Starting phenix.real_space_refine on Mon Apr 6 01:41:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qna_14072/04_2026/7qna_14072.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qna_14072/04_2026/7qna_14072.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7qna_14072/04_2026/7qna_14072.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qna_14072/04_2026/7qna_14072.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7qna_14072/04_2026/7qna_14072.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qna_14072/04_2026/7qna_14072.map" } resolution = 3.0 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= 0.003 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: 4 Type Number sf(0) Gaussians S 89 5.16 5 C 9626 2.51 5 N 2362 2.21 5 O 2700 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14777 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2693 Classifications: {'peptide': 333} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 316} Chain breaks: 1 Chain: "B" Number of atoms: 2691 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 327, 2686 Classifications: {'peptide': 327} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 327, 2686 Classifications: {'peptide': 327} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 bond proxies already assigned to first conformer: 2752 Chain: "C" Number of atoms: 2701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2701 Classifications: {'peptide': 328} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 314} Chain breaks: 1 Chain: "D" Number of atoms: 2698 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 327, 2686 Classifications: {'peptide': 327} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 327, 2686 Classifications: {'peptide': 327} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 bond proxies already assigned to first conformer: 2744 Chain: "E" Number of atoms: 2691 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 327, 2686 Classifications: {'peptide': 327} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 327, 2686 Classifications: {'peptide': 327} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 bond proxies already assigned to first conformer: 2752 Chain: "N" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "a" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATYR D 66 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR D 66 " occ=0.50 Time building chain proxies: 4.65, per 1000 atoms: 0.31 Number of scatterers: 14777 At special positions: 0 Unit cell: (119.168, 92.288, 128.128, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 89 16.00 O 2700 8.00 N 2362 7.00 C 9626 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 172 " - pdb=" SG CYS A 186 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 150 " distance=2.03 Simple disulfide: pdb=" SG CYS C 151 " - pdb=" SG CYS C 165 " distance=2.03 Simple disulfide: pdb=" SG CYS D 136 " - pdb=" SG CYS D 150 " distance=2.03 Simple disulfide: pdb=" SG CYS E 136 " - pdb=" SG CYS E 150 " distance=2.03 Simple disulfide: pdb=" SG CYS N 409 " - pdb=" SG CYS N 483 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA F 3 " - " MAN F 4 " " BMA G 3 " - " MAN G 4 " " BMA H 3 " - " MAN H 4 " " BMA a 3 " - " MAN a 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " " BMA G 3 " - " MAN G 5 " " BMA H 3 " - " MAN H 5 " " BMA a 3 " - " MAN a 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " NAG-ASN " NAG A 601 " - " ASN A 157 " " NAG C 501 " - " ASN C 208 " " NAG F 1 " - " ASN B 149 " " NAG G 1 " - " ASN D 149 " " NAG H 1 " - " ASN E 149 " " NAG a 1 " - " ASN A 144 " " NAG b 1 " - " ASN B 80 " " NAG d 1 " - " ASN D 80 " " NAG e 1 " - " ASN E 80 " Time building additional restraints: 1.45 Conformation dependent library (CDL) restraints added in 835.2 milliseconds 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3344 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 19 sheets defined 40.2% alpha, 41.0% 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 48 through 57 Processing helix chain 'A' and resid 106 through 109 Processing helix chain 'A' and resid 120 through 127 removed outlier: 3.633A pdb=" N THR A 125 " --> pdb=" O MET A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 179 removed outlier: 4.398A pdb=" N ASP A 178 " --> pdb=" O ARG A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 211 Processing helix chain 'A' and resid 215 through 219 Processing helix chain 'A' and resid 256 through 263 Processing helix chain 'A' and resid 263 through 280 removed outlier: 4.265A pdb=" N SER A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N PHE A 278 " --> pdb=" O SER A 274 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N TRP A 279 " --> pdb=" O GLN A 275 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE A 280 " --> pdb=" O VAL A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 307 Processing helix chain 'A' and resid 317 through 348 removed outlier: 3.507A pdb=" N ILE A 346 " --> pdb=" O TYR A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 544 removed outlier: 3.509A pdb=" N ILE A 524 " --> pdb=" O LYS A 520 " (cutoff:3.500A) Proline residue: A 527 - end of helix Processing helix chain 'B' and resid 8 through 21 Processing helix chain 'B' and resid 70 through 73 Processing helix chain 'B' and resid 84 through 91 Processing helix chain 'B' and resid 170 through 173 Processing helix chain 'B' and resid 177 through 181 Processing helix chain 'B' and resid 218 through 225 Processing helix chain 'B' and resid 225 through 242 removed outlier: 3.576A pdb=" N VAL B 238 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N SER B 239 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N PHE B 240 " --> pdb=" O SER B 236 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N TRP B 241 " --> pdb=" O TRP B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 270 removed outlier: 3.711A pdb=" N GLU B 270 " --> pdb=" O THR B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 307 Processing helix chain 'B' and resid 423 through 447 Proline residue: B 432 - end of helix Processing helix chain 'C' and resid 28 through 36 Processing helix chain 'C' and resid 85 through 88 Processing helix chain 'C' and resid 99 through 106 removed outlier: 3.656A pdb=" N GLY C 104 " --> pdb=" O ASN C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 240 removed outlier: 3.652A pdb=" N ILE C 238 " --> pdb=" O GLY C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 257 removed outlier: 4.061A pdb=" N SER C 254 " --> pdb=" O LEU C 250 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N PHE C 255 " --> pdb=" O SER C 251 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N TRP C 256 " --> pdb=" O TRP C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 284 removed outlier: 3.516A pdb=" N THR C 281 " --> pdb=" O THR C 277 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE C 282 " --> pdb=" O THR C 278 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG C 284 " --> pdb=" O SER C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 323 Processing helix chain 'C' and resid 409 through 435 removed outlier: 3.691A pdb=" N ILE C 416 " --> pdb=" O SER C 412 " (cutoff:3.500A) Proline residue: C 419 - end of helix removed outlier: 3.501A pdb=" N VAL C 431 " --> pdb=" O LEU C 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 21 Processing helix chain 'D' and resid 70 through 73 Processing helix chain 'D' and resid 84 through 91 Processing helix chain 'D' and resid 170 through 173 Processing helix chain 'D' and resid 177 through 181 Processing helix chain 'D' and resid 218 through 225 Processing helix chain 'D' and resid 225 through 242 removed outlier: 3.576A pdb=" N VAL D 238 " --> pdb=" O ILE D 234 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N SER D 239 " --> pdb=" O LEU D 235 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N PHE D 240 " --> pdb=" O SER D 236 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N TRP D 241 " --> pdb=" O TRP D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 270 removed outlier: 3.711A pdb=" N GLU D 270 " --> pdb=" O THR D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 307 Processing helix chain 'D' and resid 423 through 447 Proline residue: D 432 - end of helix Processing helix chain 'E' and resid 8 through 21 Processing helix chain 'E' and resid 70 through 73 Processing helix chain 'E' and resid 84 through 91 Processing helix chain 'E' and resid 170 through 173 Processing helix chain 'E' and resid 177 through 181 Processing helix chain 'E' and resid 218 through 225 Processing helix chain 'E' and resid 225 through 242 removed outlier: 3.575A pdb=" N VAL E 238 " --> pdb=" O ILE E 234 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N SER E 239 " --> pdb=" O LEU E 235 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N PHE E 240 " --> pdb=" O SER E 236 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N