Starting phenix.real_space_refine on Sat Sep 12 12:16:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6i53_4411/09_2026/6i53_4411.cif Found real_map, /net/cci-nas-00/data/ceres_data/6i53_4411/09_2026/6i53_4411.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6i53_4411/09_2026/6i53_4411.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6i53_4411/09_2026/6i53_4411.map" model { file = "/net/cci-nas-00/data/ceres_data/6i53_4411/09_2026/6i53_4411.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6i53_4411/09_2026/6i53_4411.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6i53_4411/09_2026/6i53_4411.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6i53_4411/09_2026/6i53_4411.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 9 5.49 5 S 82 5.16 5 C 9943 2.51 5 N 2474 2.21 5 O 2854 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15362 Number of models: 1 Model: "" Number of chains: 16 Chain: "E" Number of atoms: 2754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2754 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 319} Chain breaks: 1 Chain: "A" Number of atoms: 2823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2823 Classifications: {'peptide': 349} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 334} Chain breaks: 1 Chain: "B" Number of atoms: 2770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2770 Classifications: {'peptide': 338} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 321} Chain breaks: 1 Chain: "C" Number of atoms: 2701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2701 Classifications: {'peptide': 328} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 314} Chain breaks: 1 Chain: "D" Number of atoms: 2805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2805 Classifications: {'peptide': 347} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 332} Chain breaks: 1 Chain: "G" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 949 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "H" 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 chiralities: 2 Chain: "I" 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 chiralities: 7 Chain: "J" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "K" 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 chiralities: 2 Chain: "L" 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 chiralities: 2 Chain: "M" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "E" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 15 Chain: "A" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 82 Unusual residues: {'PIO': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 15 Chain: "D" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 82 Unusual residues: {'PIO': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 15 Time building chain proxies: 3.48, per 1000 atoms: 0.23 Number of scatterers: 15362 At special positions: 0 Unit cell: (97.37, 123.05, 135.89, 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 82 16.00 P 9 15.00 O 2854 8.00 N 2474 7.00 C 9943 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS E 136 " - pdb=" SG CYS E 150 " distance=2.03 Simple disulfide: pdb=" SG CYS A 139 " - pdb=" SG CYS A 153 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 150 " distance=2.03 Simple disulfide: pdb=" SG CYS C 151 " - pdb=" SG CYS C 165 " distance=2.03 Simple disulfide: pdb=" SG CYS D 139 " - pdb=" SG CYS D 153 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 95 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA F 3 " - " MAN F 4 " " BMA I 3 " - " MAN I 7 " " MAN I 4 " - " MAN I 5 " " BMA J 3 " - " MAN J 6 " " MAN J 4 " - " MAN J 5 " " BMA M 3 " - " MAN M 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " " BMA I 3 " - " MAN I 4 " " MAN I 4 " - " MAN I 6 " " BMA J 3 " - " MAN J 4 " " BMA M 3 " - " MAN M 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " NAG-ASN " NAG F 1 " - " ASN E 149 " " NAG H 1 " - " ASN E 80 " " NAG I 1 " - " ASN A 111 " " NAG J 1 " - " ASN B 149 " " NAG K 1 " - " ASN B 80 " " NAG L 1 " - " ASN C 208 " " NAG M 1 " - " ASN D 111 " Time building additional restraints: 1.38 Conformation dependent library (CDL) restraints added in 672.6 milliseconds 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3446 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 0 sheets defined 36.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'E' and resid 10 through 20 removed outlier: 3.667A pdb=" N GLU E 14 " --> pdb=" O SER E 10 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP E 17 " --> pdb=" O LYS E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 73 removed outlier: 3.756A pdb=" N ALA E 73 " --> pdb=" O LYS E 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 70 through 73' Processing helix chain 'E' and resid 84 through 91 removed outlier: 3.530A pdb=" N ASP E 89 " --> pdb=" O ARG E 86 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU E 91 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 143 removed outlier: 4.339A pdb=" N ARG E 142 " --> pdb=" O ASP E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 174 removed outlier: 3.574A pdb=" N ALA E 174 " --> pdb=" O GLY E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 225 removed outlier: 3.998A pdb=" N LEU E 223 " --> pdb=" O GLY E 219 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 234 Processing helix chain 'E' and resid 235 through 241 removed outlier: 4.050A pdb=" N VAL E 238 " --> pdb=" O LEU E 235 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER E 239 " --> pdb=" O SER E 236 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE E 240 " --> pdb=" O TRP E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 267 removed outlier: 3.681A pdb=" N ALA E 252 " --> pdb=" O ALA E 248 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY E 254 " --> pdb=" O ARG E 250 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN E 265 " --> pdb=" O MET E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 272 removed outlier: 3.549A pdb=" N THR E 271 " --> pdb=" O LEU E 268 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU E 272 " --> pdb=" O ARG E 269 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 268 through 272' Processing helix chain 'E' and resid 281 through 308 removed outlier: 3.648A pdb=" N PHE E 291 " --> pdb=" O GLY E 287 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N TYR E 299 " --> pdb=" O ALA E 295 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE E 307 " --> pdb=" O ASN E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 419 through 446 removed outlier: 3.680A pdb=" N ASP E 424 " --> pdb=" O VAL E 420 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE E 429 " --> pdb=" O ARG E 425 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE E 431 " --> pdb=" O SER E 427 " (cutoff:3.500A) Proline residue: E 432 - end of helix removed outlier: 3.636A pdb=" N SER E 436 " --> pdb=" O PRO E 432 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU E 444 " --> pdb=" O LEU E 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 23 removed outlier: 3.570A pdb=" N LEU A 23 " --> pdb=" O LEU A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 76 removed outlier: 3.981A pdb=" N LYS A 76 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 94 removed outlier: 3.641A pdb=" N ILE A 94 " --> pdb=" O ALA A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 177 Processing helix chain 'A' and resid 223 through 230 removed outlier: 3.730A pdb=" N ILE A 228 " --> pdb=" O GLY A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 242 Processing helix chain 'A' and resid 243 through 247 removed outlier: 3.670A pdb=" N LEU A 247 " --> pdb=" O SER