Starting phenix.real_space_refine on Tue Aug 26 07:14:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dmg_47003/08_2025/9dmg_47003_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dmg_47003/08_2025/9dmg_47003.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dmg_47003/08_2025/9dmg_47003.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dmg_47003/08_2025/9dmg_47003.map" model { file = "/net/cci-nas-00/data/ceres_data/9dmg_47003/08_2025/9dmg_47003_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dmg_47003/08_2025/9dmg_47003_neut_trim.cif" } resolution = 2.05 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= 0.017 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: 6 Type Number sf(0) Gaussians P 4 5.49 5 S 76 5.16 5 C 11274 2.51 5 N 2701 2.21 5 O 3168 1.98 5 H 16551 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33774 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 6433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 6433 Classifications: {'peptide': 399} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 378} Chain breaks: 1 Chain: "C" Number of atoms: 6486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 6486 Classifications: {'peptide': 401} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 380} Chain breaks: 1 Chain: "E" Number of atoms: 6575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 6575 Classifications: {'peptide': 405} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 379} Chain breaks: 3 Chain: "D" Number of atoms: 7055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 7055 Classifications: {'peptide': 433} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 402} Chain breaks: 1 Chain: "B" Number of atoms: 6480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 6480 Classifications: {'peptide': 411} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 387} Chain breaks: 1 Chain: "F" 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 dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "G" 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 dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "H" 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 dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" 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 dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 2, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'MAN': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 108 Unusual residues: {'CLR': 2, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 96 Unusual residues: {'CLR': 2, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "B" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 100 Unusual residues: {'CLR': 2, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Time building chain proxies: 6.04, per 1000 atoms: 0.18 Number of scatterers: 33774 At special positions: 0 Unit cell: (98.175, 109.395, 172.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 76 16.00 P 4 15.00 O 3168 8.00 N 2701 7.00 C 11274 6.00 H 16551 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 142 " distance=2.26 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 142 " distance=2.21 Simple disulfide: pdb=" SG CYS E 128 " - pdb=" SG CYS E 142 " distance=2.04 Simple disulfide: pdb=" SG CYS D 130 " - pdb=" SG CYS D 144 " distance=2.04 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 142 " distance=2.04 Simple disulfide: pdb=" SG CYS B 190 " - pdb=" SG CYS B 470 " 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 6 " " MAN F 4 " - " MAN F 5 " " BMA G 3 " - " MAN G 4 " " BMA H 3 " - " MAN H 4 " " BMA I 3 " - " MAN I 4 " " BMA K 3 " - " MAN K 6 " ALPHA1-6 " BMA F 3 " - " MAN F 4 " " BMA G 3 " - " MAN G 5 " " BMA H 3 " - " MAN H 5 " " BMA I 3 " - " MAN I 5 " " BMA K 4 " - " MAN K 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " BETA1-6 " BMA K 3 " - " BMA K 4 " NAG-ASN " NAG F 1 " - " ASN A 141 " " NAG G 1 " - " ASN C 141 " " NAG H 1 " - " ASN E 141 " " NAG I 1 " - " ASN D 143 " " NAG J 1 " - " ASN B 66 " " NAG K 1 " - " ASN B 141 " Time building additional restraints: 3.15 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 953.7 nanoseconds 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3920 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 19 sheets defined 45.4% alpha, 28.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 Processing helix chain 'A' and resid 68 through 73 removed outlier: 3.914A pdb=" N GLY A 73 " --> pdb=" O ASP A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 85 removed outlier: 3.579A pdb=" N LYS A 84 " --> pdb=" O PRO A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 218 Processing helix chain 'A' and resid 218 through 231 removed outlier: 3.819A pdb=" N GLY A 230 " --> pdb=" O SER A 226 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU A 231 " --> pdb=" O PHE A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 235 Processing helix chain 'A' and resid 236 through 240 Processing helix chain 'A' and resid 241 through 264 removed outlier: 3.687A pdb=" N LEU A 258 " --> pdb=" O THR A 254 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL A 259 " --> pdb=" O VAL A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 300 Processing helix chain 'A' and resid 309 through 317 Processing helix chain 'A' and resid 319 through 324 Processing helix chain 'A' and resid 369 through 435 removed outlier: 3.611A pdb=" N TRP A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N GLY A 428 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N ARG A 429 " --> pdb=" O VAL A 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 12 Processing helix chain 'C' and resid 68 through 73 removed outlier: 3.913A pdb=" N GLY C 73 " --> pdb=" O ASP C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 85 Processing helix chain 'C' and resid 211 through 218 Processing helix chain 'C' and resid 218 through 231 removed outlier: 3.877A pdb=" N GLY C 230 " --> pdb=" O SER C 226 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU C 231 " --> pdb=" O PHE C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 235 Processing helix chain 'C' and resid 236 through 240 Processing helix chain 'C' and resid 241 through 264 removed outlier: 3.977A pdb=" N LEU C 258 " --> pdb=" O THR C 254 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N VAL C 259 " --> pdb=" O VAL C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 300 Processing helix chain 'C' and