TRP E 241 " --> pdb=" O TRP E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 270 removed outlier: 3.710A pdb=" N GLU E 270 " --> pdb=" O THR E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 307 Processing helix chain 'E' and resid 423 through 447 Proline residue: E 432 - end of helix Processing helix chain 'N' and resid 415 through 418 Processing helix chain 'N' and resid 474 through 478 removed outlier: 3.639A pdb=" N THR N 478 " --> pdb=" O PRO N 475 " (cutoff:3.500A) Processing helix chain 'N' and resid 495 through 497 No H-bonds generated for 'chain 'N' and resid 495 through 497' Processing sheet with id=AA1, first strand: chain 'A' and resid 116 through 118 removed outlier: 4.278A pdb=" N THR A 159 " --> pdb=" O MET A 155 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N GLU A 92 " --> pdb=" O PRO A 85 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N THR A 94 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N PHE A 83 " --> pdb=" O THR A 94 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ASP A 96 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ILE A 104 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N GLU A 73 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N THR A 72 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N THR A 203 " --> pdb=" O THR A 72 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N VAL A 74 " --> pdb=" O THR A 203 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 141 through 142 removed outlier: 7.100A pdb=" N GLU A 92 " --> pdb=" O PRO A 85 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N THR A 94 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N PHE A 83 " --> pdb=" O THR A 94 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ASP A 96 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ILE A 104 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N GLU A 73 " --> pdb=" O ILE A 104 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 132 through 134 removed outlier: 4.266A pdb=" N SER A 192 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ILE A 244 " --> pdb=" O SER A 192 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 132 through 134 removed outlier: 4.266A pdb=" N SER A 192 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ILE A 244 " --> pdb=" O SER A 192 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY A 228 " --> pdb=" O HIS A 251 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ARG A 253 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N LEU A 226 " --> pdb=" O ARG A 253 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 81 through 83 removed outlier: 4.424A pdb=" N ILE B 116 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ASP B 56 " --> pdb=" O MET B 49 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N MET B 49 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N CYS B 37 " --> pdb=" O ARG B 68 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 101 through 106 removed outlier: 6.607A pdb=" N THR B 133 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N SER B 104 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N THR B 131 " --> pdb=" O SER B 104 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N VAL B 106 " --> pdb=" O ARG B 129 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ARG B 129 " --> pdb=" O VAL B 106 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ASP B 56 " --> pdb=" O MET B 49 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N MET B 49 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N CYS B 37 " --> pdb=" O ARG B 68 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.863A pdb=" N SER B 156 " --> pdb=" O PRO B 206 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU B 190 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LYS B 215 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ILE B 188 " --> pdb=" O LYS B 215 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 95 through 98 removed outlier: 4.090A pdb=" N LEU C 131 " --> pdb=" O LEU C 98 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ARG C 138 " --> pdb=" O TRP C 134 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N ARG C 144 " --> pdb=" O ALA C 121 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ALA C 121 " --> pdb=" O ARG C 144 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N THR C 146 " --> pdb=" O ALA C 119 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ALA C 119 " --> pdb=" O THR C 146 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ASP C 148 " --> pdb=" O LYS C 117 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 95 through 98 removed outlier: 4.090A pdb=" N LEU C 131 " --> pdb=" O LEU C 98 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ARG C 138 " --> pdb=" O TRP C 134 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N GLU C 71 " --> pdb=" O PRO C 64 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N THR C 73 " --> pdb=" O ILE C 62 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ILE C 62 " --> pdb=" O THR C 73 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ASP C 75 " --> pdb=" O ASN C 60 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N TYR C 83 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU C 52 " --> pdb=" O TYR C 83 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N THR C 51 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N GLN C 182 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ILE C 53 " --> pdb=" O GLN C 182 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N LYS C 184 " --> pdb=" O ILE C 53 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N THR C 55 " --> pdb=" O LYS C 184 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N SER C 186 " --> pdb=" O THR C 55 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N MET C 57 " --> pdb=" O SER C 186 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N VAL C 188 " --> pdb=" O MET C 57 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL C 59 " --> pdb=" O VAL C 188 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N VAL C 190 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N SER C 61 " --> pdb=" O VAL C 190 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 111 through 113 removed outlier: 4.571A pdb=" N SER C 171 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VAL C 221 " --> pdb=" O SER C 171 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N SER C 230 " --> pdb=" O PHE C 203 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N PHE C 203 " --> pdb=" O SER C 230 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 81 through 83 removed outlier: 4.424A pdb=" N ILE D 116 " --> pdb=" O LEU D 83 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ASP D 56 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N MET D 49 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N THR D 58 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE D 47 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR D 60 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ARG D 68 " --> pdb=" O CYS D 37 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N CYS D 37 " --> pdb=" O ARG D 68 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 101 through 106 removed outlier: 6.608A pdb=" N THR D 133 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N SER D 104 " --> pdb=" O THR D 131 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N THR D 131 " --> pdb=" O SER D 104 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N VAL D 106 " --> pdb=" O ARG D 129 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ARG D 129 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ASP D 56 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N MET D 49 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N THR D 58 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE D 47 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR D 60 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ARG D 68 " --> pdb=" O CYS D 37 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N CYS D 37 " --> pdb=" O ARG D 68 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 96 through 98 removed outlier: 3.862A pdb=" N SER D 156 " --> pdb=" O PRO D 206 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU D 190 " --> pdb=" O ARG D 213 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LYS D 215 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ILE D 188 " --> pdb=" O LYS D 215 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 81 through 83 removed outlier: 4.424A pdb=" N ILE E 116 " --> pdb=" O LEU E 83 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ASP E 56 " --> pdb=" O MET E 49 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N MET E 49 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N THR E 58 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE E 47 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR E 60 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ARG E 68 " --> pdb=" O CYS E 37 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N CYS E 37 " --> pdb=" O ARG E 68 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 101 through 106 removed outlier: 6.607A pdb=" N THR E 133 " --> pdb=" O LYS E 102 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N SER E 104 " --> pdb=" O THR E 131 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N THR E 131 " --> pdb=" O SER E 104 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N VAL E 106 " --> pdb=" O ARG E 129 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ARG E 129 " --> pdb=" O VAL E 106 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ASP E 56 " --> pdb=" O MET E 49 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N MET E 49 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N THR E 58 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE E 47 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR E 60 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ARG E 68 " --> pdb=" O CYS E 37 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N CYS E 37 " --> pdb=" O ARG E 68 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 96 through 98 removed outlier: 3.862A pdb=" N SER E 156 " --> pdb=" O PRO E 206 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU E 190 " --> pdb=" O ARG E 213 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LYS E 215 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ILE E 188 " --> pdb=" O LYS E 215 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 2 through 7 removed outlier: 3.550A pdb=" N THR N 465 " --> pdb=" O ASP N 460 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 433 through 439 removed outlier: 6.565A pdb=" N TRP N 423 " --> pdb=" O VAL N 435 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ALA N 437 " --> pdb=" O MET N 421 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N MET N 421 " --> pdb=" O ALA N 437 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE N 420 " --> pdb=" O LYS N 486 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N TYR N 501 " --> pdb=" O ALA N 485 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 433 through 439 removed outlier: 6.565A pdb=" N TRP N 423 " --> pdb=" O VAL N 435 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ALA N 437 " --> pdb=" O MET N 421 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N MET N 421 " --> pdb=" O ALA N 437 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE N 420 " --> pdb=" O LYS N 486 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL N 508 " --> pdb=" O ALA N 479 " (cutoff:3.500A) 862 hydrogen bonds defined for protein. 2424 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: 2.70 Time building geometry restraints manager: 1.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4447 1.34 - 1.46: 3884 1.46 - 1.58: 6678 1.58 - 1.69: 0 1.69 - 1.81: 155 Bond restraints: 15164 Sorted by residual: bond pdb=" CG ABU B 501 " pdb=" CD ABU B 501 " ideal model delta sigma weight residual 1.540 1.501 0.039 2.00e-02 2.50e+03 3.71e+00 bond pdb=" C1 MAN a 5 " pdb=" O5 MAN a 5 " ideal model delta sigma weight residual 1.399 1.429 -0.030 2.00e-02 2.50e+03 2.19e+00 bond pdb=" C1 MAN G 5 " pdb=" O5 MAN G 5 " ideal model delta sigma weight residual 1.399 1.428 -0.029 2.00e-02 2.50e+03 2.18e+00 bond pdb=" C1 MAN G 4 " pdb=" O5 MAN G 4 " ideal model delta sigma weight residual 1.399 1.428 -0.029 2.00e-02 2.50e+03 2.10e+00 bond pdb=" C1 MAN F 5 " pdb=" O5 MAN F 5 " ideal model delta sigma weight residual 1.399 1.428 -0.029 2.00e-02 2.50e+03 2.08e+00 ... (remaining 15159 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 20250 1.45 - 2.90: 282 2.90 - 4.35: 56 4.35 - 5.80: 26 5.80 - 7.25: 5 Bond angle restraints: 20619 Sorted by residual: angle pdb=" CG ABU B 501 " pdb=" CD ABU B 501 " pdb=" OE2 ABU B 501 " ideal model delta sigma weight residual 115.90 123.15 -7.25 3.00e+00 1.11e-01 5.84e+00 angle pdb=" C MET A 145 " pdb=" N THR A 146 " pdb=" CA THR A 146 " ideal model delta sigma weight residual 121.54 125.93 -4.39 1.91e+00 2.74e-01 5.27e+00 angle pdb=" C3 BMA G 3 " pdb=" C2 BMA G 3 " pdb=" O2 BMA G 3 " ideal model delta sigma weight residual 112.95 106.60 6.35 3.00e+00 1.11e-01 4.48e+00 angle pdb=" C3 BMA H 3 " pdb=" C2 BMA H 3 " pdb=" O2 BMA H 3 " ideal model delta sigma weight residual 112.95 106.61 6.34 3.00e+00 1.11e-01 4.47e+00 angle pdb=" C3 BMA a 3 " pdb=" C2 BMA a 3 " pdb=" O2 BMA a 3 " ideal model delta sigma weight residual 112.95 106.65 6.30 3.00e+00 1.11e-01 4.41e+00 ... (remaining 20614 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.64: 8992 21.64 - 43.27: 179 43.27 - 64.91: 20 64.91 - 86.55: 27 86.55 - 108.19: 19 Dihedral angle restraints: 9237 sinusoidal: 4021 harmonic: 5216 Sorted by residual: dihedral pdb=" O4 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C5 BMA G 3 " pdb=" O5 BMA G 3 " ideal model delta sinusoidal sigma weight residual -71.29 -179.48 108.19 1 3.00e+01 1.11e-03 1.40e+01 dihedral pdb=" O4 BMA a 3 " pdb=" C4 BMA a 3 " pdb=" C5 BMA a 3 " pdb=" O5 BMA a 3 " ideal model delta sinusoidal sigma weight residual -71.29 -179.24 107.95 1 3.00e+01 1.11e-03 1.40e+01 dihedral pdb=" O4 BMA H 3 " pdb=" C4 BMA H 3 " pdb=" C5 BMA H 3 " pdb=" O5 BMA H 3 " ideal model delta sinusoidal sigma weight residual -71.29 -178.67 107.38 1 3.00e+01 1.11e-03 1.39e+01 ... (remaining 9234 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2064 0.057 - 0.115: 304 0.115 - 0.172: 20 0.172 - 0.230: 5 0.230 - 0.287: 5 Chirality restraints: 2398 Sorted by residual: chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 8.46e+01 chirality pdb=" C1 BMA a 3 " pdb=" O4 NAG a 2 " pdb=" C2 BMA a 3 " pdb=" O5 BMA a 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 8.07e+01 chirality pdb=" C1 BMA G 3 " pdb=" O4 NAG G 2 " pdb=" C2 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.36e+01 ... (remaining 2395 not shown) Planarity restraints: 2514 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL D 302 " -0.008 2.00e-02 2.50e+03 1.52e-02 2.31e+00 pdb=" C VAL D 302 " 0.026 2.00e-02 2.50e+03 pdb=" O VAL D 302 " -0.010 2.00e-02 2.50e+03 pdb=" N ASN D 303 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 302 " 0.008 2.00e-02 2.50e+03 1.51e-02 2.28e+00 pdb=" C VAL B 302 " -0.026 2.00e-02 2.50e+03 pdb=" O VAL B 302 " 0.010 2.00e-02 2.50e+03 pdb=" N ASN B 303 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 302 " 0.007 2.00e-02 2.50e+03 1.49e-02 2.21e+00 pdb=" C VAL E 302 " -0.026 2.00e-02 2.50e+03 pdb=" O VAL E 302 " 0.010 2.00e-02 2.50e+03 pdb=" N ASN E 303 " 0.009 2.00e-02 2.50e+03 ... (remaining 2511 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 3590 2.80 - 3.32: 13651 3.32 - 3.85: 25161 3.85 - 4.37: 30303 4.37 - 4.90: 51630 Nonbonded interactions: 124335 Sorted by model distance: nonbonded pdb=" O VAL C 248 " pdb=" OG SER C 251 " model vdw 2.271 3.040 nonbonded pdb=" OG SER C 286 " pdb=" NZ LYS D 274 " model vdw 2.273 3.120 nonbonded pdb=" ND2 ASN D 243 " pdb=" OD2 ASP D 245 " model vdw 2.274 3.120 nonbonded pdb=" ND2 ASN B 243 " pdb=" OD2 ASP B 245 " model vdw 2.275 3.120 nonbonded pdb=" ND2 ASN E 243 " pdb=" OD2 ASP E 245 " model vdw 2.275 3.120 ... (remaining 124330 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 'B' and (resid 7 through 43 or resid 45 through 65 or resid 67 through 44 \ 7)) selection = (chain 'D' and (resid 7 through 43 or resid 45 through 65 or resid 67 through 44 \ 7)) selection = (chain 'E' and (resid 7 through 43 or resid 45 through 65 or resid 67 through 44 \ 7)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'a' } ncs_group { reference = chain 'b' selection = chain 'd' selection = chain 'e' } 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=0.50 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: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.260 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 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 : 0.003 0.039 15198 Z= 0.139 Angle : 0.490 7.250 20715 Z= 0.223 Chirality : 0.043 0.287 2398 Planarity : 0.003 0.029 2505 Dihedral : 11.462 108.185 5875 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 0.76 % Allowed : 3.02 % Favored : 96.