Starting phenix.real_space_refine on Fri Jun 13 12:16:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qna_14072/06_2025/7qna_14072.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qna_14072/06_2025/7qna_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7qna_14072/06_2025/7qna_14072.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qna_14072/06_2025/7qna_14072.map" model { file = "/net/cci-nas-00/data/ceres_data/7qna_14072/06_2025/7qna_14072.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qna_14072/06_2025/7qna_14072.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 12.95, per 1000 atoms: 0.88 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: 4.22 Conformation dependent library (CDL) restraints added in 3.3 seconds 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: 1.71 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: 5.20 Time building geometry restraints manager: 4.88 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: 1.360 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: 0.030 Extract box with map and model: 0.660 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 41.840 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.260 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (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 TRP 0.006 0.001 TRP E 443 HIS 0.002 0.001 HIS D 267 PHE 0.006 0.001 PHE A 190 TYR 0.010 0.001 TYR E 299 ARG 0.003 0.000 ARG B 196 Details of bonding type rmsd link_NAG-ASN : bond 0.00301 ( 9) link_NAG-ASN : angle 1.71157 ( 27) 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_ALPHA1-3 : bond 0.00101 ( 4) link_ALPHA1-3 : angle 0.64560 ( 12) hydrogen bonds : bond 0.22488 ( 762) hydrogen bonds : angle 7.32841 ( 2424) SS BOND : bond 0.00081 ( 6) SS BOND : angle 0.50129 ( 12) covalent geometry : bond 0.00298 (15164) covalent geometry : angle 0.48396 (20619) *********************** 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 : 1.656 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: 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: 0.7907 (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: 0.8112 (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: 0.7966 (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: 0.8266 (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: 1.2933 time to fit residues: 523.9585 Evaluate side-chains 213 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 211 time to evaluate : 1.662 ------------------------------------------------------------------------------- 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 146 optimal weight: 0.5980 chunk 131 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 70 optimal weight: 6.9990 chunk 135 optimal weight: 5.9990 chunk 52 optimal weight: 0.6980 chunk 82 optimal weight: 7.9990 chunk 100 optimal weight: 3.9990 chunk 157 optimal weight: 4.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- 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 = 0.3431 r_free = 0.3431 target = 0.086211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.062902 restraints weight = 73497.411| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 4.94 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2936 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2936 r_free = 0.2936 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2936 r_free = 0.2936 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2936 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 15198 Z= 0.208 Angle : 0.702 9.880 20715 Z= 0.360 Chirality : 0.046 0.180 2398 Planarity : 0.004 0.032 2505 Dihedral : 9.423 80.987 2548 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 2.84 % Allowed : 13.99 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.21), residues: 1744 helix: 2.10 (0.21), residues: 569 sheet: 1.04 (0.24), residues: 448 loop : 0.74 (0.25), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 241 HIS 0.003 0.001 HIS C 318 PHE 0.015 0.002 PHE B 31 TYR 0.024 0.002 TYR D 299 ARG 0.009 0.001 ARG B 180 Details of bonding type rmsd link_NAG-ASN : bond 0.00947 ( 9) link_NAG-ASN : angle 2.23165 ( 27) link_ALPHA1-6 : bond 0.00613 ( 4) link_ALPHA1-6 : angle 1.76175 ( 12) link_BETA1-4 : bond 0.00409 ( 11) link_BETA1-4 : angle 1.83771 ( 33) link_ALPHA1-3 : bond 0.00809 ( 4) link_ALPHA1-3 : angle 2.23664 ( 12) hydrogen bonds : bond 0.05077 ( 762) hydrogen bonds : angle 5.06171 ( 2424) SS BOND : bond 0.00228 ( 6) SS BOND : angle 0.60102 ( 12) covalent geometry : bond 0.00475 (15164) covalent geometry : angle 0.69106 (20619) *********************** 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 296 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 251 time to evaluate : 1.915 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: 0.8101 (m-80) cc_final: 0.7828 (m-80) REVERT: A 118 ARG cc_start: 0.7949 (mtm-85) cc_final: 0.7724 (mpp80) REVERT: A 253 ARG cc_start: 0.8045 (tpp-160) cc_final: 0.7293 (mmp-170) REVERT: B 9 MET cc_start: 0.8077 (mtp) cc_final: 0.7457 (ttm) REVERT: B 90 GLN cc_start: 0.8464 (mp10) cc_final: 0.7909 (mp10) REVERT: B 274 LYS cc_start: 0.8575 (mmtt) cc_final: 0.8168 (mmpt) REVERT: C 162 GLU cc_start: 0.8676 (tt0) cc_final: 0.8199 (tm-30) REVERT: C 209 THR cc_start: 0.8866 (OUTLIER) cc_final: 0.8522 (p) REVERT: C 259 LYS cc_start: 0.9172 (OUTLIER) cc_final: 0.8945 (pttm) REVERT: C 260 ASP cc_start: 0.8525 (m-30) cc_final: 0.8258 (m-30) REVERT: D 13 LYS cc_start: 0.8788 (tmmt) cc_final: 0.8444 (tmmt) REVERT: D 14 GLU cc_start: 0.9222 (mm-30) cc_final: 0.8648 (mp0) REVERT: D 25 ILE cc_start: 0.9035 (mt) cc_final: 0.8765 (mm) REVERT: D 55 MET cc_start: 0.8948 (mtt) cc_final: 0.8444 (mmm) REVERT: D 95 ASP cc_start: 0.8553 (p0) cc_final: 0.8104 (p0) REVERT: D 147 GLU cc_start: 0.8103 (tt0) cc_final: 0.7431 (tm-30) REVERT: D 181 ILE cc_start: 0.9075 (mt) cc_final: 0.8703 (mp) REVERT: D 224 GLN cc_start: 0.8028 (tp40) cc_final: 0.7658 (tp40) REVERT: D 230 ILE cc_start: 0.9434 (mt) cc_final: 0.8959 (mp) REVERT: D 234 ILE cc_start: 0.9557 (mt) cc_final: 0.9355 (mp) REVERT: D 444 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8650 (mm) REVERT: E 9 MET cc_start: 0.8044 (mtt) cc_final: 0.7608 (mmt) REVERT: E 90 GLN cc_start: 0.8714 (mp10) cc_final: 0.8346 (pm20) REVERT: E 155 GLU cc_start: 0.8304 (tt0) cc_final: 0.7871 (mt-10) REVERT: E 182 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8190 (mm-30) REVERT: E 190 GLU cc_start: 0.8572 (tt0) cc_final: 0.8305 (tt0) REVERT: E 298 GLU cc_start: 0.9293 (tm-30) cc_final: 0.9084 (tm-30) REVERT: N 421 MET cc_start: 0.8140 (tpp) cc_final: 0.7760 (mpp) REVERT: N 425 ARG cc_start: 0.8363 (ptt180) cc_final: 0.8156 (ptt-90) REVERT: N 426 GLN cc_start: 0.8201 (tt0) cc_final: 0.7820 (tp40) REVERT: N 433 GLU cc_start: 0.8995 (tp30) cc_final: 0.8738 (mp0) REVERT: N 452 LYS cc_start: 0.8900 (ttmt) cc_final: 0.8560 (tppp) REVERT: N 454 ARG cc_start: 0.6551 (mtm110) cc_final: 0.6275 (mtp-110) REVERT: N 472 ASN cc_start: 0.8279 (t0) cc_final: 0.7528 (t0) REVERT: N 480 VAL cc_start: 0.8803 (t) cc_final: 0.8233 (p) REVERT: N 482 TYR cc_start: 0.8211 (m-80) cc_final: 0.7978 (m-80) outliers start: 45 outliers final: 16 residues processed: 271 average time/residue: 1.7746 time to fit residues: 523.5358 Evaluate side-chains 217 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 198 time to evaluate : 1.963 ------------------------------------------------------------------------------- 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 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 132 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 50 optimal weight: 0.9990 chunk 119 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 135 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 123 optimal weight: 10.0000 chunk 116 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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** D 265 ASN ** 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 = 0.3430 r_free = 0.3430 target = 0.086517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.063204 restraints weight = 74842.285| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 4.97 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2931 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2931 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15198 Z= 0.143 Angle : 0.630 10.046 20715 Z= 0.319 Chirality : 0.044 0.206 2398 Planarity : 0.004 0.034 2505 Dihedral : 8.117 70.064 2544 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 2.33 % Allowed : 15.19 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.21), residues: 1744 helix: 2.07 (0.21), residues: 569 sheet: 0.88 (0.24), residues: 463 loop : 0.73 (0.25), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 241 HIS 0.005 0.001 HIS A 184 PHE 0.023 0.001 PHE C 417 TYR 0.027 0.001 TYR D 244 ARG 0.007 0.000 ARG D 86 Details of bonding type rmsd link_NAG-ASN : bond 0.00355 ( 9) link_NAG-ASN : angle 1.32432 ( 27) link_ALPHA1-6 : bond 0.00826 ( 4) link_ALPHA1-6 : angle 1.56288 ( 12) link_BETA1-4 : bond 0.00401 ( 11) link_BETA1-4 : angle 1.61047 ( 33) link_ALPHA1-3 : bond 0.01133 ( 4) link_ALPHA1-3 : angle 1.63527 ( 12) hydrogen bonds : bond 0.04409 ( 762) hydrogen bonds : angle 4.60041 ( 2424) SS BOND : bond 0.00173 ( 6) SS BOND : angle 0.54286 ( 12) covalent geometry : bond 0.00315 (15164) covalent geometry : angle 0.62413 (20619) *********************** 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 261 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 224 time to evaluate : 1.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 PHE cc_start: 0.8117 (m-80) cc_final: 0.7760 (m-80) REVERT: A 96 ASP cc_start: 0.8473 (t70) cc_final: 0.8190 (m-30) REVERT: A 118 ARG cc_start: 0.8010 (mtm-85) cc_final: 0.7739 (mpp80) REVERT: A 155 MET cc_start: 0.8052 (mpp) cc_final: 0.7813 (mmt) REVERT: A 262 GLN cc_start: 0.8717 (tp40) cc_final: 0.8500 (tp40) REVERT: B 9 MET cc_start: 0.7799 (mtp) cc_final: 0.7302 (ttm) REVERT: B 61 MET cc_start: 0.9053 (OUTLIER) cc_final: 0.8740 (ptt) REVERT: B 90 GLN cc_start: 0.8461 (mp10) cc_final: 0.7945 (mp10) REVERT: B 274 LYS cc_start: 0.8558 (mmtt) cc_final: 0.8102 (mmpt) REVERT: C 71 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7666 (mm-30) REVERT: C 162 GLU cc_start: 0.8669 (tt0) cc_final: 0.8177 (tm-30) REVERT: C 239 GLN cc_start: 0.8907 (tp40) cc_final: 0.8499 (tp40) REVERT: D 55 MET cc_start: 0.8963 (mtt) cc_final: 0.8455 (mmm) REVERT: D 86 ARG cc_start: 0.7505 (ttp80) cc_final: 0.7104 (tmt-80) REVERT: D 90 GLN cc_start: 0.8271 (pm20) cc_final: 0.7763 (pm20) REVERT: D 95 ASP cc_start: 0.8597 (p0) cc_final: 0.8116 (p0) REVERT: D 147 GLU cc_start: 0.8166 (tt0) cc_final: 0.7537 (tm-30) REVERT: D 185 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7765 (pm20) REVERT: D 224 GLN cc_start: 0.7993 (tp40) cc_final: 0.7645 (tp40) REVERT: D 230 ILE cc_start: 0.9334 (mt) cc_final: 0.8994 (mm) REVERT: D 444 LEU cc_start: 0.8861 (mm) cc_final: 0.8629 (mm) REVERT: E 90 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.8411 (pm20) REVERT: E 155 GLU cc_start: 0.8237 (tt0) cc_final: 0.7763 (mt-10) REVERT: E 182 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8392 (mm-30) REVERT: E 190 GLU cc_start: 0.8637 (tt0) cc_final: 0.8370 (tt0) REVERT: E 298 GLU cc_start: 0.9315 (tm-30) cc_final: 0.9087 (tm-30) REVERT: N 426 GLN cc_start: 0.8279 (tt0) cc_final: 0.8055 (tp40) REVERT: N 433 GLU cc_start: 0.8953 (tp30) cc_final: 0.8579 (tt0) REVERT: N 452 LYS cc_start: 0.8907 (ttmt) cc_final: 0.8521 (tppp) REVERT: N 469 GLU cc_start: 0.8470 (mp0) cc_final: 0.8088 (mm-30) REVERT: N 472 ASN cc_start: 0.8297 (t0) cc_final: 0.7754 (t0) REVERT: N 480 VAL cc_start: 0.8932 (t) cc_final: 0.8340 (p) REVERT: N 482 TYR cc_start: 0.8163 (m-80) cc_final: 0.7775 (m-80) REVERT: N 504 GLN cc_start: 0.8652 (mp10) cc_final: 0.8298 (pm20) outliers start: 37 outliers final: 10 residues processed: 236 average time/residue: 1.6449 time to fit residues: 426.2407 Evaluate side-chains 209 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 196 time to evaluate : 2.