Starting phenix.real_space_refine on Sat Jul 4 02:21:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7smr_25206/07_2026/7smr_25206.cif Found real_map, /net/cci-nas-00/data/ceres_data/7smr_25206/07_2026/7smr_25206.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7smr_25206/07_2026/7smr_25206.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7smr_25206/07_2026/7smr_25206.map" model { file = "/net/cci-nas-00/data/ceres_data/7smr_25206/07_2026/7smr_25206.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7smr_25206/07_2026/7smr_25206.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7smr_25206/07_2026/7smr_25206.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7smr_25206/07_2026/7smr_25206.cif" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 85 5.16 5 C 11150 2.51 5 N 2649 2.21 5 O 3147 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17037 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 3140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3140 Classifications: {'peptide': 387} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 366} Chain breaks: 1 Chain: "B" Number of atoms: 3456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3456 Classifications: {'peptide': 425} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 397} Chain breaks: 1 Chain: "C" Number of atoms: 3294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3294 Classifications: {'peptide': 406} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 382} Chain breaks: 1 Chain: "D" Number of atoms: 3204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3204 Classifications: {'peptide': 395} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 374} Chain breaks: 1 Chain: "E" Number of atoms: 3317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3317 Classifications: {'peptide': 409} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 386} Chain breaks: 1 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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 chiralities: 5 Chain: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 78 Unusual residues: {'CCE': 1, 'CLR': 1, '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: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 51 Unusual residues: {'NAG': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 104 Unusual residues: {'CLR': 1, 'DD9': 1, 'POV': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'POV:plan-1': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 73 Unusual residues: {'CCE': 1, 'CLR': 1, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'NAG': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 9 residue: pdb=" C1 CLR A 602 " occ=0.80 ... (26 atoms not shown) pdb=" O1 CLR A 602 " occ=0.80 residue: pdb=" N POV A 603 " occ=0.75 ... (38 atoms not shown) pdb="C215 POV A 603 " occ=0.75 residue: pdb=" N POV B 602 " occ=0.75 ... (35 atoms not shown) pdb="C311 POV B 602 " occ=0.75 residue: pdb=" N POV C 501 " occ=0.75 ... (33 atoms not shown) pdb="C311 POV C 501 " occ=0.75 residue: pdb=" N POV C 502 " occ=0.75 ... (30 atoms not shown) pdb=" P POV C 502 " occ=0.75 residue: pdb=" C1 CLR C 503 " occ=0.89 ... (26 atoms not shown) pdb=" O1 CLR C 503 " occ=0.89 residue: pdb=" C1 CLR D 602 " occ=0.75 ... (26 atoms not shown) pdb=" O1 CLR D 602 " occ=0.75 residue: pdb=" N POV D 603 " occ=0.75 ... (33 atoms not shown) pdb="C311 POV D 603 " occ=0.75 residue: pdb=" N POV E 502 " occ=0.75 ... (33 atoms not shown) pdb=" P POV E 502 " occ=0.75 Time building chain proxies: 3.39, per 1000 atoms: 0.20 Number of scatterers: 17037 At special positions: 0 Unit cell: (151.94, 135.89, 117.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 85 16.00 P 6 15.00 O 3147 8.00 N 2649 7.00 C 11150 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 193 " distance=2.04 Simple disulfide: pdb=" SG CYS B 130 " - pdb=" SG CYS B 144 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 142 " distance=2.03 Simple disulfide: pdb=" SG CYS D 128 " - pdb=" SG CYS D 142 " distance=2.03 Simple disulfide: pdb=" SG CYS D 192 " - pdb=" SG CYS D 193 " distance=2.05 Simple disulfide: pdb=" SG CYS E 128 " - pdb=" SG CYS E 142 " 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 ALPHA1-6 " BMA F 3 " - " MAN F 4 " " MAN F 4 " - " MAN F 5 " " BMA I 3 " - " MAN I 4 " " MAN I 4 " - " MAN I 5 " " BMA J 3 " - " MAN J 4 " " MAN J 4 " - " MAN J 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " 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 J 2 " - " BMA J 3 " NAG-ASN " NAG B 601 " - " ASN B 208 " " NAG E 501 " - " ASN E 68 " " NAG F 1 " - " ASN A 141 " " NAG G 1 " - " ASN B 143 " " NAG H 1 " - " ASN C 141 " " NAG I 1 " - " ASN D 141 " " NAG J 1 " - " ASN E 141 " Time building additional restraints: 1.49 Conformation dependent library (CDL) restraints added in 536.2 milliseconds 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3906 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 20 sheets defined 43.7% alpha, 29.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 Processing helix chain 'A' and resid 63 through 66 removed outlier: 3.528A pdb=" N ARG A 66 " --> pdb=" O VAL A 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 63 through 66' Processing helix chain 'A' and resid 68 through 73 removed outlier: 4.111A pdb=" N GLY A 73 " --> pdb=" O ALA A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 85 No H-bonds generated for 'chain 'A' and resid 83 through 85' Processing helix chain 'A' and resid 212 through 218 Processing helix chain 'A' and resid 218 through 228 Processing helix chain 'A' and resid 230 through 235 removed outlier: 3.831A pdb=" N TYR A 234 " --> pdb=" O GLY A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 240 Processing helix chain 'A' and resid 241 through 261 Processing helix chain 'A' and resid 272 through 300 Processing helix chain 'A' and resid 309 through 317 removed outlier: 3.808A pdb=" N ILE A 315 " --> pdb=" O TRP A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 324 Processing helix chain 'A' and resid 371 through 426 Processing helix chain 'B' and resid 3 through 13 Processing helix chain 'B' and resid 65 through 68 removed outlier: 3.830A pdb=" N THR B 68 " --> pdb=" O HIS B 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 65 through 68' Processing helix chain 'B' and resid 225 through 232 Processing helix chain 'B' and resid 232 through 246 removed outlier: 3.763A pdb=" N CYS B 236 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA B 243 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER B 244 " --> pdb=" O SER B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 249 No H-bonds generated for 'chain 'B' and resid 247 through 249' Processing helix chain 'B' and resid 250 through 254 removed outlier: 3.569A pdb=" N GLY B 254 " --> pdb=" O ALA B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 277 removed outlier: 3.542A pdb=" N ARG B 277 " --> pdb=" O LEU B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 314 Processing helix chain 'B' and resid 323 through 331 Processing helix chain 'B' and resid 332 through 338 removed outlier: 3.950A pdb=" N ARG B 336 " --> pdb=" O GLU B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 478 Proline residue: B 463 - end of helix removed outlier: 3.632A pdb=" N ASN B 477 " --> pdb=" O PHE B 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 12 Processing helix chain 'C' and resid 68 through 73 removed outlier: 4.062A pdb=" N GLU C 73 " --> pdb=" O ALA C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 85 Processing helix chain 'C' and resid 217 through 238 removed outlier: 4.809A pdb=" N ILE C 226 " --> pdb=" O VAL C 222 " (cutoff:3.500A) Proline residue: C 227 - end of helix Processing helix chain 'C' and