A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 272 removed outlier: 4.754A pdb=" N VAL A 257 " --> pdb=" O PRO A 253 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL A 263 " --> pdb=" O GLY A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 310 removed outlier: 4.031A pdb=" N VAL A 292 " --> pdb=" O TRP A 288 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A 297 " --> pdb=" O CYS A 293 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU A 301 " --> pdb=" O VAL A 297 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 415 removed outlier: 4.732A pdb=" N ILE A 398 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE A 400 " --> pdb=" O SER A 396 " (cutoff:3.500A) Proline residue: A 401 - end of helix removed outlier: 4.175A pdb=" N TRP A 412 " --> pdb=" O ASN A 408 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR A 415 " --> pdb=" O TYR A 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 20 removed outlier: 3.625A pdb=" N LYS B 18 " --> pdb=" O GLU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 73 removed outlier: 3.782A pdb=" N ALA B 73 " --> pdb=" O LYS B 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 70 through 73' Processing helix chain 'B' and resid 84 through 91 removed outlier: 3.523A pdb=" N ASP B 89 " --> pdb=" O ARG B 86 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU B 91 " --> pdb=" O ALA B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 143 removed outlier: 4.331A pdb=" N ARG B 142 " --> pdb=" O ASP B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 225 removed outlier: 4.223A pdb=" N LEU B 223 " --> pdb=" O GLY B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 236 removed outlier: 3.560A pdb=" N THR B 233 " --> pdb=" O SER B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 241 Processing helix chain 'B' and resid 246 through 269 removed outlier: 3.832A pdb=" N ALA B 252 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY B 254 " --> pdb=" O ARG B 250 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ASN B 265 " --> pdb=" O MET B 261 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG B 269 " --> pdb=" O ASN B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 272 No H-bonds generated for 'chain 'B' and resid 270 through 272' Processing helix chain 'B' and resid 281 through 306 removed outlier: 3.612A pdb=" N MET B 286 " --> pdb=" O ASP B 282 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY B 287 " --> pdb=" O MET B 283 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE B 291 " --> pdb=" O GLY B 287 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N TYR B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 446 removed outlier: 3.876A pdb=" N ILE B 423 " --> pdb=" O ASP B 419 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASP B 424 " --> pdb=" O VAL B 420 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ILE B 429 " --> pdb=" O ARG B 425 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE B 431 " --> pdb=" O SER B 427 " (cutoff:3.500A) Proline residue: B 432 - end of helix removed outlier: 3.889A pdb=" N SER B 436 " --> pdb=" O PRO B 432 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU B 444 " --> pdb=" O LEU B 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 36 Processing helix chain 'C' and resid 85 through 88 Processing helix chain 'C' and resid 102 through 106 removed outlier: 3.534A pdb=" N ILE C 106 " --> pdb=" O VAL C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 240 removed outlier: 3.733A pdb=" N ILE C 238 " --> pdb=" O GLY C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 249 Processing helix chain 'C' and resid 250 through 256 removed outlier: 3.705A pdb=" N SER C 254 " --> pdb=" O SER C 251 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE C 255 " --> pdb=" O TRP C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 283 removed outlier: 3.738A pdb=" N GLY C 269 " --> pdb=" O ARG C 265 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR C 271 " --> pdb=" O SER C 267 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR C 272 " --> pdb=" O LEU C 268 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N VAL C 273 " --> pdb=" O GLY C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 323 removed outlier: 3.586A pdb=" N ILE C 305 " --> pdb=" O SER C 301 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL C 307 " --> pdb=" O CYS C 303 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA C 310 " --> pdb=" O PHE C 306 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU C 311 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU C 313 " --> pdb=" O SER C 309 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR C 314 " --> pdb=" O ALA C 310 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR C 319 " --> pdb=" O GLY C 315 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL C 321 " --> pdb=" O LEU C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 433 removed outlier: 4.425A pdb=" N ILE C 416 " --> pdb=" O SER C 412 " (cutoff:3.500A) Proline residue: C 419 - end of helix removed outlier: 3.514A pdb=" N PHE C 425 " --> pdb=" O ALA C 421 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL C 431 " --> pdb=" O LEU C 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 24 removed outlier: 3.633A pdb=" N LEU D 23 " --> pdb=" O LEU D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 93 Processing helix chain 'D' and resid 142 through 146 removed outlier: 4.593A pdb=" N ASP D 145 " --> pdb=" O HIS D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 178 Processing helix chain 'D' and resid 223 through 230 removed outlier: 3.522A pdb=" N ILE D 228 " --> pdb=" O GLY D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 242 removed outlier: 3.603A pdb=" N LEU D 240 " --> pdb=" O MET D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 247 removed outlier: 3.731A pdb=" N LEU D 247 " --> pdb=" O SER D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 272 removed outlier: 4.641A pdb=" N VAL D 257 " --> pdb=" O PRO D 253 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE D 258 " --> pdb=" O ALA D 254 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N VAL D 263 " --> pdb=" O GLY D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 277 removed outlier: 3.652A pdb=" N SER D 276 " --> pdb=" O ALA D 273 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU D 277 " --> pdb=" O ARG D 274 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 273 through 277' Processing helix chain 'D' and resid 286 through 311 removed outlier: 3.628A pdb=" N VAL D 292 " --> pdb=" O TRP D 288 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU D 301 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE D 304 " --> pdb=" O ALA D 300 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE D 310 " --> pdb=" O THR D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 415 removed outlier: 3.659A pdb=" N LEU D 395 " --> pdb=" O LYS D 391 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ILE D 398 " --> pdb=" O ARG D 394 " (cutoff:3.500A) Proline residue: D 401 - end of helix removed outlier: 3.540A pdb=" N GLY D 405 " --> pdb=" O PRO D 401 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA D 413 " --> pdb=" O LEU D 409 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 90 removed outlier: 3.898A pdb=" N THR G 90 " --> pdb=" O PRO G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 110 removed outlier: 3.754A pdb=" N TYR G 110 " --> pdb=" O ALA G 107 " (cutoff:3.500A) 354 hydrogen bonds defined for protein. 975 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.98 Time building geometry restraints manager: 1.