resid 309 through 318 Processing helix chain 'C' and resid 319 through 324 Processing helix chain 'C' and resid 369 through 435 removed outlier: 3.768A pdb=" N PHE C 426 " --> pdb=" O THR C 422 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N GLY C 428 " --> pdb=" O ALA C 424 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N ARG C 429 " --> pdb=" O VAL C 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 12 Processing helix chain 'E' and resid 68 through 73 removed outlier: 4.206A pdb=" N ASP E 73 " --> pdb=" O ALA E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 85 No H-bonds generated for 'chain 'E' and resid 83 through 85' Processing helix chain 'E' and resid 222 through 229 Processing helix chain 'E' and resid 229 through 243 Processing helix chain 'E' and resid 244 through 246 No H-bonds generated for 'chain 'E' and resid 244 through 246' Processing helix chain 'E' and resid 247 through 251 Processing helix chain 'E' and resid 252 through 273 removed outlier: 4.114A pdb=" N ASP E 273 " --> pdb=" O LEU E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 311 Processing helix chain 'E' and resid 320 through 329 Processing helix chain 'E' and resid 330 through 335 removed outlier: 3.754A pdb=" N TYR E 334 " --> pdb=" O LYS E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 469 Processing helix chain 'D' and resid 2 through 13 Processing helix chain 'D' and resid 65 through 68 removed outlier: 3.613A pdb=" N LYS D 68 " --> pdb=" O ASN D 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 65 through 68' Processing helix chain 'D' and resid 70 through 75 removed outlier: 3.899A pdb=" N GLY D 75 " --> pdb=" O GLU D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'D' and resid 225 through 232 Processing helix chain 'D' and resid 232 through 243 removed outlier: 3.909A pdb=" N VAL D 243 " --> pdb=" O ILE D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 248 Processing helix chain 'D' and resid 250 through 254 removed outlier: 3.531A pdb=" N GLY D 254 " --> pdb=" O ALA D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 276 removed outlier: 3.978A pdb=" N LYS D 276 " --> pdb=" O LEU D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 314 Processing helix chain 'D' and resid 323 through 332 removed outlier: 3.678A pdb=" N GLU D 332 " --> pdb=" O LYS D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 338 Processing helix chain 'D' and resid 409 through 473 Proline residue: D 416 - end of helix Proline residue: D 458 - end of helix removed outlier: 3.851A pdb=" N GLY D 471 " --> pdb=" O ILE D 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 13 removed outlier: 3.613A pdb=" N ARG B 6 " --> pdb=" O ASN B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 66 Processing helix chain 'B' and resid 68 through 73 removed outlier: 4.159A pdb=" N GLY B 73 " --> pdb=" O ASP B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 85 Processing helix chain 'B' and resid 220 through 227 Processing helix chain 'B' and resid 227 through 237 Processing helix chain 'B' and resid 238 through 244 Processing helix chain 'B' and resid 251 through 272 removed outlier: 3.752A pdb=" N GLN B 272 " --> pdb=" O PHE B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 310 Processing helix chain 'B' and resid 319 through 328 Processing helix chain 'B' and resid 328 through 334 removed outlier: 3.934A pdb=" N ARG B 332 " --> pdb=" O GLU B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 459 removed outlier: 3.599A pdb=" N TRP B 440 " --> pdb=" O ASN B 436 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA B 457 " --> pdb=" O ILE B 453 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 80 removed outlier: 4.081A pdb=" N HIS A 115 " --> pdb=" O GLN A 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 80 removed outlier: 4.081A pdb=" N HIS A 115 " --> pdb=" O GLN A 111 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ASN A 53 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N LEU A 40 " --> pdb=" O ASN A 53 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N ARG A 55 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ILE A 38 " --> pdb=" O ARG A 55 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N LYS A 57 " --> pdb=" O GLN A 36 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N GLN A 36 " --> pdb=" O LYS A 57 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N GLN A 59 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N GLY A 34 " --> pdb=" O GLN A 59 " (cutoff:3.500A) removed outlier: 8.825A pdb=" N VAL A 61 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 9.643A pdb=" N THR A 32 " --> pdb=" O VAL A 61 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 removed outlier: 4.856A pdb=" N THR A 148 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU A 199 " --> pdb=" O THR A 148 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N THR A 196 " --> pdb=" O TYR A 190 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N TYR A 190 " --> pdb=" O THR A 196 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N GLN A 208 " --> pdb=" O ILE A 178 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ILE A 178 " --> pdb=" O GLN A 208 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 80 removed outlier: 4.141A pdb=" N HIS C 115 " --> pdb=" O GLN C 111 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 80 removed outlier: 4.141A pdb=" N HIS C 115 " --> pdb=" O GLN C 111 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ASN C 53 " --> pdb=" O LEU C 40 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N LEU C 40 " --> pdb=" O ASN C 53 " (cutoff:3.500A) removed outlier: 8.546A pdb=" N ARG C 55 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ILE C 38 " --> pdb=" O ARG C 55 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LYS C 57 " --> pdb=" O GLN C 36 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N GLN C 36 " --> pdb=" O LYS C 57 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N GLN C 59 " --> pdb=" O GLY C 34 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N GLY C 34 " --> pdb=" O GLN C 59 " (cutoff:3.500A) removed outlier: 8.764A pdb=" N VAL C 61 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 9.318A pdb=" N THR C 32 " --> pdb=" O VAL C 61 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 90 through 92 removed outlier: 4.867A pdb=" N THR C 148 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU C 199 " --> pdb=" O