resid 242 through 246 Processing helix chain 'C' and resid 247 through 267 Processing helix chain 'C' and resid 278 through 306 Processing helix chain 'C' and resid 315 through 323 Processing helix chain 'C' and resid 325 through 331 removed outlier: 3.921A pdb=" N PHE C 329 " --> pdb=" O THR C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 460 Processing helix chain 'D' and resid 2 through 12 Processing helix chain 'D' and resid 63 through 66 removed outlier: 3.802A pdb=" N ARG D 66 " --> pdb=" O VAL D 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 63 through 66' Processing helix chain 'D' and resid 68 through 73 removed outlier: 3.962A pdb=" N GLY D 73 " --> pdb=" O ALA D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 85 removed outlier: 3.587A pdb=" N VAL D 85 " --> pdb=" O SER D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 218 Processing helix chain 'D' and resid 218 through 230 removed outlier: 4.004A pdb=" N GLY D 230 " --> pdb=" O SER D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 234 Processing helix chain 'D' and resid 236 through 240 Processing helix chain 'D' and resid 241 through 264 Processing helix chain 'D' and resid 272 through 300 Processing helix chain 'D' and resid 309 through 319 removed outlier: 3.863A pdb=" N THR D 319 " --> pdb=" O ILE D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 324 Processing helix chain 'D' and resid 371 through 425 Processing helix chain 'D' and resid 428 through 433 Processing helix chain 'E' and resid 2 through 13 removed outlier: 4.257A pdb=" N ARG E 6 " --> pdb=" O ASN E 2 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 73 removed outlier: 4.011A pdb=" N GLU E 73 " --> pdb=" O SER 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 219 through 226 Processing helix chain 'E' and resid 226 through 235 Processing helix chain 'E' and resid 236 through 242 removed outlier: 3.625A pdb=" N TYR E 241 " --> pdb=" O VAL E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 271 removed outlier: 3.514A pdb=" N GLN E 271 " --> pdb=" O PHE E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 309 Processing helix chain 'E' and resid 318 through 328 removed outlier: 3.710A pdb=" N PHE E 328 " --> pdb=" O LEU E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 412 through 472 Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 81 removed outlier: 4.189A pdb=" N LYS A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 81 removed outlier: 4.189A pdb=" N LYS A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE A 49 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL A 43 " --> pdb=" O ILE A 49 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N GLU A 51 " --> pdb=" O ILE A 41 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ARG A 55 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N LEU A 37 " --> pdb=" O ARG A 55 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ARG A 57 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N LEU A 35 " --> pdb=" O ARG A 57 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N GLN A 59 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N VAL A 33 " --> pdb=" O GLN A 59 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N ILE A 61 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N ILE A 31 " --> pdb=" O ILE A 61 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 removed outlier: 3.918A pdb=" N CYS A 142 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE A 205 " --> pdb=" O CYS A 142 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE A 148 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N LEU A 199 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N GLN A 208 " --> pdb=" O MET A 178 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N MET A 178 " --> pdb=" O GLN A 208 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 80 through 82 Processing sheet with id=AA5, first strand: chain 'B' and resid 80 through 82 removed outlier: 6.248A pdb=" N THR B 51 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LEU B 45 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR B 53 " --> pdb=" O ILE B 43 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N TRP B 57 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LEU B 39 " --> pdb=" O TRP B 57 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ASP B 59 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N LEU B 37 " --> pdb=" O ASP B 59 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N ALA B 61 " --> pdb=" O LEU B 35 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N LEU B 35 " --> pdb=" O ALA B 61 " (cutoff:3.500A) removed outlier: 8.865A pdb=" N TYR B 63 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N ILE B 33 " --> pdb=" O TYR B 63 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 92 through 94 removed outlier: 5.089A pdb=" N ALA B 150 " --> pdb=" O GLN B 213 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N GLN B 213 " --> pdb=" O ALA B 150 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE B 220 " --> pdb=" O ILE B 193 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 92 through 94 removed outlier: 5.089A pdb=" N ALA B 150 " --> pdb=" O GLN B 213 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N GLN B 213 " --> pdb=" O ALA B 150 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 164 through 166 Processing sheet with id=AA9, first strand: chain 'C' and resid 77 through 80 removed outlier: 3.963A pdb=" N ALA C 115 " --> pdb=" O GLN C 111 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N GLY C 114 " --> pdb=" O ASP C 62 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N GLU C 49 " --> pdb=" O LEU C 43 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LEU C 43 " --> pdb=" O GLU C 49 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N THR C 51 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N PHE C 55 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N LEU C 37 " --> pdb=" O PHE C 55 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ASN C 57 " --> pdb=" O LEU C 35 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N LEU C 35 " --> pdb=" O ASN C 57 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N ALA C 59 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N VAL C 33 " --> pdb=" O ALA C 59 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N THR C 61 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N VAL C 31 " --> pdb=" O THR C 61 " (cutoff:3.500A) removed outlier: 11.115A pdb=" N TYR C 63 " --> pdb=" O VAL C 29 " (cutoff:3.500A) removed outlier: 13.220A pdb=" N VAL C 29 " --> pdb=" O TYR C 63 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL C 29 " --> pdb=" O THR C 157 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N GLN C 159 " --> pdb=" O VAL C 29 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL C 31 " --> pdb=" O GLN C 159 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 121 through 127 removed outlier: 6.291A pdb=" N GLU C 49 " --> pdb=" O LEU C 43 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LEU C 43 " --> pdb=" O GLU C 49 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N THR C 51 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N PHE C 55 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N LEU C 37 " --> pdb=" O PHE C 55 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ASN C 57 " --> pdb=" O LEU C 35 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N LEU C 35 " --> pdb=" O ASN C 57 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N ALA C 59 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N VAL C 33 " --> pdb=" O ALA C 59 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N THR C 61 