 Processing helix chain 'E' and resid 409 through 434 removed outlier: 4.519A pdb=" N ILE E 416 " --> pdb=" O SER E 412 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE E 418 " --> pdb=" O ALA E 414 " (cutoff:3.500A) Proline residue: E 419 - end of helix removed outlier: 3.660A pdb=" N PHE E 425 " --> pdb=" O ALA E 421 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL E 431 " --> pdb=" O LEU E 427 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.619A pdb=" N LEU I 83 " --> pdb=" O ALA I 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 65 removed outlier: 3.661A pdb=" N GLN J 65 " --> pdb=" O PRO J 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 62 through 65' Processing helix chain 'J' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 114 through 118 removed outlier: 4.958A pdb=" N ARG A 68 " --> pdb=" O CYS A 37 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N CYS A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR A 167 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 114 through 118 removed outlier: 4.958A pdb=" N ARG A 68 " --> pdb=" O CYS A 37 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N CYS A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) removed outlier: 8.946A pdb=" N THR A 176 " --> pdb=" O MET A 40 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ILE A 42 " --> pdb=" O THR A 176 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 46 through 51 removed outlier: 3.514A pdb=" N SER A 46 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N THR A 58 " --> pdb=" O ASP A 48 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N VAL A 50 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ASP A 56 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE A 105 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LYS A 103 " --> pdb=" O THR A 133 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ALA A 135 " --> pdb=" O ASP A 101 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ASP A 101 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.723A pdb=" N SER A 156 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS A 215 " --> pdb=" O SER A 187 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.723A pdb=" N SER A 156 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY A 203 " --> pdb=" O PHE A 200 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 108 through 109 removed outlier: 3.508A pdb=" N VAL B 108 " --> pdb=" O THR B 134 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU B 133 " --> pdb=" O VAL B 64 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N GLU B 59 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N THR B 61 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N PHE B 50 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ASP B 63 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE B 46 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL B 168 " --> pdb=" O THR B 39 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 108 through 109 removed outlier: 3.508A pdb=" N VAL B 108 " --> pdb=" O THR B 134 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU B 133 " --> pdb=" O VAL B 64 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N GLU B 59 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N THR B 61 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N PHE B 50 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ASP B 63 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE B 46 " --> pdb=" O PHE B 65 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 84 through 86 removed outlier: 4.469A pdb=" N LEU B 119 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 99 through 101 removed outlier: 4.083A pdb=" N SER B 159 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL B 211 " --> pdb=" O SER B 159 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 99 through 101 removed outlier: 4.083A pdb=" N SER B 159 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL B 211 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLY B 195 " --> pdb=" O HIS B 218 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N LYS B 220 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N LEU B 193 " --> pdb=" O LYS B 220 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 81 through 83 removed outlier: 4.772A pdb=" N ILE C 116 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS C 103 " --> pdb=" O THR C 133 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N ALA C 135 " --> pdb=" O ASP C 101 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ASP C 101 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 81 through 83 removed outlier: 4.772A pdb=" N ILE C 116 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ARG C 68 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ALA C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.751A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS C 192 " --> pdb=" O SER C 211 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASP C 190 " --> pdb=" O LYS C 213 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LYS C 215 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ILE C 188 " --> pdb=" O LYS C 215 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 83 through 85 removed outlier: 4.381A pdb=" N LEU D 118 " --> pdb=" O LEU D 85 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU D 127 " --> pdb=" O ARG D 119 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TRP D 69 " --> pdb=" O LEU D 126 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N VAL D 40 " --> pdb=" O ILE D 169 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 52 through 53 Processing sheet with id=AB7, first strand: chain 'D' and resid 99 through 100 Processing sheet with id=AB8, first strand: chain 'D' and resid 99 through 100 removed outlier: 4.146A pdb=" N GLY D 194 " --> pdb=" O HIS D 217 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 95 through 98 removed outlier: 3.575A pdb=" N LEU E 131 " --> pdb=" O LEU E 98 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ARG E 138 " --> pdb=" O TRP E 134 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N ARG E 144 " --> pdb=" O ALA E 121 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ALA E 121 " --> pdb=" O ARG E 144 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N THR E 146 " --> pdb=" O ALA E 119 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ALA E 119 " --> pdb=" O THR E 146 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ASP E 148 " --> pdb=" O LYS E 117 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 95 through 98 removed outlier: 3.575A pdb=" N LEU E 131 " --> pdb=" O LEU E 98 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ARG E 138 " --> pdb=" O TRP E 134 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TRP E 82 " --> pdb=" O VAL E 139 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLU E 71 " --> pdb=" O PRO E 64 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N THR E 73 " --> pdb=" O ILE E 62 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ILE E 62 " --> pdb=" O THR E 73 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ASP E 75 " --> pdb=" O ASN E 60 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TYR E 83 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU E 52 " --> pdb=" O TYR E 83 " (cutoff:3.500A) removed outlier: 9.648A pdb=" N THR E 51 " --> pdb=" O TYR E 181 " (cutoff:3.500A) removed outlier: 10.665A pdb=" N TRP E 183 " --> pdb=" O THR E 51 " (cutoff:3.500A) removed outlier: 8.751A pdb=" N ILE E 53 " --> pdb=" O TRP E 183 " (cutoff:3.500A) removed outlier: 10.698A pdb=" N ARG E 185 " --> pdb=" O ILE E 53 " (cutoff:3.500A) removed outlier: 10.850A pdb=" N THR E 55 " --> pdb=" O ARG E 185 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N SER E 187 " --> pdb=" O THR E 55 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 111 through 113 removed outlier: 4.644A pdb=" N SER E 171 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL E 221 " --> pdb=" O SER E 171 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY E 205 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N SER E 230 " --> pdb=" O PHE E 203 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N PHE E 203 " --> pdb=" O SER E 230 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 162 through 165 Processing sheet with id=AC4, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.412A pdb=" N MET I 11 " --> pdb=" O GLU I 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'I' and resid 18 through 20 Processing sheet with id=AC6, first strand: chain 'I' and resid 18 through 20 Processing sheet with id=AC7, first strand: chain 'I' and resid 53 through 54 removed outlier: 3.583A pdb=" N LYS I 45 " --> pdb=" O GLN I 37 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N TYR I 49 " --> pdb=" O VAL I 33 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR I 96 " --> pdb=" O GLN I 90 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 3 through 6 removed outlier: 3.507A pdb=" N VAL J 18 " --> pdb=" O LEU J 83 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU J 83 " --> pdb=" O VAL J 18 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR J 78 " --> pdb=" O ASP J 73 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 10 through 12 removed outlier: 7.152A pdb=" N MET J 34 " --> pdb=" O ARG J 50 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N ARG J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) 732 hydrogen bonds defined for protein. 