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.24 % 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: 1.88 (0.21), residues: 1744 helix: 2.04 (0.22), residues: 560 sheet: 1.15 (0.24), residues: 479 loop : 0.81 (0.25), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 196 TYR 0.010 0.001 TYR E 299 PHE 0.006 0.001 PHE A 190 TRP 0.006 0.001 TRP E 443 HIS 0.002 0.001 HIS D 267 Details of bonding type rmsd covalent geometry : bond 0.00298 (15164) covalent geometry : angle 0.48396 (20619) SS BOND : bond 0.00081 ( 6) SS BOND : angle 0.50129 ( 12) hydrogen bonds : bond 0.22488 ( 762) hydrogen bonds : angle 7.32841 ( 2424) link_ALPHA1-3 : bond 0.00101 ( 4) link_ALPHA1-3 : angle 0.64560 ( 12) link_ALPHA1-6 : bond 0.00091 ( 4) link_ALPHA1-6 : angle 0.45995 ( 12) link_BETA1-4 : bond 0.00203 ( 11) link_BETA1-4 : angle 1.34579 ( 33) link_NAG-ASN : bond 0.00301 ( 9) link_NAG-ASN : angle 1.71157 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 364 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 PHE cc_start: 0.8104 (m-80) cc_final: 0.7886 (m-80) REVERT: A 345 ASN cc_start: 0.7226 (m110) cc_final: 0.7005 (m-40) REVERT: B 9 MET cc_start: 0.7537 (mtp) cc_final: 0.7163 (ttm) REVERT: B 90 GLN cc_start: 0.8386 (mp10) cc_final: 0.7879 (mp10) REVERT: C 152 GLN cc_start: 0.8124 (mm-40) cc_final: 0.7906 (mm-40) REVERT: C 162 GLU cc_start: 0.8399 (tt0) cc_final: 0.8180 (tm-30) REVERT: D 55 MET cc_start: 0.8733 (mtt) cc_final: 0.8099 (mmm) REVERT: D 85 ASN cc_start: 0.8671 (p0) cc_final: 0.8362 (p0) REVERT: D 90 GLN cc_start: 0.8289 (mp10) cc_final: 0.8040 (pm20) REVERT: D 147 GLU cc_start: 0.7526 (tt0) cc_final: 0.7144 (tt0) REVERT: D 230 ILE cc_start: 0.9379 (mt) cc_final: 0.9001 (mp) REVERT: D 234 ILE cc_start: 0.9340 (mt) cc_final: 0.9098 (mp) REVERT: E 31 PHE cc_start: 0.8546 (t80) cc_final: 0.8267 (t80) REVERT: E 155 GLU cc_start: 0.7941 (tt0) cc_final: 0.7536 (tt0) REVERT: E 298 GLU cc_start: 0.9116 (tm-30) cc_final: 0.8671 (tm-30) REVERT: N 4 LEU cc_start: 0.8911 (mt) cc_final: 0.8696 (mt) REVERT: N 407 LEU cc_start: 0.7967 (mp) cc_final: 0.7685 (mp) REVERT: N 426 GLN cc_start: 0.7856 (tt0) cc_final: 0.7579 (tt0) REVERT: N 452 LYS cc_start: 0.8718 (ttmt) cc_final: 0.8512 (tppp) REVERT: N 454 ARG cc_start: 0.6827 (mtm110) cc_final: 0.6424 (mtp-110) REVERT: N 472 ASN cc_start: 0.8265 (t0) cc_final: 0.7592 (t0) REVERT: N 480 VAL cc_start: 0.8698 (t) cc_final: 0.8216 (p) outliers start: 12 outliers final: 2 residues processed: 371 average time/residue: 0.6573 time to fit residues: 264.7078 Evaluate side-chains 211 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 209 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain B residue 36 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.1980 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 8.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN A 345 ASN A 347 GLN C 33 ASN C 54 HIS ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN C 156 HIS ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.086372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.063025 restraints weight = 84801.615| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 5.27 r_work: 0.2733 rms_B_bonded: 5.23 restraints_weight: 2.0000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2740 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2740 r_free = 0.2740 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2740 r_free = 0.2740 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2740 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 15198 Z= 0.202 Angle : 0.696 9.809 20715 Z= 0.357 Chirality : 0.046 0.170 2398 Planarity : 0.004 0.033 2505 Dihedral : 9.474 81.365 2548 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 2.90 % Allowed : 13.80 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.24 % 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: 1.80 (0.21), residues: 1744 helix: 2.03 (0.21), residues: 569 sheet: 0.99 (0.24), residues: 456 loop : 0.79 (0.25), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 86 TYR 0.023 0.002 TYR D 299 PHE 0.016 0.002 PHE E 11 TRP 0.019 0.001 TRP N 440 HIS 0.003 0.001 HIS C 318 Details of bonding type rmsd covalent geometry : bond 0.00461 (15164) covalent geometry : angle 0.68525 (20619) SS BOND : bond 0.00228 ( 6) SS BOND : angle 0.58374 ( 12) hydrogen bonds : bond 0.05374 ( 762) hydrogen bonds : angle 5.08874 ( 2424) link_ALPHA1-3 : bond 0.00856 ( 4) link_ALPHA1-3 : angle 2.22046 ( 12) link_ALPHA1-6 : bond 0.00642 ( 4) link_ALPHA1-6 : angle 1.58138 ( 12) link_BETA1-4 : bond 0.00435 ( 11) link_BETA1-4 : angle 1.87496 ( 33) link_NAG-ASN : bond 0.00409 ( 9) link_NAG-ASN : angle 2.20506 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 245 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 PHE cc_start: 0.8152 (m-80) cc_final: 0.7872 (m-80) REVERT: A 118 ARG cc_start: 0.8160 (mtm-85) cc_final: 0.7878 (mpp80) REVERT: A 155 MET cc_start: 0.7714 (OUTLIER) cc_final: 0.7479 (mmt) REVERT: A 253 ARG cc_start: 0.8667 (tpp-160) cc_final: 0.7929 (mmp-170) REVERT: B 9 MET cc_start: 0.7941 (mtp) cc_final: 0.7228 (ttm) REVERT: B 90 GLN cc_start: 0.8871 (mp10) cc_final: 0.8325 (mp10) REVERT: C 162 GLU cc_start: 0.8959 (tt0) cc_final: 0.8431 (tm-30) REVERT: C 209 THR cc_start: 0.8943 (OUTLIER) cc_final: 0.8564 (p) REVERT: C 259 LYS cc_start: 0.9239 (OUTLIER) cc_final: 0.9017 (pttm) REVERT: C 260 ASP cc_start: 0.8901 (m-30) cc_final: 0.8661 (m-30) REVERT: D 9 MET cc_start: 0.8898 (pmm) cc_final: 0.8693 (mpp) REVERT: D 14 GLU cc_start: 0.9291 (mm-30) cc_final: 0.8987 (mp0) REVERT: D 18 LYS cc_start: 0.9408 (pttm) cc_final: 0.9162 (pptt) REVERT: D 25 ILE cc_start: 0.9041 (mt) cc_final: 0.8756 (mm) REVERT: D 55 MET cc_start: 0.9069 (mtt) cc_final: 0.8572 (mmm) REVERT: D 95 ASP cc_start: 0.8679 (p0) cc_final: 0.8176 (p0) REVERT: D 147 GLU cc_start: 0.8232 (tt0) cc_final: 0.7589 (tm-30) REVERT: D 181 ILE cc_start: 0.9141 (mt) cc_final: 0.8769 (mp) REVERT: D 224 GLN cc_start: 0.8380 (tp40) cc_final: 0.8052 (tp40) REVERT: D 230 ILE cc_start: 0.9458 (mt) cc_final: 0.9036 (mp) REVERT: D 444 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8677 (mm) REVERT: E 9 MET cc_start: 0.7818 (mtt) cc_final: 0.7413 (mmt) REVERT: E 90 GLN cc_start: 0.8868 (mp10) cc_final: 0.8514 (pm20) REVERT: E 137 MET cc_start: 0.8717 (mpp) cc_final: 0.8466 (mmm) REVERT: E 155 GLU cc_start: 0.8872 (tt0) cc_final: 0.8411 (mt-10) REVERT: E 182 GLU cc_start: 0.8968 (mm-30) cc_final: 0.8420 (mm-30) REVERT: E 190 GLU cc_start: 0.9028 (tt0) cc_final: 0.8753 (tt0) REVERT: E 298 GLU cc_start: 0.9541 (tm-30) cc_final: 0.9339 (tm-30) REVERT: N 421 MET cc_start: 0.8467 (tpp) cc_final: 0.8033 (mpp) REVERT: N 425 ARG cc_start: 0.8278 (ptt180) cc_final: 0.7871 (ptt-90) REVERT: N 433 GLU cc_start: 0.9028 (tp30) cc_final: 0.8669 (pt0) REVERT: N 452 LYS cc_start: 0.8819 (ttmt) cc_final: 0.8454 (tppp) REVERT: N 454 ARG cc_start: 0.6527 (mtm110) cc_final: 0.6240 (mtp-110) REVERT: N 472 ASN cc_start: 0.8300 (t0) cc_final: 0.7513 (t0) REVERT: N 480 VAL cc_start: 0.8761 (t) cc_final: 0.8184 (p) outliers start: 46 outliers final: 16 residues processed: 265 average time/residue: 0.6723 time to fit residues: 193.3545 Evaluate side-chains 223 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 203 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 222 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 78 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 chunk 50 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 72 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 116 optimal weight: 4.9990 chunk 129 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 ASN ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.086380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.063357 restraints weight = 66863.129| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 4.62 r_work: 0.2752 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2760 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2760 r_free = 0.2760 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2760 r_free = 0.2760 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2760 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15198 Z= 0.149 Angle : 0.630 10.188 20715 Z= 0.319 Chirality : 0.044 0.205 2398 Planarity : 0.004 0.035 2505 Dihedral : 8.156 70.646 2544 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 2.14 % Allowed : 15.37 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.24 % 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: 1.73 (0.21), residues: 1744 helix: 2.05 (0.21), residues: 571 sheet: 0.82 (0.24), residues: 471 loop : 0.79 (0.26), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 86 TYR 0.021 0.001 TYR D 299 PHE 0.023 0.001 PHE C 417 TRP 0.027 0.001 TRP D 241 HIS 0.005 0.001 HIS A 184 Details of bonding type rmsd covalent geometry : bond 0.00331 (15164) covalent geometry : angle 0.62349 (20619) SS BOND : bond 0.00140 ( 6) SS BOND : angle 0.56845 ( 12) hydrogen bonds : bond 0.04422 ( 762) hydrogen bonds : angle 4.62836 ( 2424) link_ALPHA1-3 : bond 0.01162 ( 4) link_ALPHA1-3 : angle 1.73046 ( 12) link_ALPHA1-6 : bond 0.00838 ( 4) link_ALPHA1-6 : angle 1.57655 ( 12) link_BETA1-4 : bond 0.00340 ( 11) link_BETA1-4 : angle 1.61315 ( 33) link_NAG-ASN : bond 0.00398 ( 9) link_NAG-ASN : angle 1.42064 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 224 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 PHE cc_start: 0.8160 (m-80) cc_final: 0.7796 (m-80) REVERT: A 118 ARG cc_start: 0.8157 (mtm-85) cc_final: 0.7859 (mpp80) REVERT: A 225 ASP cc_start: 0.8772 (m-30) cc_final: 0.8549 (m-30) REVERT: B 9 MET cc_start: 0.7634 (mtp) cc_final: 0.7005 (ttm) REVERT: B 90 GLN cc_start: 0.8811 (mp10) cc_final: 0.8321 (mp10) REVERT: C 71 GLU cc_start: 0.8464 (mt-10) cc_final: 0.7916 (mm-30) REVERT: C 162 GLU cc_start: 0.8931 (tt0) cc_final: 0.8381 (tm-30) REVERT: C 239 GLN cc_start: 0.9127 (tp40) cc_final: 0.8825 (tp40) REVERT: D 14 GLU cc_start: 0.9471 (mm-30) cc_final: 0.8945 (mp0) REVERT: D 55 MET cc_start: 0.9113 (mtt) cc_final: 0.8649 (mmm) REVERT: D 86 ARG cc_start: 0.7489 (ttp80) cc_final: 0.7048 (tmt-80) REVERT: D 90 GLN cc_start: 0.8400 (pm20) cc_final: 0.7848 (pm20) REVERT: D 95 ASP cc_start: 0.8728 (p0) cc_final: 0.8231 (p0) REVERT: D 147 GLU cc_start: 0.8323 (tt0) cc_final: 0.7732 (tm-30) REVERT: D 224 GLN cc_start: 0.8320 (tp40) cc_final: 0.8001 (tp40) REVERT: D 444 LEU cc_start: 0.8898 (mm) cc_final: 0.8647 (mm) REVERT: E 90 GLN cc_start: 0.8921 (OUTLIER) cc_final: 0.8499 (pm20) REVERT: E 147 GLU cc_start: 0.9057 (tt0) cc_final: 0.8799 (tt0) REVERT: E 155 GLU cc_start: 0.8765 (tt0) cc_final: 0.8310 (mt-10) REVERT: E 182 GLU cc_start: 0.8997 (mm-30) cc_final: 0.8616 (mm-30) REVERT: E 190 GLU cc_start: 0.9067 (tt0) cc_final: 0.8812 (tt0) REVERT: E 298 GLU cc_start: 0.9540 (tm-30) cc_final: 0.9325 (tm-30) REVERT: N 421 MET cc_start: 0.8441 (tpp) cc_final: 0.8131 (mpp) REVERT: N 425 ARG cc_start: 0.8284 (ptt180) cc_final: 0.7920 (mtm180) REVERT: N 426 GLN cc_start: 0.8127 (tt0) cc_final: 0.7641 (tp40) REVERT: N 433 GLU cc_start: 0.9008 (tp30) cc_final: 0.8703 (pt0) REVERT: N 452 LYS cc_start: 0.8810 (ttmt) cc_final: 0.8407 (tppp) REVERT: N 463 LYS cc_start: 0.9415 (OUTLIER) cc_final: 0.9204 (tppp) REVERT: N 469 GLU cc_start: 0.8463 (mp0) cc_final: 0.8048 (mm-30) REVERT: N 472 ASN cc_start: 0.8319 (t0) cc_final: 0.7755 (t0) REVERT: N 480 VAL cc_start: 0.8808 (t) cc_final: 0.8254 (p) REVERT: N 482 TYR cc_start: 0.8261 (m-80) cc_final: 0.7914 (m-80) outliers start: 34 outliers final: 13 residues processed: 237 average time/residue: 0.6691 time to fit residues: 172.4840 Evaluate side-chains 201 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 186 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain N residue 463 LYS Chi-restraints excluded: chain N residue 464 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 69 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 24 optimal weight: 0.4980 chunk 107 optimal weight: 5.9990 chunk 129 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 chunk 146 optimal weight: 5.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 ASN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.083306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.060503 restraints weight = 73254.060| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 4.74 r_work: 0.2682 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2688 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2688 r_free = 0.2688 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2688 r_free = 0.2688 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2688 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15198 Z= 0.176 Angle : 0.641 9.510 20715 Z= 0.326 Chirality : 0.045 0.228 2398 Planarity : 0.004 0.074 2505 Dihedral : 7.224 64.950 2544 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 2.84 % Allowed : 15.37 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.24 % 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: 1.54 (0.21), residues: 1744 helix: 1.97 (0.21), residues: 570 sheet: 0.81 (0.24), residues: 463 loop : 0.52 (0.25), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 50 TYR 0.026 0.001 TYR D 299 PHE 0.018 0.001 PHE A 337 TRP 0.032 0.001 TRP D 241 HIS 0.004 0.001 HIS A 184 Details of bonding type rmsd covalent geometry : bond 0.00399 (15164) covalent geometry : angle 0.63331 (20619) SS BOND : bond 0.00272 ( 6) SS BOND : angle 0.69435 ( 12) hydrogen bonds : bond 0.04138 ( 762) hydrogen bonds : angle 4.53904 ( 2424) link_ALPHA1-3 : bond 0.00917 ( 4) link_ALPHA1-3 : angle 1.94532 ( 12) link_ALPHA1-6 : bond 0.00633 ( 4) link_ALPHA1-6 : angle 1.71963 ( 12) link_BETA1-4 : bond 0.00325 ( 11) link_BETA1-4 : angle 1.82431 ( 33) link_NAG-ASN : bond 0.00210 ( 9) link_NAG-ASN : angle 1.45966 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 206 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8908 (OUTLIER) cc_final: 0.8625 (m-30) REVERT: A 253 ARG cc_start: 0.8703 (tpp-160) cc_final: 0.7973 (mmp-170) REVERT: B 9 MET cc_start: 0.7650 (mtp) cc_final: 0.7111 (ttm) REVERT: B 90 GLN cc_start: 0.8887 (mp10) cc_final: 0.8314 (mp10) REVERT: C 162 GLU cc_start: 0.8964 (tt0) cc_final: 0.8456 (tm-30) REVERT: C 189 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7646 (tm-30) REVERT: C 259 LYS cc_start: 0.9171 (OUTLIER) cc_final: 0.8954 (pttm) REVERT: D 52 GLU cc_start: 0.9058 (mp0) cc_final: 0.8764 (mp0) REVERT: D 55 MET cc_start: 0.9185 (mtt) cc_final: 0.8781 (mmm) REVERT: D 86 ARG cc_start: 0.7470 (ttp80) cc_final: 0.7172 (tmt-80) REVERT: D 90 GLN cc_start: 0.8129 (pm20) cc_final: 0.7751 (pm20) REVERT: D 95 ASP cc_start: 0.8758 (p0) cc_final: 0.8261 (p0) REVERT: D 147 GLU cc_start: 0.8540 (tt0) cc_final: 0.8064 (tm-30) REVERT: D 185 GLN cc_start: 0.8493 (mp10) cc_final: 0.8208 (pm20) REVERT: D 224 GLN cc_start: 0.8384 (tp40) cc_final: 0.8080 (tp40) REVERT: D 444 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8764 (mm) REVERT: E 90 GLN cc_start: 0.8956 (OUTLIER) cc_final: 0.8543 (pm20) REVERT: E 147 GLU cc_start: 0.9105 (tt0) cc_final: 0.8823 (tt0) REVERT: E 190 GLU cc_start: 0.9068 (tt0) cc_final: 0.8655 (tt0) REVERT: N 421 MET cc_start: 0.8445 (tpp) cc_final: 0.8203 (mpp) REVERT: N 425 ARG cc_start: 0.8295 (ptt180) cc_final: 0.7650 (ptt-90) REVERT: N 426 GLN cc_start: 0.8201 (tt0) cc_final: 0.7707 (tp40) REVERT: N 433 GLU cc_start: 0.9012 (tp30) cc_final: 0.8616 (pt0) REVERT: N 452 LYS cc_start: 0.8800 (ttmt) cc_final: 0.8423 (tppp) REVERT: N 472 ASN cc_start: 0.8265 (t0) cc_final: 0.7865 (t0) REVERT: N 480 VAL cc_start: 0.8884 (t) cc_final: 0.8366 (p) REVERT: N 482 TYR cc_start: 0.8264 (m-80) cc_final: 0.7976 (m-80) outliers start: 45 outliers final: 17 residues processed: 224 average time/residue: 0.6337 time to fit residues: 154.8748 Evaluate side-chains 214 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 193 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain N residue 407 LEU Chi-restraints excluded: chain N residue 464 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 64 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 169 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 80 optimal weight: 7.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.081785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.058374 restraints weight = 77742.535| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 4.78 r_work: 0.2636 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2640 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2640 r_free = 0.2640 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2640 r_free = 0.2640 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2640 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.4064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 15198 Z= 0.195 Angle : 0.628 8.361 20715 Z= 0.319 Chirality : 0.045 0.233 2398 Planarity : 0.004 0.045 2505 Dihedral : 6.760 60.454 2544 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.52 % Allowed : 16.51 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.24 % 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: 1.40 (0.20), residues: 1744 helix: 1.99 (0.21), residues: 570 sheet: 0.61 (0.23), residues: 472 loop : 0.41 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG E 428 TYR 0.027 0.001 TYR D 299 PHE 0.027 0.001 PHE C 417 TRP 0.048 0.002 TRP E 241 HIS 0.005 0.001 HIS D 267 Details of bonding type rmsd covalent geometry : bond 0.00447 (15164) covalent geometry : angle 0.61974 (20619) SS BOND : bond 0.00140 ( 6) SS BOND : angle 0.46082 ( 12) hydrogen bonds : bond 0.04095 ( 762) hydrogen bonds : angle 4.43336 ( 2424) link_ALPHA1-3 : bond 0.01041 ( 4) link_ALPHA1-3 : angle 1.81582 ( 12) link_ALPHA1-6 : bond 0.00802 ( 4) link_ALPHA1-6 : angle 1.64605 ( 12) link_BETA1-4 : bond 0.00306 ( 11) link_BETA1-4 : angle 1.69068 ( 33) link_NAG-ASN : bond 0.00242 ( 9) link_NAG-ASN : angle 1.59663 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 176 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8913 (OUTLIER) cc_final: 0.8632 (m-30) REVERT: B 9 MET cc_start: 0.7695 (mtp) cc_final: 0.7302 (ttm) REVERT: B 90 GLN cc_start: 0.8915 (mp10) cc_final: 0.8347 (mp10) REVERT: C 71 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8038 (mm-30) REVERT: C 162 GLU cc_start: 0.9027 (tt0) cc_final: 0.8477 (tm-30) REVERT: C 189 GLU cc_start: 0.7965 (tm-30) cc_final: 0.7672 (tm-30) REVERT: C 239 GLN cc_start: 0.8994 (tp40) cc_final: 0.8560 (tp40) REVERT: C 259 LYS cc_start: 0.9152 (OUTLIER) cc_final: 0.8929 (pttm) REVERT: D 55 MET cc_start: 0.9167 (mtt) cc_final: 0.8770 (mmm) REVERT: D 90 GLN cc_start: 0.8369 (pm20) cc_final: 0.7962 (pm20) REVERT: D 95 ASP cc_start: 0.8832 (p0) cc_final: 0.8335 (p0) REVERT: D 185 GLN cc_start: 0.8425 (mp10) cc_final: 0.8066 (pm20) REVERT: D 224 GLN cc_start: 0.8367 (tp40) cc_final: 0.7982 (tp40) REVERT: D 274 LYS cc_start: 0.8518 (mppt) cc_final: 0.8255 (mmtt) REVERT: D 444 LEU cc_start: 0.9066 (mm) cc_final: 0.8846 (mm) REVERT: E 49 MET cc_start: 0.8569 (OUTLIER) cc_final: 0.8265 (tmm) REVERT: E 90 GLN cc_start: 0.8965 (OUTLIER) cc_final: 0.8513 (pm20) REVERT: E 282 ASP cc_start: 0.8906 (m-30) cc_final: 0.8310 (m-30) REVERT: N 425 ARG cc_start: 0.8357 (ptt180) cc_final: 0.7877 (ptt-90) REVERT: N 426 GLN cc_start: 0.8217 (tt0) cc_final: 0.7665 (tp40) REVERT: N 433 GLU cc_start: 0.9019 (tp30) cc_final: 0.8619 (pt0) REVERT: N 452 LYS cc_start: 0.8811 (ttmt) cc_final: 0.8413 (tppp) REVERT: N 469 GLU cc_start: 0.8384 (mp0) cc_final: 0.8041 (mm-30) REVERT: N 480 VAL cc_start: 0.8917 (t) cc_final: 0.8457 (p) REVERT: N 482 TYR cc_start: 0.8157 (m-80) cc_final: 0.7880 (m-80) REVERT: N 504 GLN cc_start: 0.8705 (mp10) cc_final: 0.8360 (pm20) outliers start: 40 outliers final: 20 residues processed: 200 average time/residue: 0.6208 time to fit residues: 135.9877 Evaluate side-chains 195 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 171 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain E residue 49 MET Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain N residue 464 ASN Chi-restraints excluded: chain N residue 466 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 130 optimal weight: 0.9980 chunk 153 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 112 optimal weight: 6.9990 chunk 71 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 115 optimal weight: 7.9990 chunk 35 optimal weight: 0.0060 overall best weight: 1.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 GLN C 99 ASN C 154 GLN D 265 ASN ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.081657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.059110 restraints weight = 57632.212| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 4.13 r_work: 0.2673 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2680 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2680 r_free = 0.2680 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2680 r_free = 0.2680 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2680 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.4286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15198 Z= 0.159 Angle : 0.629 10.679 20715 Z= 0.318 Chirality : 0.044 0.238 2398 Planarity : 0.003 0.034 2505 Dihedral : 6.359 55.521 2544 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.46 % Allowed : 16.45 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.24 % 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: 1.41 (0.20), residues: 1744 helix: 1.98 (0.22), residues: 570 sheet: 0.90 (0.24), residues: 433 loop : 0.23 (0.24), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 180 TYR 0.025 0.001 TYR D 299 PHE 0.016 0.001 PHE A 337 TRP 0.037 0.001 TRP D 241 HIS 0.003 0.001 HIS A 184 Details of bonding type rmsd covalent geometry : bond 0.00359 (15164) covalent geometry : angle 0.62188 (20619) SS BOND : bond 0.00138 ( 6) SS BOND : angle 0.39564 ( 12) hydrogen bonds : bond 0.03911 ( 762) hydrogen bonds : angle 4.39483 ( 2424) link_ALPHA1-3 : bond 0.01001 ( 4) link_ALPHA1-3 : angle 1.83377 ( 12) link_ALPHA1-6 : bond 0.00888 ( 4) link_ALPHA1-6 : angle 1.59404 ( 12) link_BETA1-4 : bond 0.00343 ( 11) link_BETA1-4 : angle 1.62261 ( 33) link_NAG-ASN : bond 0.00222 ( 9) link_NAG-ASN : angle 1.59372 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 182 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 ARG cc_start: 0.8704 (mmt180) cc_final: 0.8002 (mmp-170) REVERT: B 9 MET cc_start: 0.7564 (mtp) cc_final: 0.7165 (ttm) REVERT: B 90 GLN cc_start: 0.8890 (mp10) cc_final: 0.8312 (mp10) REVERT: B 137 MET cc_start: 0.8207 (mmm) cc_final: 0.7340 (ttm) REVERT: C 71 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8032 (mm-30) REVERT: C 105 LYS cc_start: 0.9303 (mmtt) cc_final: 0.8758 (mppt) REVERT: C 162 GLU cc_start: 0.8994 (tt0) cc_final: 0.8431 (tm-30) REVERT: C 189 GLU cc_start: 0.8068 (tm-30) cc_final: 0.7718 (tm-30) REVERT: C 259 LYS cc_start: 0.9130 (OUTLIER) cc_final: 0.8914 (pttm) REVERT: D 55 MET cc_start: 0.9220 (mtt) cc_final: 0.8916 (mmm) REVERT: D 95 ASP cc_start: 0.8823 (p0) cc_final: 0.8365 (p0) REVERT: D 185 GLN cc_start: 0.8513 (mp10) cc_final: 0.8194 (pm20) REVERT: D 224 GLN cc_start: 0.8420 (tp40) cc_final: 0.8127 (tp40) REVERT: D 274 LYS cc_start: 0.8523 (mppt) cc_final: 0.8288 (mmtt) REVERT: D 444 LEU cc_start: 0.9029 (mm) cc_final: 0.8829 (mm) REVERT: E 49 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.8268 (tmm) REVERT: E 87 VAL cc_start: 0.9115 (OUTLIER) cc_final: 0.8707 (p) REVERT: E 90 GLN cc_start: 0.9005 (OUTLIER) cc_final: 0.8570 (pm20) REVERT: E 180 ARG cc_start: 0.8414 (mmp80) cc_final: 0.7814 (mtm180) REVERT: N 425 ARG cc_start: 0.8491 (ptt180) cc_final: 0.7931 (mtm180) REVERT: N 426 GLN cc_start: 0.8252 (tt0) cc_final: 0.7670 (tp40) REVERT: N 433 GLU cc_start: 0.9010 (tp30) cc_final: 0.8662 (pt0) REVERT: N 452 LYS cc_start: 0.8811 (ttmt) cc_final: 0.8494 (tppp) REVERT: N 472 ASN cc_start: 0.8330 (t0) cc_final: 0.8065 (t0) REVERT: N 480 VAL cc_start: 0.8935 (t) cc_final: 0.8463 (p) REVERT: N 482 TYR cc_start: 0.8172 (m-80) cc_final: 0.7880 (m-80) REVERT: N 504 GLN cc_start: 0.8690 (mp10) cc_final: 0.8417 (pm20) outliers start: 39 outliers final: 18 residues processed: 202 average time/residue: 0.5734 time to fit residues: 127.5495 Evaluate side-chains 191 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 169 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain E residue 49 MET Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain N residue 407 LEU Chi-restraints excluded: chain N residue 464 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 48 optimal weight: 6.9990 chunk 165 optimal weight: 9.9990 chunk 164 optimal weight: 0.0030 chunk 140 optimal weight: 4.9990 chunk 142 optimal weight: 0.8980 chunk 152 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 168 optimal weight: 7.9990 chunk 133 optimal weight: 4.9990 overall best weight: 1.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 154 GLN ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.081889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.058835 restraints weight = 63378.753| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 4.57 r_work: 0.2645 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2650 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2650 r_free = 0.2650 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2650 r_free = 0.2650 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2650 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.4450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15198 Z= 0.149 Angle : 0.622 9.165 20715 Z= 0.313 Chirality : 0.044 0.241 2398 Planarity : 0.003 0.032 2505 Dihedral : 6.033 51.356 2544 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.21 % Allowed : 16.95 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.24 % 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: 1.36 (0.20), residues: 1744 helix: 1.92 (0.21), residues: 577 sheet: 0.81 (0.24), residues: 442 loop : 0.23 (0.24), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 180 TYR 0.025 0.001 TYR D 299 PHE 0.028 0.001 PHE C 417 TRP 0.039 0.001 TRP D 241 HIS 0.003 0.001 HIS A 184 Details of bonding type rmsd covalent geometry : bond 0.00336 (15164) covalent geometry : angle 0.61487 (20619) SS BOND : bond 0.00164 ( 6) SS BOND : angle 0.34995 ( 12) hydrogen bonds : bond 0.03794 ( 762) hydrogen bonds : angle 4.34228 ( 2424) link_ALPHA1-3 : bond 0.00990 ( 4) link_ALPHA1-3 : angle 1.80397 ( 12) link_ALPHA1-6 : bond 0.00912 ( 4) link_ALPHA1-6 : angle 1.53901 ( 12) link_BETA1-4 : bond 0.00332 ( 11) link_BETA1-4 : angle 1.56023 ( 33) link_NAG-ASN : bond 0.00264 ( 9) link_NAG-ASN : angle 1.57479 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 179 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 ARG cc_start: 0.8750 (mmt180) cc_final: 0.8080 (mmp-170) REVERT: B 9 MET cc_start: 0.7633 (mtp) cc_final: 0.7295 (ttm) REVERT: B 90 GLN cc_start: 0.8923 (mp10) cc_final: 0.8353 (mp10) REVERT: C 71 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8153 (mm-30) REVERT: C 102 MET cc_start: 0.8860 (tpp) cc_final: 0.8288 (tpp) REVERT: C 105 LYS cc_start: 0.9329 (mmtt) cc_final: 0.8732 (mppt) REVERT: C 162 GLU cc_start: 0.9035 (tt0) cc_final: 0.8489 (tm-30) REVERT: C 189 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7885 (tm-30) REVERT: D 13 LYS cc_start: 0.8640 (mttt) cc_final: 0.8415 (tmmt) REVERT: D 18 LYS cc_start: 0.9432 (pttm) cc_final: 0.9206 (pptt) REVERT: D 55 MET cc_start: 0.9246 (mtt) cc_final: 0.8947 (mmm) REVERT: D 70 LYS cc_start: 0.9368 (mmtm) cc_final: 0.9051 (mmmm) REVERT: D 185 GLN cc_start: 0.8570 (mp10) cc_final: 0.8236 (pm20) REVERT: D 224 GLN cc_start: 0.8470 (tp40) cc_final: 0.8169 (tp40) REVERT: D 274 LYS cc_start: 0.8556 (mppt) cc_final: 0.8341 (mmtt) REVERT: D 444 LEU cc_start: 0.9076 (mm) cc_final: 0.8871 (mm) REVERT: E 49 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.8312 (tmm) REVERT: E 87 VAL cc_start: 0.9172 (OUTLIER) cc_final: 0.8838 (p) REVERT: E 90 GLN cc_start: 0.9043 (OUTLIER) cc_final: 0.8608 (pm20) REVERT: E 180 ARG cc_start: 0.8414 (mmp80) cc_final: 0.7921 (mtm180) REVERT: N 426 GLN cc_start: 0.8282 (tt0) cc_final: 0.7667 (tp40) REVERT: N 433 GLU cc_start: 0.9025 (tp30) cc_final: 0.8623 (tt0) REVERT: N 452 LYS cc_start: 0.8820 (ttmt) cc_final: 0.8488 (tppp) REVERT: N 469 GLU cc_start: 0.8450 (mp0) cc_final: 0.8121 (mm-30) REVERT: N 472 ASN cc_start: 0.8395 (t0) cc_final: 0.8157 (t0) REVERT: N 480 VAL cc_start: 0.8951 (t) cc_final: 0.8532 (p) REVERT: N 482 TYR cc_start: 0.8211 (m-80) cc_final: 0.7957 (m-80) REVERT: N 504 GLN cc_start: 0.8728 (mp10) cc_final: 0.8363 (pm20) outliers start: 35 outliers final: 16 residues processed: 198 average time/residue: 0.6230 time to fit residues: 134.7952 Evaluate side-chains 192 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 173 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain E residue 49 MET Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain N residue 464 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 66 optimal weight: 7.9990 chunk 120 optimal weight: 1.9990 chunk 119 optimal weight: 0.6980 chunk 146 optimal weight: 3.9990 chunk 100 optimal weight: 10.0000 chunk 48 optimal weight: 7.9990 chunk 16 optimal weight: 0.0060 chunk 51 optimal weight: 5.9990 chunk 118 optimal weight: 5.9990 chunk 172 optimal weight: 4.9990 chunk 147 optimal weight: 7.9990 overall best weight: 2.3402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 ASN ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.079552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.056820 restraints weight = 82838.153| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 5.13 r_work: 0.2582 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2589 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2589 r_free = 0.2589 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2589 r_free = 0.2589 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2589 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.4693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 15198 Z= 0.206 Angle : 0.681 13.585 20715 Z= 0.340 Chirality : 0.046 0.238 2398 Planarity : 0.004 0.032 2505 Dihedral : 5.902 48.588 2544 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.52 % Allowed : 16.82 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.20), residues: 1744 helix: 1.85 (0.21), residues: 576 sheet: 0.76 (0.24), residues: 442 loop : 0.06 (0.24), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 180 TYR 0.029 0.002 TYR D 299 PHE 0.020 0.002 PHE A 337 TRP 0.052 0.002 TRP D 241 HIS 0.003 0.001 HIS C 318 Details of bonding type rmsd covalent geometry : bond 0.00474 (15164) covalent geometry : angle 0.67374 (20619) SS BOND : bond 0.00145 ( 6) SS BOND : angle 0.42840 ( 12) hydrogen bonds : bond 0.04038 ( 762) hydrogen bonds : angle 4.43326 ( 2424) link_ALPHA1-3 : bond 0.00867 ( 4) link_ALPHA1-3 : angle 1.80581 ( 12) link_ALPHA1-6 : bond 0.00921 ( 4) link_ALPHA1-6 : angle 1.49988 ( 12) link_BETA1-4 : bond 0.00305 ( 11) link_BETA1-4 : angle 1.71084 ( 33) link_NAG-ASN : bond 0.00250 ( 9) link_NAG-ASN : angle 1.76465 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 174 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8913 (OUTLIER) cc_final: 0.8649 (m-30) REVERT: A 118 ARG cc_start: 0.8674 (mtm-85) cc_final: 0.8474 (mpp80) REVERT: B 9 MET cc_start: 0.7776 (mtp) cc_final: 0.7468 (ttm) REVERT: B 55 MET cc_start: 0.9064 (mtm) cc_final: 0.8422 (mmm) REVERT: B 90 GLN cc_start: 0.8982 (mp10) cc_final: 0.8413 (mp10) REVERT: B 137 MET cc_start: 0.8068 (mmm) cc_final: 0.7143 (ttm) REVERT: C 71 GLU cc_start: 0.8596 (mt-10) cc_final: 0.8082 (mm-30) REVERT: C 105 LYS cc_start: 0.9312 (mmtt) cc_final: 0.8778 (mppt) REVERT: C 162 GLU cc_start: 0.9010 (tt0) cc_final: 0.8547 (tm-30) REVERT: C 189 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7868 (tm-30) REVERT: D 13 LYS cc_start: 0.8729 (mttt) cc_final: 0.8520 (tmmt) REVERT: D 18 LYS cc_start: 0.9366 (pttm) cc_final: 0.9128 (pptt) REVERT: D 55 MET cc_start: 0.9256 (mtt) cc_final: 0.8993 (mmm) REVERT: D 70 LYS cc_start: 0.9380 (mmtm) cc_final: 0.9093 (mmmm) REVERT: D 185 GLN cc_start: 0.8638 (mp10) cc_final: 0.8267 (pm20) REVERT: D 224 GLN cc_start: 0.8425 (tp40) cc_final: 0.8072 (tp40) REVERT: E 49 MET cc_start: 0.8734 (OUTLIER) cc_final: 0.8394 (tmm) REVERT: E 87 VAL cc_start: 0.9227 (OUTLIER) cc_final: 0.8839 (p) REVERT: E 90 GLN cc_start: 0.9046 (OUTLIER) cc_final: 0.8573 (pm20) REVERT: E 180 ARG cc_start: 0.8514 (mmp80) cc_final: 0.8098 (mtm180) REVERT: E 282 ASP cc_start: 0.9065 (m-30) cc_final: 0.8780 (m-30) REVERT: N 426 GLN cc_start: 0.8267 (tt0) cc_final: 0.7650 (tp40) REVERT: N 433 GLU cc_start: 0.9090 (tp30) cc_final: 0.8659 (tt0) REVERT: N 452 LYS cc_start: 0.8828 (ttmt) cc_final: 0.8488 (tppp) REVERT: N 469 GLU cc_start: 0.8331 (mp0) cc_final: 0.7977 (mm-30) REVERT: N 472 ASN cc_start: 0.8479 (t0) cc_final: 0.8264 (t0) REVERT: N 480 VAL cc_start: 0.8968 (t) cc_final: 0.8540 (p) REVERT: N 482 TYR cc_start: 0.8182 (m-80) cc_final: 0.7912 (m-80) REVERT: N 486 LYS cc_start: 0.9029 (tttm) cc_final: 0.8580 (tttm) REVERT: N 504 GLN cc_start: 0.8662 (mp10) cc_final: 0.8315 (pm20) outliers start: 40 outliers final: 21 residues processed: 195 average time/residue: 0.6498 time to fit residues: 138.3260 Evaluate side-chains 189 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 164 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain E residue 49 MET Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain N residue 407 LEU Chi-restraints excluded: chain N residue 464 ASN Chi-restraints excluded: chain N residue 466 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 170 optimal weight: 10.0000 chunk 116 optimal weight: 3.9990 chunk 144 optimal weight: 7.9990 chunk 137 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 chunk 164 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 163 optimal weight: 9.9990 chunk 29 optimal weight: 0.8980 chunk 87 optimal weight: 0.5980 chunk 74 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.081578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.058767 restraints weight = 66612.802| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 4.60 r_work: 0.2655 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2660 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2660 r_free = 0.2660 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2660 r_free = 0.2660 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2660 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.4800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 15198 Z= 0.126 Angle : 0.636 13.873 20715 Z= 0.314 Chirality : 0.044 0.237 2398 Planarity : 0.003 0.034 2505 Dihedral : 5.557 43.561 2544 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.39 % Allowed : 17.83 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.24 % 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 (0.20), residues: 1744 helix: 1.94 (0.21), residues: 577 sheet: 0.85 (0.24), residues: 439 loop : 0.22 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 180 TYR 0.023 0.001 TYR E 299 PHE 0.031 0.001 PHE C 417 TRP 0.048 0.001 TRP D 241 HIS 0.003 0.001 HIS A 143 Details of bonding type rmsd covalent geometry : bond 0.00283 (15164) covalent geometry : angle 0.63054 (20619) SS BOND : bond 0.00164 ( 6) SS BOND : angle 0.26220 ( 12) hydrogen bonds : bond 0.03606 ( 762) hydrogen bonds : angle 4.27629 ( 2424) link_ALPHA1-3 : bond 0.00966 ( 4) link_ALPHA1-3 : angle 1.65249 ( 12) link_ALPHA1-6 : bond 0.01013 ( 4) link_ALPHA1-6 : angle 1.43186 ( 12) link_BETA1-4 : bond 0.00359 ( 11) link_BETA1-4 : angle 1.45051 ( 33) link_NAG-ASN : bond 0.00282 ( 9) link_NAG-ASN : angle 1.50470 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 188 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ARG cc_start: 0.9172 (mtm180) cc_final: 0.8921 (mtm110) REVERT: A 253 ARG cc_start: 0.8778 (mmt180) cc_final: 0.8502 (mmt-90) REVERT: A 262 GLN cc_start: 0.8932 (tp40) cc_final: 0.8652 (tp40) REVERT: B 9 MET cc_start: 0.7721 (mtp) cc_final: 0.7330 (ttm) REVERT: B 55 MET cc_start: 0.9133 (mtm) cc_final: 0.8467 (mmm) REVERT: B 90 GLN cc_start: 0.8891 (mp10) cc_final: 0.8305 (mp10) REVERT: B 137 MET cc_start: 0.8136 (mmm) cc_final: 0.7091 (ttm) REVERT: C 71 GLU cc_start: 0.8544 (mt-10) cc_final: 0.8146 (mm-30) REVERT: C 105 LYS cc_start: 0.9343 (mmtt) cc_final: 0.8885 (mppt) REVERT: C 162 GLU cc_start: 0.8995 (tt0) cc_final: 0.8464 (tm-30) REVERT: C 189 GLU cc_start: 0.8262 (tm-30) cc_final: 0.7953 (tm-30) REVERT: D 55 MET cc_start: 0.9240 (mtt) cc_final: 0.8983 (mmm) REVERT: D 153 GLU cc_start: 0.8963 (mm-30) cc_final: 0.8761 (mm-30) REVERT: D 185 GLN cc_start: 0.8575 (mp10) cc_final: 0.8146 (pm20) REVERT: D 224 GLN cc_start: 0.8469 (tp40) cc_final: 0.8141 (tp40) REVERT: E 49 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.8326 (pp-130) REVERT: E 87 VAL cc_start: 0.9199 (OUTLIER) cc_final: 0.8868 (p) REVERT: E 90 GLN cc_start: 0.9059 (OUTLIER) cc_final: 0.8641 (pm20) REVERT: E 137 MET cc_start: 0.8594 (tpp) cc_final: 0.8022 (mmm) REVERT: E 180 ARG cc_start: 0.8473 (mmp80) cc_final: 0.8102 (mtm180) REVERT: E 282 ASP cc_start: 0.9020 (m-30) cc_final: 0.8750 (m-30) REVERT: E 283 MET cc_start: 0.8483 (ttt) cc_final: 0.8134 (mmt) REVERT: N 426 GLN cc_start: 0.8309 (tt0) cc_final: 0.7733 (tp40) REVERT: N 433 GLU cc_start: 0.9054 (tp30) cc_final: 0.8611 (pt0) REVERT: N 452 LYS cc_start: 0.8874 (ttmt) cc_final: 0.8533 (tppp) REVERT: N 469 GLU cc_start: 0.8424 (mp0) cc_final: 0.8057 (mm-30) REVERT: N 472 ASN cc_start: 0.8447 (t0) cc_final: 0.8201 (t0) REVERT: N 480 VAL cc_start: 0.8988 (t) cc_final: 0.8515 (p) REVERT: N 482 TYR cc_start: 0.8188 (m-80) cc_final: 0.7888 (m-80) REVERT: N 486 LYS cc_start: 0.8948 (tttm) cc_final: 0.8473 (tttm) REVERT: N 504 GLN cc_start: 0.8714 (mp10) cc_final: 0.8449 (pm20) outliers start: 22 outliers final: 9 residues processed: 197 average time/residue: 0.6394 time to fit residues: 138.1643 Evaluate side-chains 186 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 174 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain E residue 49 MET Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain N residue 464 ASN Chi-restraints excluded: chain N residue 466 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 19 optimal weight: 3.9990 chunk 169 optimal weight: 7.9990 chunk 76 optimal weight: 0.8980 chunk 48 optimal weight: 7.9990 chunk 8 optimal weight: 0.4980 chunk 148 optimal weight: 0.5980 chunk 47 optimal weight: 5.9990 chunk 129 optimal weight: 6.9990 chunk 137 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 154 GLN D 148 GLN ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.082113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.058992 restraints weight = 76985.329| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 4.86 r_work: 0.2652 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2659 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2659 r_free = 0.2659 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2659 r_free = 0.2659 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2659 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.4892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15198 Z= 0.124 Angle : 0.651 15.094 20715 Z= 0.318 Chirality : 0.043 0.231 2398 Planarity : 0.003 0.032 2505 Dihedral : 5.325 40.314 2544 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.95 % Allowed : 18.78 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.24 % 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: 1.41 (0.20), residues: 1744 helix: 1.94 (0.21), residues: 577 sheet: 0.93 (0.24), residues: 434 loop : 0.23 (0.24), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 459 TYR 0.024 0.001 TYR E 299 PHE 0.015 0.001 PHE C 308 TRP 0.050 0.001 TRP D 241 HIS 0.003 0.001 HIS A 184 Details of bonding type rmsd covalent geometry : bond 0.00281 (15164) covalent geometry : angle 0.64540 (20619) SS BOND : bond 0.00145 ( 6) SS BOND : angle 0.26729 ( 12) hydrogen bonds : bond 0.03483 ( 762) hydrogen bonds : angle 4.22206 ( 2424) link_ALPHA1-3 : bond 0.00884 ( 4) link_ALPHA1-3 : angle 1.72296 ( 12) link_ALPHA1-6 : bond 0.00988 ( 4) link_ALPHA1-6 : angle 1.39877 ( 12) link_BETA1-4 : bond 0.00407 ( 11) link_BETA1-4 : angle 1.44054 ( 33) link_NAG-ASN : bond 0.00268 ( 9) link_NAG-ASN : angle 1.53069 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 187 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ARG cc_start: 0.9197 (mtm180) cc_final: 0.8907 (mtm110) REVERT: A 262 GLN cc_start: 0.8869 (tp40) cc_final: 0.8594 (tp40) REVERT: A 348 MET cc_start: 0.7305 (ppp) cc_final: 0.6038 (mmp) REVERT: B 9 MET cc_start: 0.7819 (mtp) cc_final: 0.7438 (ttm) REVERT: B 90 GLN cc_start: 0.8882 (mp10) cc_final: 0.8302 (mp10) REVERT: B 137 MET cc_start: 0.8112 (mmm) cc_final: 0.7121 (ttm) REVERT: C 71 GLU cc_start: 0.8532 (mt-10) cc_final: 0.8089 (mm-30) REVERT: C 105 LYS cc_start: 0.9317 (mmtt) cc_final: 0.8876 (mppt) REVERT: C 162 GLU cc_start: 0.9030 (tt0) cc_final: 0.8463 (tm-30) REVERT: C 189 GLU cc_start: 0.8248 (tm-30) cc_final: 0.7868 (tm-30) REVERT: C 239 GLN cc_start: 0.9060 (tp40) cc_final: 0.8684 (tp-100) REVERT: D 55 MET cc_start: 0.9228 (mtt) cc_final: 0.8964 (mmm) REVERT: D 153 GLU cc_start: 0.8951 (mm-30) cc_final: 0.8741 (mm-30) REVERT: D 185 GLN cc_start: 0.8547 (mp10) cc_final: 0.8142 (pm20) REVERT: D 190 GLU cc_start: 0.8858 (tt0) cc_final: 0.8583 (tt0) REVERT: D 224 GLN cc_start: 0.8468 (tp40) cc_final: 0.8139 (tp40) REVERT: E 49 MET cc_start: 0.8717 (OUTLIER) cc_final: 0.8298 (pp-130) REVERT: E 87 VAL cc_start: 0.9141 (OUTLIER) cc_final: 0.8470 (p) REVERT: E 90 GLN cc_start: 0.9056 (OUTLIER) cc_final: 0.8441 (pm20) REVERT: E 137 MET cc_start: 0.8277 (tpp) cc_final: 0.8012 (tpp) REVERT: E 180 ARG cc_start: 0.8470 (mmp80) cc_final: 0.8079 (mtm180) REVERT: E 282 ASP cc_start: 0.9024 (m-30) cc_final: 0.8743 (m-30) REVERT: E 283 MET cc_start: 0.8519 (ttt) cc_final: 0.8192 (mmt) REVERT: N 5 VAL cc_start: 0.8894 (t) cc_final: 0.8636 (p) REVERT: N 426 GLN cc_start: 0.8304 (tt0) cc_final: 0.7747 (tp40) REVERT: N 433 GLU cc_start: 0.9057 (tp30) cc_final: 0.8604 (pt0) REVERT: N 452 LYS cc_start: 0.8878 (ttmt) cc_final: 0.8532 (tppp) REVERT: N 469 GLU cc_start: 0.8407 (mp0) cc_final: 0.8029 (mm-30) REVERT: N 472 ASN cc_start: 0.8445 (t0) cc_final: 0.8229 (t0) REVERT: N 480 VAL cc_start: 0.8959 (t) cc_final: 0.8399 (p) REVERT: N 482 TYR cc_start: 0.8162 (m-80) cc_final: 0.7722 (m-80) REVERT: N 486 LYS cc_start: 0.8882 (tttm) cc_final: 0.8397 (tttm) REVERT: N 504 GLN cc_start: 0.8695 (mp10) cc_final: 0.8303 (pm20) outliers start: 15 outliers final: 8 residues processed: 194 average time/residue: 0.6516 time to fit residues: 138.0110 Evaluate side-chains 193 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 182 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain E residue 49 MET Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain N residue 466 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 15 optimal weight: 5.9990 chunk 168 optimal weight: 10.0000 chunk 102 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 172 optimal weight: 0.6980 chunk 101 optimal weight: 5.9990 chunk 117 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.080905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.057978 restraints weight = 77363.262| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 4.62 r_work: 0.2633 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2639 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2639 r_free = 0.2639 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2639 r_free = 0.2639 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2639 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.4979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 15198 Z= 0.156 Angle : 0.649 14.938 20715 Z= 0.321 Chirality : 0.044 0.227 2398 Planarity : 0.003 0.031 2505 Dihedral : 5.261 38.564 2544 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.01 % Allowed : 18.46 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.24 % 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 (0.20), residues: 1744 helix: 1.97 (0.21), residues: 573 sheet: 0.83 (0.24), residues: 437 loop : 0.17 (0.24), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG N 459 TYR 0.026 0.001 TYR D 299 PHE 0.035 0.001 PHE C 417 TRP 0.058 0.001 TRP D 241 HIS 0.003 0.001 HIS C 122 Details of bonding type rmsd covalent geometry : bond 0.00362 (15164) covalent geometry : angle 0.64247 (20619) SS BOND : bond 0.00126 ( 6) SS BOND : angle 0.22671 ( 12) hydrogen bonds : bond 0.03598 ( 762) hydrogen bonds : angle 4.23995 ( 2424) link_ALPHA1-3 : bond 0.00836 ( 4) link_ALPHA1-3 : angle 1.71031 ( 12) link_ALPHA1-6 : bond 0.00984 ( 4) link_ALPHA1-6 : angle 1.37973 ( 12) link_BETA1-4 : bond 0.00367 ( 11) link_BETA1-4 : angle 1.51366 ( 33) link_NAG-ASN : bond 0.00234 ( 9) link_NAG-ASN : angle 1.57927 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5414.71 seconds wall clock time: 92 minutes 53.82 seconds (5573.82 seconds total)