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N VAL C 31 " --> pdb=" O THR C 61 " (cutoff:3.500A) removed outlier: 11.115A pdb=" N TYR C 63 " --> pdb=" O VAL C 29 " (cutoff:3.500A) removed outlier: 13.220A pdb=" N VAL C 29 " --> pdb=" O TYR C 63 " (cutoff:3.500A) removed outlier: 9.121A pdb=" N VAL C 174 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU C 35 " --> pdb=" O VAL C 174 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 90 through 92 removed outlier: 5.226A pdb=" N SER C 148 " --> pdb=" O GLU C 205 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N GLU C 205 " --> pdb=" O SER C 148 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE C 212 " --> pdb=" O GLU C 189 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 90 through 92 removed outlier: 5.226A pdb=" N SER C 148 " --> pdb=" O GLU C 205 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N GLU C 205 " --> pdb=" O SER C 148 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N TYR C 204 " --> pdb=" O ARG C 198 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ARG C 198 " --> pdb=" O TYR C 204 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 77 through 80 removed outlier: 4.278A pdb=" N LYS D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 77 through 80 removed outlier: 4.278A pdb=" N LYS D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ILE D 49 " --> pdb=" O SER D 42 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N SER D 42 " --> pdb=" O ILE D 49 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N GLU D 51 " --> pdb=" O LEU D 40 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N LEU D 40 " --> pdb=" O GLU D 51 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ASN D 53 " --> pdb=" O ILE D 38 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ILE D 61 " --> pdb=" O ASP D 30 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ASP D 30 " --> pdb=" O ILE D 61 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N VAL D 29 " --> pdb=" O SER D 157 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N SER D 159 " --> pdb=" O VAL D 29 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ILE D 31 " --> pdb=" O SER D 159 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 90 through 92 removed outlier: 3.768A pdb=" N CYS D 142 " --> pdb=" O PHE D 205 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE D 205 " --> pdb=" O CYS D 142 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE D 148 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N LEU D 199 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP D 180 " --> pdb=" O ILE D 206 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLN D 208 " --> pdb=" O MET D 178 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N MET D 178 " --> pdb=" O GLN D 208 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 77 through 81 removed outlier: 3.989A pdb=" N SER E 115 " --> pdb=" O TYR E 111 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 77 through 81 removed outlier: 3.989A pdb=" N SER E 115 " --> pdb=" O TYR E 111 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ALA E 49 " --> pdb=" O SER E 42 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N SER E 42 " --> pdb=" O ALA E 49 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR E 51 " --> pdb=" O LEU E 40 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N LEU E 40 " --> pdb=" O THR E 51 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASN E 53 " --> pdb=" O THR E 38 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ASN E 61 " --> pdb=" O ASP E 30 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ASP E 30 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE E 29 " --> pdb=" O ASN E 157 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N GLN E 159 " --> pdb=" O ILE E 29 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL E 31 " --> pdb=" O GLN E 159 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 90 through 92 removed outlier: 5.128A pdb=" N SER E 148 " --> pdb=" O GLN E 207 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N GLN E 207 " --> pdb=" O SER E 148 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE E 214 " --> pdb=" O ARG E 187 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 90 through 92 removed outlier: 5.128A pdb=" N SER E 148 " --> pdb=" O GLN E 207 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N GLN E 207 " --> pdb=" O SER E 148 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 162 through 163 921 hydrogen bonds defined for protein. 2661 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.82 Time building geometry restraints manager: 1.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2651 1.31 - 1.44: 4774 1.44 - 1.58: 9881 1.58 - 1.71: 13 1.71 - 1.84: 139 Bond restraints: 17458 Sorted by residual: bond pdb=" C TRP D 184 " pdb=" N LYS D 185 " ideal model delta sigma weight residual 1.329 1.278 0.051 1.43e-02 4.89e+03 1.29e+01 bond pdb=" C THR A 143 " pdb=" N MET A 144 " ideal model delta sigma weight residual 1.332 1.373 -0.041 1.35e-02 5.49e+03 9.27e+00 bond pdb=" N POV A 603 " pdb=" C12 POV A 603 " ideal model delta sigma weight residual 1.508 1.448 0.060 2.00e-02 2.50e+03 8.95e+00 bond pdb=" N POV E 502 " pdb=" C12 POV E 502 " ideal model delta sigma weight residual 1.508 1.451 0.057 2.00e-02 2.50e+03 8.26e+00 bond pdb=" N POV C 502 " pdb=" C12 POV C 502 " ideal model delta sigma weight residual 1.508 1.453 0.055 2.00e-02 2.50e+03 7.46e+00 ... (remaining 17453 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 23406 2.48 - 4.97: 335 4.97 - 7.45: 47 7.45 - 9.93: 4 9.93 - 12.41: 12 Bond angle restraints: 23804 Sorted by residual: angle pdb=" O11 POV B 602 " pdb=" P POV B 602 " pdb=" O12 POV B 602 " ideal model delta sigma weight residual 97.67 110.08 -12.41 3.00e+00 1.11e-01 1.71e+01 angle pdb=" O11 POV D 603 " pdb=" P POV D 603 " pdb=" O12 POV D 603 " ideal model delta sigma weight residual 97.67 109.48 -11.81 3.00e+00 1.11e-01 1.55e+01 angle pdb=" O13 POV D 603 " pdb=" P POV D 603 " pdb=" O14 POV D 603 " ideal model delta sigma weight residual 121.11 109.32 11.79 3.00e+00 1.11e-01 1.54e+01 angle pdb=" O13 POV C 502 " pdb=" P POV C 502 " pdb=" O14 POV C 502 " ideal model delta sigma weight residual 121.11 109.36 11.75 3.00e+00 1.11e-01 1.53e+01 angle pdb=" O11 POV C 501 " pdb=" P POV C 501 " pdb=" O12 POV C 501 " ideal model delta sigma weight residual 97.67 109.39 -11.72 3.00e+00 1.11e-01 1.53e+01 ... (remaining 23799 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.71: 9811 27.71 - 55.41: 317 55.41 - 83.12: 36 83.12 - 110.83: 8 110.83 - 138.53: 4 Dihedral angle restraints: 10176 sinusoidal: 4177 harmonic: 5999 Sorted by residual: dihedral pdb=" CA CYS D 142 " pdb=" C CYS D 142 " pdb=" N THR D 143 " pdb=" CA THR D 143 " ideal model delta harmonic sigma weight residual -180.00 -151.44 -28.56 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA CYS A 142 " pdb=" C CYS A 142 " pdb=" N THR A 143 " pdb=" CA THR A 143 " ideal model delta harmonic sigma weight residual -180.00 -151.90 -28.10 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA CYS D 192 " pdb=" C CYS D 192 " pdb=" N CYS D 193 " pdb=" CA CYS D 193 " ideal model delta harmonic sigma weight residual -180.00 -157.89 -22.11 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 10173 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 2544 0.079 - 0.157: 246 0.157 - 0.236: 9 0.236 - 0.315: 5 0.315 - 0.393: 1 Chirality restraints: 2805 Sorted by residual: chirality pdb=" C1 NAG B 601 " pdb=" ND2 ASN B 208 " pdb=" C2 NAG B 601 " pdb=" O5 NAG B 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.86e+00 chirality pdb=" C5 BMA J 3 " pdb=" C4 BMA J 3 " pdb=" C6 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN D 