Starting phenix.real_space_refine on Sun Jun 29 15:18:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dmg_47003/06_2025/9dmg_47003_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dmg_47003/06_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_47003/06_2025/9dmg_47003.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dmg_47003/06_2025/9dmg_47003.map" model { file = "/net/cci-nas-00/data/ceres_data/9dmg_47003/06_2025/9dmg_47003_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dmg_47003/06_2025/9dmg_47003_neut_trim.cif" } resolution = 2.05 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 17.98, per 1000 atoms: 0.53 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: 12.11 Conformation dependent library (CDL) restraints added in 2.9 seconds 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: 2.92 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: 13.52 Time building geometry restraints manager: 13.16 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: 10.630 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: 0.510 Extract box with map and model: 1.170 Check model and map are aligned: 0.250 Set scattering table: 0.310 Process input model: 76.780 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.770 ------------------------------------------------------------------------------- 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 : 3.92 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.020 0.002 TRP B 55 HIS 0.013 0.002 HIS D 60 PHE 0.027 0.002 PHE C 284 TYR 0.017 0.002 TYR C 213 ARG 0.009 0.001 ARG D 277 Details of bonding type rmsd link_NAG-ASN : bond 0.13414 ( 6) link_NAG-ASN : angle 6.86369 ( 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_ALPHA1-3 : bond 0.00416 ( 6) link_ALPHA1-3 : angle 2.57065 ( 18) hydrogen bonds : bond 0.11914 ( 902) hydrogen bonds : angle 5.70793 ( 2799) link_BETA1-6 : bond 0.00511 ( 1) link_BETA1-6 : angle 1.58647 ( 3) SS BOND : bond 0.11942 ( 6) SS BOND : angle 5.98798 ( 12) covalent geometry : bond 0.00576 (17666) covalent geometry : angle 0.90061 (24107) *********************** 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 : 2.709 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: 0.7886 (ttmt) outliers start: 7 outliers final: 3 residues processed: 225 average time/residue: 2.7840 time to fit residues: 704.7926 Evaluate side-chains 205 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 202 time to evaluate : 2.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 323 ILE 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 171 optimal weight: 0.2980 chunk 153 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 159 optimal weight: 0.0570 chunk 61 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 118 optimal weight: 0.9980 chunk 184 optimal weight: 0.3980 overall best weight: 0.5098 ------------------------------------------------------------------------------- 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 299 HIS C 394 ASN D 422 ASN D 491 GLN B 272 GLN B 432 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.139435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.110783 restraints weight = 50683.003| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.69 r_work: 0.3263 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.0777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17701 Z= 0.137 Angle : 0.601 9.176 24206 Z= 0.294 Chirality : 0.044 0.222 2887 Planarity : 0.005 0.049 2914 Dihedral : 13.063 173.494 3395 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.63 % Favored : 98.32 % Rotamer: Outliers : 1.18 % Allowed : 8.