THR C 148 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU C 180 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLN C 208 " --> pdb=" O ILE C 178 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N ILE C 178 " --> pdb=" O GLN C 208 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 77 through 81 removed outlier: 4.059A pdb=" N SER E 115 " --> pdb=" O SER E 111 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N GLY E 114 " --> pdb=" O ASP E 62 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 77 through 81 removed outlier: 4.059A pdb=" N SER E 115 " --> pdb=" O SER E 111 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N GLY E 114 " --> pdb=" O ASP E 62 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N GLU E 49 " --> pdb=" O SER E 42 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N SER E 42 " --> pdb=" O GLU E 49 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N SER E 51 " --> pdb=" O LEU E 40 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N LEU E 40 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LYS E 53 " --> pdb=" O ALA E 38 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N THR E 61 " --> pdb=" O ARG E 30 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ARG E 30 " --> pdb=" O THR E 61 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 90 through 92 removed outlier: 6.913A pdb=" N ILE E 217 " --> pdb=" O ILE E 188 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 90 through 92 Processing sheet with id=AB2, first strand: chain 'D' and resid 79 through 82 removed outlier: 3.981A pdb=" N PHE D 117 " --> pdb=" O TYR D 113 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 79 through 82 removed outlier: 3.981A pdb=" N PHE D 117 " --> pdb=" O TYR D 113 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N THR D 51 " --> pdb=" O SER D 44 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N SER D 44 " --> pdb=" O THR D 51 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N THR D 53 " --> pdb=" O LEU D 42 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N LEU D 42 " --> pdb=" O THR D 53 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ASN D 55 " --> pdb=" O SER D 40 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N THR D 63 " --> pdb=" O ASP D 32 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ASP D 32 " --> pdb=" O THR D 63 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 93 through 94 removed outlier: 6.884A pdb=" N ILE D 220 " --> pdb=" O VAL D 193 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 93 through 94 Processing sheet with id=AB6, first strand: chain 'D' and resid 164 through 167 Processing sheet with id=AB7, first strand: chain 'B' and resid 77 through 80 removed outlier: 3.723A pdb=" N SER B 115 " --> pdb=" O TYR B 111 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 77 through 80 removed outlier: 3.723A pdb=" N SER B 115 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N THR B 49 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N SER B 42 " --> pdb=" O THR B 49 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N THR B 51 " --> pdb=" O LEU B 40 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N LEU B 40 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N SER B 53 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N GLN B 61 " --> pdb=" O THR B 30 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N THR B 30 " --> pdb=" O GLN B 61 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 90 through 92 removed outlier: 5.162A pdb=" N SER B 148 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N THR B 208 " --> pdb=" O SER B 148 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE B 215 " --> pdb=" O ASP B 188 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 90 through 92 removed outlier: 5.162A pdb=" N SER B 148 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N THR B 208 " --> pdb=" O SER B 148 " (cutoff:3.500A) 988 hydrogen bonds defined for protein. 2799 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: 8.32 Time building geometry restraints manager: 4.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 16532 1.04 - 1.23: 308 1.23 - 1.43: 6918 1.43 - 1.62: 10338 1.62 - 1.82: 121 Bond restraints: 34217 Sorted by residual: bond pdb=" NZ LYS B 273 " pdb=" HZ3 LYS B 273 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" NZ LYS D 167 " pdb=" HZ1 LYS D 167 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" NZ LYS A 76 " pdb=" HZ1 LYS A 76 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" NZ LYS B 219 " pdb=" HZ1 LYS B 219 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.62e+01 bond pdb=" NZ LYS D 415 " pdb=" HZ3 LYS D 415 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.62e+01 ... (remaining 34212 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.09: 61708 11.09 - 22.18: 3 22.18 - 33.27: 3 33.27 - 44.36: 0 44.36 - 55.45: 4 Bond angle restraints: 61718 Sorted by residual: angle pdb=" CA LEU C 366 " pdb=" N LEU C 366 " pdb=" H LEU C 366 " ideal model delta sigma weight residual 114.00 169.45 -55.45 3.00e+00 1.11e-01 3.42e+02 angle pdb=" CA LYS A 368 " pdb=" N LYS A 368 " pdb=" H LYS A 368 " ideal model delta sigma weight residual 114.00 167.64 -53.64 3.00e+00 1.11e-01 3.20e+02 angle pdb=" CA LEU E 407 " pdb=" N LEU E 407 " pdb=" H LEU E 407 " ideal model delta sigma weight residual 114.00 160.45 -46.45 3.00e+00 1.11e-01 2.40e+02 angle pdb=" CA ALA B 397 " pdb=" N ALA B 397 " pdb=" H ALA B 397 " ideal model delta sigma weight residual 114.00 159.93 -45.93 3.00e+00 1.11e-01 2.34e+02 angle pdb=" CA GLU E 206 " pdb=" N GLU E 206 " pdb=" H GLU E 206 " ideal model delta sigma weight residual 114.00 145.56 -31.56 3.00e+00 1.11e-01 1.11e+02 ... (remaining 61713 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.26: 16460 35.26 - 70.51: 439 70.51 - 105.77: 71 105.77 - 141.03: 16 141.03 - 176.28: 2 Dihedral angle restraints: 16988 sinusoidal: 9713 harmonic: 7275 Sorted by residual: dihedral pdb=" CB CYS A 128 " pdb=" SG CYS A 128 " pdb=" SG CYS A 142 " pdb=" CB CYS A 142 " ideal model delta sinusoidal sigma weight residual 93.00 17.31 75.69 1 1.00e+01 1.00e-02 7.23e+01 dihedral pdb=" C29 POV E 503 " pdb="C210 POV E 503 " pdb="C211 POV E 503 " pdb="C212 POV E 503 " ideal model delta sinusoidal sigma weight residual 112.25 -64.03 176.28 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C3 POV E 503 " pdb=" C31 POV E 503 " pdb=" O31 POV E 503 " pdb=" C32 POV E 503 " ideal model delta sinusoidal sigma weight residual 172.61 29.50 143.11 1 3.00e+01 1.11e-03 1.92e+01 ... (remaining 16985 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.509: 2885 0.509 - 1.019: 0 1.019 - 1.528: 0 1.528 - 2.037: 1 2.037 - 2.547: 1 Chirality restraints: 2887 Sorted by residual: chirality pdb=" C1 BMA G 3 " pdb=" O4 NAG G 2 " pdb=" C2 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.40 -0.87 -1.53 2.00e-02 2.50e+03 5.88e+03 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-02 2.50e+03 1.90e+02 chirality pdb=" C2 MAN A 502 " pdb=" C1 MAN A 502 " pdb=" C3 MAN A 502 " pdb=" O2 MAN A 502 " both_signs ideal model delta sigma weight residual False 2.52 -0.03 2.55 2.00e-01 2.50e+01 1.62e+02 ... (remaining 2884 not shown) Planarity restraints: 4839 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 2 " -0.273 2.00e-02 2.50e+03 2.33e-01 6.79e+02 pdb=" C7 NAG J 2 " 0.062 2.00e-02 2.50e+03 pdb=" C8 NAG J 2 " -0.165 2.00e-02 2.50e+03 pdb=" N2 NAG J 2 " 0.406 2.00e-02 2.50e+03 pdb=" O7 NAG J 2 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 1 " -0.197 2.00e-02 2.50e+03 1.69e-01 3.57e+02 pdb=" C7 NAG G 1 " 0.043 2.00e-02 2.50e+03 pdb=" C8 NAG G 1 " 0.030 2.00e-02 2.50e+03 pdb=" N2 NAG G 1 " 0.279 2.00e-02 2.50e+03 pdb=" O7 NAG G 1 " -0.154 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 301 " 0.725 9.50e-02 1.11e+02 2.56e-01 2.16e+02 pdb=" NE ARG A 301 " 0.051 2.00e-02 2.50e+03 pdb=" CZ ARG A 301 " 0.022 2.00e-02 2.50e+03 pdb=" NH1 ARG A 301 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 301 " -0.018 2.00e-02 2.50e+03 pdb="HH11 ARG A 301 " -0.181 2.00e-02 2.50e+03 pdb="HH12 ARG A 301 " 0.157 2.00e-02 2.50e+03 pdb="HH21 ARG A 301 " -0.039 2.00e-02 2.50e+03 pdb="HH22 ARG A 301 " -0.028 2.00e-02 2.50e+03 ... (remaining 4836 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.08: 364 2.08 - 2.71: 53674 2.71 - 3.34: 96991 3.34 - 3.97: 131703 3.97 - 4.60: 202149 Nonbonded interactions: 484881 Sorted by model distance: nonbonded pdb=" HH TYR D 17 " pdb=" H TRP D 88 " model vdw 1.444 2.100 nonbonded pdb="HD22 ASN B 301 " pdb=" HB3 CYS B 438 " model vdw 1.485 2.270 nonbonded pdb=" HH TYR C 381 " pdb="HD21 ASN D 432 " model vdw 1.510 2.100 nonbonded pdb=" HH TYR A 15 " pdb=" H TRP A 86 " model vdw 1.576 2.100 nonbonded pdb=" HE1 PHE D 241 " pdb=" HG1 THR D 464 " model vdw 1.589 2.100 ... (remaining 484876 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 1 through 436) selection = (chain 'C' and (resid 1 through 330 or resid 369 through 436)) } ncs_group { reference = (chain 'F' and (resid 1 through 3 or resid 5 through 6)) selection = (chain 'K' and (resid 1 through 3 or resid 5 through 6)) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 12.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.210 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 30.890 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 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 0.232 17701 Z= 0.325 Angle : 0.941 27.103 24206 Z= 0.480 Chirality : 0.076 2.547 2887 Planarity : 0.010 0.258 2914 Dihedral : 17.346 176.285 7311 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.83 % Favored : 98.12 % Rotamer: Outliers : 0.37 % Allowed : 8.02 % Favored : 91.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.19), residues: 2025 helix: 2.32 (0.18), residues: 780 sheet: 0.14 (0.25), residues: 415 loop : -0.08 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 277 TYR 0.017 0.002 TYR C 213 PHE 0.027 0.002 PHE C 284 TRP 0.020 0.002 TRP B 55 HIS 0.013 0.002 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00576 (17666) covalent geometry : angle 0.90061 (24107) SS BOND : bond 0.11942 ( 6) SS BOND : angle 5.98798 ( 12) hydrogen bonds : bond 0.11914 ( 902) hydrogen bonds : angle 5.70793 ( 2799) link_ALPHA1-3 : bond 0.00416 ( 6) link_ALPHA1-3 : angle 2.57065 ( 18) link_ALPHA1-6 : bond 0.00379 ( 5) link_ALPHA1-6 : angle 1.19010 ( 15) link_BETA1-4 : bond 0.00660 ( 11) link_BETA1-4 : angle 3.62337 ( 33) link_BETA1-6 : bond 0.00511 ( 1) link_BETA1-6 : angle 1.58647 ( 3) link_NAG-ASN : bond 0.13414 ( 6) link_NAG-ASN : angle 6.86369 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 220 time to evaluate : 0.988 Fit side-chains revert: symmetry clash REVERT: A 278 MET cc_start: 0.7999 (ttp) cc_final: 0.7790 (tmm) REVERT: A 308 MET cc_start: 0.8469 (tpp) cc_final: 0.8126 (tpp) REVERT: A 387 LYS cc_start: 0.8239 (tttp) cc_final: 0.7880 (ttmt) outliers start: 7 outliers final: 4 residues processed: 225 average time/residue: 1.1893 time to fit residues: 299.9470 Evaluate side-chains 206 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 202 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain E residue 452 PHE Chi-restraints excluded: chain B residue 450 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 98 optimal weight: 0.0060 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN C 394 ASN D 422 ASN D 491 GLN B 272 GLN B 301 ASN B 432 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.138238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.109297 restraints weight = 51062.318| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.70 r_work: 0.3204 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.0759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17701 Z= 0.141 Angle : 0.606 9.194 24206 Z= 0.297 Chirality : 0.044 0.216 2887 Planarity : 0.005 0.056 2914 Dihedral : 13.292 173.639 3397 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.68 % Favored : 98.27 % Rotamer: Outliers : 1.12 % Allowed : 8.23 % Favored : 90.