141 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 2802 not shown) Planarity restraints: 2888 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 141 " 0.029 2.00e-02 2.50e+03 2.87e-02 1.03e+01 pdb=" CG ASN A 141 " -0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN A 141 " -0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN A 141 " -0.042 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 217 " 0.171 9.50e-02 1.11e+02 7.68e-02 3.91e+00 pdb=" NE ARG E 217 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG E 217 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG E 217 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG E 217 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 223 " -0.009 2.00e-02 2.50e+03 1.86e-02 3.47e+00 pdb=" C ILE E 223 " 0.032 2.00e-02 2.50e+03 pdb=" O ILE E 223 " -0.012 2.00e-02 2.50e+03 pdb=" N ILE E 224 " -0.011 2.00e-02 2.50e+03 ... (remaining 2885 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 270 2.69 - 3.24: 16464 3.24 - 3.79: 27287 3.79 - 4.35: 37730 4.35 - 4.90: 62199 Nonbonded interactions: 143950 Sorted by model distance: nonbonded pdb=" OE2 GLU D 45 " pdb=" NH2 ARG D 209 " model vdw 2.131 3.120 nonbonded pdb=" OG SER A 82 " pdb=" O THR A 106 " model vdw 2.176 3.040 nonbonded pdb=" OD2 ASP D 89 " pdb=" OG1 THR D 150 " model vdw 2.194 3.040 nonbonded pdb=" OD2 ASP E 138 " pdb=" NE2 GLN E 140 " model vdw 2.196 3.120 nonbonded pdb=" OE2 GLU D 4 " pdb=" O HOH D 701 " model vdw 2.198 3.040 ... (remaining 143945 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 602 or (resid 603 and (name N or name C1 or name \ C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or n \ ame C22 or name C23 or name C24 or name C25 or name C26 or name C3 or name C31 o \ r name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name O \ 11 or name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or na \ me O32 or name P )))) selection = (chain 'D' and (resid 1 through 330 or resid 370 through 426 or resid 601 throug \ h 602 or (resid 603 and (name N or name C1 or name C11 or name C12 or name C13 o \ r name C14 or name C15 or name C2 or name C21 or name C22 or name C23 or name C2 \ 4 or name C25 or name C26 or name C3 or name C31 or name C32 or name C33 or name \ C34 or name C35 or name C36 or name C37 or name O11 or name O12 or name O13 or \ name O14 or name O21 or name O22 or name O31 or name O32 or name P )))) } ncs_group { reference = chain 'F' selection = chain 'I' selection = chain 'J' } 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=0.75 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.190 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: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 14.610 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 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 : 0.006 0.060 17487 Z= 0.263 Angle : 0.740 12.415 23884 Z= 0.322 Chirality : 0.047 0.393 2805 Planarity : 0.004 0.077 2881 Dihedral : 14.125 138.532 6249 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.19), residues: 2002 helix: 2.62 (0.19), residues: 768 sheet: -0.54 (0.25), residues: 384 loop : -0.51 (0.21), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 217 TYR 0.012 0.001 TYR C 124 PHE 0.015 0.001 PHE D 256 TRP 0.007 0.001 TRP E 170 HIS 0.006 0.001 HIS D 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00567 / 0.26 (17458) covalent geometry : angle 0.72715 / 0.32 (23804) SS BOND : bond 0.00794 / 0.40 ( 7) SS BOND : angle 2.19138 / 1.23 ( 14) hydrogen bonds : bond 0.11378 / 7.79 ( 845) hydrogen bonds : angle 5.84317 / 4.18 ( 2661) link_ALPHA1-6 : bond 0.00431 / 0.21 ( 6) link_ALPHA1-6 : angle 1.80833 / 1.09 ( 18) link_BETA1-4 : bond 0.00534 / 0.34 ( 9) link_BETA1-4 : angle 2.41630 / 1.47 ( 27) link_NAG-ASN : bond 0.02059 / 1.14 ( 7) link_NAG-ASN : angle 3.09607 / 2.42 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.469 Fit side-chains REVERT: A 105 MET cc_start: 0.9184 (mmt) cc_final: 0.8981 (mmp) REVERT: A 278 MET cc_start: 0.7913 (mmm) cc_final: 0.7443 (mmt) REVERT: A 324 MET cc_start: 0.6599 (tpt) cc_final: 0.6028 (ptm) REVERT: A 410 LEU cc_start: 0.8834 (mm) cc_final: 0.8566 (mm) REVERT: B 454 ASP cc_start: 0.7832 (p0) cc_final: 0.7413 (p0) REVERT: C 233 ILE cc_start: 0.8885 (mt) cc_final: 0.8661 (mm) REVERT: C 420 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7636 (mt-10) REVERT: D 14 ASN cc_start: 0.8168 (p0) cc_final: 0.7490 (p0) REVERT: D 171 MET cc_start: 0.7260 (ttm) cc_final: 0.7038 (ttt) REVERT: D 278 MET cc_start: 0.7932 (mmm) cc_final: 0.7649 (mmm) REVERT: E 429 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7810 (mm-30) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.6716 time to fit residues: 128.9158 Evaluate side-chains 116 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 98 optimal weight: 0.0470 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.1980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.0040 chunk 91 optimal weight: 4.9990 overall best weight: 0.3490 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 20 HIS B 305 ASN C 466 ASN D 310 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.090457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.070420 restraints weight = 28075.759| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 2.13 r_work: 0.2720 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2581 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2573 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2573 r_free = 0.2573 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2571 r_free = 0.2571 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.2571 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17487 Z= 0.118 Angle : 0.509 6.937 23884 Z= 0.262 Chirality : 0.043 0.285 2805 Planarity : 0.004 0.038 2881 Dihedral : 9.523 119.137 2327 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.02 % Allowed : 4.82 % Favored : 94.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.19), residues: 2002 helix: 2.87 (0.18), residues: 769 sheet: -0.38 (0.25), residues: 387 loop : -0.39 (0.22), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 168 TYR 0.012 0.001 TYR E 117 PHE 0.019 0.001 PHE D 325 TRP 0.010 0.001 TRP A 60 HIS 0.004 0.001 HIS D 385 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (17458) covalent geometry : angle 0.49839 / 0.26 (23804) SS BOND : bond 0.00840 / 0.41 ( 7) SS BOND : angle 1.76169 / 0.92 ( 14) hydrogen bonds : bond 0.04373 / 2.94 ( 845) hydrogen bonds : angle 4.34600 / 3.15 ( 2661) link_ALPHA1-6 : bond 0.00683 / 0.35 ( 6) link_ALPHA1-6 : angle 1.57142 / 1.00 ( 18) link_BETA1-4 : bond 0.00520 / 0.34 ( 9) link_BETA1-4 : angle 1.62380 / 1.16 ( 27) link_NAG-ASN : bond 0.00250 / 0.14 ( 7) link_NAG-ASN : angle 2.28480 / 1.79 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 0.656 Fit side-chains REVERT: A 97 ASP cc_start: 0.8276 (t0) cc_final: 0.8007 (t0) REVERT: A 278 MET cc_start: 0.8439 (mmm) cc_final: 0.8152 (mmt) REVERT: A 324 MET cc_start: 0.6557 (tpt) cc_final: 0.5711 (ptm) REVERT: A 410 LEU cc_start: 0.9000 (mm) cc_final: 0.8711 (mm) REVERT: B 441 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7421 (mp0) REVERT: B 454 ASP cc_start: 0.8351 (p0) cc_final: 0.7933 (p0) REVERT: C 233 ILE cc_start: 0.8906 (mt) cc_final: 0.8700 (mm) REVERT: C 420 GLU cc_start: 0.8368 (mt-10) cc_final: 0.8132 (mt-10) REVERT: D 13 GLU cc_start: 0.7611 (pm20) cc_final: 0.7369 (pm20) REVERT: D 14 ASN cc_start: 0.8384 (p0) cc_final: 0.8085 (p0) REVERT: D 129 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.8078 (tt0) REVERT: D 171 MET cc_start: 0.8055 (ttm) cc_final: 0.7749 (ttp) REVERT: E 429 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7942 (mm-30) outliers start: 19 outliers final: 3 residues processed: 141 average time/residue: 0.5942 time to fit residues: 93.5908 Evaluate side-chains 121 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 116 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain C residue 268 ASP Chi-restraints excluded: chain D residue 129 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 166 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 136 optimal weight: 0.0870 chunk 163 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 181 optimal weight: 4.9990 chunk 180 optimal weight: 1.