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 2299 1.30 - 1.43: 4524 1.43 - 1.56: 8729 1.56 - 1.68: 45 1.68 - 1.81: 147 Bond restraints: 15744 Sorted by residual: bond pdb=" C21 POV A 609 " pdb=" O21 POV A 609 " ideal model delta sigma weight residual 1.330 1.474 -0.144 2.00e-02 2.50e+03 5.16e+01 bond pdb=" C21 POV E 508 " pdb=" O21 POV E 508 " ideal model delta sigma weight residual 1.330 1.473 -0.143 2.00e-02 2.50e+03 5.11e+01 bond pdb=" C21 POV D 507 " pdb=" O21 POV D 507 " ideal model delta sigma weight residual 1.330 1.472 -0.142 2.00e-02 2.50e+03 5.06e+01 bond pdb=" O4 PIO A 601 " pdb=" P4 PIO A 601 " ideal model delta sigma weight residual 1.710 1.596 0.114 2.00e-02 2.50e+03 3.24e+01 bond pdb=" O4 PIO D 501 " pdb=" P4 PIO D 501 " ideal model delta sigma weight residual 1.710 1.600 0.110 2.00e-02 2.50e+03 3.04e+01 ... (remaining 15739 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 20852 2.37 - 4.75: 443 4.75 - 7.12: 68 7.12 - 9.49: 13 9.49 - 11.87: 9 Bond angle restraints: 21385 Sorted by residual: angle pdb=" C GLY G 103 " pdb=" N LEU G 104 " pdb=" CA LEU G 104 " ideal model delta sigma weight residual 121.54 131.68 -10.14 1.91e+00 2.74e-01 2.82e+01 angle pdb=" C ASP C 192 " pdb=" N THR C 193 " pdb=" CA THR C 193 " ideal model delta sigma weight residual 121.54 130.01 -8.47 1.91e+00 2.74e-01 1.97e+01 angle pdb=" N PRO D 175 " pdb=" CA PRO D 175 " pdb=" C PRO D 175 " ideal model delta sigma weight residual 112.47 120.66 -8.19 2.06e+00 2.36e-01 1.58e+01 angle pdb=" O11 POV A 609 " pdb=" P POV A 609 " pdb=" O12 POV A 609 " ideal model delta sigma weight residual 97.67 109.54 -11.87 3.00e+00 1.11e-01 1.57e+01 angle pdb=" O11 POV D 507 " pdb=" P POV D 507 " pdb=" O12 POV D 507 " ideal model delta sigma weight residual 97.67 109.54 -11.87 3.00e+00 1.11e-01 1.56e+01 ... (remaining 21380 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.24: 8735 17.24 - 34.48: 203 34.48 - 51.71: 48 51.71 - 68.95: 7 68.95 - 86.19: 7 Dihedral angle restraints: 9000 sinusoidal: 3640 harmonic: 5360 Sorted by residual: dihedral pdb=" CB CYS E 136 " pdb=" SG CYS E 136 " pdb=" SG CYS E 150 " pdb=" CB CYS E 150 " ideal model delta sinusoidal sigma weight residual 93.00 161.27 -68.27 1 1.00e+01 1.00e-02 6.05e+01 dihedral pdb=" CA GLU D 174 " pdb=" C GLU D 174 " pdb=" N PRO D 175 " pdb=" CA PRO D 175 " ideal model delta harmonic sigma weight residual -180.00 -152.72 -27.28 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CA PRO D 154 " pdb=" C PRO D 154 " pdb=" N LEU D 155 " pdb=" CA LEU D 155 " ideal model delta harmonic sigma weight residual 180.00 156.96 23.04 0 5.00e+00 4.00e-02 2.12e+01 ... (remaining 8997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 2231 0.081 - 0.162: 239 0.162 - 0.243: 9 0.243 - 0.324: 4 0.324 - 0.405: 1 Chirality restraints: 2484 Sorted by residual: chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN D 111 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.09e+00 chirality pdb=" C1 NAG L 1 " pdb=" ND2 ASN C 208 " pdb=" C2 NAG L 1 " pdb=" O5 NAG L 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" C5 BMA J 3 " pdb=" C4 BMA J 3 " pdb=" C6 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 2481 not shown) Planarity restraints: 2603 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 1 " -0.051 2.00e-02 2.50e+03 4.21e-02 2.22e+01 pdb=" C7 NAG M 1 " 0.019 2.00e-02 2.50e+03 pdb=" C8 NAG M 1 " -0.040 2.00e-02 2.50e+03 pdb=" N2 NAG M 1 " 0.065 2.00e-02 2.50e+03 pdb=" O7 NAG M 1 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 1 " -0.030 2.00e-02 2.50e+03 2.49e-02 7.76e+00 pdb=" C7 NAG I 1 " 0.010 2.00e-02 2.50e+03 pdb=" C8 NAG I 1 " -0.023 2.00e-02 2.50e+03 pdb=" N2 NAG I 1 " 0.039 2.00e-02 2.50e+03 pdb=" O7 NAG I 1 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 431 " -0.042 5.00e-02 4.00e+02 6.32e-02 6.39e+00 pdb=" N PRO B 432 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO B 432 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 432 " -0.036 5.00e-02 4.00e+02 ... (remaining 2600 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3816 2.79 - 3.32: 12881 3.32 - 3.85: 25379 3.85 - 4.37: 30841 4.37 - 4.90: 52228 Nonbonded interactions: 125145 Sorted by model distance: nonbonded pdb=" O THR D 172 " pdb=" OG SER D 178 " model vdw 2.264 3.040 nonbonded pdb=" O ALA E 280 " pdb=" OH TYR E 442 " model vdw 2.326 3.040 nonbonded pdb=" NE2 HIS A 110 " pdb=" OG1 THR A 134 " model vdw 2.327 3.120 nonbonded pdb=" OH TYR A 60 " pdb=" O PRO A 154 " model vdw 2.332 3.040 nonbonded pdb=" NE2 HIS D 110 " pdb=" OG1 THR D 134 " model vdw 2.335 3.120 ... (remaining 125140 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 10 through 322 or resid 384 through 417 or resid 601 throu \ gh 609)) selection = chain 'D' } ncs_group { reference = (chain 'B' and resid 10 through 447) selection = (chain 'E' and resid 10 through 447) } ncs_group { reference = chain 'F' selection = chain 'M' } ncs_group { reference = chain 'H' selection = chain 'K' selection = chain 'L' } ncs_group { reference = (chain 'I' and (resid 2 or resid 5 through 7)) selection = (chain 'J' and (resid 1 or resid 4 through 6)) } 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: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 14.250 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 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 0.144 15779 Z= 0.312 Angle : 0.886 11.869 21484 Z= 0.436 Chirality : 0.051 0.405 2484 Planarity : 0.007 0.063 2596 Dihedral : 9.056 86.191 5536 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % 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: -4.72 (0.15), residues: 1799 helix: -4.37 (0.08), residues: 537 sheet: -2.48 (0.20), residues: 494 loop : -2.39 (0.19), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 231 TYR 0.021 0.002 TYR B 66 PHE 0.031 0.002 PHE A 65 TRP 0.025 0.002 TRP A 95 HIS 0.005 0.001 HIS B 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00658 / 0.31 (15744) covalent geometry : angle 0.87627 / 0.43 (21385) SS BOND : bond 0.00139 / 0.07 ( 6) SS BOND : angle 1.54474 / 0.91 ( 12) hydrogen bonds : bond 0.31881 / 21.55 ( 354) hydrogen bonds : angle 9.75310 / 6.58 ( 975) link_ALPHA1-3 : bond 0.00690 / 0.37 ( 6) link_ALPHA1-3 : angle 1.41971 / 0.77 ( 18) link_ALPHA1-6 : bond 0.00576 / 0.29 ( 5) link_ALPHA1-6 : angle 1.33938 / 0.75 ( 15) link_BETA1-4 : bond 0.00771 / 0.48 ( 11) link_BETA1-4 : angle 1.82763 / 1.14 ( 33) link_NAG-ASN : bond 0.00542 / 0.29 ( 7) link_NAG-ASN : angle 3.45435 / 2.32 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 469 time to evaluate : 0.578 Fit side-chains revert: symmetry clash REVERT: E 68 ARG cc_start: 0.7300 (ptm160) cc_final: 0.7046 (ttt180) REVERT: E 90 GLN cc_start: 0.7924 (mt0) cc_final: 0.7664 (mt0) REVERT: E 147 GLU cc_start: 0.8379 (mt-10) cc_final: 0.7721 (mt-10) REVERT: E 173 LYS cc_start: 0.8688 (mtmm) cc_final: 0.8367 (mmmm) REVERT: E 179 GLU cc_start: 0.7955 (mp0) cc_final: 0.7342 (mp0) REVERT: E 213 ARG cc_start: 0.7459 (ttm-80) cc_final: 0.7216 (mmm-85) REVERT: E 262 THR cc_start: 0.7543 (m) cc_final: 0.7244 (p) REVERT: E 283 MET cc_start: 0.7214 (tpp) cc_final: 0.6958 (ttp) REVERT: E 286 MET cc_start: 0.8069 (mtm) cc_final: 0.7807 (mtm) REVERT: A 17 ARG cc_start: 0.7644 (ttm110) cc_final: 0.7151 (mtm110) REVERT: A 76 LYS cc_start: 0.7839 (mttt) cc_final: 0.7592 (mtpp) REVERT: A 78 LYS cc_start: 0.8078 (mttt) cc_final: 0.7808 (tttp) REVERT: A 112 MET cc_start: 0.8289 (tpp) cc_final: 0.7775 (tpp) REVERT: A 114 MET cc_start: 0.7428 (mmm) cc_final: 0.7166 (mmp) REVERT: A 136 ARG cc_start: 0.7359 (ttp-170) cc_final: 0.7032 (ttp80) REVERT: A 222 LYS cc_start: 0.7469 (mttt) cc_final: 0.7189 (mtmt) REVERT: A 391 LYS cc_start: 0.6590 (mtmm) cc_final: 