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.19), residues: 2025 helix: 2.57 (0.18), residues: 784 sheet: 0.24 (0.25), residues: 422 loop : 0.10 (0.22), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 55 HIS 0.005 0.001 HIS E 169 PHE 0.016 0.001 PHE C 284 TYR 0.012 0.001 TYR D 119 ARG 0.002 0.000 ARG E 23 Details of bonding type rmsd link_NAG-ASN : bond 0.00457 ( 6) link_NAG-ASN : angle 2.11406 ( 18) link_ALPHA1-6 : bond 0.00724 ( 5) link_ALPHA1-6 : angle 1.90485 ( 15) link_BETA1-4 : bond 0.00989 ( 11) link_BETA1-4 : angle 2.60142 ( 33) link_ALPHA1-3 : bond 0.00876 ( 6) link_ALPHA1-3 : angle 2.60935 ( 18) hydrogen bonds : bond 0.05118 ( 902) hydrogen bonds : angle 4.57258 ( 2799) link_BETA1-6 : bond 0.00686 ( 1) link_BETA1-6 : angle 2.14751 ( 3) SS BOND : bond 0.00423 ( 6) SS BOND : angle 1.76063 ( 12) covalent geometry : bond 0.00282 (17666) covalent geometry : angle 0.58367 (24107) *********************** 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 231 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 209 time to evaluate : 2.470 Fit side-chains revert: symmetry clash REVERT: A 278 MET cc_start: 0.7646 (ttp) cc_final: 0.7377 (tmm) REVERT: A 308 MET cc_start: 0.8340 (tpp) cc_final: 0.7857 (tpp) REVERT: A 387 LYS cc_start: 0.7988 (tttp) cc_final: 0.7564 (ttmt) REVERT: A 416 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7752 (mp) REVERT: C 324 MET cc_start: 0.5871 (OUTLIER) cc_final: 0.5614 (mtm) REVERT: B 83 GLU cc_start: 0.8058 (mp0) cc_final: 0.7736 (pm20) REVERT: B 314 THR cc_start: 0.7775 (OUTLIER) cc_final: 0.7546 (m) REVERT: B 435 ASP cc_start: 0.7368 (OUTLIER) cc_final: 0.6532 (t0) outliers start: 22 outliers final: 8 residues processed: 218 average time/residue: 2.6036 time to fit residues: 641.2586 Evaluate side-chains 214 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 202 time to evaluate : 3.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 89 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 127 optimal weight: 0.9990 chunk 139 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 199 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 142 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 HIS A 322 ASN A 393 ASN A 408 HIS C 394 ASN D 60 HIS D 97 ASN D 164 GLN D 491 GLN B 95 ASN B 272 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.136718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.107532 restraints weight = 50798.230| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.72 r_work: 0.3215 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 17701 Z= 0.193 Angle : 0.614 10.129 24206 Z= 0.312 Chirality : 0.045 0.264 2887 Planarity : 0.005 0.046 2914 Dihedral : 11.785 172.244 3390 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.22 % Favored : 97.73 % Rotamer: Outliers : 1.39 % Allowed : 7.75 % Favored : 90.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.18), residues: 2025 helix: 2.50 (0.17), residues: 785 sheet: 0.24 (0.25), residues: 418 loop : 0.09 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 55 HIS 0.007 0.001 HIS E 169 PHE 0.023 0.002 PHE E 267 TYR 0.015 0.002 TYR A 72 ARG 0.004 0.001 ARG D 81 Details of bonding type rmsd link_NAG-ASN : bond 0.00237 ( 6) link_NAG-ASN : angle 1.70552 ( 18) link_ALPHA1-6 : bond 0.00869 ( 5) link_ALPHA1-6 : angle 1.63993 ( 15) link_BETA1-4 : bond 0.00968 ( 11) link_BETA1-4 : angle 2.72009 ( 33) link_ALPHA1-3 : bond 0.01067 ( 6) link_ALPHA1-3 : angle 1.98501 ( 18) hydrogen bonds : bond 0.05635 ( 902) hydrogen bonds : angle 4.60971 ( 2799) link_BETA1-6 : bond 0.00655 ( 1) link_BETA1-6 : angle 2.12715 ( 3) SS BOND : bond 0.00898 ( 6) SS BOND : angle 2.38188 ( 12) covalent geometry : bond 0.00428 (17666) covalent geometry : angle 0.59868 (24107) *********************** 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 227 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 201 time to evaluate : 2.907 Fit side-chains revert: symmetry clash REVERT: A 278 MET cc_start: 0.7713 (ttp) cc_final: 0.7454 (tmm) REVERT: A 308 MET cc_start: 0.8406 (tpp) cc_final: 0.7952 (tpp) REVERT: A 387 LYS cc_start: 0.8110 (tttp) cc_final: 0.7766 (ttmt) REVERT: A 416 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7798 (mp) REVERT: D 186 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7161 (tt0) REVERT: B 314 THR cc_start: 0.7905 (OUTLIER) cc_final: 0.7669 (m) REVERT: B 435 ASP cc_start: 0.7408 (OUTLIER) cc_final: 0.6657 (t0) outliers start: 26 outliers final: 13 residues processed: 213 average time/residue: 3.3960 time to fit residues: 837.3479 Evaluate