2073 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: 2.32 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2560 1.32 - 1.45: 4507 1.45 - 1.57: 8683 1.57 - 1.69: 10 1.69 - 1.81: 154 Bond restraints: 15914 Sorted by residual: bond pdb=" C SER D 250 " pdb=" O SER D 250 " ideal model delta sigma weight residual 1.231 1.307 -0.076 1.62e-02 3.81e+03 2.23e+01 bond pdb=" C THR A 225 " pdb=" O THR A 225 " ideal model delta sigma weight residual 1.235 1.291 -0.056 1.26e-02 6.30e+03 1.97e+01 bond pdb=" O4 PIO B 601 " pdb=" P4 PIO B 601 " ideal model delta sigma weight residual 1.710 1.626 0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" O4 PIO D 601 " pdb=" P4 PIO D 601 " ideal model delta sigma weight residual 1.710 1.626 0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" O5 PIO B 601 " pdb=" P5 PIO B 601 " ideal model delta sigma weight residual 1.699 1.626 0.073 2.00e-02 2.50e+03 1.34e+01 ... (remaining 15909 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 20328 2.14 - 4.29: 1191 4.29 - 6.43: 87 6.43 - 8.57: 22 8.57 - 10.71: 4 Bond angle restraints: 21632 Sorted by residual: angle pdb=" N GLU A 270 " pdb=" CA GLU A 270 " pdb=" C GLU A 270 " ideal model delta sigma weight residual 114.56 106.93 7.63 1.27e+00 6.20e-01 3.61e+01 angle pdb=" C ASP C 171 " pdb=" CA ASP C 171 " pdb=" CB ASP C 171 " ideal model delta sigma weight residual 116.63 110.01 6.62 1.16e+00 7.43e-01 3.25e+01 angle pdb=" CA PHE A 221 " pdb=" C PHE A 221 " pdb=" O PHE A 221 " ideal model delta sigma weight residual 120.55 114.73 5.82 1.06e+00 8.90e-01 3.02e+01 angle pdb=" C CYS A 136 " pdb=" CA CYS A 136 " pdb=" CB CYS A 136 " ideal model delta sigma weight residual 111.82 104.71 7.11 1.38e+00 5.25e-01 2.65e+01 angle pdb=" N VAL B 227 " pdb=" CA VAL B 227 " pdb=" C VAL B 227 " ideal model delta sigma weight residual 112.80 107.16 5.64 1.15e+00 7.56e-01 2.41e+01 ... (remaining 21627 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.78: 9239 30.78 - 61.56: 251 61.56 - 92.34: 40 92.34 - 123.11: 13 123.11 - 153.89: 1 Dihedral angle restraints: 9544 sinusoidal: 4019 harmonic: 5525 Sorted by residual: dihedral pdb=" C3 POV B 602 " pdb=" C31 POV B 602 " pdb=" O31 POV B 602 " pdb=" C32 POV B 602 " ideal model delta sinusoidal sigma weight residual 172.61 -33.50 -153.89 1 3.00e+01 1.11e-03 2.02e+01 dihedral pdb=" CB CYS J 22 " pdb=" SG CYS J 22 " pdb=" SG CYS J 96 " pdb=" CB CYS J 96 " ideal model delta sinusoidal sigma weight residual 93.00 130.18 -37.18 1 1.00e+01 1.00e-02 1.95e+01 dihedral pdb=" CA TYR I 94 " pdb=" C TYR I 94 " pdb=" N PRO I 95 " pdb=" CA PRO I 95 " ideal model delta harmonic sigma weight residual -180.00 -160.87 -19.13 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 9541 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.132: 2316 0.132 - 0.265: 170 0.265 - 0.397: 6 0.397 - 0.530: 0 0.530 - 0.662: 1 Chirality restraints: 2493 Sorted by residual: chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-02 2.50e+03 2.65e+02 chirality pdb=" C1 MAN G 5 " pdb=" O2 MAN G 4 " pdb=" C2 MAN G 5 " pdb=" O5 MAN G 5 " both_signs ideal model delta sigma weight residual False 2.40 2.22 0.18 2.00e-02 2.50e+03 7.77e+01 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.39e+01 ... (remaining 2490 not shown) Planarity restraints: 2644 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG O 2 " -0.341 2.00e-02 2.50e+03 2.95e-01 1.08e+03 pdb=" C7 NAG O 2 " 0.078 2.00e-02 2.50e+03 pdb=" C8 NAG O 2 " -0.103 2.00e-02 2.50e+03 pdb=" N2 NAG O 2 " 0.525 2.00e-02 2.50e+03 pdb=" O7 NAG O 2 " -0.160 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 501 " 0.327 2.00e-02 2.50e+03 2.83e-01 1.00e+03 pdb=" C7 NAG E 501 " -0.077 2.00e-02 2.50e+03 pdb=" C8 NAG E 501 " 0.134 2.00e-02 2.50e+03 pdb=" N2 NAG E 501 " -0.506 2.00e-02 2.50e+03 pdb=" O7 NAG E 501 " 0.121 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 2 " -0.108 2.00e-02 2.50e+03 8.99e-02 1.01e+02 pdb=" C7 NAG G 2 " 0.028 2.00e-02 2.50e+03 pdb=" C8 NAG G 2 " -0.081 2.00e-02 2.50e+03 pdb=" N2 NAG G 2 " 0.145 2.00e-02 2.50e+03 pdb=" O7 NAG G 2 " 0.016 2.00e-02 2.50e+03 ... (remaining 2641 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.43: 40 2.43 - 3.05: 9232 3.05 - 3.67: 23117 3.67 - 4.28: 35503 4.28 - 4.90: 58704 Nonbonded interactions: 126596 Sorted by model distance: nonbonded pdb=" OD1 ASP E 56 " pdb=" O SER E 187 " model vdw 1.818 3.040 nonbonded pdb=" O ASP A 245 " pdb=" OD1 ASP A 245 " model vdw 2.214 3.040 nonbonded pdb=" O THR C 256 " pdb=" OG1 THR C 260 " model vdw 2.293 3.040 nonbonded pdb=" OG1 THR B 122 " pdb=" OD1 ASP B 124 " model vdw 2.307 3.040 nonbonded pdb=" O LEU C 259 " pdb=" OG1 THR C 263 " model vdw 2.316 3.040 ... (remaining 126591 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 through 10 or resid 12 through 17 or resid 19 through 36 \ or resid 38 through 65 or resid 67 through 72 or resid 74 or resid 77 through 1 \ 70 or resid 172 or resid 174 through 178 or resid 181 through 189 or resid 193 o \ r resid 198 through 200 or resid 202 through 203 or resid 205 through 212 or res \ id 214 through 293 or resid 295 through 300 or resid 302 through 308 or resid 42 \ 1 through 429 or resid 431 through 432 or resid 435 through 436 or resid 438 thr \ ough 439 or resid 441 through 447)) selection = (chain 'C' and (resid 8 through 10 or resid 12 through 17 or resid 19 through 36 \ or resid 38 through 65 or resid 67 through 72 or resid 74 or resid 77 through 1 \ 70 or resid 172 or resid 174 through 178 or resid 181 through 189 or resid 193 o \ r resid 198 through 200 or resid 202 through 203 or resid 205 through 212 or res \ id 214 through 293 or resid 295 through 300 or resid 302 through 469 or resid 47 \ 1 through 472 or resid 475 through 476 or resid 478 through 479 or resid 481 thr \ ough 487)) } ncs_group { reference = (chain 'B' and (resid 13 or resid 15 through 35 or resid 39 through 41 or resid \ 43 or resid 45 or resid 47 through 55 or resid 57 through 68 or resid 70 through \ 81 or resid 84 through 121 or resid 124 through 135 or resid 137 through 151 or \ resid 153 through 163 or resid 166 through 167 or resid 169 or resid 171 throug \ h 172 or resid 178 through 179 or resid 181 through 182 or resid 184 through 196 \ or resid 205 through 210 or resid 212 through 214 or resid 216 through 311 or r \ esid 388 through 394 or resid 396 through 398 or resid 400 through 401 or resid \ 403 through 405 or resid 407 through 416)) selection = (chain 'D' and (resid 12 or resid 14 through 34 or resid 38 through 40 or resid \ 42 or resid 44 or resid 46 through 54 or resid 56 through 67 or resid 69 through \ 80 or resid 83 through 120 or resid 123 through 134 or resid 136 through 150 or \ resid 152 through 162 or resid 165 through 166 or resid 168 or resid 170 throug \ h 171 or resid 177 through 178 or resid 180 through 181 or resid 183 through 195 \ or resid 204 through 209 or resid 211 through 213 or resid 215 through 310 or r \ esid 385 through 391 or resid 393 through 395 or resid 397 through 398 or resid \ 400 through 402 or resid 404 through 413)) } ncs_group { reference = chain 'F' selection = chain 'H' } 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: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 12.340 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 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 : 0.007 0.092 15937 Z= 0.477 Angle : 1.055 28.405 21694 Z= 0.672 Chirality : 0.069 0.662 2493 Planarity : 0.013 0.295 2639 Dihedral : 15.392 153.893 5969 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 1.37 % Allowed : 1.96 % Favored : 96.