0.6208 (mmtm) REVERT: B 21 LYS cc_start: 0.8085 (tttt) cc_final: 0.7618 (mttm) REVERT: B 49 MET cc_start: 0.7390 (ptp) cc_final: 0.6820 (ptp) REVERT: B 68 ARG cc_start: 0.7745 (ttt180) cc_final: 0.7306 (ttt-90) REVERT: B 84 ASP cc_start: 0.7655 (t70) cc_final: 0.7328 (t70) REVERT: B 103 LYS cc_start: 0.7559 (tttt) cc_final: 0.7137 (tptp) REVERT: B 153 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7526 (mm-30) REVERT: B 162 ASP cc_start: 0.8283 (m-30) cc_final: 0.8010 (m-30) REVERT: B 172 ASP cc_start: 0.8213 (m-30) cc_final: 0.7885 (m-30) REVERT: B 213 ARG cc_start: 0.7330 (ttm-80) cc_final: 0.7071 (mmm-85) REVERT: B 217 ASN cc_start: 0.7985 (m-40) cc_final: 0.7736 (m110) REVERT: B 243 ASN cc_start: 0.7149 (t0) cc_final: 0.6799 (t0) REVERT: B 245 ASP cc_start: 0.7362 (m-30) cc_final: 0.6846 (m-30) REVERT: B 265 ASN cc_start: 0.7772 (t0) cc_final: 0.7404 (t0) REVERT: B 283 MET cc_start: 0.7343 (mmm) cc_final: 0.6477 (mtm) REVERT: B 286 MET cc_start: 0.8135 (mtp) cc_final: 0.7933 (mtp) REVERT: B 421 ASN cc_start: 0.7105 (t0) cc_final: 0.6603 (t0) REVERT: B 425 ARG cc_start: 0.6722 (mtt180) cc_final: 0.6504 (mtm110) REVERT: C 57 MET cc_start: 0.8579 (ttm) cc_final: 0.8279 (ttp) REVERT: C 69 ASN cc_start: 0.8239 (m-40) cc_final: 0.7932 (m110) REVERT: C 85 ARG cc_start: 0.7630 (mtm180) cc_final: 0.6686 (mmt180) REVERT: C 92 THR cc_start: 0.8468 (m) cc_final: 0.8256 (p) REVERT: C 94 LYS cc_start: 0.8013 (ttpt) cc_final: 0.7334 (mttp) REVERT: C 105 LYS cc_start: 0.8400 (mttt) cc_final: 0.8024 (mttt) REVERT: C 168 GLU cc_start: 0.8323 (mt-10) cc_final: 0.8085 (mt-10) REVERT: C 189 GLU cc_start: 0.6988 (tt0) cc_final: 0.6335 (mp0) REVERT: C 199 TYR cc_start: 0.7504 (m-10) cc_final: 0.6565 (m-80) REVERT: C 211 GLU cc_start: 0.7142 (pt0) cc_final: 0.6914 (pt0) REVERT: C 214 LYS cc_start: 0.8460 (ttmp) cc_final: 0.7982 (tptp) REVERT: C 236 PHE cc_start: 0.7609 (m-80) cc_final: 0.7401 (m-80) REVERT: C 320 PHE cc_start: 0.7139 (m-80) cc_final: 0.6769 (m-80) REVERT: D 42 LYS cc_start: 0.7120 (mttt) cc_final: 0.6901 (mttm) REVERT: D 71 LYS cc_start: 0.8176 (tttt) cc_final: 0.7638 (ttmt) REVERT: D 105 LYS cc_start: 0.8461 (mttt) cc_final: 0.8203 (mttt) REVERT: D 106 LYS cc_start: 0.8429 (ttmm) cc_final: 0.7684 (tppt) REVERT: D 117 LYS cc_start: 0.7311 (mttt) cc_final: 0.7045 (mttm) REVERT: D 123 GLU cc_start: 0.8286 (pt0) cc_final: 0.7871 (mt-10) REVERT: D 144 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7331 (mt-10) REVERT: D 156 LYS cc_start: 0.6763 (mttt) cc_final: 0.6306 (mtmt) REVERT: D 170 GLU cc_start: 0.7250 (pt0) cc_final: 0.6957 (pt0) REVERT: D 204 GLN cc_start: 0.8512 (tp40) cc_final: 0.8229 (mm-40) REVERT: D 209 GLU cc_start: 0.7386 (mt-10) cc_final: 0.7013 (mt-10) REVERT: D 220 LYS cc_start: 0.6997 (tttt) cc_final: 0.6760 (tttm) REVERT: D 279 LYS cc_start: 0.7436 (mttt) cc_final: 0.6591 (mptt) REVERT: D 318 ASP cc_start: 0.7138 (m-30) cc_final: 0.6117 (p0) REVERT: D 391 LYS cc_start: 0.7450 (mtmm) cc_final: 0.6993 (tptp) REVERT: G 25 SER cc_start: 0.7955 (t) cc_final: 0.7477 (p) REVERT: G 27 ARG cc_start: 0.7209 (ttm-80) cc_final: 0.6987 (ttm-80) REVERT: G 28 THR cc_start: 0.8449 (p) cc_final: 0.8240 (t) REVERT: G 45 ARG cc_start: 0.5470 (mtt180) cc_final: 0.5222 (mtm180) REVERT: G 64 ARG cc_start: 0.6789 (ttm-80) cc_final: 0.6426 (ttm170) REVERT: G 83 ASP cc_start: 0.8466 (t0) cc_final: 0.8254 (t0) REVERT: G 110 TYR cc_start: 0.8588 (m-80) cc_final: 0.8132 (m-80) outliers start: 0 outliers final: 0 residues processed: 469 average time/residue: 0.1613 time to fit residues: 104.7472 Evaluate side-chains 312 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 312 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 303 ASN E 421 ASN A 142 HIS A 190 GLN A 308 ASN ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 ASN B 54 ASN B 113 ASN B 303 ASN C 80 GLN C 128 ASN C 323 ASN D 56 HIS D 151 HIS G 111 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.117832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.099147 restraints weight = 20369.723| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 1.81 r_work: 0.2969 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15779 Z= 0.139 Angle : 0.566 6.676 21484 Z= 0.293 Chirality : 0.042 0.222 2484 Planarity : 0.005 0.045 2596 Dihedral : 7.801 89.508 2134 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.99 % Allowed : 6.84 % Favored : 92.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % 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: -3.11 (0.18), residues: 1799 helix: -1.98 (0.18), residues: 539 sheet: -2.23 (0.21), residues: 496 loop : -1.78 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 136 TYR 0.019 0.001 TYR B 299 PHE 0.019 0.002 PHE E 301 TRP 0.013 0.001 TRP E 92 HIS 0.005 0.001 HIS B 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (15744) covalent geometry : angle 0.55763 / 0.29 (21385) SS BOND : bond 0.00063 / 0.04 ( 6) SS BOND : angle 0.72720 / 0.43 ( 12) hydrogen bonds : bond 0.05564 / 3.82 ( 354) hydrogen bonds : angle 4.57162 / 3.10 ( 975) link_ALPHA1-3 : bond 0.00582 / 0.31 ( 6) link_ALPHA1-3 : angle 1.46484 / 0.88 ( 18) link_ALPHA1-6 : bond 0.00463 / 0.25 ( 5) link_ALPHA1-6 : angle 1.57111 / 0.97 ( 15) link_BETA1-4 : bond 0.00377 / 0.25 ( 11) link_BETA1-4 : angle 1.33477 / 0.87 ( 33) link_NAG-ASN : bond 0.00256 / 0.15 ( 7) link_NAG-ASN : angle 2.04026 / 1.33 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 332 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 147 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8385 (mt-10) REVERT: A 17 ARG cc_start: 0.8257 (ttm110) cc_final: 0.7958 (mtm110) REVERT: A 58 MET cc_start: 0.9024 (mtm) cc_final: 0.8812 (mtm) REVERT: A 112 MET cc_start: 0.8837 (tpp) cc_final: 0.8283 (tpp) REVERT: A 114 MET cc_start: 0.8795 (mmm) cc_final: 0.8584 (mmp) REVERT: A 170 GLU cc_start: 0.8693 (tt0) cc_final: 0.8405 (pt0) REVERT: A 279 LYS cc_start: 0.8894 (mttt) cc_final: 0.8055 (mmtt) REVERT: B 84 ASP cc_start: 0.8799 (t70) cc_final: 0.8427 (t70) REVERT: B 103 LYS cc_start: 0.8751 (tttt) cc_final: 0.8538 (tptp) REVERT: B 137 MET cc_start: 0.6214 (mmm) cc_final: 0.5269 (mtp) REVERT: B 153 GLU cc_start: 0.8763 (mm-30) cc_final: 0.8402 (mm-30) REVERT: B 172 ASP cc_start: 0.8061 (m-30) cc_final: 0.7832 (m-30) REVERT: B 265 ASN cc_start: 0.7980 (t0) cc_final: 0.7661 (t0) REVERT: B 445 TYR cc_start: 0.9024 (t80) cc_final: 0.8818 (t80) REVERT: C 85 ARG cc_start: 0.8260 (mtm180) cc_final: 0.7904 (mmt180) REVERT: C 94 LYS cc_start: 0.8701 (ttpt) cc_final: 0.8193 (mttp) REVERT: C 99 ASN cc_start: 0.8083 (OUTLIER) cc_final: 0.7823 (m-40) REVERT: C 250 LEU cc_start: 0.9261 (tt) cc_final: 0.9030 (tp) REVERT: C 285 LYS cc_start: 0.8877 (mmmt) cc_final: 0.8614 (mttm) REVERT: D 156 LYS cc_start: 0.8765 (mttt) cc_final: 0.8466 (mtmt) REVERT: D 209 GLU cc_start: 0.8244 (mt-10) cc_final: 0.8037 (mt-10) REVERT: D 279 LYS cc_start: 0.8699 (mttt) cc_final: 0.7936 (mptt) REVERT: D 318 ASP cc_start: 0.7766 (m-30) cc_final: 0.6972 (p0) REVERT: G 17 SER cc_start: 0.9026 (p) cc_final: 0.8731 (t) REVERT: G 110 TYR cc_start: 0.9468 (m-80) cc_final: 0.9148 (m-80) outliers start: 16 outliers final: 9 residues processed: 342 average time/residue: 0.1412 time to fit residues: 68.5559 Evaluate side-chains 291 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 281 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 211 SER Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain D residue 88 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 133 optimal weight: 0.8980 chunk 163 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 123 optimal weight: 0.0670 chunk 170 optimal weight: 4.9990 overall best