side-chains 215 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 198 time to evaluate : 2.491 ------------------------------------------------------------------------------- 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 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 E residue 452 PHE Chi-restraints excluded: chain D residue 60 HIS 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 53 optimal weight: 0.9980 chunk 172 optimal weight: 0.9990 chunk 121 optimal weight: 0.9980 chunk 51 optimal weight: 0.0070 chunk 11 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 196 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN A 408 HIS C 394 ASN 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 = 0.3726 r_free = 0.3726 target = 0.137090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.108084 restraints weight = 51212.817| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.71 r_work: 0.3187 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 17701 Z= 0.136 Angle : 0.554 8.788 24206 Z= 0.282 Chirality : 0.043 0.244 2887 Planarity : 0.004 0.044 2914 Dihedral : 10.862 168.656 3390 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.78 % Favored : 98.17 % Rotamer: Outliers : 1.34 % Allowed : 7.96 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.18), residues: 2025 helix: 2.63 (0.18), residues: 785 sheet: 0.34 (0.25), residues: 420 loop : 0.12 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 55 HIS 0.035 0.001 HIS D 60 PHE 0.017 0.001 PHE C 284 TYR 0.012 0.001 TYR D 119 ARG 0.002 0.000 ARG D 81 Details of bonding type rmsd link_NAG-ASN : bond 0.00213 ( 6) link_NAG-ASN : angle 1.68384 ( 18) link_ALPHA1-6 : bond 0.00830 ( 5) link_ALPHA1-6 : angle 1.74291 ( 15) link_BETA1-4 : bond 0.00818 ( 11) link_BETA1-4 : angle 2.36130 ( 33) link_ALPHA1-3 : bond 0.01069 ( 6) link_ALPHA1-3 : angle 2.12278 ( 18) hydrogen bonds : bond 0.05009 ( 902) hydrogen bonds : angle 4.47797 ( 2799) link_BETA1-6 : bond 0.00426 ( 1) link_BETA1-6 : angle 1.85292 ( 3) SS BOND : bond 0.01724 ( 6) SS BOND : angle 2.37779 ( 12) covalent geometry : bond 0.00289 (17666) covalent geometry : angle 0.53866 (24107) *********************** 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 228 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 203 time to evaluate : 2.506 Fit side-chains revert: symmetry clash REVERT: A 26 ARG cc_start: 0.8232 (mtm-85) cc_final: 0.7842 (mtt90) REVERT: A 278 MET cc_start: 0.7749 (ttp) cc_final: 0.7517 (tmm) REVERT: A 308 MET cc_start: 0.8400 (tpp) cc_final: 0.7929 (tpp) REVERT: A 387 LYS cc_start: 0.8085 (tttp) cc_final: 0.7690 (ttmt) REVERT: A 416 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7780 (mp) REVERT: C 324 MET cc_start: 0.6006 (ttp) cc_final: 0.5555 (mtm) REVERT: D 9 ARG cc_start: 0.7824 (ttp-110) cc_final: 0.7602 (ttp-110) REVERT: D 186 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.7158 (tt0) REVERT: B 314 THR cc_start: 0.7902 (OUTLIER) cc_final: 0.7659 (m) REVERT: B 435 ASP cc_start: 0.7444 (OUTLIER) cc_final: 0.6648 (t0) outliers start: 25 outliers final: 13 residues processed: 214 average time/residue: 2.5640 time to fit residues: 618.5356 Evaluate side-chains 218 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 201 time to evaluate : 3.008 ------------------------------------------------------------------------------- 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 389 ASP 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 286 ILE 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 58 optimal weight: 0.0170 chunk 133 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 chunk 142 optimal weight: 0.9980 chunk 172 optimal weight: 0.0050 chunk 24 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 135 optimal weight: 1.9990 overall best weight: 0.5632 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN A 408 HIS C 394 ASN 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 = 0.3740 r_free = 0.3740 target = 0.138568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.109649 restraints weight = 50827.718| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.73 r_work: 0.3246 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17701 Z= 0.129 Angle : 0.549 8.550 24206 Z= 0.279 Chirality : 0.044 0.248 2887 Planarity : 0.004 0.043 2914 Dihedral : 10.372 166.633 3390 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.88 % Favored : 98.07 % Rotamer: Outliers : 1.28 % Allowed : 8.12 % Favored : 90.