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.22 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.53 (0.18), residues: 1849 helix: -1.88 (0.17), residues: 554 sheet: -1.22 (0.22), residues: 526 loop : -1.65 (0.21), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 269 TYR 0.032 0.002 TYR A 299 PHE 0.028 0.002 PHE A 221 TRP 0.029 0.002 TRP E 183 HIS 0.004 0.001 HIS A 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00716 / 0.48 (15914) covalent geometry : angle 1.02074 / 0.67 (21632) SS BOND : bond 0.00230 / 0.15 ( 7) SS BOND : angle 0.85115 / 0.46 ( 14) hydrogen bonds : bond 0.22203 / 14.41 ( 669) hydrogen bonds : angle 8.78295 / 6.02 ( 2073) link_ALPHA1-2 : bond 0.00288 / 0.18 ( 1) link_ALPHA1-2 : angle 1.16551 / 0.69 ( 3) link_ALPHA1-3 : bond 0.00198 / 0.11 ( 2) link_ALPHA1-3 : angle 2.70376 / 1.36 ( 6) link_ALPHA1-6 : bond 0.00647 / 0.40 ( 1) link_ALPHA1-6 : angle 1.01621 / 0.47 ( 3) link_BETA1-4 : bond 0.01320 / 0.82 ( 7) link_BETA1-4 : angle 2.78927 / 1.60 ( 21) link_NAG-ASN : bond 0.04308 / 2.67 ( 5) link_NAG-ASN : angle 9.66244 / 5.85 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 549 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LYS cc_start: 0.8385 (tttp) cc_final: 0.8112 (ttmt) REVERT: A 49 MET cc_start: 0.7061 (ptp) cc_final: 0.6665 (mtp) REVERT: A 70 LYS cc_start: 0.8694 (mtpt) cc_final: 0.7747 (tmmt) REVERT: A 77 ILE cc_start: 0.8323 (mm) cc_final: 0.8033 (mm) REVERT: A 95 ASP cc_start: 0.7932 (p0) cc_final: 0.7357 (p0) REVERT: A 190 GLU cc_start: 0.7055 (pt0) cc_final: 0.6671 (pt0) REVERT: A 192 ARG cc_start: 0.8137 (mtp85) cc_final: 0.7384 (ttm170) REVERT: A 260 THR cc_start: 0.8504 (m) cc_final: 0.8266 (t) REVERT: A 275 ILE cc_start: 0.8105 (OUTLIER) cc_final: 0.7855 (pt) REVERT: A 282 ASP cc_start: 0.8486 (m-30) cc_final: 0.7934 (m-30) REVERT: A 283 MET cc_start: 0.7125 (tpp) cc_final: 0.6476 (tmm) REVERT: A 305 ILE cc_start: 0.8380 (OUTLIER) cc_final: 0.8142 (mt) REVERT: B 20 ASP cc_start: 0.7439 (m-30) cc_final: 0.7166 (m-30) REVERT: B 44 ASP cc_start: 0.8663 (p0) cc_final: 0.8446 (p0) REVERT: B 57 ASP cc_start: 0.8566 (m-30) cc_final: 0.8199 (m-30) REVERT: B 114 MET cc_start: 0.8407 (mmp) cc_final: 0.7664 (mmm) REVERT: B 230 THR cc_start: 0.8562 (m) cc_final: 0.8201 (t) REVERT: B 275 ASN cc_start: 0.6966 (t0) cc_final: 0.6317 (m110) REVERT: B 310 PHE cc_start: 0.8299 (m-80) cc_final: 0.7865 (m-10) REVERT: B 391 LYS cc_start: 0.7198 (mttm) cc_final: 0.6759 (mttm) REVERT: C 49 MET cc_start: 0.7387 (mtp) cc_final: 0.6790 (mtt) REVERT: C 99 LEU cc_start: 0.8266 (tp) cc_final: 0.8053 (tp) REVERT: C 171 ASP cc_start: 0.6553 (m-30) cc_final: 0.6302 (t0) REVERT: C 227 MET cc_start: 0.8064 (tpp) cc_final: 0.7844 (ttt) REVERT: C 234 ILE cc_start: 0.8886 (mm) cc_final: 0.8597 (mp) REVERT: C 256 THR cc_start: 0.7987 (p) cc_final: 0.7770 (p) REVERT: C 277 TYR cc_start: 0.8282 (p90) cc_final: 0.8007 (p90) REVERT: C 286 MET cc_start: 0.8001 (mtp) cc_final: 0.7546 (mtp) REVERT: C 294 MET cc_start: 0.8188 (mmm) cc_final: 0.7908 (mmp) REVERT: C 465 ARG cc_start: 0.7440 (ttt-90) cc_final: 0.6558 (tpt170) REVERT: D 43 ASN cc_start: 0.7536 (m-40) cc_final: 0.7253 (m-40) REVERT: D 57 MET cc_start: 0.8203 (mtt) cc_final: 0.7946 (mtp) REVERT: D 62 ASP cc_start: 0.8058 (m-30) cc_final: 0.7195 (m-30) REVERT: D 89 MET cc_start: 0.8401 (tpp) cc_final: 0.8130 (tpt) REVERT: D 95 THR cc_start: 0.9182 (OUTLIER) cc_final: 0.8947 (m) REVERT: D 144 ASP cc_start: 0.7855 (m-30) cc_final: 0.7312 (t0) REVERT: D 147 MET cc_start: 0.8760 (mpp) cc_final: 0.8128 (mpp) REVERT: D 159 TYR cc_start: 0.8727 (t80) cc_final: 0.8025 (t80) REVERT: D 179 GLN cc_start: 0.8172 (mt0) cc_final: 0.7554 (mm110) REVERT: D 199 LYS cc_start: 0.8859 (tttt) cc_final: 0.8525 (tttm) REVERT: D 233 CYS cc_start: 0.8745 (m) cc_final: 0.8507 (m) REVERT: D 285 MET cc_start: 0.8809 (tpp) cc_final: 0.8317 (tpp) REVERT: D 390 ASP cc_start: 0.8067 (t0) cc_final: 0.7640 (t70) REVERT: E 75 ASP cc_start: 0.7597 (t0) cc_final: 0.7348 (m-30) REVERT: E 94 LYS cc_start: 0.8206 (mmpt) cc_final: 0.7931 (mmmt) REVERT: E 118 LYS cc_start: 0.7811 (pptt) cc_final: 0.7548 (tptm) REVERT: E 160 MET cc_start: 0.7955 (mtp) cc_final: 0.7507 (mpp) REVERT: E 182 GLN cc_start: 0.7658 (tt0) cc_final: 0.7403 (tt0) REVERT: E 248 VAL cc_start: 0.8035 (m) cc_final: 0.7806 (p) REVERT: E 417 PHE cc_start: 0.6795 (t80) cc_final: 0.5885 (t80) REVERT: I 28 TYR cc_start: 0.8517 (t80) cc_final: 0.7828 (t80) REVERT: I 49 TYR cc_start: 0.7800 (p90) cc_final: 0.7593 (p90) REVERT: J 46 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7704 (mt-10) outliers start: 23 outliers final: 5 residues processed: 557 average time/residue: 0.1223 time to fit residues: 99.2866 Evaluate side-chains 369 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 361 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain E residue 155 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 HIS ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 ASN ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 10 ASN D 87 ASN D 110 ASN D 115 ASN E 157 ASN E 163 HIS I 42 GLN J 55 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.145387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.111388 restraints weight = 25371.224| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.93 r_work: 0.3374 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15937 Z= 0.146 Angle : 0.654 14.395 21694 Z= 0.332 Chirality : 0.044 0.313 2493 Planarity : 0.005 0.051 2639 Dihedral : 10.281 122.892 2490 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.62 % Allowed : 12.50 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.22 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.19), residues: 1849 helix: 0.15 (0.20), residues: 557 sheet: -1.13 (0.21), residues: 548 loop : -1.09 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 273 TYR 0.025 0.002 TYR A 143 PHE 0.018 0.002 PHE A 221 TRP 0.028 0.001 TRP E 252 HIS 0.005 0.001 HIS B 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 (15914) covalent geometry : angle 0.64490 / 0.33 (21632) SS BOND : bond 0.00336 / 0.21 ( 7) SS BOND : angle 0.60925 / 0.41 ( 14) hydrogen bonds : bond 0.04705 / 3.10 ( 669) hydrogen bonds : angle 5.54783 / 3.82 ( 2073) link_ALPHA1-2 : bond 0.00559 / 0.35 ( 1) link_ALPHA1-2 : angle 1.31830 / 0.77 ( 3) link_ALPHA1-3 : bond 0.00562 / 0.34 ( 2) link_ALPHA1-3 : angle 1.50665 / 0.78 ( 6) link_ALPHA1-6 : bond 0.00016 / 0.01 ( 1) link_ALPHA1-6 : angle 1.51677 / 0.79 ( 3) link_BETA1-4 : bond 0.00448 / 0.31 ( 7) link_BETA1-4 : angle 2.48209 / 1.44 ( 21) link_NAG-ASN : bond 0.00634 / 0.39 ( 5) link_NAG-ASN : angle 2.75092 / 1.72 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 382 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 PHE cc_start: 0.6988 (t80) cc_final: 0.6775 (t80) REVERT: A 70 LYS cc_start: 0.8795 (mtpt) cc_final: 0.7964 (tmmt) REVERT: A 251 VAL cc_start: 0.9015 (t) cc_final: 0.8749 (m) REVERT: A 282 ASP cc_start: 0.8642 (m-30) cc_final: 0.8333 (m-30) REVERT: A 283 MET cc_start: 0.7641 (tpp) cc_final: 0.7228 (tmm) REVERT: A 305 ILE cc_start: 0.8690 (mm) cc_final: 0.8423 (mt) REVERT: A 424 ASP cc_start: 0.8141 (t0) cc_final: 0.7865 (t0) REVERT: A 428 ARG cc_start: 0.8207 (ttm110) cc_final: 0.7847 (ttm110) REVERT: B 20 ASP cc_start: 0.7863 (m-30) cc_final: 0.7613 (m-30) REVERT: B 57 ASP cc_start: 0.8693 (m-30) cc_final: 0.8473 (m-30) REVERT: B 114 MET cc_start: 0.8609 (mmp) cc_final: 0.7989 (mmm) REVERT: B 242 GLN cc_start: 0.7834 (mm110) cc_final: 0.7302 (mp10) REVERT: B 275 ASN cc_start: 0.7065 (t0) cc_final: 0.6400 (m-40) REVERT: B 310 PHE cc_start: 0.8433 (m-80) cc_final: 0.7952 (m-10) REVERT: C 49 MET cc_start: 0.7540 (mtp) cc_final: 0.7224 (mtt) REVERT: C 52 GLU cc_start: 0.7320 (mp0) cc_final: 0.6936 (mp0) REVERT: C 153 GLU cc_start: 0.8826 (mm-30) cc_final: 0.8601 (mm-30) REVERT: C 216 ARG cc_start: 0.8240 (ttm-80) cc_final: 0.7971 (ttm-80) REVERT: C 227 MET cc_start: 0.8493 (tpp) cc_final: 0.8219 (ttt) REVERT: C 241 TRP cc_start: 0.8547 (m100) cc_final: 0.8241 (m100) REVERT: C 286 MET cc_start: 0.8426 (mtp) cc_final: 0.8014 (mtp) REVERT: C 294 MET cc_start: 0.8347 (mmm) cc_final: 0.8102 (mmp) REVERT: C 303 ASN cc_start: 0.8960 (t0) cc_final: 0.8755 (t0) REVERT: C 465 ARG cc_start: 0.7479 (ttt-90) cc_final: 0.6918 (tpt170) REVERT: D 62 ASP cc_start: 0.7832 (m-30) cc_final: 0.7193 (m-30) REVERT: D 84 ARG cc_start: 0.8140 (mtm-85) cc_final: 0.7919 (mtm-85) REVERT: D 113 MET cc_start: 0.7988 (mmp) cc_final: 0.7538 (mmm) REVERT: D 159 TYR cc_start: 0.8770 (t80) cc_final: 0.8307 (t80) REVERT: D 179 GLN cc_start: 0.8426 (mt0) cc_final: 0.8040 (mm-40) REVERT: D 199 LYS cc_start: 0.8590 (tttt) cc_final: 0.8377 (tttm) REVERT: D 233 CYS cc_start: 0.8886 (m) cc_final: 0.8660 (m) REVERT: D 390 ASP cc_start: 0.7851 (t0) cc_final: 0.7469 (t70) REVERT: D 408 TYR cc_start: 0.7618 (t80) cc_final: 0.7355 (t80) REVERT: E 36 GLU cc_start: 0.8945 (tt0) cc_final: 0.8740 (tm-30) REVERT: E 71 GLU cc_start: 0.8110 (pm20) cc_final: 0.7811 (pt0) REVERT: E 150 GLU cc_start: 0.7503 (tt0) cc_final: 0.7208 (tm-30) REVERT: E 160 MET cc_start: 0.7835 (mtp) cc_final: 0.7596 (mpp) REVERT: E 182 GLN cc_start: 0.7754 (tt0) cc_final: 0.7545 (tt0) REVERT: E 223 MET cc_start: 0.6749 (mtt) cc_final: 0.6502 (mtt) REVERT: E 279 LEU cc_start: 0.9096 (mt) cc_final: 0.8849 (mt) REVERT: J 46 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7514 (mp0) outliers start: 44 outliers final: 23 residues processed: 408 average time/residue: 0.1122 time to fit residues: 68.9028 Evaluate side-chains 349 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 326 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 288 CYS Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 471 PHE Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 322 SER Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 37 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 51 optimal weight: 6.9990 chunk 50 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 178 optimal weight: 6.9990 chunk 1 optimal weight: 0.7980 chunk 172 optimal weight: 3.9990 chunk 147 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 chunk 88 optimal weight: 8.9990 chunk 129 optimal weight: 0.6980 chunk 152 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 56 HIS ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 ASN E 101 ASN ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.143892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.109820 restraints weight = 25626.399| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.94 r_work: 0.3347 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 15937 Z= 0.129 Angle : 0.583 10.381 21694 Z= 0.294 Chirality : 0.044 0.259 2493 Planarity : 0.004 0.049 2639 Dihedral : 8.923 114.883 2480 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.04 % Allowed : 13.33 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.22 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.19), residues: 1849 helix: 1.10 (0.21), residues: 552 sheet: -1.00 (0.21), residues: 543 loop : -0.91 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 18 TYR 0.023 0.002 TYR A 299 PHE 0.022 0.001 PHE E 425 TRP 0.043 0.001 TRP E 252 HIS 0.003 0.001 HIS A 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (15914) covalent geometry : angle 0.57600 / 0.29 (21632) SS BOND : bond 0.00234 / 0.15 ( 7) SS BOND : angle 0.50344 / 0.33 ( 14) hydrogen bonds : bond 0.03825 / 2.50 ( 669) hydrogen bonds : angle 4.89315 / 3.39 ( 2073) link_ALPHA1-2 : bond 0.00447 / 0.28 ( 1) link_ALPHA1-2 : angle 1.14852 / 0.67 ( 3) link_ALPHA1-3 : bond 0.00653 / 0.38 ( 2) link_ALPHA1-3 : angle 1.55921 / 0.80 ( 6) link_ALPHA1-6 : bond 0.00201 / 0.13 ( 1) link_ALPHA1-6 : angle 1.97029 / 1.01 ( 3) link_BETA1-4 : bond 0.00586 / 0.43 ( 7) link_BETA1-4 : angle 2.12838 / 1.31 ( 21) link_NAG-ASN : bond 0.00178 / 0.11 ( 5) link_NAG-ASN : angle 2.20143 / 1.39 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 341 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LYS cc_start: 0.8824 (mtpt) cc_final: 0.8100 (tmmt) REVERT: A 103 LYS cc_start: 0.8032 (tttp) cc_final: 0.7790 (tttp) REVERT: A 251 VAL cc_start: 0.9037 (t) cc_final: 0.8795 (m) REVERT: A 282 ASP cc_start: 0.8613 (m-30) cc_final: 0.8302 (m-30) REVERT: A 283 MET cc_start: 0.7570 (tpp) cc_final: 0.7202 (tmm) REVERT: A 305 ILE cc_start: 0.8717 (mm) cc_final: 0.8448 (mt) REVERT: A 424 ASP cc_start: 0.8220 (t0) cc_final: 0.7931 (t0) REVERT: B 20 ASP cc_start: 0.7817 (m-30) cc_final: 0.7457 (m-30) REVERT: B 114 MET cc_start: 0.8652 (mmp) cc_final: 0.8024 (mmm) REVERT: B 242 GLN cc_start: 0.7937 (mm110) cc_final: 0.7516 (mp10) REVERT: B 264 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8135 (tp) REVERT: B 275 ASN cc_start: 0.7257 (t0) cc_final: 0.6566 (m-40) REVERT: B 310 PHE cc_start: 0.8404 (m-80) cc_final: 0.7853 (m-10) REVERT: C 49 MET cc_start: 0.7521 (mtp) cc_final: 0.7203 (mtt) REVERT: C 52 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.6808 (mp0) REVERT: C 141 ARG cc_start: 0.8140 (mtt90) cc_final: 0.7760 (mmm160) REVERT: C 153 GLU cc_start: 0.8887 (mm-30) cc_final: 0.7949 (mm-30) REVERT: C 216 ARG cc_start: 0.8202 (ttm-80) cc_final: 0.7939 (ttm-80) REVERT: C 227 MET cc_start: 0.8402 (tpp) cc_final: 0.8113 (ttt) REVERT: C 241 TRP cc_start: 0.8564 (m100) cc_final: 0.8287 (m100) REVERT: C 286 MET cc_start: 0.8597 (mtp) cc_final: 0.8279 (mtp) REVERT: C 294 MET cc_start: 0.8248 (mmm) cc_final: 0.7966 (mmp) REVERT: C 465 ARG cc_start: 0.7473 (ttt-90) cc_final: 0.7000 (tpt170) REVERT: D 62 ASP cc_start: 0.7818 (m-30) cc_final: 0.7156 (m-30) REVERT: D 84 ARG cc_start: 0.8096 (mtm-85) cc_final: 0.7513 (mtm-85) REVERT: D 89 MET cc_start: 0.8557 (mmm) cc_final: 0.8260 (tpt) REVERT: D 113 MET cc_start: 0.8349 (mmp) cc_final: 0.7852 (mmm) REVERT: D 159 TYR cc_start: 0.8860 (t80) cc_final: 0.8409 (t80) REVERT: D 179 GLN cc_start: 0.8467 (mt0) cc_final: 0.8110 (mm-40) REVERT: D 199 LYS cc_start: 0.8492 (tttt) cc_final: 0.8241 (tttm) REVERT: D 233 CYS cc_start: 0.8796 (m) cc_final: 0.8551 (m) REVERT: D 390 ASP cc_start: 0.7924 (t0) cc_final: 0.7576 (t70) REVERT: D 404 PHE cc_start: 0.8609 (t80) cc_final: 0.8307 (t80) REVERT: E 71 GLU cc_start: 0.8246 (pm20) cc_final: 0.7863 (pt0) REVERT: E 177 GLU cc_start: 0.8665 (mp0) cc_final: 0.8404 (mp0) REVERT: E 223 MET cc_start: 0.7311 (mtt) cc_final: 0.7093 (mtt) REVERT: E 236 PHE cc_start: 0.4876 (p90) cc_final: 0.4195 (p90) REVERT: E 241 TYR cc_start: 0.8212 (m-80) cc_final: 0.7940 (m-80) REVERT: E 285 LYS cc_start: 0.6649 (mtpt) cc_final: 0.6150 (tptt) REVERT: J 46 GLU cc_start: 0.8318 (mm-30) cc_final: 0.7481 (mp0) outliers start: 51 outliers final: 36 residues processed: 371 average time/residue: 0.1173 time to fit residues: 65.4525 Evaluate side-chains 351 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 313 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 52 GLU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 471 PHE Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 179 ILE Chi-restraints excluded: chain E residue 252 TRP Chi-restraints excluded: chain E residue 274 LEU Chi-restraints excluded: chain E residue 320 PHE Chi-restraints excluded: chain E residue 322 SER Chi-restraints excluded: chain J residue 37 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 133 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 101 optimal weight: 5.9990 chunk 175 optimal weight: 20.0000 chunk 64 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 145 optimal weight: 7.9990 chunk 26 optimal weight: 0.0770 chunk 141 optimal weight: 0.9990 chunk 179 optimal weight: 10.0000 overall best weight: 2.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 56 HIS ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 87 ASN D 247 ASN J 55 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.140481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.106328 restraints weight = 25688.280| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.92 r_work: 0.3303 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 15937 Z= 0.173 Angle : 0.598 9.458 21694 Z= 0.301 Chirality : 0.044 0.241 2493 Planarity : 0.004 0.056 2639 Dihedral : 8.427 112.364 2480 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.75 % Allowed : 15.00 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.22 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.19), residues: 1849 helix: 1.24 (0.21), residues: 563 sheet: -0.95 (0.21), residues: 544 loop : -0.80 (0.23), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 18 TYR 0.024 0.002 TYR A 299 PHE 0.030 0.002 PHE E 425 TRP 0.038 0.001 TRP E 252 HIS 0.002 0.001 HIS C 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.17 (15914) covalent geometry : angle 0.59150 / 0.30 (21632) SS BOND : bond 0.00231 / 0.14 ( 7) SS BOND : angle 0.47552 / 0.30 ( 14) hydrogen bonds : bond 0.03607 / 2.38 ( 669) hydrogen bonds : angle 4.70665 / 3.27 ( 2073) link_ALPHA1-2 : bond 0.00840 / 0.52 ( 1) link_ALPHA1-2 : angle 1.42576 / 0.81 ( 3) link_ALPHA1-3 : bond 0.00476 / 0.29 ( 2) link_ALPHA1-3 : angle 1.54010 / 0.80 ( 6) link_ALPHA1-6 : bond 0.00101 / 0.06 ( 1) link_ALPHA1-6 : angle 2.23197 / 1.08 ( 3) link_BETA1-4 : bond 0.00422 / 0.29 ( 7) link_BETA1-4 : angle 1.99761 / 1.22 ( 21) link_NAG-ASN : bond 0.00247 / 0.17 ( 5) link_NAG-ASN : angle 2.05314 / 1.24 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 332 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.8589 (mp0) cc_final: 0.8140 (mp0) REVERT: A 70 LYS cc_start: 0.8854 (mtpt) cc_final: 0.8090 (tmmt) REVERT: A 251 VAL cc_start: 0.9041 (t) cc_final: 0.8827 (m) REVERT: A 282 ASP cc_start: 0.8677 (m-30) cc_final: 0.8386 (m-30) REVERT: A 283 MET cc_start: 0.7537 (tpp) cc_final: 0.7224 (tmm) REVERT: A 305 ILE cc_start: 0.8728 (mm) cc_final: 0.8465 (mt) REVERT: A 424 ASP cc_start: 0.8264 (t0) cc_final: 0.7963 (t0) REVERT: B 20 ASP cc_start: 0.7849 (m-30) cc_final: 0.7481 (m-30) REVERT: B 114 MET cc_start: 0.8715 (mmp) cc_final: 0.8000 (mmm) REVERT: B 242 GLN cc_start: 0.8143 (mm110) cc_final: 0.7822 (mp10) REVERT: B 310 PHE cc_start: 0.8461 (m-80) cc_final: 0.7949 (m-10) REVERT: C 49 MET cc_start: 0.7495 (mtp) cc_final: 0.7255 (mtt) REVERT: C 52 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.6877 (mp0) REVERT: C 55 MET cc_start: 0.8336 (mtt) cc_final: 0.8058 (mtm) REVERT: C 141 ARG cc_start: 0.8071 (mtt90) cc_final: 0.7708 (mmm160) REVERT: C 153 GLU cc_start: 0.8867 (mm-30) cc_final: 0.8014 (mm-30) REVERT: C 216 ARG cc_start: 0.8272 (ttm-80) cc_final: 0.7998 (ttm-80) REVERT: C 227 MET cc_start: 0.8305 (tpp) cc_final: 0.8089 (ttt) REVERT: C 241 TRP cc_start: 0.8615 (m100) cc_final: 0.8288 (m100) REVERT: C 286 MET cc_start: 0.8598 (mtp) cc_final: 0.8344 (mtp) REVERT: C 294 MET cc_start: 0.8239 (mmm) cc_final: 0.7915 (mmp) REVERT: C 465 ARG cc_start: 0.7543 (ttt-90) cc_final: 0.6992 (tpt170) REVERT: D 39 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.7909 (mt-10) REVERT: D 62 ASP cc_start: 0.7808 (m-30) cc_final: 0.7162 (m-30) REVERT: D 89 MET cc_start: 0.8592 (mmm) cc_final: 0.8227 (tpt) REVERT: D 113 MET cc_start: 0.8572 (mmp) cc_final: 0.8148 (mmm) REVERT: D 143 GLU cc_start: 0.6932 (mp0) cc_final: 0.6650 (mp0) REVERT: D 159 TYR cc_start: 0.9022 (t80) cc_final: 0.8694 (t80) REVERT: D 179 GLN cc_start: 0.8493 (mt0) cc_final: 0.8145 (mm-40) REVERT: D 199 LYS cc_start: 0.8472 (tttt) cc_final: 0.8230 (tttm) REVERT: D 390 ASP cc_start: 0.8020 (t0) cc_final: 0.7683 (t70) REVERT: E 71 GLU cc_start: 0.8425 (pm20) cc_final: 0.8036 (pm20) REVERT: E 236 PHE cc_start: 0.5137 (p90) cc_final: 0.4438 (p90) REVERT: E 241 TYR cc_start: 0.8117 (m-80) cc_final: 0.7905 (m-80) REVERT: E 304 PHE cc_start: 0.8140 (OUTLIER) cc_final: 0.7756 (t80) REVERT: I 11 MET cc_start: 0.7191 (mtt) cc_final: 0.6969 (mtm) REVERT: J 46 GLU cc_start: 0.8384 (mm-30) cc_final: 0.7484 (mp0) REVERT: J 59 LYS cc_start: 0.7454 (tptm) cc_final: 0.6455 (mmtt) outliers start: 63 outliers final: 48 residues processed: 366 average time/residue: 0.1070 time to fit residues: 58.7928 Evaluate side-chains 366 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 315 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 52 GLU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 471 PHE Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 179 ILE Chi-restraints excluded: chain E residue 252 TRP Chi-restraints excluded: chain E residue 304 PHE Chi-restraints excluded: chain E residue 320 PHE Chi-restraints excluded: chain E residue 322 SER Chi-restraints excluded: chain I residue 70 ASP Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 93 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 18 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 169 optimal weight: 20.0000 chunk 127 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 156 optimal weight: 0.9990 chunk 155 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 138 optimal weight: 4.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 56 HIS ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 ASN C 185 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.141550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.109067 restraints weight = 25239.985| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.78 r_work: 0.3315 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 15937 Z= 0.145 Angle : 0.573 9.368 21694 Z= 0.289 Chirality : 0.043 0.226 2493 Planarity : 0.004 0.044 2639 Dihedral : 8.085 108.655 2480 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.57 % Allowed : 16.25 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.22 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.20), residues: 1849 helix: 1.44 (0.21), residues: 562 sheet: -0.84 (0.21), residues: 533 loop : -0.80 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 18 TYR 0.023 0.001 TYR A 299 PHE 0.034 0.002 PHE E 425 TRP 0.039 0.001 TRP E 252 HIS 0.002 0.001 HIS B 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (15914) covalent geometry : angle 0.56747 / 0.29 (21632) SS BOND : bond 0.00182 / 0.11 ( 7) SS BOND : angle 0.41508 / 0.27 ( 14) hydrogen bonds : bond 0.03445 / 2.28 ( 669) hydrogen bonds : angle 4.49787 / 3.14 ( 2073) link_ALPHA1-2 : bond 0.00684 / 0.43 ( 1) link_ALPHA1-2 : angle 1.35966 / 0.77 ( 3) link_ALPHA1-3 : bond 0.00522 / 0.31 ( 2) link_ALPHA1-3 : angle 1.47290 / 0.76 ( 6) link_ALPHA1-6 : bond 0.00018 / 0.01 ( 1) link_ALPHA1-6 : angle 2.07686 / 0.98 ( 3) link_BETA1-4 : bond 0.00425 / 0.30 ( 7) link_BETA1-4 : angle 1.78839 / 1.12 ( 21) link_NAG-ASN : bond 0.00174 / 0.10 ( 5) link_NAG-ASN : angle 1.88594 / 1.15 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 335 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.8663 (mp0) cc_final: 0.8311 (mp0) REVERT: A 70 LYS cc_start: 0.8844 (mtpt) cc_final: 0.8283 (tmmt) REVERT: A 251 VAL cc_start: 0.9050 (t) cc_final: 0.8828 (m) REVERT: A 282 ASP cc_start: 0.8626 (m-30) cc_final: 0.8332 (m-30) REVERT: A 283 MET cc_start: 0.7415 (tpp) cc_final: 0.7137 (tmm) REVERT: A 305 ILE cc_start: 0.8759 (mm) cc_final: 0.8480 (mt) REVERT: A 424 ASP cc_start: 0.8340 (t0) cc_final: 0.8093 (t0) REVERT: B 20 ASP cc_start: 0.7882 (m-30) cc_final: 0.7543 (m-30) REVERT: B 114 MET cc_start: 0.8663 (mmp) cc_final: 0.8057 (mmm) REVERT: B 242 GLN cc_start: 0.8137 (mm110) cc_final: 0.7879 (mp10) REVERT: B 264 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8211 (tp) REVERT: B 310 PHE cc_start: 0.8453 (m-80) cc_final: 0.7892 (m-10) REVERT: C 49 MET cc_start: 0.7542 (mtp) cc_final: 0.7312 (mtt) REVERT: C 52 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6856 (mp0) REVERT: C 55 MET cc_start: 0.8355 (mtt) cc_final: 0.8050 (mtm) REVERT: C 141 ARG cc_start: 0.8021 (mtt90) cc_final: 0.7637 (mmm160) REVERT: C 153 GLU cc_start: 0.8820 (mm-30) cc_final: 0.8205 (mm-30) REVERT: C 216 ARG cc_start: 0.8264 (ttm-80) cc_final: 0.7986 (ttm-80) REVERT: C 227 MET cc_start: 0.8231 (tpp) cc_final: 0.8017 (ttt) REVERT: C 234 ILE cc_start: 0.9178 (OUTLIER) cc_final: 0.8844 (mp) REVERT: C 241 TRP cc_start: 0.8642 (m100) cc_final: 0.8325 (m100) REVERT: C 277 TYR cc_start: 0.8332 (p90) cc_final: 0.7928 (p90) REVERT: C 294 MET cc_start: 0.8197 (mmm) cc_final: 0.7869 (mmp) REVERT: C 465 ARG cc_start: 0.7550 (ttt-90) cc_final: 0.7002 (tpt170) REVERT: D 39 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.7890 (mt-10) REVERT: D 62 ASP cc_start: 0.7867 (m-30) cc_final: 0.7159 (m-30) REVERT: D 89 MET cc_start: 0.8558 (mmm) cc_final: 0.8202 (tpt) REVERT: D 113 MET cc_start: 0.8619 (mmp) cc_final: 0.8310 (mmt) REVERT: D 143 GLU cc_start: 0.6944 (mp0) cc_final: 0.6689 (mp0) REVERT: D 159 TYR cc_start: 0.9009 (t80) cc_final: 0.8753 (t80) REVERT: D 179 GLN cc_start: 0.8475 (mt0) cc_final: 0.8125 (mm-40) REVERT: D 199 LYS cc_start: 0.8462 (tttt) cc_final: 0.8225 (tttm) REVERT: D 390 ASP cc_start: 0.8032 (t0) cc_final: 0.7666 (t70) REVERT: D 404 PHE cc_start: 0.8661 (t80) cc_final: 0.8362 (t80) REVERT: D 408 TYR cc_start: 0.7436 (t80) cc_final: 0.7200 (t80) REVERT: E 71 GLU cc_start: 0.8450 (pm20) cc_final: 0.8049 (pm20) REVERT: E 197 ARG cc_start: 0.7996 (mmm-85) cc_final: 0.7673 (tpp80) REVERT: E 223 MET cc_start: 0.7569 (mtt) cc_final: 0.7078 (mtt) REVERT: E 236 PHE cc_start: 0.5049 (p90) cc_final: 0.4356 (p90) REVERT: E 304 PHE cc_start: 0.8017 (OUTLIER) cc_final: 0.7773 (t80) REVERT: I 11 MET cc_start: 0.7348 (mtt) cc_final: 0.6959 (mtp) REVERT: J 46 GLU cc_start: 0.8331 (mm-30) cc_final: 0.7879 (mt-10) REVERT: J 59 LYS cc_start: 0.7454 (tptm) cc_final: 0.6521 (mmtt) outliers start: 60 outliers final: 41 residues processed: 367 average time/residue: 0.1016 time to fit residues: 56.6655 Evaluate side-chains 361 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 315 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain C residue 9 MET Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 52 GLU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 471 PHE Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 179 ILE Chi-restraints excluded: chain E residue 252 TRP Chi-restraints excluded: chain E residue 304 PHE Chi-restraints excluded: chain E residue 320 PHE Chi-restraints excluded: chain E residue 322 SER Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 93 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 175 optimal weight: 8.9990 chunk 53 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 26 optimal weight: 8.9990 chunk 154 optimal weight: 10.0000 chunk 182 optimal weight: 6.9990 chunk 114 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 GLN B 56 HIS ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.143066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.109503 