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.19), residues: 2025 helix: 2.55 (0.18), residues: 784 sheet: 0.23 (0.25), residues: 423 loop : 0.11 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 23 TYR 0.012 0.001 TYR D 119 PHE 0.017 0.002 PHE C 284 TRP 0.018 0.001 TRP B 55 HIS 0.005 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00293 (17666) covalent geometry : angle 0.58867 (24107) SS BOND : bond 0.00506 ( 6) SS BOND : angle 1.89878 ( 12) hydrogen bonds : bond 0.05272 ( 902) hydrogen bonds : angle 4.60708 ( 2799) link_ALPHA1-3 : bond 0.00809 ( 6) link_ALPHA1-3 : angle 2.58840 ( 18) link_ALPHA1-6 : bond 0.00663 ( 5) link_ALPHA1-6 : angle 1.84814 ( 15) link_BETA1-4 : bond 0.01096 ( 11) link_BETA1-4 : angle 2.62576 ( 33) link_BETA1-6 : bond 0.00743 ( 1) link_BETA1-6 : angle 2.14122 ( 3) link_NAG-ASN : bond 0.00517 ( 6) link_NAG-ASN : angle 2.09422 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 209 time to evaluate : 0.703 Fit side-chains revert: symmetry clash REVERT: A 278 MET cc_start: 0.7734 (ttp) cc_final: 0.7501 (tmm) REVERT: A 308 MET cc_start: 0.8365 (tpp) cc_final: 0.7887 (tpp) REVERT: A 387 LYS cc_start: 0.8066 (tttp) cc_final: 0.7626 (ttmt) REVERT: A 416 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7825 (mp) REVERT: C 324 MET cc_start: 0.5904 (OUTLIER) cc_final: 0.5643 (mtm) REVERT: B 314 THR cc_start: 0.7794 (OUTLIER) cc_final: 0.7563 (m) REVERT: B 435 ASP cc_start: 0.7437 (OUTLIER) cc_final: 0.6595 (t0) outliers start: 21 outliers final: 10 residues processed: 218 average time/residue: 1.1848 time to fit residues: 290.1951 Evaluate side-chains 216 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 202 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 324 MET Chi-restraints excluded: chain E residue 1 SER Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain E residue 452 PHE Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 242 MET Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 435 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 39 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 132 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 118 optimal weight: 0.3980 chunk 61 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 ASN C 299 HIS C 394 ASN D 60 HIS D 164 GLN D 491 GLN B 95 ASN B 272 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.137256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.108175 restraints weight = 51161.586| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.71 r_work: 0.3188 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.0957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17701 Z= 0.145 Angle : 0.569 9.222 24206 Z= 0.286 Chirality : 0.044 0.240 2887 Planarity : 0.004 0.046 2914 Dihedral : 11.599 169.544 3394 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.88 % Favored : 98.07 % Rotamer: Outliers : 1.34 % Allowed : 7.91 % Favored : 90.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.18), residues: 2025 helix: 2.63 (0.18), residues: 785 sheet: 0.25 (0.25), residues: 415 loop : 0.08 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 81 TYR 0.012 0.001 TYR D 119 PHE 0.018 0.002 PHE C 284 TRP 0.016 0.001 TRP B 55 HIS 0.006 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00311 (17666) covalent geometry : angle 0.55518 (24107) SS BOND : bond 0.01025 ( 6) SS BOND : angle 1.59175 ( 12) hydrogen bonds : bond 0.05155 ( 902) hydrogen bonds : angle 4.48684 ( 2799) link_ALPHA1-3 : bond 0.01072 ( 6) link_ALPHA1-3 : angle 1.88993 ( 18) link_ALPHA1-6 : bond 0.00841 ( 5) link_ALPHA1-6 : angle 1.66947 ( 15) link_BETA1-4 : bond 0.00907 ( 11) link_BETA1-4 : angle 2.47988 ( 33) link_BETA1-6 : bond 0.00684 ( 1) link_BETA1-6 : angle 2.14166 ( 3) link_NAG-ASN : bond 0.00255 ( 6) link_NAG-ASN : angle 1.62107 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 197 time to evaluate : 0.857 Fit side-chains revert: symmetry clash REVERT: A 278 MET cc_start: 0.7752 (ttp) cc_final: 0.7521 (tmm) REVERT: A 308 MET cc_start: 0.8393 (tpp) cc_final: 0.7929 (tpp) REVERT: A 416 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7805 (mp) REVERT: C 324 MET cc_start: 0.5831 (OUTLIER) cc_final: 0.5545 (mtm) REVERT: D 186 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.7148 (tt0) REVERT: B 314 THR cc_start: 0.7840 (OUTLIER) cc_final: 0.7608 (m) REVERT: B 435 ASP cc_start: 0.7429 (OUTLIER) cc_final: 0.6663 (t0) outliers start: 25 outliers final: 15 residues processed: 208 average time/residue: 1.3755 time to fit residues: 321.4578 Evaluate side-chains 213 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 193 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain C residue 324 MET Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain E residue 452 PHE Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 242 MET Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 435 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 150 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 171 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 198 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 152 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN C 394 ASN D 491 GLN B 272 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.136849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.107809 restraints weight = 50766.399| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.71 r_work: 0.3219 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 17701 Z= 0.182 Angle : 0.591 9.656 24206 Z= 0.302 Chirality : 0.044 0.272 2887 Planarity : 0.005 0.043 2914 Dihedral : 11.079 170.480 3394 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.22 % Favored : 97.73 % Rotamer: Outliers : 1.50 % Allowed : 7.80 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.65 (0.18), residues: 2025 helix: 2.57 (0.17), residues: 785 sheet: 0.31 (0.24), residues: 423 loop : 0.12 (0.22), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 6 TYR 0.014 0.002 TYR A 72 PHE 0.021 0.002 PHE C 284 TRP 0.017 0.002 TRP B 55 HIS 0.026 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00405 (17666) covalent geometry : angle 0.57268 (24107) SS BOND : bond 0.01230 ( 6) SS BOND : angle 3.01893 ( 12) hydrogen bonds : bond 0.05425 ( 902) hydrogen bonds : angle 4.56616 ( 2799) link_ALPHA1-3 : bond 0.01026 ( 6) link_ALPHA1-3 : angle 2.23114 ( 18) link_ALPHA1-6 : bond 0.00790 ( 5) link_ALPHA1-6 : angle 1.76440 ( 15) link_BETA1-4 : bond 0.00938 ( 11) link_BETA1-4 : angle 2.57168 ( 33) link_BETA1-6 : bond 0.00385 ( 1) link_BETA1-6 : angle 1.81261 ( 3) link_NAG-ASN : bond 0.00252 ( 6) link_NAG-ASN : angle 1.83590 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 202 time to evaluate : 0.885 Fit side-chains revert: symmetry clash REVERT: A 278 MET cc_start: 0.7728 (ttp) cc_final: 0.7469 (tmm) REVERT: A 308 MET cc_start: 0.8393 (tpp) cc_final: 0.7929 (tpp) REVERT: A 416 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7777 (mp) REVERT: C 264 ILE cc_start: 0.8257 (tt) cc_final: 0.8048 (mp) REVERT: D 186 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.7150 (tt0) REVERT: B 314 THR cc_start: 0.7944 (OUTLIER) cc_final: 0.7700 (m) REVERT: B 318 MET cc_start: 0.7661 (tpt) cc_final: 0.7451 (tpt) REVERT: B 435 ASP cc_start: 0.7380 (OUTLIER) cc_final: 0.6573 (t0) outliers start: 28 