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.19), residues: 2025 helix: 2.71 (0.18), residues: 785 sheet: 0.38 (0.25), residues: 421 loop : 0.14 (0.22), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 55 HIS 0.004 0.001 HIS E 169 PHE 0.017 0.001 PHE C 284 TYR 0.011 0.001 TYR D 119 ARG 0.002 0.000 ARG D 22 Details of bonding type rmsd link_NAG-ASN : bond 0.00248 ( 6) link_NAG-ASN : angle 1.81789 ( 18) link_ALPHA1-6 : bond 0.00854 ( 5) link_ALPHA1-6 : angle 1.72071 ( 15) link_BETA1-4 : bond 0.00813 ( 11) link_BETA1-4 : angle 2.23854 ( 33) link_ALPHA1-3 : bond 0.01053 ( 6) link_ALPHA1-3 : angle 2.02361 ( 18) hydrogen bonds : bond 0.04902 ( 902) hydrogen bonds : angle 4.38648 ( 2799) link_BETA1-6 : bond 0.00314 ( 1) link_BETA1-6 : angle 1.62683 ( 3) SS BOND : bond 0.00652 ( 6) SS BOND : angle 2.98136 ( 12) covalent geometry : bond 0.00277 (17666) covalent geometry : angle 0.53271 (24107) *********************** 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 231 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 207 time to evaluate : 2.956 Fit side-chains revert: symmetry clash REVERT: A 26 ARG cc_start: 0.8190 (mtm-85) cc_final: 0.7791 (mtt90) REVERT: A 278 MET cc_start: 0.7693 (ttp) cc_final: 0.7431 (tmm) REVERT: A 301 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.7911 (mtt90) REVERT: A 308 MET cc_start: 0.8351 (tpp) cc_final: 0.7858 (tpp) REVERT: A 387 LYS cc_start: 0.8075 (tttp) cc_final: 0.7702 (ttmt) REVERT: A 416 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7743 (mp) REVERT: C 264 ILE cc_start: 0.8220 (tt) cc_final: 0.8014 (mp) REVERT: E 28 ARG cc_start: 0.8347 (mtp180) cc_final: 0.8104 (mtp-110) REVERT: E 30 ARG cc_start: 0.7744 (mtp85) cc_final: 0.7446 (mtt90) REVERT: D 186 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7150 (tt0) REVERT: B 314 THR cc_start: 0.7910 (OUTLIER) cc_final: 0.7666 (m) REVERT: B 318 MET cc_start: 0.7642 (tpt) cc_final: 0.7216 (tpt) REVERT: B 435 ASP cc_start: 0.7348 (OUTLIER) cc_final: 0.6570 (t0) outliers start: 24 outliers final: 13 residues processed: 217 average time/residue: 2.5091 time to fit residues: 616.0314 Evaluate side-chains 218 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 200 time to evaluate : 2.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 MET 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 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 E residue 452 PHE 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 426 ASP 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 40 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 51 optimal weight: 0.1980 chunk 15 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN A 408 HIS C 394 ASN 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 = 0.3719 r_free = 0.3719 target = 0.136917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.108035 restraints weight = 50729.582| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.70 r_work: 0.3222 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 17701 Z= 0.177 Angle : 0.584 9.320 24206 Z= 0.300 Chirality : 0.044 0.275 2887 Planarity : 0.005 0.042 2914 Dihedral : 10.318 167.611 3390 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.17 % Favored : 97.78 % Rotamer: Outliers : 1.50 % Allowed : 7.96 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.18), residues: 2025 helix: 2.63 (0.17), residues: 785 sheet: 0.35 (0.24), residues: 423 loop : 0.13 (0.22), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 55 HIS 0.015 0.001 HIS D 60 PHE 0.022 0.002 PHE C 284 TYR 0.013 0.001 TYR A 72 ARG 0.003 0.000 ARG D 81 Details of bonding type rmsd link_NAG-ASN : bond 0.00216 ( 6) link_NAG-ASN : angle 1.80902 ( 18) link_ALPHA1-6 : bond 0.00789 ( 5) link_ALPHA1-6 : angle 1.69744 ( 15) link_BETA1-4 : bond 0.00881 ( 11) link_BETA1-4 : angle 2.44275 ( 33) link_ALPHA1-3 : bond 0.01011 ( 6) link_ALPHA1-3 : angle 2.24154 ( 18) hydrogen bonds : bond 0.05324 ( 902) hydrogen bonds : angle 4.47357 ( 2799) link_BETA1-6 : bond 0.00288 ( 1) link_BETA1-6 : angle 1.42639 ( 3) SS BOND : bond 0.00327 ( 6) SS BOND : angle 3.10908 ( 12) covalent geometry : bond 0.00389 (17666) covalent geometry : angle 0.56700 (24107) *********************** 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 226 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 198 time to evaluate : 2.613 Fit side-chains revert: symmetry clash REVERT: A 26 ARG cc_start: 0.8199 (mtm-85) cc_final: 0.7798 (mtt90) REVERT: A 278 MET cc_start: 0.7726 (ttp) cc_final: 0.7465 (tmm) REVERT: A 301 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.7951 (mtt90) REVERT: A 308 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.7845 (tpp) REVERT: A 387 LYS cc_start: 0.8110 (tttp) cc_final: 0.7708 (ttmt) REVERT: A 416 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7737 (mp) REVERT: D 186 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7189 (tt0) REVERT: B 314 THR cc_start: 0.7965 (OUTLIER) cc_final: 0.7716 (m) REVERT: B 435 ASP cc_start: 0.7369 (OUTLIER) cc_final: 0.6565 (t0) outliers start: 28 outliers final: 15 residues processed: 210 average time/residue: 2.5681 time to fit residues: 611.8652 Evaluate side-chains 217 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 196 time to evaluate : 2.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 274 ILE 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 E residue 452 PHE 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 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 87 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 182 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 200 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN A 408 HIS ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3700 r_free = 0.3700 target = 0.135359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.106372 restraints weight = 50973.483| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.70 r_work: 0.3198 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1444 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= 0.234 Angle : 0.642 10.448 24206 Z= 0.332 Chirality : 0.047 0.335 2887 Planarity : 0.005 0.046 2914 Dihedral : 10.717 168.997 3390 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.52 % Favored : 97.43 % Rotamer: Outliers : 1.44 % Allowed : 7.96 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.18), residues: 2025 helix: 2.47 (0.17), residues: 785 sheet: 0.32 (0.24), residues: 424 loop : 0.06 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 176 HIS 0.031 0.002 HIS D 60 PHE 0.027 0.002 PHE C 284 TYR 0.015 0.002 TYR A 72 ARG 0.004 0.001 ARG D 81 Details of bonding type rmsd link_NAG-ASN : bond 0.00256 ( 6) link_NAG-ASN : angle 1.78946 ( 18) link_ALPHA1-6 : bond 0.00731 ( 5) link_ALPHA1-6 : angle 1.68735 ( 15) link_BETA1-4 : bond 0.00982 ( 11) link_BETA1-4 : angle 2.71654 ( 33) link_ALPHA1-3 : bond 0.01021 ( 6) link_ALPHA1-3 : angle 2.49371 ( 18) hydrogen bonds : bond 0.05874 ( 902) hydrogen bonds : angle 4.63305 ( 2799) link_BETA1-6 : bond 0.00250 ( 1) link_BETA1-6 : angle 1.64312 ( 3) SS BOND : bond 0.00445 ( 6) SS BOND : angle 3.85268 ( 12) covalent geometry : bond 0.00524 (17666) covalent geometry : angle 0.62265 (24107) *********************** 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 223 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 196 time to evaluate : 2.767 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 278 MET cc_start: 0.7733 (ttp) cc_final: 0.7469 (tmm) REVERT: A 308 MET cc_start: 0.8354 (OUTLIER) cc_final: 0.7849 (tpp) REVERT: A 387 LYS cc_start: 0.8152 (tttp) cc_final: 0.7772 (ttmt) REVERT: A 416 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7767 (tp) REVERT: E 9 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7161 (tp30) REVERT: E 28 ARG cc_start: 0.8406 (mtp180) cc_final: 0.8117 (mtp180) REVERT: E 30 ARG cc_start: 0.7736 (mtp85) cc_final: 0.7468 (mtt90) REVERT: D 186 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7208 (tt0) REVERT: B 314 THR cc_start: 0.7956 (OUTLIER) cc_final: 0.7697 (m) REVERT: B 435 ASP cc_start: 0.7453 (OUTLIER) cc_final: 0.6682 (t0) outliers start: 27 outliers final: 16 residues processed: 209 average time/residue: 2.5636 time to fit residues: 606.9325 Evaluate side-chains 213 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 191 time to evaluate : 2.469 ------------------------------------------------------------------------------- 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 389 ASP 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 9 GLU 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 422 ASN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 75 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 141 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 104 optimal weight: 0.6980 chunk 58 optimal weight: 0.0370 chunk 67 optimal weight: 0.9980 chunk 121 optimal weight: 0.9980 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN A 408 HIS C 394 ASN 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 = 0.3723 r_free = 0.3723 target = 0.137275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.108529 restraints weight = 50777.950| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.69 r_work: 0.3229 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1451 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 : 0.554 8.931 24206 Z= 0.284 Chirality : 0.043 0.246 2887 Planarity : 0.004 0.039 2914 Dihedral : 9.929 160.642 3390 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.83 % Favored : 98.12 % Rotamer: Outliers : 1.18 % Allowed : 8.34 % Favored : 90.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.19), residues: 2025 helix: 2.66 (0.18), residues: 784 sheet: 0.35 (0.24), residues: 422 loop : 0.13 (0.22), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 55 HIS 0.014 0.001 HIS D 60 PHE 0.018 0.002 PHE C 284 TYR 0.011 0.001 TYR D 119 ARG 0.002 0.000 ARG D 22 Details of bonding type rmsd link_NAG-ASN : bond 0.00196 ( 6) link_NAG-ASN : angle 1.70968 ( 18) link_ALPHA1-6 : bond 0.00827 ( 5) link_ALPHA1-6 : angle 1.46029 ( 15) link_BETA1-4 : bond 0.00841 ( 11) link_BETA1-4 : angle 2.35985 ( 33) link_ALPHA1-3 : bond 0.01013 ( 6) link_ALPHA1-3 : angle 1.98770 ( 18) hydrogen bonds : bond 0.05047 ( 902) hydrogen bonds : angle 4.43688 ( 2799) link_BETA1-6 : bond 0.00396 ( 1) link_BETA1-6 : angle 1.46219 ( 3) SS BOND : bond 0.00179 ( 6) SS BOND : angle 2.14634 ( 12) covalent geometry : bond 0.00293 (17666) covalent geometry : angle 0.54013 (24107) *********************** 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 215 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 193 time to evaluate : 2.930 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 ARG cc_start: 0.8199 (mtm-85) cc_final: 0.7794 (mtt90) REVERT: A 278 MET cc_start: 0.7694 (ttp) cc_final: 0.7439 (tmm) REVERT: A 387 LYS cc_start: 0.8132 (tttp) cc_final: 0.7701 (ttmt) REVERT: A 416 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7757 (tp) REVERT: E 28 ARG cc_start: 0.8346 (mtp180) cc_final: 0.8135 (mtp-110) REVERT: E 30 ARG cc_start: 0.7764 (mtp85) cc_final: 0.7475 (mtt90) REVERT: D 186 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7203 (tt0) REVERT: D 460 MET cc_start: 0.8298 (ttm) cc_final: 0.8017 (ttm) REVERT: B 314 THR cc_start: 0.7942 (OUTLIER) cc_final: 0.7684 (m) REVERT: B 435 ASP cc_start: 0.7396 (OUTLIER) cc_final: 0.6597 (t0) outliers start: 22 outliers final: 12 residues processed: 202 average time/residue: 2.6773 time to fit residues: 610.0109 Evaluate side-chains 207 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 191 time to evaluate : 2.