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 97 ASN D 310 GLN E 250 GLN E 437 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.090230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.070150 restraints weight = 28147.278| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 2.14 r_work: 0.2717 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2580 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2574 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2574 r_free = 0.2574 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2574 r_free = 0.2574 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.2574 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17487 Z= 0.123 Angle : 0.484 6.792 23884 Z= 0.247 Chirality : 0.042 0.276 2805 Planarity : 0.003 0.034 2881 Dihedral : 8.671 102.404 2327 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.86 % Allowed : 6.80 % Favored : 92.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.19), residues: 2002 helix: 2.98 (0.18), residues: 769 sheet: -0.38 (0.25), residues: 394 loop : -0.36 (0.22), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 168 TYR 0.011 0.001 TYR B 439 PHE 0.014 0.001 PHE E 467 TRP 0.010 0.001 TRP A 60 HIS 0.004 0.001 HIS B 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (17458) covalent geometry : angle 0.47318 / 0.24 (23804) SS BOND : bond 0.00787 / 0.39 ( 7) SS BOND : angle 1.64245 / 0.86 ( 14) hydrogen bonds : bond 0.04103 / 2.74 ( 845) hydrogen bonds : angle 4.06541 / 2.95 ( 2661) link_ALPHA1-6 : bond 0.00563 / 0.29 ( 6) link_ALPHA1-6 : angle 1.58453 / 1.02 ( 18) link_BETA1-4 : bond 0.00411 / 0.28 ( 9) link_BETA1-4 : angle 1.74700 / 1.20 ( 27) link_NAG-ASN : bond 0.00154 / 0.10 ( 7) link_NAG-ASN : angle 2.26725 / 1.73 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 0.533 Fit side-chains REVERT: A 97 ASP cc_start: 0.8260 (t0) cc_final: 0.8016 (t0) REVERT: A 278 MET cc_start: 0.8493 (mmm) cc_final: 0.8190 (mmt) REVERT: A 324 MET cc_start: 0.6529 (tpt) cc_final: 0.5703 (ptm) REVERT: A 397 GLU cc_start: 0.8549 (mt-10) cc_final: 0.8262 (mt-10) REVERT: B 163 MET cc_start: 0.9115 (ttp) cc_final: 0.8796 (mtp) REVERT: B 454 ASP cc_start: 0.8393 (p0) cc_final: 0.7954 (p0) REVERT: C 233 ILE cc_start: 0.8908 (mt) cc_final: 0.8694 (mm) REVERT: C 420 GLU cc_start: 0.8343 (mt-10) cc_final: 0.8138 (mt-10) REVERT: D 171 MET cc_start: 0.8189 (ttm) cc_final: 0.7913 (ttp) REVERT: D 324 MET cc_start: 0.7850 (OUTLIER) cc_final: 0.7530 (mtp) REVERT: D 380 LYS cc_start: 0.8340 (mmmm) cc_final: 0.8028 (mmmm) REVERT: E 83 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8395 (mp0) REVERT: E 483 ASP cc_start: 0.8604 (OUTLIER) cc_final: 0.8347 (t0) outliers start: 16 outliers final: 3 residues processed: 130 average time/residue: 0.5811 time to fit residues: 84.3765 Evaluate side-chains 121 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 115 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain C residue 268 ASP Chi-restraints excluded: chain D residue 324 MET Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 483 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 77 optimal weight: 4.9990 chunk 195 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 197 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 139 optimal weight: 0.9990 chunk 192 optimal weight: 8.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 39 ASN C 466 ASN D 310 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.087465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.067260 restraints weight = 28102.847| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 2.11 r_work: 0.2655 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2517 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2517 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2520 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2520 r_free = 0.2520 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2520 r_free = 0.2520 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (12 function evaluations) r_final: 0.2520 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 17487 Z= 0.247 Angle : 0.569 7.952 23884 Z= 0.287 Chirality : 0.045 0.302 2805 Planarity : 0.004 0.036 2881 Dihedral : 8.476 94.001 2327 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.23 % Allowed : 7.92 % Favored : 90.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.19), residues: 2002 helix: 2.81 (0.18), residues: 770 sheet: -0.33 (0.24), residues: 406 loop : -0.47 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 217 TYR 0.014 0.002 TYR B 74 PHE 0.018 0.002 PHE D 256 TRP 0.008 0.001 TRP D 86 HIS 0.007 0.001 HIS B 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00588 / 0.25 (17458) covalent geometry : angle 0.55553 / 0.28 (23804) SS BOND : bond 0.00858 / 0.44 ( 7) SS BOND : angle 2.21874 / 1.26 ( 14) hydrogen bonds : bond 0.04653 / 3.11 ( 845) hydrogen bonds : angle 4.23593 / 3.05 ( 2661) link_ALPHA1-6 : bond 0.00434 / 0.22 ( 6) link_ALPHA1-6 : angle 1.71470 / 1.10 ( 18) link_BETA1-4 : bond 0.00397 / 0.28 ( 9) link_BETA1-4 : angle 2.18511 / 1.43 ( 27) link_NAG-ASN : bond 0.00328 / 0.21 ( 7) link_NAG-ASN : angle 2.53841 / 1.96 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.436 Fit side-chains REVERT: A 97 ASP cc_start: 0.8292 (t0) cc_final: 0.8026 (t0) REVERT: A 278 MET cc_start: 0.8434 (mmm) cc_final: 0.8111 (mmt) REVERT: A 324 MET cc_start: 0.6505 (tpt) cc_final: 0.5721 (ptm) REVERT: B 26 HIS cc_start: 0.8329 (t-90) cc_final: 0.7864 (t-90) REVERT: B 441 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7325 (mp0) REVERT: B 454 ASP cc_start: 0.8408 (p0) cc_final: 0.7970 (p0) REVERT: C 233 ILE cc_start: 0.8963 (mt) cc_final: 0.8752 (mm) REVERT: D 13 GLU cc_start: 0.7645 (pm20) cc_final: 0.7430 (pm20) REVERT: D 14 ASN cc_start: 0.8436 (p0) cc_final: 0.8007 (p0) REVERT: D 117 MET cc_start: 0.9298 (OUTLIER) cc_final: 0.8822 (ttp) REVERT: D 171 MET cc_start: 0.8074 (ttm) cc_final: 0.7802 (ttp) REVERT: D 324 MET cc_start: 0.7821 (OUTLIER) cc_final: 0.7058 (mtp) REVERT: E 83 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8406 (mp0) REVERT: E 483 ASP cc_start: 0.8666 (OUTLIER) cc_final: 0.8435 (t0) outliers start: 23 outliers final: 10 residues processed: 132 average time/residue: 0.5972 time to fit residues: 87.8959 Evaluate side-chains 127 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 268 ASP Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain D residue 117 MET Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 324 MET Chi-restraints excluded: chain D residue 407 ASP Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain E residue 483 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 127 optimal weight: 0.0870 chunk 191 optimal weight: 7.9990 chunk 148 optimal weight: 0.9990 chunk 14 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 140 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 178 optimal weight: 0.0060 chunk 197 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 overall best weight: 0.5576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 466 ASN D 310 GLN E 315 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.090569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.070576 restraints weight = 27897.729| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 2.12 r_work: 0.2726 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2590 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2586 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2586 r_free = 0.2586 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2586 r_free = 0.2586 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2586 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 17487 Z= 0.107 Angle : 0.475 7.186 23884 Z= 0.242 Chirality : 0.042 0.281 2805 Planarity : 0.003 0.036 2881 Dihedral : 7.781 89.606 2327 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.12 % Allowed : 8.89 % Favored : 89.