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 14 GLU Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 61 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 185 GLN Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain E residue 90 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 151 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 11 optimal weight: 7.9990 chunk 165 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 161 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 121 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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** C 154 GLN D 265 ASN ** E 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.081437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.058537 restraints weight = 69856.547| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 4.67 r_work: 0.2642 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2647 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2647 r_free = 0.2647 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2647 r_free = 0.2647 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2647 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 15198 Z= 0.216 Angle : 0.667 9.940 20715 Z= 0.339 Chirality : 0.046 0.233 2398 Planarity : 0.005 0.108 2505 Dihedral : 7.125 64.292 2544 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 3.47 % Allowed : 14.87 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.20), residues: 1744 helix: 1.89 (0.21), residues: 570 sheet: 0.69 (0.24), residues: 454 loop : 0.42 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 241 HIS 0.004 0.001 HIS C 318 PHE 0.020 0.002 PHE A 337 TYR 0.029 0.002 TYR D 299 ARG 0.006 0.001 ARG A 50 Details of bonding type rmsd link_NAG-ASN : bond 0.00203 ( 9) link_NAG-ASN : angle 1.62898 ( 27) link_ALPHA1-6 : bond 0.00735 ( 4) link_ALPHA1-6 : angle 1.73698 ( 12) link_BETA1-4 : bond 0.00302 ( 11) link_BETA1-4 : angle 2.03581 ( 33) link_ALPHA1-3 : bond 0.01035 ( 4) link_ALPHA1-3 : angle 2.12099 ( 12) hydrogen bonds : bond 0.04326 ( 762) hydrogen bonds : angle 4.58971 ( 2424) SS BOND : bond 0.00278 ( 6) SS BOND : angle 0.84373 ( 12) covalent geometry : bond 0.00491 (15164) covalent geometry : angle 0.65688 (20619) *********************** 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 248 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 193 time to evaluate : 1.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8889 (OUTLIER) cc_final: 0.8632 (m-30) REVERT: A 253 ARG cc_start: 0.8688 (tpp-160) cc_final: 0.7956 (mmp-170) REVERT: B 9 MET cc_start: 0.7713 (mtp) cc_final: 0.7285 (ttm) REVERT: B 90 GLN cc_start: 0.8951 (mp10) cc_final: 0.8377 (mp10) REVERT: C 105 LYS cc_start: 0.9295 (mmtt) cc_final: 0.8696 (mppt) REVERT: C 162 GLU cc_start: 0.8949 (tt0) cc_final: 0.8491 (tm-30) REVERT: C 189 GLU cc_start: 0.7844 (tm-30) cc_final: 0.7545 (tm-30) REVERT: C 211 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7683 (mm-30) REVERT: C 259 LYS cc_start: 0.9211 (OUTLIER) cc_final: 0.8992 (pttm) REVERT: D 55 MET cc_start: 0.9205 (mtt) cc_final: 0.8847 (mmm) REVERT: D 86 ARG cc_start: 0.7553 (ttp80) cc_final: 0.7240 (tmt-80) REVERT: D 90 GLN cc_start: 0.8159 (pm20) cc_final: 0.7751 (pm20) REVERT: D 95 ASP cc_start: 0.8806 (p0) cc_final: 0.8319 (p0) REVERT: D 224 GLN cc_start: 0.8399 (tp40) cc_final: 0.7998 (tp40) REVERT: D 444 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8846 (mm) REVERT: E 90 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.8521 (pm20) REVERT: N 433 GLU cc_start: 0.9025 (tp30) cc_final: 0.8563 (tt0) REVERT: N 452 LYS cc_start: 0.8809 (ttmt) cc_final: 0.8434 (tppp) REVERT: N 472 ASN cc_start: 0.8317 (t0) cc_final: 0.7795 (t0) REVERT: N 480 VAL cc_start: 0.8957 (t) cc_final: 0.8439 (p) REVERT: N 482 TYR cc_start: 0.8338 (m-80) cc_final: 0.8024 (m-80) outliers start: 55 outliers final: 22 residues processed: 224 average time/residue: 1.3010 time to fit residues: 321.4727 Evaluate side-chains 199 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 173 time to evaluate : 1.640 ------------------------------------------------------------------------------- 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 345 ASN Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 36 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 209 THR 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 440 LEU Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain E residue 222 ILE 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 132 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 100 optimal weight: 7.9990 chunk 46 optimal weight: 0.0970 chunk 96 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN D 265 ASN E 8 ASN ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 426 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.082755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.059586 restraints weight = 73537.185| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 4.82 r_work: 0.2668 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2670 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2670 r_free = 0.2670 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2670 r_free = 0.2670 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2670 