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 173 optimal weight: 1.9990 chunk 199 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 176 optimal weight: 0.6980 chunk 137 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 chunk 138 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN A 408 HIS 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 = 0.3714 r_free = 0.3714 target = 0.136611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.107735 restraints weight = 50965.204| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.70 r_work: 0.3219 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: 0.8093 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17701 Z= 0.166 Angle : 0.573 9.172 24206 Z= 0.294 Chirality : 0.044 0.284 2887 Planarity : 0.004 0.039 2914 Dihedral : 9.567 161.689 3390 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.32 % Favored : 97.63 % Rotamer: Outliers : 1.18 % Allowed : 8.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.18), residues: 2025 helix: 2.63 (0.17), residues: 785 sheet: 0.33 (0.24), residues: 424 loop : 0.13 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 55 HIS 0.017 0.001 HIS D 60 PHE 0.023 0.002 PHE C 284 TYR 0.011 0.001 TYR A 72 ARG 0.003 0.000 ARG D 81 Details of bonding type rmsd link_NAG-ASN : bond 0.00153 ( 6) link_NAG-ASN : angle 1.74212 ( 18) link_ALPHA1-6 : bond 0.00944 ( 5) link_ALPHA1-6 : angle 2.03622 ( 15) link_BETA1-4 : bond 0.00864 ( 11) link_BETA1-4 : angle 2.46754 ( 33) link_ALPHA1-3 : bond 0.01010 ( 6) link_ALPHA1-3 : angle 2.13193 ( 18) hydrogen bonds : bond 0.05236 ( 902) hydrogen bonds : angle 4.46036 ( 2799) link_BETA1-6 : bond 0.00322 ( 1) link_BETA1-6 : angle 1.46400 ( 3) SS BOND : bond 0.00313 ( 6) SS BOND : angle 2.53926 ( 12) covalent geometry : bond 0.00364 (17666) covalent geometry : angle 0.55612 (24107) *********************** 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 214 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 192 time to evaluate : 2.627 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 ARG cc_start: 0.8201 (mtm-85) cc_final: 0.7799 (mtt90) REVERT: A 278 MET cc_start: 0.7668 (ttp) cc_final: 0.7409 (tmm) REVERT: A 308 MET cc_start: 0.8246 (tpp) cc_final: 0.7960 (tpp) REVERT: A 387 LYS cc_start: 0.8124 (tttp) cc_final: 0.7724 (ttmt) REVERT: A 416 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7763 (tp) REVERT: E 28 ARG cc_start: 0.8360 (mtp180) cc_final: 0.8150 (mtp-110) REVERT: E 30 ARG cc_start: 0.7736 (mtp85) cc_final: 0.7466 (mtt90) REVERT: D 186 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.7189 (tt0) REVERT: D 460 MET cc_start: 0.8327 (ttm) cc_final: 0.8035 (ttm) REVERT: B 314 THR cc_start: 0.7931 (OUTLIER) cc_final: 0.7675 (m) REVERT: B 435 ASP cc_start: 0.7406 (OUTLIER) cc_final: 0.6588 (t0) outliers start: 22 outliers final: 15 residues processed: 204 average time/residue: 2.7022 time to fit residues: 627.0546 Evaluate side-chains 210 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 191 time to evaluate : 2.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 389 ASP Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 269 SER 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 60 HIS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 36 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 178 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 184 optimal weight: 0.2980 chunk 7 optimal weight: 0.4980 chunk 201 optimal weight: 0.9990 chunk 196 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 177 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN A 408 HIS 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 = 0.3723 r_free = 0.3723 target = 0.137345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.108613 restraints weight = 50846.852| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.69 r_work: 0.3232 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1515 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= 0.139 Angle : 0.548 8.698 24206 Z= 0.281 Chirality : 0.043 0.256 2887 Planarity : 0.004 0.040 2914 Dihedral : 9.223 160.721 3390 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.88 % Favored : 98.07 % Rotamer: Outliers : 1.02 % Allowed : 8.50 % Favored : 90.