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.19), residues: 2002 helix: 2.94 (0.18), residues: 770 sheet: -0.36 (0.24), residues: 406 loop : -0.41 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 168 TYR 0.013 0.001 TYR E 117 PHE 0.015 0.001 PHE E 467 TRP 0.011 0.001 TRP A 60 HIS 0.004 0.001 HIS D 385 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (17458) covalent geometry : angle 0.46344 / 0.24 (23804) SS BOND : bond 0.00755 / 0.37 ( 7) SS BOND : angle 1.55422 / 0.81 ( 14) hydrogen bonds : bond 0.03928 / 2.60 ( 845) hydrogen bonds : angle 3.94934 / 2.86 ( 2661) link_ALPHA1-6 : bond 0.00590 / 0.31 ( 6) link_ALPHA1-6 : angle 1.52956 / 0.98 ( 18) link_BETA1-4 : bond 0.00453 / 0.29 ( 9) link_BETA1-4 : angle 1.62872 / 1.12 ( 27) link_NAG-ASN : bond 0.00217 / 0.12 ( 7) link_NAG-ASN : angle 2.40196 / 1.87 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 0.656 Fit side-chains REVERT: A 97 ASP cc_start: 0.8241 (t0) cc_final: 0.7960 (t0) REVERT: A 278 MET cc_start: 0.8481 (mmm) cc_final: 0.8216 (mmt) REVERT: A 324 MET cc_start: 0.6433 (tpt) cc_final: 0.5524 (ptm) REVERT: A 397 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8259 (mt-10) REVERT: B 244 SER cc_start: 0.9026 (OUTLIER) cc_final: 0.8752 (m) REVERT: B 454 ASP cc_start: 0.8396 (p0) cc_final: 0.8009 (p0) REVERT: C 233 ILE cc_start: 0.8903 (mt) cc_final: 0.8665 (mm) REVERT: D 14 ASN cc_start: 0.8459 (p0) cc_final: 0.8118 (p0) REVERT: D 129 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7926 (tt0) REVERT: D 324 MET cc_start: 0.7801 (OUTLIER) cc_final: 0.7072 (mtp) REVERT: D 380 LYS cc_start: 0.8298 (mmmm) cc_final: 0.7932 (mmmm) REVERT: E 83 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8400 (mp0) REVERT: E 483 ASP cc_start: 0.8581 (OUTLIER) cc_final: 0.8305 (t0) outliers start: 21 outliers final: 7 residues processed: 137 average time/residue: 0.5995 time to fit residues: 91.6892 Evaluate side-chains 128 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 426 PHE Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain C residue 268 ASP Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 324 MET Chi-restraints excluded: chain D residue 407 ASP Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 483 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 155 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 150 optimal weight: 0.0970 chunk 122 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 184 optimal weight: 0.9990 chunk 191 optimal weight: 8.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 310 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.088319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.068221 restraints weight = 27959.199| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 2.11 r_work: 0.2675 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2539 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2540 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2540 r_free = 0.2540 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2540 r_free = 0.2540 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (13 function evaluations) r_final: 0.2540 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 17487 Z= 0.196 Angle : 0.537 7.380 23884 Z= 0.270 Chirality : 0.044 0.288 2805 Planarity : 0.004 0.036 2881 Dihedral : 7.683 87.811 2327 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.39 % Allowed : 9.48 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.19), residues: 2002 helix: 2.87 (0.18), residues: 770 sheet: -0.38 (0.24), residues: 402 loop : -0.45 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 168 TYR 0.013 0.001 TYR B 439 PHE 0.019 0.001 PHE D 325 TRP 0.008 0.001 TRP A 60 HIS 0.005 0.001 HIS B 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.20 (17458) covalent geometry : angle 0.52461 / 0.27 (23804) SS BOND : bond 0.00835 / 0.43 ( 7) SS BOND : angle 2.08367 / 1.14 ( 14) hydrogen bonds : bond 0.04308 / 2.87 ( 845) hydrogen bonds : angle 4.06419 / 2.93 ( 2661) link_ALPHA1-6 : bond 0.00441 / 0.22 ( 6) link_ALPHA1-6 : angle 1.64649 / 1.05 ( 18) link_BETA1-4 : bond 0.00346 / 0.25 ( 9) link_BETA1-4 : angle 2.02561 / 1.33 ( 27) link_NAG-ASN : bond 0.00211 / 0.13 ( 7) link_NAG-ASN : angle 2.42529 / 1.86 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 115 time to evaluate : 0.573 Fit side-chains REVERT: A 97 ASP cc_start: 0.8318 (t0) cc_final: 0.8027 (t0) REVERT: A 278 MET cc_start: 0.8416 (mmm) cc_final: 0.8109 (mmt) REVERT: A 324 MET cc_start: 0.6459 (tpt) cc_final: 0.5535 (ptm) REVERT: A 397 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8301 (mt-10) REVERT: B 244 SER cc_start: 0.9112 (OUTLIER) cc_final: 0.8886 (m) REVERT: B 454 ASP cc_start: 0.8400 (p0) cc_final: 0.8009 (p0) REVERT: C 233 ILE cc_start: 0.8932 (mt) cc_final: 0.8714 (mm) REVERT: C 314 MET cc_start: 0.9369 (OUTLIER) cc_final: 0.9138 (ttp) REVERT: D 14 ASN cc_start: 0.8536 (p0) cc_final: 0.8167 (p0) REVERT: D 171 MET cc_start: 0.8296 (ttp) cc_final: 0.8090 (ptm) REVERT: D 278 MET cc_start: 0.8407 (tpp) cc_final: 0.8153 (mmm) REVERT: D 324 MET cc_start: 0.7829 (OUTLIER) cc_final: 0.7132 (mtp) REVERT: D 377 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8224 (mp0) REVERT: E 83 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8398 (mp0) REVERT: E 483 ASP cc_start: 0.8707 (OUTLIER) cc_final: 0.8438 (t0) outliers start: 26 outliers final: 10 residues processed: 127 average time/residue: 0.5825 time to fit residues: 82.4526 Evaluate side-chains 128 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 426 PHE Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 268 ASP Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 324 MET Chi-restraints excluded: chain D residue 377 GLU Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 483 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 7 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 190 optimal weight: 0.0370 chunk 137 optimal weight: 0.9980 chunk 117 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 159 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 overall best weight: 1.0062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 466 ASN D 310 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.089544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.069509 restraints weight = 27719.201| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 2.11 r_work: 0.2706 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2570 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2572 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2572 r_free = 0.2572 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2572 r_free = 0.2572 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.2572 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17487 Z= 0.133 Angle : 0.495 7.136 23884 Z= 0.251 Chirality : 0.043 0.280 2805 Planarity : 0.003 0.036 2881 Dihedral : 7.454 86.098 2327 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.02 % Allowed : 9.90 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.19), residues: 2002 helix: 2.93 (0.18), residues: 770 sheet: -0.33 (0.24), residues: 413 loop : -0.39 (0.22), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 168 TYR 0.012 0.001 TYR E 117 PHE 0.016 0.001 PHE E 467 TRP 0.010 0.001 TRP A 60 HIS 0.004 0.001 HIS D 385 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (17458) covalent geometry : angle 0.48268 / 0.25 (23804) SS BOND : bond 0.00772 / 0.39 ( 7) SS BOND : angle 1.91082 / 1.04 ( 14) hydrogen bonds : bond 0.04029 / 2.68 ( 845) hydrogen bonds : angle 3.94746 / 2.86 ( 2661) link_ALPHA1-6 : bond 0.00498 / 0.26 ( 6) link_ALPHA1-6 : angle 1.55320 / 0.99 ( 18) link_BETA1-4 : bond 0.00370 / 0.26 ( 9) link_BETA1-4 : angle 1.77184 / 1.19 ( 27) link_NAG-ASN : bond 0.00110 / 0.06 ( 7) link_NAG-ASN : angle 2.37334 / 1.84 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.462 Fit side-chains REVERT: A 97 ASP cc_start: 0.8254 (t0) cc_final: 0.7976 (t0) REVERT: A 278 MET cc_start: 0.8405 (mmm) cc_final: 0.8104 (mmt) REVERT: A 324 MET cc_start: 0.6447 (tpt) cc_final: 0.5530 (ptm) REVERT: A 397 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8275 (mt-10) REVERT: B 163 MET cc_start: 0.9078 (ttp) cc_final: 0.8832 (mtp) REVERT: B 244 SER cc_start: 0.9053 (OUTLIER) cc_final: 0.8849 (m) REVERT: B 454 ASP cc_start: 0.8395 (p0) cc_final: 0.7991 (p0) REVERT: C 233 ILE cc_start: 0.8922 (mt) cc_final: 0.8702 (mm) REVERT: C 314 MET cc_start: 0.9330 (OUTLIER) cc_final: 0.9060 (ttp) REVERT: D 13 GLU cc_start: 0.7575 (pm20) cc_final: 0.7370 (pm20) REVERT: D 14 ASN cc_start: 0.8519 (p0) cc_final: 0.8185 (p0) REVERT: D 278 MET cc_start: 0.8463 (tpp) cc_final: 0.8200 (mmm) REVERT: D 324 MET cc_start: 0.7791 (OUTLIER) cc_final: 0.7060 (mtp) REVERT: D 377 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8104 (mp0) REVERT: E 83 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8391 (mp0) outliers start: 19 outliers final: 9 residues processed: 127 average time/residue: 0.5964 time to fit residues: 84.4702 Evaluate side-chains 129 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 426 PHE Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 268 ASP Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain D residue 324 MET Chi-restraints excluded: chain D residue 377 GLU Chi-restraints excluded: chain D residue 407 ASP Chi-restraints excluded: chain E residue 83 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 189 optimal weight: 3.9990 chunk 172 optimal weight: 0.0470 chunk 53 optimal weight: 3.9990 chunk 188 optimal weight: 0.9990 chunk 184 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 chunk 182 optimal weight: 0.9990 chunk 167 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 overall best weight: 1.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 310 ASN D 310 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.088980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.068863 restraints weight = 28025.886| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 2.12 r_work: 0.2692 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2556 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2551 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2551 r_free = 0.2551 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2551 r_free = 0.2551 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2551 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17487 Z= 0.162 Angle : 0.515 7.123 23884 Z= 0.260 Chirality : 0.043 0.280 2805 Planarity : 0.003 0.036 2881 Dihedral : 7.401 83.978 2327 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.28 % Allowed : 10.06 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.19), residues: 2002 helix: 2.92 (0.18), residues: 770 sheet: -0.36 (0.24), residues: 412 loop : -0.39 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 168 TYR 0.012 0.001 TYR B 439 PHE 0.022 0.001 PHE D 325 TRP 0.008 0.001 TRP A 60 HIS 0.004 0.001 HIS B 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 (17458) covalent geometry : angle 0.50241 / 0.26 (23804) SS BOND : bond 0.00792 / 0.40 ( 7) SS BOND : angle 1.98024 / 1.08 ( 14) hydrogen bonds : bond 0.04135 / 2.75 ( 845) hydrogen bonds : angle 3.98156 / 2.88 ( 2661) link_ALPHA1-6 : bond 0.00465 / 0.24 ( 6) link_ALPHA1-6 : angle 1.60603 / 1.03 ( 18) link_BETA1-4 : bond 0.00337 / 0.24 ( 9) link_BETA1-4 : angle 1.89994 / 1.26 ( 27) link_NAG-ASN : bond 0.00163 / 0.10 ( 7) link_NAG-ASN : angle 2.36556 / 1.81 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 0.619 Fit side-chains REVERT: A 97 ASP cc_start: 0.8300 (t0) cc_final: 0.8019 (t0) REVERT: A 278 MET cc_start: 0.8414 (mmm) cc_final: 0.8121 (mmt) REVERT: A 324 MET cc_start: 0.6476 (tpt) cc_final: 0.5610 (ptm) REVERT: A 397 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8300 (mt-10) REVERT: B 163 MET cc_start: 0.9073 (ttp) cc_final: 0.8845 (mtp) REVERT: B 454 ASP cc_start: 0.8407 (p0) cc_final: 0.8005 (p0) REVERT: C 233 ILE cc_start: 0.8922 (mt) cc_final: 0.8711 (mm) REVERT: C 314 MET cc_start: 0.9354 (OUTLIER) cc_final: 0.9103 (ttp) REVERT: D 14 ASN cc_start: 0.8503 (p0) cc_final: 0.8228 (p0) REVERT: D 278 MET cc_start: 0.8496 (tpp) cc_final: 0.8203 (mmm) REVERT: D 324 MET cc_start: 0.7791 (OUTLIER) cc_final: 0.7101 (mtp) REVERT: D 377 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8114 (mp0) REVERT: E 83 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8398 (mp0) outliers start: 24 outliers final: 12 residues processed: 127 average time/residue: 0.6105 time to fit residues: 86.3551 Evaluate side-chains 127 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 426 PHE Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 268 ASP Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 324 MET Chi-restraints excluded: chain D residue 377 GLU Chi-restraints excluded: chain D residue 415 MET Chi-restraints excluded: chain E residue 83 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 90 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 188 optimal weight: 0.7980 chunk 121 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 178 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 148 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 113 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.089558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.069530 restraints weight = 27920.951| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 2.11 r_work: 0.2706 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2569 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2569 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2569 r_free = 0.2569 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2569 r_free = 0.2569 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2569 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17487 Z= 0.137 Angle : 0.501 7.037 23884 Z= 0.254 Chirality : 0.043 0.276 2805 Planarity : 0.003 0.053 2881 Dihedral : 7.290 82.322 2327 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.91 % Allowed : 10.55 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.19), residues: 2002 helix: 2.95 (0.18), residues: 770 sheet: -0.37 (0.24), residues: 415 loop : -0.36 (0.22), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 168 TYR 0.011 0.001 TYR B 439 PHE 0.016 0.001 PHE E 467 TRP 0.010 0.001 TRP A 60 HIS 0.004 0.001 HIS D 385 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (17458) covalent geometry : angle 0.48951 / 0.25 (23804) SS BOND : bond 0.00768 / 0.38 ( 7) SS BOND : angle 1.91536 / 1.05 ( 14) hydrogen bonds : bond 0.04004 / 2.66 ( 845) hydrogen bonds : angle 3.93026 / 2.84 ( 2661) link_ALPHA1-6 : bond 0.00493 / 0.25 ( 6) link_ALPHA1-6 : angle 1.56437 / 0.99 ( 