restraints weight = 25488.955| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.88 r_work: 0.3322 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 15937 Z= 0.121 Angle : 0.557 10.955 21694 Z= 0.280 Chirality : 0.043 0.221 2493 Planarity : 0.004 0.044 2639 Dihedral : 7.836 102.433 2480 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.15 % Allowed : 17.44 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.22 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.20), residues: 1849 helix: 1.46 (0.21), residues: 570 sheet: -0.75 (0.21), residues: 554 loop : -0.73 (0.24), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 18 TYR 0.023 0.001 TYR A 299 PHE 0.020 0.001 PHE E 417 TRP 0.038 0.001 TRP E 252 HIS 0.002 0.001 HIS I 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (15914) covalent geometry : angle 0.55196 / 0.28 (21632) SS BOND : bond 0.00159 / 0.09 ( 7) SS BOND : angle 0.31102 / 0.21 ( 14) hydrogen bonds : bond 0.03292 / 2.18 ( 669) hydrogen bonds : angle 4.36858 / 3.05 ( 2073) link_ALPHA1-2 : bond 0.00756 / 0.47 ( 1) link_ALPHA1-2 : angle 1.40115 / 0.79 ( 3) link_ALPHA1-3 : bond 0.00763 / 0.47 ( 2) link_ALPHA1-3 : angle 1.48845 / 0.78 ( 6) link_ALPHA1-6 : bond 0.00163 / 0.10 ( 1) link_ALPHA1-6 : angle 1.91756 / 0.89 ( 3) link_BETA1-4 : bond 0.00444 / 0.30 ( 7) link_BETA1-4 : angle 1.70767 / 1.06 ( 21) link_NAG-ASN : bond 0.00184 / 0.12 ( 5) link_NAG-ASN : angle 1.80004 / 1.12 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 336 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 LYS cc_start: 0.8856 (mtpt) cc_final: 0.8284 (tmmt) REVERT: A 224 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.8118 (tt0) REVERT: A 237 TRP cc_start: 0.8404 (m-10) cc_final: 0.8123 (m-10) REVERT: A 251 VAL cc_start: 0.9046 (t) cc_final: 0.8836 (m) REVERT: A 282 ASP cc_start: 0.8610 (m-30) cc_final: 0.8296 (m-30) REVERT: A 283 MET cc_start: 0.7402 (tpp) cc_final: 0.7100 (tmm) REVERT: A 305 ILE cc_start: 0.8741 (mm) cc_final: 0.8431 (mt) REVERT: A 424 ASP cc_start: 0.8297 (t0) cc_final: 0.8027 (t0) REVERT: B 20 ASP cc_start: 0.7821 (m-30) cc_final: 0.7483 (m-30) REVERT: B 114 MET cc_start: 0.8669 (mmp) cc_final: 0.8050 (mmm) REVERT: B 242 GLN cc_start: 0.8154 (mm110) cc_final: 0.7887 (mp10) REVERT: B 310 PHE cc_start: 0.8453 (m-80) cc_final: 0.7869 (m-10) REVERT: B 393 ASP cc_start: 0.9195 (m-30) cc_final: 0.8488 (t70) REVERT: B 397 ARG cc_start: 0.8254 (ttm170) cc_final: 0.7594 (ttm110) REVERT: C 49 MET cc_start: 0.7519 (mtp) cc_final: 0.7318 (mtt) REVERT: C 52 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6865 (mp0) REVERT: C 55 MET cc_start: 0.8371 (mtt) cc_final: 0.8072 (mtm) REVERT: C 141 ARG cc_start: 0.7999 (mtt90) cc_final: 0.7625 (mmm160) REVERT: C 153 GLU cc_start: 0.8786 (mm-30) cc_final: 0.8173 (mm-30) REVERT: C 216 ARG cc_start: 0.8251 (ttm-80) cc_final: 0.7995 (ttm-80) REVERT: C 241 TRP cc_start: 0.8619 (m100) cc_final: 0.8315 (m100) REVERT: C 244 TYR cc_start: 0.7362 (p90) cc_final: 0.7144 (p90) REVERT: C 277 TYR cc_start: 0.8287 (p90) cc_final: 0.7858 (p90) REVERT: C 294 MET cc_start: 0.8230 (mmm) cc_final: 0.7856 (mmp) REVERT: C 303 ASN cc_start: 0.8890 (t0) cc_final: 0.8652 (t0) REVERT: C 463 ILE cc_start: 0.6931 (tp) cc_final: 0.6637 (mm) REVERT: C 465 ARG cc_start: 0.7517 (ttt-90) cc_final: 0.6908 (tpt170) REVERT: D 39 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.7856 (mt-10) REVERT: D 89 MET cc_start: 0.8567 (mmm) cc_final: 0.8200 (tpt) REVERT: D 113 MET cc_start: 0.8640 (mmp) cc_final: 0.8379 (mmm) REVERT: D 143 GLU cc_start: 0.6851 (mp0) cc_final: 0.6636 (mp0) REVERT: D 159 TYR cc_start: 0.8995 (t80) cc_final: 0.8700 (t80) REVERT: D 179 GLN cc_start: 0.8456 (mt0) cc_final: 0.8117 (mm-40) REVERT: D 199 LYS cc_start: 0.8436 (tttt) cc_final: 0.8211 (tttm) REVERT: D 390 ASP cc_start: 0.7989 (t0) cc_final: 0.7646 (t70) REVERT: D 404 PHE cc_start: 0.8682 (t80) cc_final: 0.8385 (t80) REVERT: E 36 GLU cc_start: 0.8891 (tt0) cc_final: 0.8674 (tm-30) REVERT: E 71 GLU cc_start: 0.8533 (pm20) cc_final: 0.8169 (pm20) REVERT: E 93 ILE cc_start: 0.8144 (tp) cc_final: 0.7868 (tt) REVERT: E 197 ARG cc_start: 0.7938 (mmm-85) cc_final: 0.7618 (tpp80) REVERT: E 223 MET cc_start: 0.7676 (mtt) cc_final: 0.7301 (mtt) REVERT: I 4 MET cc_start: 0.7580 (mmp) cc_final: 0.7152 (mmp) REVERT: I 11 MET cc_start: 0.7288 (mtt) cc_final: 0.7048 (mtm) REVERT: J 46 GLU cc_start: 0.8361 (mm-30) cc_final: 0.7882 (mt-10) REVERT: J 59 LYS cc_start: 0.7419 (tptm) cc_final: 0.6521 (mmtt) outliers start: 53 outliers final: 40 residues processed: 366 average time/residue: 0.1050 time to fit residues: 57.9754 Evaluate side-chains 357 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 314 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain C residue 9 MET Chi-restraints excluded: chain C residue 52 GLU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 179 ILE Chi-restraints excluded: chain E residue 252 TRP Chi-restraints excluded: chain E residue 320 PHE Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 93 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 71 optimal weight: 6.9990 chunk 151 optimal weight: 2.9990 chunk 174 optimal weight: 8.9990 chunk 56 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 118 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 HIS B 190 GLN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 ASN J 55 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.139536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.105879 restraints weight = 25730.788| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.89 r_work: 0.3272 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 15937 Z= 0.214 Angle : 0.632 11.349 21694 Z= 0.317 Chirality : 0.045 0.252 2493 Planarity : 0.004 0.041 2639 Dihedral : 7.938 105.113 2480 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.51 % Allowed : 17.50 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.22 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.20), residues: 1849 helix: 1.38 (0.21), residues: 566 sheet: -0.80 (0.21), residues: 548 loop : -0.79 (0.24), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 284 TYR 0.023 0.002 TYR A 299 PHE 0.033 0.002 PHE E 304 TRP 0.040 0.001 TRP E 252 HIS 0.003 0.001 HIS D 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.21 (15914) covalent geometry : angle 0.62724 / 0.32 (21632) SS BOND : bond 0.00241 / 0.14 ( 7) SS BOND : angle 0.36663 / 0.23 ( 14) hydrogen bonds : bond 0.03579 / 2.38 ( 669) hydrogen bonds : angle 4.51400 / 3.15 ( 2073) link_ALPHA1-2 : bond 0.00779 / 0.49 ( 1) link_ALPHA1-2 : angle 1.33335 / 0.75 ( 3) link_ALPHA1-3 : bond 0.00649 / 0.40 ( 2) link_ALPHA1-3 : angle 1.53974 / 0.80 ( 6) link_ALPHA1-6 : bond 0.00032 / 0.02 ( 1) link_ALPHA1-6 : angle 2.26201 / 1.07 ( 3) link_BETA1-4 : bond 0.00365 / 0.25 ( 7) link_BETA1-4 : angle 1.76453 / 1.11 ( 21) link_NAG-ASN : bond 0.00229 / 0.13 ( 5) link_NAG-ASN : angle 2.07819 / 1.24 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 321 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LYS cc_start: 0.8856 (mtpt) cc_final: 0.8278 (tmmt) REVERT: A 180 ARG cc_start: 0.8018 (mmp80) cc_final: 0.7313 (mmm-85) REVERT: A 237 TRP cc_start: 0.8425 (m-10) cc_final: 0.8155 (m-10) REVERT: A 283 MET cc_start: 0.7522 (tpp) cc_final: 0.7197 (tmm) REVERT: A 305 ILE cc_start: 0.8757 (mm) cc_final: 0.8495 (mt) REVERT: A 424 ASP cc_start: 0.8387 (t0) cc_final: 0.8157 (t0) REVERT: B 20 ASP cc_start: 0.7869 (m-30) cc_final: 0.7530 (m-30) REVERT: B 114 MET cc_start: 0.8733 (mmp) cc_final: 0.8132 (mmm) REVERT: B 242 GLN cc_start: 0.8184 (mm110) cc_final: 0.7966 (mp10) REVERT: B 310 PHE cc_start: 0.8508 (m-80) cc_final: 0.7950 (m-10) REVERT: B 393 ASP cc_start: 0.9249 (m-30) cc_final: 0.8595 (t70) REVERT: B 397 ARG cc_start: 0.8259 (ttm170) cc_final: 0.7598 (ttm110) REVERT: C 52 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.6948 (mp0) REVERT: C 55 MET cc_start: 0.8369 (mtt) cc_final: 0.8075 (mtm) REVERT: C 141 ARG cc_start: 0.8046 (mtt90) cc_final: 0.7662 (mmm160) REVERT: C 153 GLU cc_start: 0.8829 (mm-30) cc_final: 0.8189 (mm-30) REVERT: C 220 TYR cc_start: 0.8118 (t80) cc_final: 0.7872 (t80) REVERT: C 241 TRP cc_start: 0.8639 (m100) cc_final: 0.8321 (m100) REVERT: C 277 TYR cc_start: 0.8345 (p90) cc_final: 0.7967 (p90) REVERT: C 294 MET cc_start: 0.8240 (mmm) cc_final: 0.7875 (mmp) REVERT: C 303 ASN cc_start: 0.8931 (t0) cc_final: 0.8665 (t0) REVERT: C 463 ILE cc_start: 0.6931 (tp) cc_final: 0.6611 (mm) REVERT: C 465 ARG cc_start: 0.7550 (ttt-90) cc_final: 0.6998 (tpt170) REVERT: D 39 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.7827 (mt-10) REVERT: D 89 MET cc_start: 0.8548 (mmm) cc_final: 0.8189 (tpt) REVERT: D 113 MET cc_start: 0.8694 (mmp) cc_final: 