outliers final: 14 residues processed: 214 average time/residue: 1.2959 time to fit residues: 312.9453 Evaluate side-chains 217 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 199 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 242 MET Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 435 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 37 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 202 optimal weight: 0.6980 chunk 12 optimal weight: 0.0570 chunk 120 optimal weight: 0.2980 chunk 95 optimal weight: 2.9990 chunk 114 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 chunk 165 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN C 394 ASN D 491 GLN B 272 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.137557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.108734 restraints weight = 50921.388| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.70 r_work: 0.3197 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17701 Z= 0.121 Angle : 0.544 8.452 24206 Z= 0.277 Chirality : 0.043 0.240 2887 Planarity : 0.004 0.043 2914 Dihedral : 10.402 165.984 3392 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.88 % Favored : 98.07 % Rotamer: Outliers : 1.28 % Allowed : 8.07 % Favored : 90.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.76 (0.19), residues: 2025 helix: 2.71 (0.18), residues: 785 sheet: 0.37 (0.25), residues: 421 loop : 0.14 (0.22), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 81 TYR 0.011 0.001 TYR D 119 PHE 0.016 0.001 PHE C 284 TRP 0.016 0.001 TRP B 55 HIS 0.004 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00257 (17666) covalent geometry : angle 0.52838 (24107) SS BOND : bond 0.00251 ( 6) SS BOND : angle 2.70145 ( 12) hydrogen bonds : bond 0.04895 ( 902) hydrogen bonds : angle 4.39967 ( 2799) link_ALPHA1-3 : bond 0.01035 ( 6) link_ALPHA1-3 : angle 1.97225 ( 18) link_ALPHA1-6 : bond 0.00846 ( 5) link_ALPHA1-6 : angle 1.69173 ( 15) link_BETA1-4 : bond 0.00823 ( 11) link_BETA1-4 : angle 2.21126 ( 33) link_BETA1-6 : bond 0.00335 ( 1) link_BETA1-6 : angle 1.60394 ( 3) link_NAG-ASN : bond 0.00184 ( 6) link_NAG-ASN : angle 1.80683 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 202 time to evaluate : 1.033 Fit side-chains revert: symmetry clash REVERT: A 26 ARG cc_start: 0.8202 (mtm-85) cc_final: 0.7825 (mtt90) REVERT: A 278 MET cc_start: 0.7728 (ttp) cc_final: 0.7502 (tmm) REVERT: A 301 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.7962 (mtt90) REVERT: A 308 MET cc_start: 0.8351 (OUTLIER) cc_final: 0.7867 (tpp) REVERT: A 416 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7761 (mp) REVERT: D 9 ARG cc_start: 0.7854 (ttp-110) cc_final: 0.7624 (ttp-110) REVERT: D 186 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7178 (tt0) REVERT: B 314 THR cc_start: 0.7908 (OUTLIER) cc_final: 0.7665 (m) REVERT: B 435 ASP cc_start: 0.7448 (OUTLIER) cc_final: 0.6624 (t0) outliers start: 24 outliers final: 14 residues processed: 210 average time/residue: 1.3959 time to fit residues: 329.4843 Evaluate side-chains 216 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 196 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 301 ARG Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 242 MET Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 435 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 144 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 177 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 141 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN D 60 HIS D 491 GLN B 272 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.135945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.106802 restraints weight = 50806.125| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.72 r_work: 0.3204 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 17701 Z= 0.216 Angle : 0.621 9.916 24206 Z= 0.320 Chirality : 0.046 0.302 2887 Planarity : 0.005 0.040 2914 Dihedral : 10.658 169.930 3392 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.42 % Favored : 97.53 % Rotamer: Outliers : 1.39 % Allowed : 7.91 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.61 (0.18), residues: 2025 helix: 2.53 (0.17), residues: 785 sheet: 0.34 (0.24), residues: 423 loop : 0.09 (0.22), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 81 TYR 0.015 0.002 TYR A 72 PHE 0.024 0.002 PHE C 284 TRP 0.019 0.002 TRP D 176 HIS 0.021 0.002 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00483 (17666) covalent geometry : angle 0.60155 (24107) SS BOND : bond 0.00402 ( 6) SS BOND : angle 3.97499 ( 12) hydrogen bonds : bond 0.05663 ( 902) hydrogen bonds : angle 4.57042 ( 2799) link_ALPHA1-3 : bond 0.00979 ( 6) link_ALPHA1-3 : angle 2.35542 ( 18) link_ALPHA1-6 : bond 0.00746 ( 5) link_ALPHA1-6 : angle 1.71382 ( 15) link_BETA1-4 : bond 0.00945 ( 11) link_BETA1-4 : angle 2.60236 ( 33) link_BETA1-6 : bond 0.00230 ( 1) link_BETA1-6 : angle 1.50492 ( 3) link_NAG-ASN : bond 0.00258 ( 6) link_NAG-ASN : angle 1.82101 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 195 time to evaluate : 0.868 Fit side-chains revert: symmetry clash REVERT: A 26 ARG cc_start: 0.8207 (mtm-85) cc_final: 0.7807 (mtt90) REVERT: A 278 MET cc_start: 0.7738 (ttp) cc_final: 0.7480 (tmm) REVERT: A 301 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.7876 (mtt90) REVERT: A 308 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.7852 (tpp) REVERT: A 416 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7761 (tp) REVERT: E 30 ARG cc_start: 0.7735 (mtp85) cc_final: 0.7438 (mtt90) REVERT: D 9 ARG cc_start: 0.7877 (ttp-110) cc_final: 0.7622 (ttp-110) REVERT: D 186 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7213 (tt0) REVERT: B 314 THR cc_start: 0.7937 (OUTLIER) cc_final: 0.7685 (m) REVERT: B 435 ASP cc_start: 0.7389 (OUTLIER) cc_final: 0.6597 (t0) outliers start: 26 outliers final: 19 residues processed: 207 average time/residue: 1.1496 time to fit residues: 267.9162 Evaluate side-chains 216 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 191 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 301 ARG Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 242 MET Chi-restraints excluded: chain D residue 449 ASP Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 435 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 71 optimal weight: 0.8980 chunk 187 optimal weight: 1.9990 chunk 96 optimal weight: 0.0670 chunk 86 optimal weight: 1.9990 chunk 137 optimal weight: 0.8980 chunk 163 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 193 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN D 491 GLN B 272 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.137673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.108712 restraints weight = 50855.004| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.72 r_work: 0.3232 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17701 Z= 0.138 Angle : 0.553 8.764 24206 Z= 0.283 Chirality : 0.044 0.253 2887 Planarity : 0.004 0.040 2914 Dihedral : 10.118 164.306 3392 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.78 % Favored : 98.17 % Rotamer: Outliers : 1.23 % Allowed : 8.18 % Favored : 90.