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.4079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 15198 Z= 0.133 Angle : 0.615 9.437 20715 Z= 0.312 Chirality : 0.044 0.238 2398 Planarity : 0.003 0.033 2505 Dihedral : 6.639 58.652 2544 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.27 % Allowed : 16.45 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.20), residues: 1744 helix: 1.96 (0.21), residues: 571 sheet: 0.65 (0.24), residues: 463 loop : 0.47 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP E 241 HIS 0.002 0.001 HIS A 184 PHE 0.025 0.001 PHE C 417 TYR 0.023 0.001 TYR B 299 ARG 0.017 0.001 ARG E 428 Details of bonding type rmsd link_NAG-ASN : bond 0.00305 ( 9) link_NAG-ASN : angle 1.37976 ( 27) link_ALPHA1-6 : bond 0.00851 ( 4) link_ALPHA1-6 : angle 1.62038 ( 12) link_BETA1-4 : bond 0.00348 ( 11) link_BETA1-4 : angle 1.54740 ( 33) link_ALPHA1-3 : bond 0.01073 ( 4) link_ALPHA1-3 : angle 1.74182 ( 12) hydrogen bonds : bond 0.03867 ( 762) hydrogen bonds : angle 4.40014 ( 2424) SS BOND : bond 0.00121 ( 6) SS BOND : angle 0.35542 ( 12) covalent geometry : bond 0.00300 (15164) covalent geometry : angle 0.60896 (20619) *********************** 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 224 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 188 time to evaluate : 1.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.8158 (mpp) cc_final: 0.7906 (mmt) REVERT: A 253 ARG cc_start: 0.8655 (tpp-160) cc_final: 0.8444 (mmt180) REVERT: A 345 ASN cc_start: 0.7053 (OUTLIER) cc_final: 0.6789 (t0) REVERT: B 9 MET cc_start: 0.7692 (mtp) cc_final: 0.7192 (ttm) REVERT: B 90 GLN cc_start: 0.8891 (mp10) cc_final: 0.8343 (mp10) REVERT: C 71 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8095 (mm-30) REVERT: C 162 GLU cc_start: 0.8993 (tt0) cc_final: 0.8467 (tm-30) REVERT: C 189 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7793 (tm-30) REVERT: C 211 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7583 (mm-30) REVERT: C 239 GLN cc_start: 0.9023 (tp40) cc_final: 0.8502 (tp40) REVERT: C 259 LYS cc_start: 0.9150 (OUTLIER) cc_final: 0.8937 (pttm) REVERT: D 55 MET cc_start: 0.9207 (mtt) cc_final: 0.8807 (mmm) REVERT: D 90 GLN cc_start: 0.8522 (pm20) cc_final: 0.8108 (pm20) REVERT: D 95 ASP cc_start: 0.8876 (p0) cc_final: 0.8406 (p0) REVERT: D 185 GLN cc_start: 0.8488 (mp10) cc_final: 0.8114 (pm20) REVERT: D 224 GLN cc_start: 0.8421 (tp40) cc_final: 0.8053 (tp40) REVERT: D 274 LYS cc_start: 0.8465 (mppt) cc_final: 0.8258 (mmtt) REVERT: D 306 PHE cc_start: 0.6922 (m-10) cc_final: 0.6707 (m-10) REVERT: D 444 LEU cc_start: 0.9066 (mm) cc_final: 0.8857 (mm) REVERT: E 87 VAL cc_start: 0.9152 (OUTLIER) cc_final: 0.8487 (p) REVERT: E 90 GLN cc_start: 0.8995 (OUTLIER) cc_final: 0.8392 (pm20) REVERT: E 155 GLU cc_start: 0.8733 (tt0) cc_final: 0.8299 (tt0) REVERT: N 433 GLU cc_start: 0.8987 (tp30) cc_final: 0.8533 (tt0) REVERT: N 452 LYS cc_start: 0.8802 (ttmt) cc_final: 0.8478 (tppp) REVERT: N 472 ASN cc_start: 0.8375 (t0) cc_final: 0.8158 (t0) REVERT: N 480 VAL cc_start: 0.8967 (t) cc_final: 0.8455 (p) REVERT: N 482 TYR cc_start: 0.8389 (m-80) cc_final: 0.8114 (m-80) REVERT: N 504 GLN cc_start: 0.8779 (mp10) cc_final: 0.8484 (pm20) outliers start: 36 outliers final: 17 residues processed: 208 average time/residue: 1.2561 time to fit residues: 288.4947 Evaluate side-chains 192 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 171 time to evaluate : 1.595 ------------------------------------------------------------------------------- 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 14 GLU 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 130 MET 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 D residue 440 LEU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain E residue 283 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 38 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 149 optimal weight: 7.9990 chunk 164 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 142 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 101 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 265 ASN ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 426 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.081094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.057575 restraints weight = 78284.550| |-----------------------------------------------------------------------------| r_work (start): 0.2811 rms_B_bonded: 4.77 r_work: 0.2618 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2622 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2622 r_free = 0.2622 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2622 r_free = 0.2622 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2622 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.4392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 15198 Z= 0.198 Angle : 0.650 11.738 20715 Z= 0.327 Chirality : 0.045 0.239 2398 Planarity : 0.004 0.032 2505 Dihedral : 6.348 55.331 2544 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.21 % Allowed : 16.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.20), residues: 1744 helix: 1.97 (0.21), residues: 569 sheet: 0.83 (0.24), residues: 424 loop : 0.16 (0.23), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP D 241 HIS 0.003 0.001 HIS C 318 PHE 0.021 0.002 PHE A 337 TYR 0.028 0.002 TYR D 299 ARG 0.009 0.001 ARG D 26 Details of bonding type rmsd link_NAG-ASN : bond 0.00225 ( 9) link_NAG-ASN : angle 1.69767 ( 27) link_ALPHA1-6 : bond 0.00831 ( 4) link_ALPHA1-6 : angle 1.54980 ( 12) link_BETA1-4 : bond 0.00352 ( 11) link_BETA1-4 : angle 1.74902 ( 33) link_ALPHA1-3 : bond 0.00988 ( 4) link_ALPHA1-3 : angle 1.88388 ( 12) hydrogen bonds : bond 0.04047 ( 762) hydrogen bonds : angle 4.40234 ( 2424) SS BOND : bond 0.00129 ( 6) SS BOND : angle 0.48340 ( 12) covalent geometry : bond 0.00454 (15164) covalent geometry : angle 0.64179 (20619) *********************** 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 209 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 174 time to evaluate : 1.