weight: 1.5522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 100 ASN E 113 ASN E 303 ASN A 68 GLN A 308 ASN A 387 ASN B 113 ASN B 243 ASN D 56 HIS G 111 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.110990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.091622 restraints weight = 20889.211| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 1.84 r_work: 0.2897 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 15779 Z= 0.201 Angle : 0.576 6.692 21484 Z= 0.296 Chirality : 0.043 0.209 2484 Planarity : 0.004 0.042 2596 Dihedral : 7.449 89.332 2134 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.40 % Allowed : 9.43 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % 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: -2.26 (0.19), residues: 1799 helix: -0.71 (0.21), residues: 540 sheet: -2.06 (0.22), residues: 492 loop : -1.51 (0.23), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 231 TYR 0.024 0.002 TYR B 66 PHE 0.018 0.002 PHE E 301 TRP 0.011 0.001 TRP C 107 HIS 0.005 0.001 HIS A 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.20 (15744) covalent geometry : angle 0.56595 / 0.29 (21385) SS BOND : bond 0.00419 / 0.21 ( 6) SS BOND : angle 1.63726 / 1.00 ( 12) hydrogen bonds : bond 0.04324 / 2.95 ( 354) hydrogen bonds : angle 4.10739 / 2.78 ( 975) link_ALPHA1-3 : bond 0.00436 / 0.24 ( 6) link_ALPHA1-3 : angle 1.58862 / 0.94 ( 18) link_ALPHA1-6 : bond 0.00351 / 0.19 ( 5) link_ALPHA1-6 : angle 1.61005 / 0.97 ( 15) link_BETA1-4 : bond 0.00410 / 0.28 ( 11) link_BETA1-4 : angle 1.38851 / 0.86 ( 33) link_NAG-ASN : bond 0.00310 / 0.18 ( 7) link_NAG-ASN : angle 2.06487 / 1.39 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 259 time to evaluate : 0.569 Fit side-chains revert: symmetry clash REVERT: E 68 ARG cc_start: 0.8366 (ttt180) cc_final: 0.8049 (ttt90) REVERT: E 87 VAL cc_start: 0.9224 (OUTLIER) cc_final: 0.9019 (p) REVERT: E 261 MET cc_start: 0.9253 (tpp) cc_final: 0.9008 (mmm) REVERT: A 17 ARG cc_start: 0.8256 (ttm110) cc_final: 0.7901 (mtm110) REVERT: A 148 MET cc_start: 0.9388 (mtm) cc_final: 0.9129 (mtm) REVERT: A 170 GLU cc_start: 0.8710 (tt0) cc_final: 0.8403 (pt0) REVERT: A 242 GLN cc_start: 0.9114 (mt0) cc_final: 0.8913 (mt0) REVERT: B 84 ASP cc_start: 0.8774 (t70) cc_final: 0.8459 (t70) REVERT: B 103 LYS cc_start: 0.8697 (tttt) cc_final: 0.8463 (tttp) REVERT: B 153 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8352 (mm-30) REVERT: B 172 ASP cc_start: 0.8133 (m-30) cc_final: 0.7912 (m-30) REVERT: B 245 ASP cc_start: 0.8274 (m-30) cc_final: 0.8054 (m-30) REVERT: B 265 ASN cc_start: 0.8186 (t0) cc_final: 0.7811 (t0) REVERT: C 85 ARG cc_start: 0.8277 (mtm180) cc_final: 0.7865 (mmt180) REVERT: C 94 LYS cc_start: 0.8693 (ttpt) cc_final: 0.8191 (mttp) REVERT: C 160 MET cc_start: 0.9137 (mtm) cc_final: 0.8929 (mpp) REVERT: C 285 LYS cc_start: 0.8812 (mmmt) cc_final: 0.8543 (mttm) REVERT: C 304 PHE cc_start: 0.7697 (OUTLIER) cc_final: 0.7408 (t80) REVERT: C 409 LYS cc_start: 0.7580 (mtmt) cc_final: 0.7195 (mttp) REVERT: D 156 LYS cc_start: 0.8821 (mttt) cc_final: 0.8483 (mtmt) REVERT: D 279 LYS cc_start: 0.8816 (mttt) cc_final: 0.8078 (mptt) REVERT: D 318 ASP cc_start: 0.7796 (m-30) cc_final: 0.6876 (p0) REVERT: G 83 ASP cc_start: 0.9004 (OUTLIER) cc_final: 0.8578 (m-30) outliers start: 39 outliers final: 25 residues processed: 276 average time/residue: 0.1434 time to fit residues: 57.1950 Evaluate side-chains 272 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 244 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 211 SER Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 436 SER Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 83 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 162 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 107 optimal weight: 0.0980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 56 HIS D 308 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.116167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.096925 restraints weight = 20330.263| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 1.80 r_work: 0.2938 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15779 Z= 0.111 Angle : 0.495 6.623 21484 Z= 0.254 Chirality : 0.041 0.201 2484 Planarity : 0.004 0.036 2596 Dihedral : 6.901 88.099 2134 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.97 % Allowed : 11.47 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % 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: -1.72 (0.20), residues: 1799 helix: 0.03 (0.23), residues: 528 sheet: -1.87 (0.22), residues: 488 loop : -1.32 (0.22), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 68 TYR 0.020 0.001 TYR E 299 PHE 0.013 0.001 PHE D 258 TRP 0.008 0.001 TRP C 107 HIS 0.004 0.001 HIS A 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (15744) covalent geometry : angle 0.48722 / 0.25 (21385) SS BOND : bond 0.00183 / 0.09 ( 6) SS BOND : angle 1.08988 / 0.65 ( 12) hydrogen bonds : bond 0.03501 / 2.39 ( 354) hydrogen bonds : angle 3.74597 / 2.52 ( 975) link_ALPHA1-3 : bond 0.00520 / 0.28 ( 6) link_ALPHA1-3 : angle 1.44001 / 0.86 ( 18) link_ALPHA1-6 : bond 0.00460 / 0.24 ( 5) link_ALPHA1-6 : angle 1.47607 / 0.90 ( 15) link_BETA1-4 : bond 0.00371 / 0.24 ( 11) link_BETA1-4 : angle 1.26901 / 0.84 ( 33) link_NAG-ASN : bond 0.00275 / 0.14 ( 7) link_NAG-ASN : angle 1.67783 / 1.10 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 259 time to evaluate : 0.521 Fit side-chains revert: symmetry clash REVERT: E 68 ARG cc_start: 0.8385 (ttt180) cc_final: 0.8069 (ttt90) REVERT: E 79 LEU cc_start: 0.8812 (mt) cc_final: 0.8604 (mt) REVERT: E 87 VAL cc_start: 0.9199 (OUTLIER) cc_final: 0.8987 (p) REVERT: E 261 MET cc_start: 0.9239 (tpp) cc_final: 0.8908 (mmm) REVERT: A 17 ARG cc_start: 0.8190 (ttm110) cc_final: 0.7949 (mtm110) REVERT: A 170 GLU cc_start: 0.8681 (tt0) cc_final: 0.8407 (pt0) REVERT: B 137 MET cc_start: 0.6368 (mmm) cc_final: 0.4882 (mtt) REVERT: B 153 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8312 (mm-30) REVERT: B 172 ASP cc_start: 0.8016 (m-30) cc_final: 0.7804 (m-30) REVERT: B 265 ASN cc_start: 0.8142 (t0) cc_final: 0.7709 (t0) REVERT: B 283 MET cc_start: 0.8403 (mmm) cc_final: 0.8127 (mtp) REVERT: C 85 ARG cc_start: 0.8226 (mtm180) cc_final: 0.7906 (mmt180) REVERT: C 94 LYS cc_start: 0.8617 (ttpt) cc_final: 0.8168 (mttp) REVERT: C 160 MET cc_start: 0.9135 (mtm) cc_final: 0.8893 (mpp) REVERT: C 285 LYS cc_start: 0.8745 (mmmt) cc_final: 0.8490 (mttm) REVERT: C 304 PHE cc_start: 0.7682 (OUTLIER) cc_final: 0.7448 (t80) REVERT: C 409 LYS cc_start: 0.7596 (mtmt) cc_final: 0.7195 (mttp) REVERT: D 156 LYS cc_start: 0.8787 (mttt) cc_final: 0.8469 (mtmt) REVERT: D 279 LYS cc_start: 0.8805 (mttt) cc_final: 0.8086 (mptt) REVERT: D 318 ASP cc_start: 0.7736 (m-30) cc_final: 0.6777 (p0) REVERT: G 83 ASP cc_start: 0.8963 (OUTLIER) cc_final: 0.8577 (m-30) outliers start: 32 outliers final: 18 residues processed: 278 average time/residue: 0.1346 time to fit residues: 54.3394 Evaluate side-chains 255 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 234 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 211 SER Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 83 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 90 optimal weight: 4.9990 chunk 175 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 163 optimal weight: 8.9990 chunk 103 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 130 optimal weight: 10.0000 chunk 160 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 chunk 150 optimal weight: 1.