0.8461 (mmt) REVERT: D 179 GLN cc_start: 0.8521 (mt0) cc_final: 0.8149 (mm-40) REVERT: D 199 LYS cc_start: 0.8498 (tttt) cc_final: 0.8223 (tttm) REVERT: D 212 MET cc_start: 0.9069 (mpp) cc_final: 0.8842 (mpp) REVERT: D 390 ASP cc_start: 0.8073 (t0) cc_final: 0.7675 (t70) REVERT: D 395 ILE cc_start: 0.8185 (mm) cc_final: 0.7697 (pt) REVERT: E 71 GLU cc_start: 0.8568 (pm20) cc_final: 0.8247 (pm20) REVERT: E 93 ILE cc_start: 0.8127 (tp) cc_final: 0.7903 (tt) REVERT: E 223 MET cc_start: 0.7882 (mtt) cc_final: 0.7646 (mtt) REVERT: E 304 PHE cc_start: 0.8504 (t80) cc_final: 0.8244 (t80) REVERT: I 4 MET cc_start: 0.7715 (mmp) cc_final: 0.7218 (mmp) REVERT: J 36 TRP cc_start: 0.7440 (m100) cc_final: 0.7185 (m100) REVERT: J 46 GLU cc_start: 0.8330 (mm-30) cc_final: 0.7836 (mt-10) REVERT: J 59 LYS cc_start: 0.7517 (tptm) cc_final: 0.6555 (mmtt) outliers start: 59 outliers final: 50 residues processed: 360 average time/residue: 0.0973 time to fit residues: 53.6250 Evaluate side-chains 357 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 305 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain C residue 9 MET Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 52 GLU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 140 MET Chi-restraints excluded: chain D residue 141 HIS Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 179 ILE Chi-restraints excluded: chain E residue 252 TRP Chi-restraints excluded: chain E residue 320 PHE Chi-restraints excluded: chain E residue 322 SER Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 93 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 157 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 137 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 123 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 GLN B 56 HIS ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN D 87 ASN E 101 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.142314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.108595 restraints weight = 25654.059| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.89 r_work: 0.3306 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 15937 Z= 0.130 Angle : 0.590 11.678 21694 Z= 0.294 Chirality : 0.043 0.258 2493 Planarity : 0.004 0.033 2639 Dihedral : 7.700 98.219 2478 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.04 % Allowed : 17.92 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.22 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.20), residues: 1849 helix: 1.49 (0.21), residues: 564 sheet: -0.65 (0.22), residues: 543 loop : -0.76 (0.23), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 284 TYR 0.022 0.001 TYR A 66 PHE 0.030 0.001 PHE E 304 TRP 0.040 0.001 TRP E 252 HIS 0.003 0.001 HIS D 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (15914) covalent geometry : angle 0.58520 / 0.29 (21632) SS BOND : bond 0.00185 / 0.11 ( 7) SS BOND : angle 0.35965 / 0.24 ( 14) hydrogen bonds : bond 0.03396 / 2.27 ( 669) hydrogen bonds : angle 4.37842 / 3.05 ( 2073) link_ALPHA1-2 : bond 0.00722 / 0.45 ( 1) link_ALPHA1-2 : angle 1.32163 / 0.75 ( 3) link_ALPHA1-3 : bond 0.00712 / 0.44 ( 2) link_ALPHA1-3 : angle 1.42222 / 0.74 ( 6) link_ALPHA1-6 : bond 0.00440 / 0.28 ( 1) link_ALPHA1-6 : angle 1.79393 / 0.86 ( 3) link_BETA1-4 : bond 0.00428 / 0.29 ( 7) link_BETA1-4 : angle 1.61462 / 1.00 ( 21) link_NAG-ASN : bond 0.00165 / 0.10 ( 5) link_NAG-ASN : angle 1.82415 / 1.13 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 329 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LYS cc_start: 0.8815 (mtpt) cc_final: 0.8225 (tmmt) REVERT: A 180 ARG cc_start: 0.7812 (mmp80) cc_final: 0.7318 (mmm-85) REVERT: A 237 TRP cc_start: 0.8401 (m-10) cc_final: 0.8107 (m-10) REVERT: A 283 MET cc_start: 0.7439 (tpp) cc_final: 0.7123 (tmm) REVERT: A 305 ILE cc_start: 0.8758 (mm) cc_final: 0.8474 (mt) REVERT: A 424 ASP cc_start: 0.8369 (t0) cc_final: 0.8138 (t0) REVERT: B 114 MET cc_start: 0.8707 (mmp) cc_final: 0.8101 (mmm) REVERT: B 242 GLN cc_start: 0.8171 (mm110) cc_final: 0.7862 (mp10) REVERT: B 393 ASP cc_start: 0.9220 (m-30) cc_final: 0.8582 (t70) REVERT: B 397 ARG cc_start: 0.8212 (ttm170) cc_final: 0.7571 (ttm110) REVERT: C 55 MET cc_start: 0.8374 (mtt) cc_final: 0.8073 (mtm) REVERT: C 141 ARG cc_start: 0.7995 (mtt90) cc_final: 0.7628 (mmm160) REVERT: C 153 GLU cc_start: 0.8776 (mm-30) cc_final: 0.8183 (mm-30) REVERT: C 220 TYR cc_start: 0.7996 (t80) cc_final: 0.7791 (t80) REVERT: C 241 TRP cc_start: 0.8622 (m100) cc_final: 0.8322 (m100) REVERT: C 277 TYR cc_start: 0.8273 (p90) cc_final: 0.7873 (p90) REVERT: C 294 MET cc_start: 0.8228 (mmm) cc_final: 0.7849 (mmp) REVERT: C 463 ILE cc_start: 0.6803 (tp) cc_final: 0.6559 (mm) REVERT: C 465 ARG cc_start: 0.7567 (ttt-90) cc_final: 0.7042 (tpt170) REVERT: D 39 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.7845 (mt-10) REVERT: D 89 MET cc_start: 0.8522 (mmm) cc_final: 0.8178 (tpt) REVERT: D 113 MET cc_start: 0.8633 (mmp) cc_final: 0.8399 (mmt) REVERT: D 179 GLN cc_start: 0.8524 (mt0) cc_final: 0.8166 (mm-40) REVERT: D 199 LYS cc_start: 0.8439 (tttt) cc_final: 0.8190 (tttm) REVERT: D 212 MET cc_start: 0.8989 (mpp) cc_final: 0.8787 (mpp) REVERT: E 71 GLU cc_start: 0.8577 (pm20) cc_final: 0.8288 (pm20) REVERT: E 93 ILE cc_start: 0.8179 (tp) cc_final: 0.7961 (tt) REVERT: E 197 ARG cc_start: 0.7931 (mmm-85) cc_final: 0.7608 (tpp80) REVERT: E 223 MET cc_start: 0.7738 (mtt) cc_final: 0.7530 (mtt) REVERT: I 4 MET cc_start: 0.7673 (mmp) cc_final: 0.7233 (mmp) REVERT: J 36 TRP cc_start: 0.7449 (m100) cc_final: 0.7185 (m100) REVERT: J 46 GLU cc_start: 0.8310 (mm-30) cc_final: 0.7815 (mt-10) REVERT: J 59 LYS cc_start: 0.7488 (tptm) cc_final: 0.6556 (mmtt) outliers start: 51 outliers final: 43 residues processed: 356 average time/residue: 0.1025 time to fit residues: 55.0803 Evaluate side-chains 361 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 317 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain C residue 9 MET Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 179 ILE Chi-restraints excluded: chain E residue 252 TRP Chi-restraints excluded: chain E residue 320 PHE Chi-restraints excluded: chain E residue 322 SER Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 93 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 43 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 70 optimal weight: 0.6980 chunk 162 optimal weight: 6.9990 chunk 114 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 HIS ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 ASN C 267 HIS ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 55 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.146926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.114489 restraints weight = 24688.742| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.61 r_work: 0.3356 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15937 Z= 0.115 Angle : 0.593 12.029 21694 Z= 0.296 Chirality : 0.043 0.280 2493 Planarity : 0.004 0.035 2639 Dihedral : 7.445 92.047 2476 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.74 % Allowed : 18.75 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.22 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.20), residues: 1849 helix: 1.52 (0.21), residues: 564 sheet: -0.59 (0.22), residues: 539 loop : -0.71 (0.23), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 284 TYR 0.024 0.001 TYR I 36 PHE 0.047 0.002 PHE D 404 TRP 0.039 0.001 TRP E 252 HIS 0.018 0.001 HIS C 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (15914) covalent geometry : angle 0.58914 / 0.30 (21632) SS BOND : bond 0.00175 / 0.11 ( 7) SS BOND : angle 0.36697 / 0.24 ( 14) hydrogen bonds : bond 0.03333 / 2.22 ( 669) hydrogen bonds : angle 4.34428 / 3.01 ( 2073) link_ALPHA1-2 : bond 0.00694 / 0.43 ( 1) link_ALPHA1-2 : angle 1.31389 / 0.74 ( 3) link_ALPHA1-3 : bond 0.00681 / 0.41 ( 2) link_ALPHA1-3 : angle 1.38527 / 0.73 ( 6) link_ALPHA1-6 : bond 0.00478 / 0.30 ( 1) link_ALPHA1-6 : angle 1.63434 / 0.78 ( 3) link_BETA1-4 : bond 0.00415 / 0.28 ( 7) link_BETA1-4 : angle 1.56487 / 0.97 ( 21) link_NAG-ASN : bond 0.00169 / 0.11 ( 5) link_NAG-ASN : angle 1.74865 / 1.09 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 315 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LYS cc_start: 0.8718 (mtpt) cc_final: 0.8290 (tmmt) REVERT: A 180 ARG cc_start: 0.7669 (mmp80) cc_final: 0.7464 (mmm-85) REVERT: A 237 TRP cc_start: 0.8315 (m-10) cc_final: 0.8040 (m-10) REVERT: A 282 ASP cc_start: 0.8575 (m-30) cc_final: 0.8267 (m-30) REVERT: A 283 MET cc_start: 0.7382 (tpp) cc_final: 0.7147 (tmm) REVERT: A 305 ILE cc_start: 0.8783 (mm) cc_final: 0.8474 (mt) REVERT: A 424 ASP cc_start: 0.8234 (t0) cc_final: 0.8012 (t0) REVERT: B 114 MET cc_start: 0.8759 (mmp) cc_final: 0.8192 (mmm) REVERT: B 242 GLN cc_start: 0.8157 (mm110) cc_final: 0.7840 (mp10) REVERT: B 310 PHE cc_start: 0.8335 (m-80) cc_final: 0.8046 (m-10) REVERT: C 55 MET cc_start: 0.8272 (mtt) cc_final: 0.7946 (mtm) REVERT: C 153 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8196 (mm-30) REVERT: C 241 TRP cc_start: 0.8645 (m100) cc_final: 0.8377 (m100) REVERT: C 259 LEU cc_start: 0.8174 (mp) cc_final: 0.7910 (tt) REVERT: C 277 TYR cc_start: 0.8208 (p90) cc_final: 0.7930 (p90) REVERT: C 294 MET cc_start: 0.8185 (mmm) cc_final: 0.7842 (mmp) REVERT: C 463 ILE cc_start: 0.6753 (tp) cc_final: 0.6456 (mm) REVERT: C 465 ARG cc_start: 0.7569 (ttt-90) cc_final: 0.7030 (tpt170) REVERT: D 39 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7609 (mt-10) REVERT: D 89 MET cc_start: 0.8487 (mmm) cc_final: 0.8208 (tpt) REVERT: D 179 GLN cc_start: 0.8438 (mt0) cc_final: 0.8174 (mm-40) REVERT: E 71 GLU cc_start: 0.8568 (pm20) cc_final: 0.8351 (pm20) REVERT: E 93 ILE cc_start: 0.8233 (tp) cc_final: 0.7985 (tt) REVERT: E 197 ARG cc_start: 0.7835 (mmm-85) cc_final: 0.7444 (tpp80) REVERT: J 36 TRP cc_start: 0.7522 (m100) cc_final: 0.7266 (m100) REVERT: J 46 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7749 (mt-10) REVERT: J 59 LYS cc_start: 0.7413 (tptm) cc_final: 0.6578 (mmtt) outliers start: 46 outliers final: 42 residues processed: 341 average time/residue: 0.1006 time to fit residues: 52.3136 Evaluate side-chains 347 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 304 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain C residue 9 MET Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 140 MET Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 179 ILE Chi-restraints excluded: chain E residue 252 TRP Chi-restraints excluded: chain E residue 320 PHE Chi-restraints excluded: chain E residue 322 SER Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 55 ASN Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 93 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 176 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 163 optimal weight: 9.9990 chunk 132 optimal weight: 3.9990 chunk 171 optimal weight: 20.0000 chunk 15 optimal weight: 5.9990 chunk 11 optimal weight: 40.0000 chunk 8 optimal weight: 2.9990 chunk 116 optimal weight: 7.9990 chunk 69 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 HIS B 190 GLN ** B 242 GLN ** 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 = 0.3865 r_free = 0.3865 target = 0.142707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.111139 restraints weight = 25314.428| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.68 r_work: 0.3331 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 15937 Z= 0.155 Angle : 0.625 12.257 21694 Z= 0.312 Chirality : 0.044 0.298 2493 Planarity : 0.004 0.068 2639 Dihedral : 7.462 89.473 2476 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.80 % Allowed : 18.69 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.22 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.20), residues: 1849 helix: 1.52 (0.21), residues: 564 sheet: -0.62 (0.22), residues: 543 loop : -0.68 (0.24), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 180 TYR 0.042 0.002 TYR C 220 PHE 0.041 0.002 PHE D 404 TRP 0.040 0.001 TRP E 252 HIS 0.002 0.001 HIS B 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 (15914) covalent geometry : angle 0.62090 / 0.31 (21632) SS BOND : bond 0.00206 / 0.12 ( 7) SS BOND : angle 0.38398 / 0.24 ( 14) hydrogen bonds : bond 0.03410 / 2.27 ( 669) hydrogen bonds : angle 4.40612 / 3.06 ( 2073) link_ALPHA1-2 : bond 0.00767 / 0.48 ( 1) link_ALPHA1-2 : angle 1.29983 / 0.74 ( 3) link_ALPHA1-3 : bond 0.00737 / 0.45 ( 2) link_ALPHA1-3 : angle 1.41953 / 0.74 ( 6) link_ALPHA1-6 : bond 0.00394 / 0.25 ( 1) link_ALPHA1-6 : angle 1.80713 / 0.87 ( 3) link_BETA1-4 : bond 0.00392 / 0.27 ( 7) link_BETA1-4 : angle 1.58967 / 0.99 ( 21) link_NAG-ASN : bond 0.00169 / 0.09 ( 5) link_NAG-ASN : angle 1.85941 / 1.14 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 310 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LYS cc_start: 0.8682 (mtpt) cc_final: 0.8263 (tmmt) REVERT: A 179 GLU cc_start: 0.7938 (pm20) cc_final: 0.7556 (pm20) REVERT: A 237 TRP cc_start: 0.8299 (m-10) cc_final: 0.8020 (m-10) REVERT: A 282 ASP cc_start: 0.8596 (m-30) cc_final: 0.8293 (m-30) REVERT: A 283 MET cc_start: 0.7462 (tpp) cc_final: 0.7220 (tmm) REVERT: A 305 ILE cc_start: 0.8794 (mm) cc_final: 0.8509 (mt) REVERT: A 424 ASP cc_start: 0.8235 (t0) cc_final: 0.8018 (t0) REVERT: B 114 MET cc_start: 0.8747 (mmp) cc_final: 0.8207 (mmm) REVERT: B 242 GLN cc_start: 0.8150 (mm110) cc_final: 0.7844 (mp10) REVERT: B 310 PHE cc_start: 0.8357 (m-80) cc_final: 0.8037 (m-10) REVERT: C 55 MET cc_start: 0.8234 (mtt) cc_final: 0.7920 (mtm) REVERT: C 153 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8229 (mm-30) REVERT: C 234 ILE cc_start: 0.9219 (OUTLIER) cc_final: 0.8871 (mp) REVERT: C 241 TRP cc_start: 0.8654 (m100) cc_final: 0.8409 (m100) REVERT: C 259 LEU cc_start: 0.8140 (mp) cc_final: 0.7905 (tt) REVERT: C 294 MET cc_start: 0.8136 (mmm) cc_final: 0.7802 (mmp) REVERT: C 463 ILE cc_start: 0.6828 (tp) cc_final: 0.6532 (mm) REVERT: C 465 ARG cc_start: 0.7588 (ttt-90) cc_final: 0.7023 (tpt170) REVERT: D 39 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7638 (mt-10) REVERT: D 89 MET cc_start: 0.8480 (mmm) cc_final: 0.8201 (tpt) REVERT: D 179 GLN cc_start: 0.8432 (mt0) cc_final: 0.8155 (mm-40) REVERT: D 395 ILE cc_start: 0.8234 (mm) cc_final: 0.7786 (pt) REVERT: E 71 GLU cc_start: 0.8575 (pm20) cc_final: 0.8370 (pm20) REVERT: E 93 ILE cc_start: 0.8248 (tp) cc_final: 0.8010 (tt) REVERT: E 197 ARG cc_start: 0.7863 (mmm-85) cc_final: 0.7490 (tpp80) REVERT: E 223 MET cc_start: 0.7709 (mtt) cc_final: 0.6907 (mtt) REVERT: J 36 TRP cc_start: 0.7514 (m100) cc_final: 0.7266 (m100) REVERT: J 46 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7785 (mt-10) REVERT: J 59 LYS cc_start: 0.7468 (tptm) cc_final: 0.6597 (mmtt) outliers start: 47 outliers final: 41 residues processed: 336 average time/residue: 0.1012 time to fit residues: 52.2412 Evaluate side-chains 344 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 301 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain C residue 9 MET Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 140 MET Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 179 ILE Chi-restraints excluded: chain E residue 252 TRP Chi-restraints excluded: chain E residue 320 PHE Chi-restraints excluded: chain E residue 322 SER Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 93 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 117 optimal weight: 9.9990 chunk 50 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 83 optimal weight: 6.9990 chunk 166 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 9 optimal weight: 0.9990 chunk 178 optimal weight: 3.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 HIS ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 405 ASN E 101 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.140156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.106439 restraints weight = 25682.847| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.88 r_work: 0.3279 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.4324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 15937 Z= 0.189 Angle : 0.653 11.638 21694 Z= 0.326 Chirality : 0.045 0.284 2493 Planarity : 0.004 0.044 2639 Dihedral : 7.542 85.390 2476 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.86 % Allowed : 19.05 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.22 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.20), residues: 1849 helix: 1.53 (0.21), residues: 558 sheet: -0.64 (0.22), residues: 552 loop : -0.76 (0.23), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 397 TYR 0.038 0.002 TYR C 220 PHE 0.028 0.002 PHE E 304 TRP 0.041 0.001 TRP E 252 HIS 0.002 0.001 HIS C 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.19 (15914) covalent geometry : angle 0.64830 / 0.33 (21632) SS BOND : bond 0.00227 / 0.14 ( 7) SS BOND : angle 0.39217 / 0.24 ( 14) hydrogen bonds : bond 0.03595 / 2.39 ( 669) hydrogen bonds : angle 4.53247 / 3.15 ( 2073) link_ALPHA1-2 : bond 0.00837 / 0.52 ( 1) link_ALPHA1-2 : angle 1.32055 / 0.75 ( 3) link_ALPHA1-3 : bond 0.00654 / 0.40 ( 2) link_ALPHA1-3 : angle 1.39724 / 0.73 ( 6) link_ALPHA1-6 : bond 0.00283 / 0.18 ( 1) link_ALPHA1-6 : angle 1.99797 / 0.96 ( 3) link_BETA1-4 : bond 0.00363 / 0.25 ( 7) link_BETA1-4 : angle 1.62460 / 1.01 ( 21) link_NAG-ASN : bond 0.00224 / 0.12 ( 5) link_NAG-ASN : angle 2.09546 / 1.25 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3166.49 seconds wall clock time: 55 minutes 16.90 seconds (3316.90 seconds total)