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8901 (OUTLIER) cc_final: 0.8628 (m-30) REVERT: A 118 ARG cc_start: 0.8608 (mtm-85) cc_final: 0.8339 (mpp80) REVERT: A 253 ARG cc_start: 0.8675 (tpp-160) cc_final: 0.8436 (mmt180) REVERT: A 262 GLN cc_start: 0.8994 (tp40) cc_final: 0.8766 (tp40) REVERT: B 9 MET cc_start: 0.7694 (mtp) cc_final: 0.7245 (ttm) REVERT: B 90 GLN cc_start: 0.8957 (mp10) cc_final: 0.8391 (mp10) REVERT: B 137 MET cc_start: 0.8203 (mmm) cc_final: 0.7287 (ttm) REVERT: C 102 MET cc_start: 0.8851 (tpp) cc_final: 0.8560 (tpp) REVERT: C 105 LYS cc_start: 0.9295 (mmtt) cc_final: 0.8769 (mppt) REVERT: C 162 GLU cc_start: 0.9012 (tt0) cc_final: 0.8522 (tm-30) REVERT: C 189 GLU cc_start: 0.8120 (tm-30) cc_final: 0.7910 (tm-30) REVERT: C 211 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7620 (mm-30) REVERT: C 239 GLN cc_start: 0.9044 (tp40) cc_final: 0.8558 (tp40) REVERT: C 259 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8976 (pttm) REVERT: D 55 MET cc_start: 0.9247 (mtt) cc_final: 0.8954 (mmm) REVERT: D 95 ASP cc_start: 0.8861 (p0) cc_final: 0.8425 (p0) REVERT: D 185 GLN cc_start: 0.8554 (mp10) cc_final: 0.8188 (pm20) REVERT: D 224 GLN cc_start: 0.8478 (tp40) cc_final: 0.8056 (tp40) REVERT: D 274 LYS cc_start: 0.8570 (mppt) cc_final: 0.8358 (mmtt) REVERT: D 282 ASP cc_start: 0.8887 (m-30) cc_final: 0.8655 (m-30) REVERT: E 87 VAL cc_start: 0.9187 (OUTLIER) cc_final: 0.8786 (p) REVERT: E 90 GLN cc_start: 0.9035 (OUTLIER) cc_final: 0.8572 (pm20) REVERT: E 155 GLU cc_start: 0.8765 (tt0) cc_final: 0.8302 (tt0) REVERT: E 180 ARG cc_start: 0.8463 (mmp80) cc_final: 0.7930 (mtm180) REVERT: E 282 ASP cc_start: 0.8983 (m-30) cc_final: 0.8304 (m-30) REVERT: N 433 GLU cc_start: 0.9032 (tp30) cc_final: 0.8549 (tt0) REVERT: N 452 LYS cc_start: 0.8805 (ttmt) cc_final: 0.8478 (tppp) REVERT: N 469 GLU cc_start: 0.8396 (mp0) cc_final: 0.8084 (mm-30) REVERT: N 472 ASN cc_start: 0.8456 (t0) cc_final: 0.8158 (t0) REVERT: N 480 VAL cc_start: 0.8992 (t) cc_final: 0.8493 (p) REVERT: N 482 TYR cc_start: 0.8344 (m-80) cc_final: 0.8010 (m-80) REVERT: N 504 GLN cc_start: 0.8655 (mp10) cc_final: 0.8273 (pm20) outliers start: 35 outliers final: 18 residues processed: 196 average time/residue: 1.3419 time to fit residues: 288.3964 Evaluate side-chains 192 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 170 time to evaluate : 1.788 ------------------------------------------------------------------------------- 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 14 GLU 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 444 LEU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 179 ILE 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 7 optimal weight: 5.9990 chunk 146 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 154 optimal weight: 0.8980 chunk 147 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 153 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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** N 426 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.082114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.059470 restraints weight = 58051.046| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 4.11 r_work: 0.2688 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2694 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2694 r_free = 0.2694 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2694 r_free = 0.2694 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2694 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.4527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15198 Z= 0.125 Angle : 0.606 9.423 20715 Z= 0.304 Chirality : 0.043 0.241 2398 Planarity : 0.003 0.032 2505 Dihedral : 5.928 49.782 2544 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.02 % Allowed : 17.08 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.20), residues: 1744 helix: 2.08 (0.21), residues: 570 sheet: 0.90 (0.24), residues: 433 loop : 0.23 (0.24), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP D 241 HIS 0.003 0.001 HIS A 184 PHE 0.029 0.001 PHE C 417 TYR 0.024 0.001 TYR E 299 ARG 0.006 0.000 ARG E 180 Details of bonding type rmsd link_NAG-ASN : bond 0.00283 ( 9) link_NAG-ASN : angle 1.46867 ( 27) link_ALPHA1-6 : bond 0.00944 ( 4) link_ALPHA1-6 : angle 1.51205 ( 12) link_BETA1-4 : bond 0.00368 ( 11) link_BETA1-4 : angle 1.48347 ( 33) link_ALPHA1-3 : bond 0.01011 ( 4) link_ALPHA1-3 : angle 1.73939 ( 12) hydrogen bonds : bond 0.03617 ( 762) hydrogen bonds : angle 4.24904 ( 2424) SS BOND : bond 0.00102 ( 6) SS BOND : angle 0.28209 ( 12) covalent geometry : bond 0.00277 (15164) covalent geometry : angle 0.59974 (20619) *********************** 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 219 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 187 time to evaluate : 1.