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.19), residues: 2025 helix: 2.71 (0.18), residues: 784 sheet: 0.35 (0.24), residues: 422 loop : 0.16 (0.22), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 55 HIS 0.012 0.001 HIS D 60 PHE 0.021 0.002 PHE C 284 TYR 0.011 0.001 TYR D 119 ARG 0.002 0.000 ARG D 81 Details of bonding type rmsd link_NAG-ASN : bond 0.00131 ( 6) link_NAG-ASN : angle 1.67065 ( 18) link_ALPHA1-6 : bond 0.00862 ( 5) link_ALPHA1-6 : angle 1.94747 ( 15) link_BETA1-4 : bond 0.00818 ( 11) link_BETA1-4 : angle 2.31274 ( 33) link_ALPHA1-3 : bond 0.00927 ( 6) link_ALPHA1-3 : angle 1.89962 ( 18) hydrogen bonds : bond 0.04977 ( 902) hydrogen bonds : angle 4.39732 ( 2799) link_BETA1-6 : bond 0.00386 ( 1) link_BETA1-6 : angle 1.44163 ( 3) SS BOND : bond 0.00216 ( 6) SS BOND : angle 2.07751 ( 12) covalent geometry : bond 0.00297 (17666) covalent geometry : angle 0.53373 (24107) ********************** 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: 19 poor density : 193 time to evaluate : 2.659 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 ARG cc_start: 0.8196 (mtm-85) cc_final: 0.7799 (mtt90) REVERT: A 278 MET cc_start: 0.7665 (ttp) cc_final: 0.7397 (tmm) REVERT: A 387 LYS cc_start: 0.8085 (tttp) cc_final: 0.7701 (ttmt) REVERT: A 416 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7699 (tp) REVERT: E 28 ARG cc_start: 0.8350 (mtp180) cc_final: 0.8145 (mtp-110) REVERT: E 30 ARG cc_start: 0.7751 (mtp85) cc_final: 0.7475 (mtt90) REVERT: D 186 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7205 (tt0) REVERT: D 460 MET cc_start: 0.8280 (ttm) cc_final: 0.7979 (ttm) REVERT: B 314 THR cc_start: 0.7951 (OUTLIER) cc_final: 0.7687 (m) REVERT: B 318 MET cc_start: 0.7804 (tpt) cc_final: 0.7022 (tpp) REVERT: B 435 ASP cc_start: 0.7402 (OUTLIER) cc_final: 0.6573 (t0) outliers start: 19 outliers final: 14 residues processed: 203 average time/residue: 2.6054 time to fit residues: 596.3723 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 : 2.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 407 ASP Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 269 SER 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 124 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 163 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 141 optimal weight: 0.9990 chunk 133 optimal weight: 0.6980 chunk 91 optimal weight: 0.0000 chunk 39 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 174 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN A 408 HIS 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 = 0.3727 r_free = 0.3727 target = 0.137591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.108856 restraints weight = 50878.752| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.70 r_work: 0.3234 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1537 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= 0.139 Angle : 0.544 8.667 24206 Z= 0.279 Chirality : 0.043 0.245 2887 Planarity : 0.004 0.039 2914 Dihedral : 8.988 163.699 3390 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.22 % Favored : 97.73 % Rotamer: Outliers : 1.18 % Allowed : 8.34 % Favored : 90.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.19), residues: 2025 helix: 2.75 (0.17), residues: 784 sheet: 0.34 (0.24), residues: 422 loop : 0.17 (0.22), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 55 HIS 0.014 0.001 HIS D 60 PHE 0.021 0.002 PHE C 284 TYR 0.011 0.001 TYR D 119 ARG 0.002 0.000 ARG D 81 Details of bonding type rmsd link_NAG-ASN : bond 0.00122 ( 6) link_NAG-ASN : angle 1.64973 ( 18) link_ALPHA1-6 : bond 0.00819 ( 5) link_ALPHA1-6 : angle 1.78523 ( 15) link_BETA1-4 : bond 0.00799 ( 11) link_BETA1-4 : angle 2.27389 ( 33) link_ALPHA1-3 : bond 0.00939 ( 6) link_ALPHA1-3 : angle 1.92354 ( 18) hydrogen bonds : bond 0.04912 ( 902) hydrogen bonds : angle 4.35939 ( 2799) link_BETA1-6 : bond 0.00373 ( 1) link_BETA1-6 : angle 1.41877 ( 3) SS BOND : bond 0.00249 ( 6) SS BOND : angle 2.10257 ( 12) covalent geometry : bond 0.00302 (17666) covalent geometry : angle 0.52996 (24107) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27326.12 seconds wall clock time: 469 minutes 4.77 seconds (28144.77 seconds total)