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.74 (0.18), residues: 2025 helix: 2.70 (0.18), residues: 785 sheet: 0.35 (0.24), residues: 422 loop : 0.13 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 461 TYR 0.013 0.001 TYR D 119 PHE 0.018 0.001 PHE C 284 TRP 0.016 0.001 TRP B 55 HIS 0.006 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00294 (17666) covalent geometry : angle 0.53733 (24107) SS BOND : bond 0.00225 ( 6) SS BOND : angle 2.66671 ( 12) hydrogen bonds : bond 0.05048 ( 902) hydrogen bonds : angle 4.46007 ( 2799) link_ALPHA1-3 : bond 0.01002 ( 6) link_ALPHA1-3 : angle 2.05513 ( 18) link_ALPHA1-6 : bond 0.00802 ( 5) link_ALPHA1-6 : angle 1.64576 ( 15) link_BETA1-4 : bond 0.00827 ( 11) link_BETA1-4 : angle 2.29379 ( 33) link_BETA1-6 : bond 0.00362 ( 1) link_BETA1-6 : angle 1.50848 ( 3) link_NAG-ASN : bond 0.00199 ( 6) link_NAG-ASN : angle 1.72441 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 196 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 ARG cc_start: 0.8199 (mtm-85) cc_final: 0.7809 (mtt90) REVERT: A 278 MET cc_start: 0.7733 (ttp) cc_final: 0.7471 (tmm) REVERT: A 308 MET cc_start: 0.8333 (OUTLIER) cc_final: 0.7840 (tpp) REVERT: A 416 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7754 (tp) REVERT: E 30 ARG cc_start: 0.7760 (mtp85) cc_final: 0.7462 (mtt90) REVERT: D 9 ARG cc_start: 0.7834 (ttp-110) cc_final: 0.7609 (ttp-110) REVERT: D 186 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.7200 (tt0) REVERT: D 460 MET cc_start: 0.8372 (ttm) cc_final: 0.8089 (ttm) REVERT: B 314 THR cc_start: 0.7938 (OUTLIER) cc_final: 0.7685 (m) REVERT: B 435 ASP cc_start: 0.7371 (OUTLIER) cc_final: 0.6572 (t0) outliers start: 23 outliers final: 13 residues processed: 206 average time/residue: 1.1168 time to fit residues: 259.0645 Evaluate side-chains 210 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 192 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 301 ARG Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 435 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 145 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 193 optimal weight: 0.9990 chunk 154 optimal weight: 0.0170 chunk 158 optimal weight: 0.4980 chunk 69 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 102 optimal weight: 0.3980 chunk 202 optimal weight: 0.0870 overall best weight: 0.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN C 394 ASN D 491 GLN B 272 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.139630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.111166 restraints weight = 50849.093| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.69 r_work: 0.3270 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17701 Z= 0.105 Angle : 0.511 7.667 24206 Z= 0.259 Chirality : 0.043 0.220 2887 Planarity : 0.004 0.041 2914 Dihedral : 9.205 159.119 3392 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.93 % Favored : 98.02 % Rotamer: Outliers : 1.12 % Allowed : 8.34 % Favored : 90.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.91 (0.19), residues: 2025 helix: 2.91 (0.18), residues: 783 sheet: 0.36 (0.24), residues: 420 loop : 0.19 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 22 TYR 0.010 0.001 TYR D 434 PHE 0.017 0.001 PHE C 284 TRP 0.016 0.001 TRP B 55 HIS 0.013 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00222 (17666) covalent geometry : angle 0.49877 (24107) SS BOND : bond 0.00113 ( 6) SS BOND : angle 1.56216 ( 12) hydrogen bonds : bond 0.04436 ( 902) hydrogen bonds : angle 4.23044 ( 2799) link_ALPHA1-3 : bond 0.00990 ( 6) link_ALPHA1-3 : angle 1.84137 ( 18) link_ALPHA1-6 : bond 0.00887 ( 5) link_ALPHA1-6 : angle 1.40379 ( 15) link_BETA1-4 : bond 0.00767 ( 11) link_BETA1-4 : angle 2.07842 ( 33) link_BETA1-6 : bond 0.00448 ( 1) link_BETA1-6 : angle 1.51224 ( 3) link_NAG-ASN : bond 0.00286 ( 6) link_NAG-ASN : angle 1.69416 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 200 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 278 MET cc_start: 0.7689 (ttp) cc_final: 0.7414 (tmm) REVERT: A 308 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.7833 (tpp) REVERT: A 416 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7688 (tp) REVERT: E 28 ARG cc_start: 0.8239 (mtp180) cc_final: 0.8019 (mtp180) REVERT: E 30 ARG cc_start: 0.7710 (mtp85) cc_final: 0.7365 (mtt90) REVERT: D 9 ARG cc_start: 0.7784 (ttp-110) cc_final: 0.7567 (ttp-110) REVERT: D 460 MET cc_start: 0.8288 (ttm) cc_final: 0.8005 (ttm) REVERT: B 83 GLU cc_start: 0.8006 (mp0) cc_final: 0.7755 (pm20) REVERT: B 314 THR cc_start: 0.7950 (OUTLIER) cc_final: 0.7696 (m) outliers start: 21 outliers final: 10 residues processed: 208 average time/residue: 1.1542 time to fit residues: 271.3406 Evaluate side-chains 210 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 197 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 301 ARG Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 314 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 167 optimal weight: 1.9990 chunk 186 optimal weight: 0.8980 chunk 156 optimal weight: 1.9990 chunk 154 optimal weight: 0.9990 chunk 169 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 153 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN D 491 GLN B 272 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.136657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.107804 restraints weight = 50753.186| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.70 r_work: 0.3220 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17701 Z= 0.200 Angle : 0.586 8.724 24206 Z= 0.301 Chirality : 0.045 0.281 2887 Planarity : 0.005 0.041 2914 Dihedral : 9.432 167.104 3392 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.22 % Favored : 97.73 % Rotamer: Outliers : 1.12 % Allowed : 8.66 % Favored : 90.