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.8113 (mpp) cc_final: 0.7890 (mmt) REVERT: A 253 ARG cc_start: 0.8607 (tpp-160) cc_final: 0.8389 (mmt180) REVERT: A 262 GLN cc_start: 0.8947 (tp40) cc_final: 0.8707 (tp40) REVERT: B 9 MET cc_start: 0.7650 (mtp) cc_final: 0.7128 (ttm) REVERT: B 90 GLN cc_start: 0.8891 (mp10) cc_final: 0.8326 (mp10) REVERT: B 137 MET cc_start: 0.8258 (mmm) cc_final: 0.7865 (tpp) REVERT: C 105 LYS cc_start: 0.9262 (mmtt) cc_final: 0.8793 (mppt) REVERT: C 162 GLU cc_start: 0.8973 (tt0) cc_final: 0.8462 (tm-30) REVERT: C 189 GLU cc_start: 0.8177 (tm-30) cc_final: 0.7885 (tm-30) REVERT: C 211 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7512 (mm-30) REVERT: D 13 LYS cc_start: 0.8858 (tmmt) cc_final: 0.8651 (tmmt) REVERT: D 18 LYS cc_start: 0.9369 (pttp) cc_final: 0.9058 (pptt) REVERT: D 55 MET cc_start: 0.9244 (mtt) cc_final: 0.8951 (mmm) REVERT: D 70 LYS cc_start: 0.9289 (mmtm) cc_final: 0.8961 (mmmm) REVERT: D 95 ASP cc_start: 0.8846 (p0) cc_final: 0.8415 (p0) REVERT: D 185 GLN cc_start: 0.8542 (mp10) cc_final: 0.8196 (pm20) REVERT: D 224 GLN cc_start: 0.8420 (tp40) cc_final: 0.8055 (tp40) REVERT: D 282 ASP cc_start: 0.8888 (m-30) cc_final: 0.8640 (m-30) REVERT: E 87 VAL cc_start: 0.9151 (OUTLIER) cc_final: 0.8809 (p) REVERT: E 90 GLN cc_start: 0.9052 (OUTLIER) cc_final: 0.8627 (pm20) REVERT: E 155 GLU cc_start: 0.8729 (tt0) cc_final: 0.8268 (tt0) REVERT: E 180 ARG cc_start: 0.8359 (mmp80) cc_final: 0.7944 (mtm180) REVERT: N 433 GLU cc_start: 0.8994 (tp30) cc_final: 0.8528 (tt0) REVERT: N 452 LYS cc_start: 0.8789 (ttmt) cc_final: 0.8465 (tppp) REVERT: N 469 GLU cc_start: 0.8419 (mp0) cc_final: 0.8037 (mm-30) REVERT: N 472 ASN cc_start: 0.8583 (t0) cc_final: 0.8350 (t0) REVERT: N 480 VAL cc_start: 0.8994 (t) cc_final: 0.8499 (p) REVERT: N 482 TYR cc_start: 0.8345 (m-80) cc_final: 0.8022 (m-80) REVERT: N 504 GLN cc_start: 0.8712 (mp10) cc_final: 0.8416 (pm20) outliers start: 32 outliers final: 16 residues processed: 203 average time/residue: 1.2881 time to fit residues: 287.7672 Evaluate side-chains 190 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 172 time to evaluate : 1.546 ------------------------------------------------------------------------------- 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 345 ASN Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 132 THR 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 E residue 87 VAL Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain N residue 440 TRP 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 70 optimal weight: 5.9990 chunk 137 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 138 optimal weight: 3.9990 chunk 100 optimal weight: 8.9990 chunk 127 optimal weight: 3.9990 chunk 166 optimal weight: 7.9990 chunk 15 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 139 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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** N 426 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.080851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.058094 restraints weight = 81289.103| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 5.06 r_work: 0.2616 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2623 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2623 r_free = 0.2623 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2623 r_free = 0.2623 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2623 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.4662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15198 Z= 0.166 Angle : 0.626 12.118 20715 Z= 0.314 Chirality : 0.044 0.240 2398 Planarity : 0.003 0.031 2505 Dihedral : 5.785 47.539 2544 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.33 % Allowed : 16.89 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.20), residues: 1744 helix: 2.00 (0.21), residues: 575 sheet: 0.82 (0.24), residues: 439 loop : 0.12 (0.24), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP D 241 HIS 0.003 0.001 HIS C 122 PHE 0.019 0.001 PHE A 337 TYR 0.027 0.001 TYR D 299 ARG 0.005 0.000 ARG E 180 Details of bonding type rmsd link_NAG-ASN : bond 0.00235 ( 9) link_NAG-ASN : angle 1.61877 ( 27) link_ALPHA1-6 : bond 0.00917 ( 4) link_ALPHA1-6 : angle 1.49102 ( 12) link_BETA1-4 : bond 0.00337 ( 11) link_BETA1-4 : angle 1.61493 ( 33) link_ALPHA1-3 : bond 0.00896 ( 4) link_ALPHA1-3 : angle 1.79588 ( 12) hydrogen bonds : bond 0.03732 ( 762) hydrogen bonds : angle 4.27594 ( 2424) SS BOND : bond 0.00097 ( 6) SS BOND : angle 0.31749 ( 12) covalent geometry : bond 0.00381 (15164) covalent geometry : angle 0.61832 (20619) *********************** 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 208 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 171 time to evaluate : 1.558 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: A 118 ARG cc_start: 0.8640 (mtm-85) cc_final: 0.8439 (mpp80) REVERT: A 155 MET cc_start: 0.8081 (mpp) cc_final: 0.7869 (mmt) REVERT: B 9 MET cc_start: 0.7875 (mtp) cc_final: 0.7496 (ttm) REVERT: B 90 GLN cc_start: 0.8944 (mp10) cc_final: 0.8370 (mp10) REVERT: C 71 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7789 (mm-30) REVERT: C 162 GLU cc_start: 0.9003 (tt0) cc_final: 0.8526 (tm-30) REVERT: C 189 GLU cc_start: 0.8239 (tm-30) cc_final: 0.7923 (tm-30) REVERT: C 211 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7615 (mm-30) REVERT: C 239 GLN cc_start: 0.9066 (tp40) cc_final: 0.8622 (tp-100) REVERT: D 55 MET cc_start: 0.9249 (mtt) cc_final: 0.8969 (mmm) REVERT: D 95 ASP cc_start: 0.8873 (p0) cc_final: 0.8434 (p0) REVERT: D 185 GLN cc_start: 0.8553 (mp10) cc_final: 0.8111 (pm20) REVERT: D 224 GLN cc_start: 0.8481 (tp40) cc_final: 0.8083 (tp40) REVERT: D 282 ASP cc_start: 0.9034 (m-30) cc_final: 0.8808 (m-30) REVERT: E 49 MET cc_start: 0.8702 (OUTLIER) cc_final: 0.8381 (pp-130) REVERT: E 87 VAL cc_start: 0.9194 (OUTLIER) cc_final: 0.8876 (p) REVERT: E 90 GLN cc_start: 0.9065 (OUTLIER) cc_final: 0.8657 (pm20) REVERT: E 180 ARG cc_start: 0.8466 (mmp80) cc_final: 0.8041 (mtm180) REVERT: E 282 ASP cc_start: 0.9042 (m-30) cc_final: 0.8772 (m-30) REVERT: N 433 GLU cc_start: 0.9040 (tp30) cc_final: 0.8600 (tt0) REVERT: N 452 LYS cc_start: 0.8835 (ttmt) cc_final: 0.8495 (tppp) REVERT: N 469 GLU cc_start: 0.8427 (mp0) cc_final: 0.8020 (mm-30) REVERT: N 472 ASN cc_start: 0.8446 (t0) cc_final: 0.8153 (t0) REVERT: N 480 VAL cc_start: 0.9009 (t) cc_final: 0.8522 (p) REVERT: N 482 TYR cc_start: 0.8341 (m-80) cc_final: 0.8029 (m-80) REVERT: N 504 GLN cc_start: 0.8690 (mp10) cc_final: 0.8396 (pm20) outliers start: 37 outliers final: 19 residues processed: 190 average time/residue: 1.2997 time to fit residues: 271.7050 Evaluate side-chains 187 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 165 time to evaluate : 1.606 ------------------------------------------------------------------------------- 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 345 ASN Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 227 MET 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 105 optimal weight: 0.3980 chunk 86 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 24 optimal weight: 0.7980 chunk 93 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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** N 426 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.082796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.058945 restraints weight = 91113.243| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 5.12 r_work: 0.2652 rms_B_bonded: 5.09 restraints_weight: 2.0000 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 = 0.32 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 = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2659 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.4765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15198 Z= 0.121 Angle : 0.625 13.186 20715 Z= 0.307 Chirality : 0.043 0.237 2398 Planarity : 0.003 0.034 2505 Dihedral : 5.464 42.784 2544 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.70 % Allowed : 17.45 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.20), residues: 1744 helix: 2.11 (0.21), residues: 570 sheet: 0.88 (0.24), residues: 439 loop : 0.26 (0.24), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP D 241 HIS 0.003 0.001 HIS A 143 PHE 0.033 0.001 PHE C 417 TYR 0.023 0.001 TYR E 299 ARG 0.006 0.000 ARG E 180 Details of bonding type rmsd link_NAG-ASN : bond 0.00271 ( 9) link_NAG-ASN : angle 1.45086 ( 27) link_ALPHA1-6 : bond 0.01011 ( 4) link_ALPHA1-6 : angle 1.44071 ( 12) link_BETA1-4 : bond 0.00380 ( 11) link_BETA1-4 : angle 1.43575 ( 33) link_ALPHA1-3 : bond 0.00967 ( 4) link_ALPHA1-3 : angle 1.67947 ( 12) hydrogen bonds : bond 0.03480 ( 762) hydrogen bonds : angle 4.17734 ( 2424) SS BOND : bond 0.00152 ( 6) SS BOND : angle 0.25606 ( 12) covalent geometry : bond 0.00272 (15164) covalent geometry : angle 0.61920 (20619) *********************** 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 218 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 191 time to evaluate : 1.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 MET cc_start: 0.7911 (mtp) cc_final: 0.7385 (ttm) REVERT: B 90 GLN cc_start: 0.8899 (mp10) cc_final: 0.8319 (mp10) REVERT: B 137 MET cc_start: 0.8114 (tpp) cc_final: 0.7117 (ttm) REVERT: C 71 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7846 (mp0) REVERT: C 105 LYS cc_start: 0.9314 (mmtt) cc_final: 0.8826 (mppt) REVERT: C 162 GLU cc_start: 0.9026 (tt0) cc_final: 0.8455 (tm-30) REVERT: C 189 GLU cc_start: 0.8270 (tm-30) cc_final: 0.7964 (tm-30) REVERT: C 211 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7560 (mm-30) REVERT: C 239 GLN cc_start: 0.9065 (tp40) cc_final: 0.8647 (tp-100) REVERT: D 52 GLU cc_start: 0.9260 (mp0) cc_final: 0.8974 (mp0) REVERT: D 55 MET cc_start: 0.9216 (mtt) cc_final: 0.8916 (mmm) REVERT: D 95 ASP cc_start: 0.8872 (p0) cc_final: 0.8437 (p0) REVERT: D 147 GLU cc_start: 0.8631 (tt0) cc_final: 0.8402 (tt0) REVERT: D 153 GLU cc_start: 0.8882 (mm-30) cc_final: 0.8662 (mm-30) REVERT: D 185 GLN cc_start: 0.8506 (mp10) cc_final: 0.8075 (pm20) REVERT: D 190 GLU cc_start: 0.8936 (tt0) cc_final: 0.8169 (tt0) REVERT: D 224 GLN cc_start: 0.8519 (tp40) cc_final: 0.8145 (tp40) REVERT: E 49 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.8374 (pp-130) REVERT: E 87 VAL cc_start: 0.9133 (OUTLIER) cc_final: 0.8793 (p) REVERT: E 90 GLN cc_start: 0.9063 (OUTLIER) cc_final: 0.8620 (pm20) REVERT: E 137 MET cc_start: 0.8389 (mmm) cc_final: 0.8006 (mmm) REVERT: E 155 GLU cc_start: 0.8805 (tt0) cc_final: 0.8342 (tt0) REVERT: E 180 ARG cc_start: 0.8449 (mmp80) cc_final: 0.8059 (mtm180) REVERT: E 282 ASP cc_start: 0.9031 (m-30) cc_final: 0.8701 (m-30) REVERT: N 426 GLN cc_start: 0.8066 (tt0) cc_final: 0.7762 (tp-100) REVERT: N 433 GLU cc_start: 0.9039 (tp30) cc_final: 0.8567 (tt0) REVERT: N 452 LYS cc_start: 0.8876 (ttmt) cc_final: 0.8533 (tppp) REVERT: N 469 GLU cc_start: 0.8415 (mp0) cc_final: 0.7989 (mm-30) REVERT: N 472 ASN cc_start: 0.8351 (t0) cc_final: 0.8071 (t0) REVERT: N 480 VAL cc_start: 0.8973 (t) cc_final: 0.8501 (p) REVERT: N 482 TYR cc_start: 0.8306 (m-80) cc_final: 0.8031 (m-80) REVERT: N 504 GLN cc_start: 0.8684 (mp10) cc_final: 0.8389 (pm20) outliers start: 27 outliers final: 12 residues processed: 205 average time/residue: 1.2618 time to fit residues: 284.2251 Evaluate side-chains 186 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 171 time to evaluate : 1.573 ------------------------------------------------------------------------------- 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 14 GLU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 179 ILE 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 464 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 81 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 105 optimal weight: 0.6980 chunk 85 optimal weight: 7.9990 chunk 170 optimal weight: 9.9990 chunk 63 optimal weight: 10.0000 chunk 132 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 118 optimal weight: 7.9990 chunk 101 optimal weight: 0.0040 overall best weight: 1.2996 ------------------------------------------------------------------------------- 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 = 0.3345 r_free = 0.3345 target = 0.081871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.058105 