18) link_BETA1-4 : bond 0.00357 / 0.25 ( 9) link_BETA1-4 : angle 1.79382 / 1.20 ( 27) link_NAG-ASN : bond 0.00121 / 0.08 ( 7) link_NAG-ASN : angle 2.33905 / 1.81 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.631 Fit side-chains REVERT: A 97 ASP cc_start: 0.8289 (t0) cc_final: 0.8008 (t0) REVERT: A 278 MET cc_start: 0.8411 (mmm) cc_final: 0.8112 (mmt) REVERT: A 324 MET cc_start: 0.6415 (tpt) cc_final: 0.5508 (ptp) REVERT: A 397 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8302 (mt-10) REVERT: B 163 MET cc_start: 0.9069 (ttp) cc_final: 0.8820 (mtp) REVERT: B 454 ASP cc_start: 0.8424 (p0) cc_final: 0.8022 (p0) REVERT: C 168 ARG cc_start: 0.8386 (ttm110) cc_final: 0.8184 (ttm110) REVERT: C 233 ILE cc_start: 0.8908 (mt) cc_final: 0.8693 (mm) REVERT: C 314 MET cc_start: 0.9323 (OUTLIER) cc_final: 0.9058 (ttp) REVERT: C 400 ASP cc_start: 0.8055 (m-30) cc_final: 0.7784 (m-30) REVERT: D 14 ASN cc_start: 0.8580 (p0) cc_final: 0.8325 (p0) REVERT: D 278 MET cc_start: 0.8488 (tpp) cc_final: 0.8208 (mmm) REVERT: D 324 MET cc_start: 0.7743 (OUTLIER) cc_final: 0.7031 (mtp) REVERT: D 377 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8092 (mp0) REVERT: D 380 LYS cc_start: 0.8299 (mmmm) cc_final: 0.8062 (mmmm) REVERT: D 407 ASP cc_start: 0.8312 (m-30) cc_final: 0.7969 (t0) REVERT: E 83 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8385 (mp0) outliers start: 17 outliers final: 11 residues processed: 126 average time/residue: 0.5961 time to fit residues: 83.9560 Evaluate side-chains 126 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 426 PHE Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 268 ASP Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 324 MET Chi-restraints excluded: chain D residue 377 GLU Chi-restraints excluded: chain E residue 83 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 18 optimal weight: 3.9990 chunk 196 optimal weight: 0.9980 chunk 189 optimal weight: 0.7980 chunk 175 optimal weight: 2.9990 chunk 193 optimal weight: 3.9990 chunk 118 optimal weight: 0.7980 chunk 161 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 184 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 chunk 16 optimal weight: 0.0770 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 310 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.090681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.070653 restraints weight = 27692.201| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 2.12 r_work: 0.2726 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2590 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2589 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2589 r_free = 0.2589 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2589 r_free = 0.2589 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2589 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17487 Z= 0.113 Angle : 0.497 8.722 23884 Z= 0.251 Chirality : 0.042 0.266 2805 Planarity : 0.003 0.057 2881 Dihedral : 7.122 79.971 2327 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.86 % Allowed : 10.55 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.19), residues: 2002 helix: 3.00 (0.18), residues: 770 sheet: -0.30 (0.24), residues: 415 loop : -0.35 (0.22), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 168 TYR 0.012 0.001 TYR E 117 PHE 0.023 0.001 PHE D 325 TRP 0.010 0.001 TRP D 60 HIS 0.003 0.001 HIS D 385 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (17458) covalent geometry : angle 0.48635 / 0.25 (23804) SS BOND : bond 0.00743 / 0.37 ( 7) SS BOND : angle 1.84230 / 1.01 ( 14) hydrogen bonds : bond 0.03801 / 2.51 ( 845) hydrogen bonds : angle 3.83754 / 2.78 ( 2661) link_ALPHA1-6 : bond 0.00506 / 0.26 ( 6) link_ALPHA1-6 : angle 1.51415 / 0.96 ( 18) link_BETA1-4 : bond 0.00397 / 0.27 ( 9) link_BETA1-4 : angle 1.66214 / 1.13 ( 27) link_NAG-ASN : bond 0.00119 / 0.06 ( 7) link_NAG-ASN : angle 2.25918 / 1.74 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.528 Fit side-chains REVERT: A 97 ASP cc_start: 0.8251 (t0) cc_final: 0.7985 (t0) REVERT: A 278 MET cc_start: 0.8475 (mmm) cc_final: 0.8198 (mmt) REVERT: A 324 MET cc_start: 0.6423 (tpt) cc_final: 0.5451 (ptp) REVERT: A 397 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8282 (mt-10) REVERT: B 163 MET cc_start: 0.9068 (ttp) cc_final: 0.8844 (mtp) REVERT: B 454 ASP cc_start: 0.8411 (p0) cc_final: 0.8027 (p0) REVERT: C 233 ILE cc_start: 0.8892 (mt) cc_final: 0.8672 (mm) REVERT: C 314 MET cc_start: 0.9290 (OUTLIER) cc_final: 0.9013 (ttp) REVERT: D 14 ASN cc_start: 0.8517 (p0) cc_final: 0.8284 (p0) REVERT: D 241 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7839 (mt-10) REVERT: D 278 MET cc_start: 0.8468 (tpp) cc_final: 0.8205 (mmm) REVERT: D 324 MET cc_start: 0.7762 (OUTLIER) cc_final: 0.7055 (mtp) REVERT: D 377 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8101 (mp0) REVERT: D 380 LYS cc_start: 0.8273 (mmmm) cc_final: 0.8052 (mmmm) REVERT: D 407 ASP cc_start: 0.8306 (m-30) cc_final: 0.7992 (t0) REVERT: E 83 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8395 (mp0) outliers start: 16 outliers final: 10 residues processed: 124 average time/residue: 0.5934 time to fit residues: 82.1292 Evaluate side-chains 127 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 426 PHE Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 268 ASP Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 324 MET Chi-restraints excluded: chain D residue 377 GLU Chi-restraints excluded: chain E residue 83 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 177 optimal weight: 1.9990 chunk 79 optimal weight: 0.0980 chunk 188 optimal weight: 0.8980 chunk 125 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 198 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 173 optimal weight: 4.9990 chunk 176 optimal weight: 1.9990 chunk 158 optimal weight: 5.9990 chunk 151 optimal weight: 0.8980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 466 ASN D 310 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.089750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.069727 restraints weight = 27808.328| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 2.10 r_work: 0.2708 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2572 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2576 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2576 r_free = 0.2576 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2576 r_free = 0.2576 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2576 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17487 Z= 0.144 Angle : 0.507 8.791 23884 Z= 0.256 Chirality : 0.043 0.271 2805 Planarity : 0.003 0.039 2881 Dihedral : 7.115 78.213 2327 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.91 % Allowed : 10.60 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.19), residues: 2002 helix: 2.98 (0.18), residues: 770 sheet: -0.29 (0.24), residues: 417 loop : -0.34 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 168 TYR 0.012 0.001 TYR B 439 PHE 0.022 0.001 PHE D 325 TRP 0.009 0.001 TRP A 60 HIS 0.004 0.001 HIS D 385 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 (17458) covalent geometry : angle 0.49617 / 0.25 (23804) SS BOND : bond 0.00770 / 0.39 ( 7) SS BOND : angle 1.92870 / 1.05 ( 14) hydrogen bonds : bond 0.03933 / 2.61 ( 845) hydrogen bonds : angle 3.87319 / 2.80 ( 2661) link_ALPHA1-6 : bond 0.00461 / 0.24 ( 6) link_ALPHA1-6 : angle 1.55896 / 0.99 ( 18) link_BETA1-4 : bond 0.00342 / 0.24 ( 9) link_BETA1-4 : angle 1.79086 / 1.20 ( 27) link_NAG-ASN : bond 0.00127 / 0.08 ( 7) link_NAG-ASN : angle 2.25868 / 1.73 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4926.72 seconds wall clock time: 84 minutes 53.91 seconds (5093.91 seconds total)