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.79 (0.18), residues: 2025 helix: 2.72 (0.17), residues: 785 sheet: 0.37 (0.24), residues: 424 loop : 0.18 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 81 TYR 0.015 0.002 TYR E 419 PHE 0.024 0.002 PHE C 284 TRP 0.018 0.002 TRP D 176 HIS 0.014 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00449 (17666) covalent geometry : angle 0.56943 (24107) SS BOND : bond 0.00402 ( 6) SS BOND : angle 2.86207 ( 12) hydrogen bonds : bond 0.05331 ( 902) hydrogen bonds : angle 4.44983 ( 2799) link_ALPHA1-3 : bond 0.00971 ( 6) link_ALPHA1-3 : angle 2.20138 ( 18) link_ALPHA1-6 : bond 0.00853 ( 5) link_ALPHA1-6 : angle 1.76793 ( 15) link_BETA1-4 : bond 0.00852 ( 11) link_BETA1-4 : angle 2.43964 ( 33) link_BETA1-6 : bond 0.00287 ( 1) link_BETA1-6 : angle 1.49008 ( 3) link_NAG-ASN : bond 0.00181 ( 6) link_NAG-ASN : angle 1.74934 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 195 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 278 MET cc_start: 0.7714 (ttp) cc_final: 0.7455 (tmm) REVERT: A 308 MET cc_start: 0.8319 (OUTLIER) cc_final: 0.7850 (tpp) REVERT: A 416 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7710 (tp) REVERT: E 30 ARG cc_start: 0.7727 (mtp85) cc_final: 0.7465 (mtt90) REVERT: E 319 MET cc_start: 0.8238 (ttm) cc_final: 0.8037 (ttm) REVERT: D 9 ARG cc_start: 0.7859 (ttp-110) cc_final: 0.7607 (ttp-110) REVERT: D 460 MET cc_start: 0.8311 (ttm) cc_final: 0.8042 (ttm) REVERT: B 314 THR cc_start: 0.7943 (OUTLIER) cc_final: 0.7685 (m) outliers start: 21 outliers final: 14 residues processed: 203 average time/residue: 1.1671 time to fit residues: 267.2387 Evaluate side-chains 210 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 193 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 301 ARG Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 278 MET Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 426 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 184 optimal weight: 0.8980 chunk 69 optimal weight: 0.2980 chunk 78 optimal weight: 3.9990 chunk 188 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN D 491 GLN B 272 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.137466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.108737 restraints weight = 51051.479| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.69 r_work: 0.3233 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17701 Z= 0.147 Angle : 0.549 8.457 24206 Z= 0.282 Chirality : 0.043 0.248 2887 Planarity : 0.004 0.040 2914 Dihedral : 9.181 166.338 3392 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.93 % Favored : 98.02 % Rotamer: Outliers : 0.86 % Allowed : 8.61 % Favored : 90.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.84 (0.19), residues: 2025 helix: 2.78 (0.17), residues: 784 sheet: 0.38 (0.24), residues: 422 loop : 0.19 (0.22), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 313 TYR 0.011 0.001 TYR D 119 PHE 0.020 0.002 PHE C 284 TRP 0.015 0.001 TRP B 55 HIS 0.011 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00319 (17666) covalent geometry : angle 0.53465 (24107) SS BOND : bond 0.00245 ( 6) SS BOND : angle 2.20301 ( 12) hydrogen bonds : bond 0.04997 ( 902) hydrogen bonds : angle 4.39173 ( 2799) link_ALPHA1-3 : bond 0.00953 ( 6) link_ALPHA1-3 : angle 1.90908 ( 18) link_ALPHA1-6 : bond 0.00893 ( 5) link_ALPHA1-6 : angle 1.98379 ( 15) link_BETA1-4 : bond 0.00792 ( 11) link_BETA1-4 : angle 2.28380 ( 33) link_BETA1-6 : bond 0.00392 ( 1) link_BETA1-6 : angle 1.46098 ( 3) link_NAG-ASN : bond 0.00134 ( 6) link_NAG-ASN : angle 1.67869 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 196 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 278 MET cc_start: 0.7697 (ttp) cc_final: 0.7425 (tmm) REVERT: A 308 MET cc_start: 0.8314 (OUTLIER) cc_final: 0.7834 (tpp) REVERT: A 416 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7704 (tp) REVERT: E 30 ARG cc_start: 0.7772 (mtp85) cc_final: 0.7473 (mtt90) REVERT: D 9 ARG cc_start: 0.7850 (ttp-110) cc_final: 0.7596 (ttp-110) REVERT: D 460 MET cc_start: 0.8288 (ttm) cc_final: 0.7995 (ttm) REVERT: B 314 THR cc_start: 0.7934 (OUTLIER) cc_final: 0.7674 (m) outliers start: 16 outliers final: 11 residues processed: 202 average time/residue: 1.2960 time to fit residues: 294.6481 Evaluate side-chains 208 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 194 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 301 ARG Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 314 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 145 optimal weight: 0.9980 chunk 181 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 195 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 chunk 201 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 179 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN D 491 GLN B 272 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.137075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.108350 restraints weight = 50819.875| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.69 r_work: 0.3227 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17701 Z= 0.156 Angle : 0.556 8.520 24206 Z= 0.286 Chirality : 0.043 0.252 2887 Planarity : 0.004 0.039 2914 Dihedral : 9.133 174.082 3392 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.22 % Favored : 97.73 % Rotamer: Outliers : 1.02 % Allowed : 8.39 % Favored : 90.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.84 (0.19), residues: 2025 helix: 2.78 (0.17), residues: 784 sheet: 0.38 (0.24), residues: 422 loop : 0.20 (0.22), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 81 TYR 0.012 0.001 TYR E 419 PHE 0.022 0.002 PHE C 284 TRP 0.014 0.001 TRP B 55 HIS 0.011 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00343 (17666) covalent geometry : angle 0.54158 (24107) SS BOND : bond 0.00296 ( 6) SS BOND : angle 2.36574 ( 12) hydrogen bonds : bond 0.05093 ( 902) hydrogen bonds : angle 4.41210 ( 2799) link_ALPHA1-3 : bond 0.00879 ( 6) link_ALPHA1-3 : angle 1.99562 ( 18) link_ALPHA1-6 : bond 0.00792 ( 5) link_ALPHA1-6 : angle 1.79187 ( 15) link_BETA1-4 : bond 0.00788 ( 11) link_BETA1-4 : angle 2.29747 ( 33) link_BETA1-6 : bond 0.00357 ( 1) link_BETA1-6 : angle 1.42833 ( 3) link_NAG-ASN : bond 0.00141 ( 6) link_NAG-ASN : angle 1.68850 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12896.26 seconds wall clock time: 218 minutes 24.12 seconds (13104.12 seconds total)