restraints weight = 88321.281| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 5.05 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2828 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2828 r_free = 0.2828 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2828 r_free = 0.2828 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2828 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.4873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 15198 Z= 0.147 Angle : 0.647 12.443 20715 Z= 0.323 Chirality : 0.044 0.234 2398 Planarity : 0.003 0.031 2505 Dihedral : 5.396 40.975 2544 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.20 % Allowed : 18.34 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.20), residues: 1744 helix: 2.12 (0.21), residues: 570 sheet: 0.85 (0.24), residues: 442 loop : 0.26 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP D 241 HIS 0.003 0.001 HIS A 184 PHE 0.016 0.001 PHE A 337 TYR 0.030 0.001 TYR D 299 ARG 0.007 0.000 ARG N 459 Details of bonding type rmsd link_NAG-ASN : bond 0.00435 ( 9) link_NAG-ASN : angle 2.07154 ( 27) link_ALPHA1-6 : bond 0.00956 ( 4) link_ALPHA1-6 : angle 1.40779 ( 12) link_BETA1-4 : bond 0.00371 ( 11) link_BETA1-4 : angle 1.50531 ( 33) link_ALPHA1-3 : bond 0.00867 ( 4) link_ALPHA1-3 : angle 1.74605 ( 12) hydrogen bonds : bond 0.03538 ( 762) hydrogen bonds : angle 4.21772 ( 2424) SS BOND : bond 0.00113 ( 6) SS BOND : angle 0.26225 ( 12) covalent geometry : bond 0.00341 (15164) covalent geometry : angle 0.63929 (20619) ********************** 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 190 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 171 time to evaluate : 1.730 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: B 9 MET cc_start: 0.8041 (mtp) cc_final: 0.7646 (ttm) REVERT: B 90 GLN cc_start: 0.8611 (mp10) cc_final: 0.8006 (mp10) REVERT: B 137 MET cc_start: 0.7823 (tpp) cc_final: 0.7576 (tpp) REVERT: C 71 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7531 (mp0) REVERT: C 162 GLU cc_start: 0.8710 (tt0) cc_final: 0.8213 (tm-30) REVERT: C 189 GLU cc_start: 0.7916 (tm-30) cc_final: 0.7664 (tm-30) REVERT: D 55 MET cc_start: 0.9040 (mtt) cc_final: 0.8767 (mmm) REVERT: D 185 GLN cc_start: 0.8365 (mp10) cc_final: 0.8040 (pm20) REVERT: D 224 GLN cc_start: 0.8238 (tp40) cc_final: 0.7829 (tp40) REVERT: E 87 VAL cc_start: 0.9106 (OUTLIER) cc_final: 0.8767 (p) REVERT: E 90 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.8523 (pm20) REVERT: E 180 ARG cc_start: 0.8237 (mmp80) cc_final: 0.7989 (mtm180) REVERT: E 282 ASP cc_start: 0.8554 (m-30) cc_final: 0.8274 (m-30) REVERT: N 426 GLN cc_start: 0.8171 (tt0) cc_final: 0.7907 (tp-100) REVERT: N 433 GLU cc_start: 0.9003 (tp30) cc_final: 0.8564 (tt0) REVERT: N 452 LYS cc_start: 0.8953 (ttmt) cc_final: 0.8624 (tppp) REVERT: N 469 GLU cc_start: 0.8257 (mp0) cc_final: 0.7857 (mm-30) REVERT: N 472 ASN cc_start: 0.8390 (t0) cc_final: 0.8150 (t0) REVERT: N 480 VAL cc_start: 0.8975 (t) cc_final: 0.8506 (p) REVERT: N 482 TYR cc_start: 0.8153 (m-80) cc_final: 0.7834 (m-80) REVERT: N 504 GLN cc_start: 0.8558 (mp10) cc_final: 0.8271 (pm20) outliers start: 19 outliers final: 13 residues processed: 184 average time/residue: 1.3088 time to fit residues: 264.8120 Evaluate side-chains 180 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 165 time to evaluate : 1.582 ------------------------------------------------------------------------------- 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 B residue 14 GLU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain N residue 440 TRP Chi-restraints excluded: chain N residue 464 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 122 optimal weight: 2.9990 chunk 162 optimal weight: 7.9990 chunk 114 optimal weight: 9.9990 chunk 62 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 154 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 160 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 ASN C 152 GLN D 303 ASN ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.080473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.057074 restraints weight = 88966.987| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 4.91 r_work: 0.2604 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2609 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2609 r_free = 0.2609 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2609 r_free = 0.2609 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2609 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.4989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 15198 Z= 0.180 Angle : 0.666 13.529 20715 Z= 0.331 Chirality : 0.044 0.230 2398 Planarity : 0.003 0.035 2505 Dihedral : 5.376 39.880 2544 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.51 % Allowed : 18.40 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.20), residues: 1744 helix: 2.08 (0.21), residues: 570 sheet: 0.85 (0.24), residues: 439 loop : 0.16 (0.24), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP D 241 HIS 0.003 0.001 HIS A 184 PHE 0.036 0.001 PHE C 417 TYR 0.026 0.001 TYR D 299 ARG 0.010 0.000 ARG N 459 Details of bonding type rmsd link_NAG-ASN : bond 0.00358 ( 9) link_NAG-ASN : angle 2.08041 ( 27) link_ALPHA1-6 : bond 0.00987 ( 4) link_ALPHA1-6 : angle 1.39036 ( 12) link_BETA1-4 : bond 0.00350 ( 11) link_BETA1-4 : angle 1.58190 ( 33) link_ALPHA1-3 : bond 0.00829 ( 4) link_ALPHA1-3 : angle 1.72600 ( 12) hydrogen bonds : bond 0.03730 ( 762) hydrogen bonds : angle 4.26862 ( 2424) SS BOND : bond 0.00114 ( 6) SS BOND : angle 0.28341 ( 12) covalent geometry : bond 0.00418 (15164) covalent geometry : angle 0.65849 (20619) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10938.41 seconds wall clock time: 189 minutes 33.40 seconds (11373.40 seconds total)