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.109047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.089307 restraints weight = 20768.392| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 1.84 r_work: 0.2855 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 15779 Z= 0.198 Angle : 0.558 7.134 21484 Z= 0.284 Chirality : 0.043 0.204 2484 Planarity : 0.004 0.048 2596 Dihedral : 6.985 89.939 2134 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.65 % Allowed : 11.22 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % 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: -1.50 (0.20), residues: 1799 helix: 0.24 (0.22), residues: 539 sheet: -1.80 (0.23), residues: 469 loop : -1.23 (0.22), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 250 TYR 0.029 0.002 TYR B 66 PHE 0.017 0.002 PHE C 113 TRP 0.008 0.001 TRP C 107 HIS 0.004 0.001 HIS D 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.20 (15744) covalent geometry : angle 0.54938 / 0.28 (21385) SS BOND : bond 0.00189 / 0.10 ( 6) SS BOND : angle 0.95555 / 0.58 ( 12) hydrogen bonds : bond 0.03756 / 2.52 ( 354) hydrogen bonds : angle 3.73125 / 2.52 ( 975) link_ALPHA1-3 : bond 0.00527 / 0.28 ( 6) link_ALPHA1-3 : angle 1.70250 / 1.00 ( 18) link_ALPHA1-6 : bond 0.00353 / 0.19 ( 5) link_ALPHA1-6 : angle 1.65118 / 1.00 ( 15) link_BETA1-4 : bond 0.00399 / 0.27 ( 11) link_BETA1-4 : angle 1.35719 / 0.87 ( 33) link_NAG-ASN : bond 0.00289 / 0.16 ( 7) link_NAG-ASN : angle 1.83110 / 1.26 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 242 time to evaluate : 0.594 Fit side-chains REVERT: E 68 ARG cc_start: 0.8454 (ttt180) cc_final: 0.8115 (ttt90) REVERT: E 261 MET cc_start: 0.9311 (tpp) cc_final: 0.9060 (mmm) REVERT: E 262 THR cc_start: 0.8820 (OUTLIER) cc_final: 0.8077 (p) REVERT: A 17 ARG cc_start: 0.8199 (ttm110) cc_final: 0.7912 (mtm110) REVERT: A 170 GLU cc_start: 0.8736 (tt0) cc_final: 0.8421 (pt0) REVERT: B 153 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8358 (mm-30) REVERT: B 265 ASN cc_start: 0.8305 (t0) cc_final: 0.7896 (t0) REVERT: B 283 MET cc_start: 0.8392 (mmm) cc_final: 0.8029 (mtt) REVERT: C 85 ARG cc_start: 0.8203 (mtm180) cc_final: 0.7892 (mmt180) REVERT: C 94 LYS cc_start: 0.8670 (ttpt) cc_final: 0.8188 (mttp) REVERT: C 102 MET cc_start: 0.8832 (tpp) cc_final: 0.8620 (mmm) REVERT: C 285 LYS cc_start: 0.8753 (mmmt) cc_final: 0.8470 (mttm) REVERT: C 304 PHE cc_start: 0.7810 (OUTLIER) cc_final: 0.7558 (t80) REVERT: C 409 LYS cc_start: 0.7690 (mtmt) cc_final: 0.7294 (mttp) REVERT: D 156 LYS cc_start: 0.8859 (mttt) cc_final: 0.8512 (mtmt) REVERT: D 236 MET cc_start: 0.8822 (tpp) cc_final: 0.8593 (mmm) REVERT: D 279 LYS cc_start: 0.8884 (mttt) cc_final: 0.8072 (mmtt) REVERT: D 318 ASP cc_start: 0.7717 (m-30) cc_final: 0.6757 (p0) outliers start: 43 outliers final: 33 residues processed: 267 average time/residue: 0.1405 time to fit residues: 54.8832 Evaluate side-chains 268 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 233 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 211 SER Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 436 SER Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 71 LYS Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 62 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 88 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 141 optimal weight: 0.9980 chunk 135 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 150 optimal weight: 0.0970 chunk 155 optimal weight: 3.9990 overall best weight: 0.7978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 GLN C 99 ASN C 323 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.113787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.094431 restraints weight = 20409.563| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 1.80 r_work: 0.2916 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15779 Z= 0.119 Angle : 0.497 6.444 21484 Z= 0.253 Chirality : 0.041 0.198 2484 Planarity : 0.003 0.046 2596 Dihedral : 6.674 87.700 2134 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.03 % Allowed : 12.39 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % 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: -1.15 (0.20), residues: 1799 helix: 0.67 (0.23), residues: 534 sheet: -1.58 (0.24), residues: 442 loop : -1.15 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 68 TYR 0.021 0.001 TYR B 66 PHE 0.012 0.001 PHE C 113 TRP 0.009 0.001 TRP C 107 HIS 0.003 0.001 HIS A 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (15744) covalent geometry : angle 0.48922 / 0.25 (21385) SS BOND : bond 0.00142 / 0.07 ( 6) SS BOND : angle 0.71857 / 0.42 ( 12) hydrogen bonds : bond 0.03241 / 2.18 ( 354) hydrogen bonds : angle 3.54576 / 2.38 ( 975) link_ALPHA1-3 : bond 0.00524 / 0.28 ( 6) link_ALPHA1-3 : angle 1.46980 / 0.88 ( 18) link_ALPHA1-6 : bond 0.00450 / 0.24 ( 5) link_ALPHA1-6 : angle 1.49843 / 0.92 ( 15) link_BETA1-4 : bond 0.00360 / 0.24 ( 11) link_BETA1-4 : angle 1.28688 / 0.85 ( 33) link_NAG-ASN : bond 0.00258 / 0.13 ( 7) link_NAG-ASN : angle 1.70272 / 1.14 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 249 time to evaluate : 0.622 Fit side-chains REVERT: E 68 ARG cc_start: 0.8418 (ttt180) cc_final: 0.8076 (ttt90) REVERT: E 179 GLU cc_start: 0.8315 (mp0) cc_final: 0.8067 (mm-30) REVERT: E 262 THR cc_start: 0.8872 (m) cc_final: 0.8230 (p) REVERT: A 17 ARG cc_start: 0.8207 (ttm110) cc_final: 0.7875 (mtm110) REVERT: A 170 GLU cc_start: 0.8679 (tt0) cc_final: 0.8411 (pt0) REVERT: A 279 LYS cc_start: 0.8969 (mttt) cc_final: 0.8176 (mmtm) REVERT: B 153 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8311 (mm-30) REVERT: B 265 ASN cc_start: 0.8324 (t0) cc_final: 0.7905 (t0) REVERT: B 283 MET cc_start: 0.8346 (mmm) cc_final: 0.7979 (mtp) REVERT: C 85 ARG cc_start: 0.8156 (mtm180) cc_final: 0.7867 (mmt180) REVERT: C 94 LYS cc_start: 0.8624 (ttpt) cc_final: 0.8200 (mttp) REVERT: C 285 LYS cc_start: 0.8714 (mmmt) cc_final: 0.8492 (mttm) REVERT: D 17 ARG cc_start: 0.8508 (ttm110) cc_final: 0.8277 (ttp-110) REVERT: D 156 LYS cc_start: 0.8832 (mttt) cc_final: 0.8505 (mtmt) REVERT: D 236 MET cc_start: 0.8718 (tpp) cc_final: 0.8497 (mmm) REVERT: D 279 LYS cc_start: 0.8838 (mttt) cc_final: 0.8070 (mmtt) REVERT: D 318 ASP cc_start: 0.7681 (m-30) cc_final: 0.6630 (p0) REVERT: G 83 ASP cc_start: 0.9004 (OUTLIER) cc_final: 0.8648 (m-30) outliers start: 33 outliers final: 24 residues processed: 269 average time/residue: 0.1383 time to fit residues: 54.5581 Evaluate side-chains 256 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 231 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 211 SER Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 83 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 103 optimal weight: 0.9980 chunk 125 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 chunk 119 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 150 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 12 optimal weight: 0.2980 chunk 173 optimal weight: 0.0270 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.115579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.096335 restraints weight = 20166.666| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 1.79 r_work: 0.2865 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15779 Z= 0.108 Angle : 0.490 6.540 21484 Z= 0.248 Chirality : 0.041 0.205 2484 Planarity : 0.003 0.048 2596 Dihedral : 6.468 87.491 2134 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.03 % Allowed : 12.52 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % 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: -0.97 (0.20), residues: 1799 helix: 0.90 (0.23), residues: 532 sheet: -1.52 (0.24), residues: 439 loop : -1.08 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 37 TYR 0.021 0.001 TYR B 66 PHE 0.016 0.001 PHE C 236 TRP 0.008 0.001 TRP C 107 HIS 0.003 0.001 HIS A 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (15744) covalent geometry : angle 0.48134 / 0.25 (21385) SS BOND : bond 0.00136 / 0.07 ( 6) SS BOND : angle 1.02431 / 0.60 ( 12) hydrogen bonds : bond 0.03124 / 2.10 ( 354) hydrogen bonds : angle 3.45472 / 2.30 ( 975) link_ALPHA1-3 : bond 0.00509 / 0.28 ( 6) link_ALPHA1-3 : angle 1.48908 / 0.89 ( 18) link_ALPHA1-6 : bond 0.00451 / 0.24 ( 5) link_ALPHA1-6 : angle 1.48530 / 0.91 ( 15) link_BETA1-4 : bond 0.00388 / 0.26 ( 11) link_BETA1-4 : angle 1.26948 / 0.84 ( 33) link_NAG-ASN : bond 0.00261 / 0.13 ( 7) link_NAG-ASN : angle 1.67013 / 1.12 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 240 time to evaluate : 0.597 Fit side-chains REVERT: E 68 ARG cc_start: 0.8406 (ttt180) cc_final: 0.8056 (ttt90) REVERT: E 179 GLU cc_start: 0.8330 (mp0) cc_final: 0.8062 (mm-30) REVERT: E 261 MET cc_start: 0.9191 (mmm) cc_final: 0.8628 (mmm) REVERT: E 262 THR cc_start: 0.8865 (m) cc_final: 0.8234 (p) REVERT: A 17 ARG cc_start: 0.8223 (ttm110) cc_final: 0.7916 (mtm110) REVERT: A 170 GLU cc_start: 0.8689 (tt0) cc_final: 0.8420 (pt0) REVERT: A 279 LYS cc_start: 0.8960 (mttt) cc_final: 0.8129 (mmtm) REVERT: B 153 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8297 (mm-30) REVERT: B 265 ASN cc_start: 0.8251 (t0) cc_final: 0.7784 (t0) REVERT: B 283 MET cc_start: 0.8310 (mmm) cc_final: 0.7985 (mtp) REVERT: C 85 ARG cc_start: 0.8128 (mtm180) cc_final: 0.7865 (mmt180) REVERT: C 94 LYS cc_start: 0.8613 (ttpt) cc_final: 0.8191 (mttp) REVERT: C 285 LYS cc_start: 0.8659 (mmmt) cc_final: 0.8433 (mttm) REVERT: D 156 LYS cc_start: 0.8773 (mttt) cc_final: 0.8500 (mtmt) REVERT: D 236 MET cc_start: 0.8718 (tpp) cc_final: 0.8507 (mmm) REVERT: D 277 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.7975 (mt) REVERT: D 279 LYS cc_start: 0.8815 (mttt) cc_final: 0.8043 (mmtt) REVERT: D 318 ASP cc_start: 0.7648 (m-30) cc_final: 0.6549 (p0) REVERT: G 83 ASP cc_start: 0.9006 (OUTLIER) cc_final: 0.8673 (m-30) outliers start: 33 outliers final: 26 residues processed: 263 average time/residue: 0.1337 time to fit residues: 52.0000 Evaluate side-chains 267 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 239 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 211 SER Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 305 ILE Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain D residue 24 ASP Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 83 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 73 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 142 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 96 optimal weight: 0.6980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 323 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.111539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.092336 restraints weight = 20595.542| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 1.80 r_work: 0.2895 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15779 Z= 0.158 Angle : 0.522 6.381 21484 Z= 0.264 Chirality : 0.042 0.203 2484 Planarity : 0.004 0.051 2596 Dihedral : 6.543 88.727 2134 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.91 % Allowed : 12.82 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % 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: -0.91 (0.20), residues: 1799 helix: 0.89 (0.23), residues: 542 sheet: -1.51 (0.24), residues: 444 loop : -1.01 (0.22), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 169 TYR 0.033 0.001 TYR B 66 PHE 0.015 0.001 PHE C 113 TRP 0.007 0.001 TRP E 168 HIS 0.003 0.001 HIS A 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 (15744) covalent geometry : angle 0.51307 / 0.26 (21385) SS BOND : bond 0.00164 / 0.09 ( 6) SS BOND : angle 1.13295 / 0.67 ( 12) hydrogen bonds : bond 0.03277 / 2.20 ( 354) hydrogen bonds : angle 3.50460 / 2.34 ( 975) link_ALPHA1-3 : bond 0.00472 / 0.26 ( 6) link_ALPHA1-3 : angle 1.57476 / 0.93 ( 18) link_ALPHA1-6 : bond 0.00321 / 0.17 ( 5) link_ALPHA1-6 : angle 1.53444 / 0.94 ( 15) link_BETA1-4 : bond 0.00341 / 0.23 ( 11) link_BETA1-4 : angle 1.29869 / 0.84 ( 33) link_NAG-ASN : bond 0.00246 / 0.13 ( 7) link_NAG-ASN : angle 1.76160 / 1.20 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 246 time to evaluate : 0.594 Fit side-chains REVERT: E 68 ARG cc_start: 0.8414 (ttt180) cc_final: 0.8053 (ttt90) REVERT: E 262 THR cc_start: 0.8823 (m) cc_final: 0.8217 (p) REVERT: A 17 ARG cc_start: 0.8299 (ttm110) cc_final: 0.7942 (mtm110) REVERT: A 170 GLU cc_start: 0.8669 (tt0) cc_final: 0.8405 (pt0) REVERT: A 279 LYS cc_start: 0.8980 (mttt) cc_final: 0.8172 (mmtm) REVERT: B 153 GLU cc_start: 0.8581 (mm-30) cc_final: 0.8330 (mm-30) REVERT: B 245 ASP cc_start: 0.8235 (m-30) cc_final: 0.8021 (m-30) REVERT: B 265 ASN cc_start: 0.8335 (t0) cc_final: 0.7929 (t0) REVERT: B 283 MET cc_start: 0.8315 (mmm) cc_final: 0.8000 (mtp) REVERT: C 85 ARG cc_start: 0.8154 (mtm180) cc_final: 0.7880 (mmt180) REVERT: C 94 LYS cc_start: 0.8638 (ttpt) cc_final: 0.8166 (mttp) REVERT: D 156 LYS cc_start: 0.8784 (mttt) cc_final: 0.8498 (mtmt) REVERT: D 236 MET cc_start: 0.8733 (tpp) cc_final: 0.8505 (mmm) REVERT: D 277 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8112 (mt) REVERT: D 279 LYS cc_start: 0.8848 (mttt) cc_final: 0.8083 (mmtt) REVERT: D 318 ASP cc_start: 0.7682 (m-30) cc_final: 0.6643 (p0) outliers start: 31 outliers final: 29 residues processed: 267 average time/residue: 0.1397 time to fit residues: 54.5178 Evaluate side-chains 270 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 240 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 211 SER Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 305 ILE Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain D residue 24 ASP Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain G residue 28 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 11 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 17 optimal weight: 0.1980 chunk 32 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 157 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.114126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.095083 restraints weight = 20302.003| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 1.78 r_work: 0.2916 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15779 Z= 0.119 Angle : 0.500 7.474 21484 Z= 0.253 Chirality : 0.041 0.202 2484 Planarity : 0.003 0.054 2596 Dihedral : 6.375 87.540 2134 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.85 % Allowed : 13.26 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % 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: -0.78 (0.20), residues: 1799 helix: 0.99 (0.23), residues: 542 sheet: -1.42 (0.25), residues: 437 loop : -0.94 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 425 TYR 0.021 0.001 TYR E 299 PHE 0.011 0.001 PHE C 113 TRP 0.008 0.001 TRP C 107 HIS 0.003 0.001 HIS A 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (15744) covalent geometry : angle 0.49201 / 0.25 (21385) SS BOND : bond 0.00103 / 0.05 ( 6) SS BOND : angle 0.85543 / 0.50 ( 12) hydrogen bonds : bond 0.03096 / 2.08 ( 354) hydrogen bonds : angle 3.43158 / 2.29 ( 975) link_ALPHA1-3 : bond 0.00520 / 0.28 ( 6) link_ALPHA1-3 : angle 1.48759 / 0.88 ( 18) link_ALPHA1-6 : bond 0.00446 / 0.23 ( 5) link_ALPHA1-6 : angle 1.50316 / 0.92 ( 15) link_BETA1-4 : bond 0.00364 / 0.24 ( 11) link_BETA1-4 : angle 1.27393 / 0.84 ( 33) link_NAG-ASN : bond 0.00253 / 0.13 ( 7) link_NAG-ASN : angle 1.71578 / 1.16 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 244 time to evaluate : 0.592 Fit side-chains REVERT: E 68 ARG cc_start: 0.8409 (ttt180) cc_final: 0.8048 (ttt90) REVERT: E 179 GLU cc_start: 0.8296 (mp0) cc_final: 0.8063 (mm-30) REVERT: E 261 MET cc_start: 0.9295 (tpp) cc_final: 0.8883 (mmm) REVERT: E 262 THR cc_start: 0.8838 (m) cc_final: 0.8248 (p) REVERT: A 17 ARG cc_start: 0.8273 (ttm110) cc_final: 0.7926 (mtm110) REVERT: A 170 GLU cc_start: 0.8663 (tt0) cc_final: 0.8397 (pt0) REVERT: A 279 LYS cc_start: 0.8953 (mttt) cc_final: 0.8161 (mmtm) REVERT: B 21 LYS cc_start: 0.8432 (ttmt) cc_final: 0.7641 (tptp) REVERT: B 153 GLU cc_start: 0.8518 (mm-30) cc_final: 0.8310 (mm-30) REVERT: B 265 ASN cc_start: 0.8227 (t0) cc_final: 0.7812 (t0) REVERT: B 283 MET cc_start: 0.8312 (mmm) cc_final: 0.8005 (mtp) REVERT: C 85 ARG cc_start: 0.8127 (mtm180) cc_final: 0.7871 (mmt180) REVERT: C 94 LYS cc_start: 0.8630 (ttpt) cc_final: 0.8161 (mttp) REVERT: C 276 MET cc_start: 0.8719 (mmm) cc_final: 0.8443 (mmm) REVERT: D 156 LYS cc_start: 0.8779 (mttt) cc_final: 0.8496 (mtmt) REVERT: D 236 MET cc_start: 0.8686 (tpp) cc_final: 0.8470 (mmm) REVERT: D 277 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.7950 (mt) REVERT: D 279 LYS cc_start: 0.8825 (mttt) cc_final: 0.8070 (mmtt) REVERT: D 318 ASP cc_start: 0.7661 (m-30) cc_final: 0.6619 (p0) REVERT: G 55 ARG cc_start: 0.8009 (mtp85) cc_final: 0.7782 (mtp85) REVERT: G 110 TYR cc_start: 0.9526 (m-80) cc_final: 0.9269 (m-80) outliers start: 30 outliers final: 26 residues processed: 267 average time/residue: 0.1402 time to fit residues: 55.0287 Evaluate side-chains 264 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 237 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 211 SER Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 305 ILE Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain D residue 24 ASP Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain G residue 28 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 2 optimal weight: 0.0770 chunk 27 optimal weight: 0.6980 chunk 158 optimal weight: 0.0870 chunk 39 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 141 optimal weight: 0.9990 chunk 108 optimal weight: 0.0570 chunk 161 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 147 optimal weight: 0.9980 overall best weight: 0.3434 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.115262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.096273 restraints weight = 20415.889| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 1.79 r_work: 0.2955 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 15779 Z= 0.087 Angle : 0.470 7.088 21484 Z= 0.238 Chirality : 0.040 0.208 2484 Planarity : 0.003 0.056 2596 Dihedral : 6.032 85.475 2134 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.60 % Allowed : 13.44 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % 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: -0.59 (0.20), residues: 1799 helix: 1.18 (0.23), residues: 542 sheet: -1.32 (0.25), residues: 435 loop : -0.85 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 68 TYR 0.017 0.001 TYR B 66 PHE 0.010 0.001 PHE D 258 TRP 0.007 0.001 TRP B 168 HIS 0.003 0.001 HIS A 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00199 / 0.09 (15744) covalent geometry : angle 0.46197 / 0.24 (21385) SS BOND : bond 0.00086 / 0.04 ( 6) SS BOND : angle 0.61149 / 0.36 ( 12) hydrogen bonds : bond 0.02806 / 1.89 ( 354) hydrogen bonds : angle 3.28670 / 2.18 ( 975) link_ALPHA1-3 : bond 0.00547 / 0.29 ( 6) link_ALPHA1-3 : angle 1.41751 / 0.85 ( 18) link_ALPHA1-6 : bond 0.00499 / 0.26 ( 5) link_ALPHA1-6 : angle 1.43364 / 0.89 ( 15) link_BETA1-4 : bond 0.00404 / 0.26 ( 11) link_BETA1-4 : angle 1.24195 / 0.82 ( 33) link_NAG-ASN : bond 0.00314 / 0.16 ( 7) link_NAG-ASN : angle 1.61673 / 1.06 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 261 time to evaluate : 0.622 Fit side-chains REVERT: E 68 ARG cc_start: 0.8399 (ttt180) cc_final: 0.8039 (ttt90) REVERT: E 179 GLU cc_start: 0.8273 (mp0) cc_final: 0.8062 (mm-30) REVERT: E 261 MET cc_start: 0.9282 (tpp) cc_final: 0.8908 (mmm) REVERT: E 262 THR cc_start: 0.8830 (m) cc_final: 0.8334 (p) REVERT: A 17 ARG cc_start: 0.8377 (ttm110) cc_final: 0.8036 (mtm110) REVERT: A 170 GLU cc_start: 0.8638 (tt0) cc_final: 0.8382 (pt0) REVERT: A 279 LYS cc_start: 0.8872 (mttt) cc_final: 0.8111 (mmtm) REVERT: B 21 LYS cc_start: 0.8405 (ttmt) cc_final: 0.7638 (tptp) REVERT: B 137 MET cc_start: 0.6340 (mmm) cc_final: 0.5130 (mtt) REVERT: B 153 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8231 (mm-30) REVERT: B 265 ASN cc_start: 0.8183 (t0) cc_final: 0.7729 (t0) REVERT: B 283 MET cc_start: 0.8199 (mmm) cc_final: 0.7989 (mtp) REVERT: C 94 LYS cc_start: 0.8593 (ttpt) cc_final: 0.8166 (mttp) REVERT: C 266 THR cc_start: 0.9032 (m) cc_final: 0.8809 (m) REVERT: C 276 MET cc_start: 0.8665 (mmm) cc_final: 0.8411 (mmm) REVERT: D 17 ARG cc_start: 0.8564 (ttp-110) cc_final: 0.8330 (ttm110) REVERT: D 156 LYS cc_start: 0.8746 (mttt) cc_final: 0.8474 (mtmt) REVERT: D 164 ARG cc_start: 0.8801 (ptm-80) cc_final: 0.8590 (ptm160) REVERT: D 236 MET cc_start: 0.8584 (tpp) cc_final: 0.8364 (mmm) REVERT: D 279 LYS cc_start: 0.8798 (mttt) cc_final: 0.8154 (mptt) REVERT: D 318 ASP cc_start: 0.7574 (m-30) cc_final: 0.6514 (p0) REVERT: G 27 ARG cc_start: 0.8188 (ttm-80) cc_final: 0.7733 (ttm-80) REVERT: G 110 TYR cc_start: 0.9509 (m-80) cc_final: 0.9294 (m-80) outliers start: 26 outliers final: 25 residues processed: 280 average time/residue: 0.1334 time to fit residues: 55.4758 Evaluate side-chains 270 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 245 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 211 SER Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 305 ILE Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain D residue 24 ASP Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain G residue 28 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 176 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 62 optimal weight: 0.4980 chunk 1 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 142 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 144 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 100 ASN C 323 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.115405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.096405 restraints weight = 20211.680| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 1.78 r_work: 0.2934 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15779 Z= 0.110 Angle : 0.483 6.959 21484 Z= 0.244 Chirality : 0.041 0.209 2484 Planarity : 0.003 0.055 2596 Dihedral : 6.033 86.112 2134 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.54 % Allowed : 14.06 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % 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: -0.51 (0.20), residues: 1799 helix: 1.25 (0.23), residues: 542 sheet: -1.27 (0.25), residues: 435 loop : -0.81 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 37 TYR 0.020 0.001 TYR B 299 PHE 0.019 0.001 PHE E 301 TRP 0.007 0.001 TRP E 168 HIS 0.003 0.001 HIS A 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 (15744) covalent geometry : angle 0.47484 / 0.24 (21385) SS BOND : bond 0.00089 / 0.05 ( 6) SS BOND : angle 0.76579 / 0.45 ( 12) hydrogen bonds : bond 0.02850 / 1.92 ( 354) hydrogen bonds : angle 3.30492 / 2.20 ( 975) link_ALPHA1-3 : bond 0.00515 / 0.28 ( 6) link_ALPHA1-3 : angle 1.47972 / 0.88 ( 18) link_ALPHA1-6 : bond 0.00454 / 0.24 ( 5) link_ALPHA1-6 : angle 1.48572 / 0.92 ( 15) link_BETA1-4 : bond 0.00386 / 0.25 ( 11) link_BETA1-4 : angle 1.25652 / 0.83 ( 33) link_NAG-ASN : bond 0.00261 / 0.13 ( 7) link_NAG-ASN : angle 1.65279 / 1.11 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3617.58 seconds wall clock time: 62 minutes 57.71 seconds (3777.71 seconds total)