Starting phenix.real_space_refine on Tue Dec 31 06:25:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qna_14072/12_2024/7qna_14072.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qna_14072/12_2024/7qna_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_14072/12_2024/7qna_14072.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qna_14072/12_2024/7qna_14072.map" model { file = "/net/cci-nas-00/data/ceres_data/7qna_14072/12_2024/7qna_14072.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qna_14072/12_2024/7qna_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-5532/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: 12.01, per 1000 atoms: 0.81 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: 4.32 Conformation dependent library (CDL) restraints added in 2.8 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: 1.75 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: 5.40 Time building geometry restraints manager: 4.79 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: 1.450 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: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 39.930 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.650 ------------------------------------------------------------------------------- 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 15164 Z= 0.194 Angle : 0.484 7.250 20619 Z= 0.222 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 *********************** 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 : 1.727 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: 1.4540 time to fit residues: 588.5243 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 : 1.611 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 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 15164 Z= 0.305 Angle : 0.691 9.880 20619 Z= 0.358 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 *********************** 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 : 1.636 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: 0.8095 (m-80) cc_final: 0.7828 (m-80) REVERT: A 253 ARG cc_start: 0.8010 (tpp-160) cc_final: 0.7320 (mmp-170) REVERT: B 9 MET cc_start: 0.7396 (mtp) cc_final: 0.6841 (ttm) REVERT: B 90 GLN cc_start: 0.8481 (mp10) cc_final: 0.7991 (mp10) REVERT: B 274 LYS cc_start: 0.8535 (mmtt) cc_final: 0.8211 (mmpt) REVERT: C 162 GLU cc_start: 0.8369 (tt0) cc_final: 0.8166 (tm-30) REVERT: C 209 THR cc_start: 0.8926 (OUTLIER) cc_final: 0.8670 (p) REVERT: C 260 ASP cc_start: 0.8324 (m-30) cc_final: 0.8079 (m-30) REVERT: D 9 MET cc_start: 0.8676 (pmm) cc_final: 0.8410 (mpp) REVERT: D 13 LYS cc_start: 0.8824 (tmmt) cc_final: 0.8419 (tmmt) REVERT: D 14 GLU cc_start: 0.9106 (mm-30) cc_final: 0.8556 (mp0) REVERT: D 25 ILE cc_start: 0.9022 (mt) cc_final: 0.8780 (mm) REVERT: D 55 MET cc_start: 0.8954 (mtt) cc_final: 0.8582 (mmm) REVERT: D 95 ASP cc_start: 0.8424 (p0) cc_final: 0.8047 (p0) REVERT: D 147 GLU cc_start: 0.7764 (tt0) cc_final: 0.7339 (tm-30) REVERT: D 181 ILE cc_start: 0.9159 (mt) cc_final: 0.8840 (mp) REVERT: D 224 GLN cc_start: 0.8034 (tp40) cc_final: 0.7652 (tp40) REVERT: D 230 ILE cc_start: 0.9434 (mt) cc_final: 0.8973 (mp) REVERT: E 90 GLN cc_start: 0.8713 (mp10) cc_final: 0.8412 (pm20) REVERT: E 155 GLU cc_start: 0.8125 (tt0) cc_final: 0.7750 (mt-10) REVERT: E 182 GLU cc_start: 0.8405 (mm-30) cc_final: 0.8039 (mm-30) REVERT: E 298 GLU cc_start: 0.9305 (tm-30) cc_final: 0.9092 (tm-30) REVERT: N 421 MET cc_start: 0.8216 (tpp) cc_final: 0.7799 (mpp) REVERT: N 425 ARG cc_start: 0.8375 (ptt180) cc_final: 0.8175 (ptt-90) REVERT: N 426 GLN cc_start: 0.8084 (tt0) cc_final: 0.7788 (tp40) REVERT: N 452 LYS cc_start: 0.8718 (ttmt) cc_final: 0.8465 (tppp) REVERT: N 454 ARG cc_start: 0.6867 (mtm110) cc_final: 0.6577 (mtp-110) REVERT: N 472 ASN cc_start: 0.8309 (t0) cc_final: 0.7588 (t0) REVERT: N 480 VAL cc_start: 0.8849 (t) cc_final: 0.8263 (p) REVERT: N 482 TYR cc_start: 0.8262 (m-80) cc_final: 0.8031 (m-80) outliers start: 45 outliers final: 16 residues processed: 271 average time/residue: 1.4531 time to fit residues: 428.8433 Evaluate side-chains 214 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 197 time to evaluate : 1.685 ------------------------------------------------------------------------------- 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 D residue 227 MET Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain D residue 440 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 87 optimal weight: 0.7980 chunk 48 optimal weight: 5.9990 chunk 130 optimal weight: 0.0870 chunk 106 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 157 optimal weight: 1.9990 chunk 170 optimal weight: 9.9990 chunk 140 optimal weight: 7.9990 chunk 156 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 overall best weight: 0.9560 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15164 Z= 0.196 Angle : 0.626 10.087 20619 Z= 0.320 Chirality : 0.044 0.203 2398 Planarity : 0.004 0.033 2505 Dihedral : 8.192 70.931 2544 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 2.21 % Allowed : 15.63 % Favored : 82.17 % 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: 2.05 (0.21), residues: 569 sheet: 0.88 (0.24), residues: 463 loop : 0.74 (0.25), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 237 HIS 0.005 0.001 HIS A 184 PHE 0.022 0.001 PHE C 417 TYR 0.027 0.001 TYR D 244 ARG 0.008 0.001 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 223 time to evaluate : 1.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 PHE cc_start: 0.8112 (m-80) cc_final: 0.7809 (m-80) REVERT: B 9 MET cc_start: 0.7044 (mtp) cc_final: 0.6689 (ttm) REVERT: B 61 MET cc_start: 0.8861 (OUTLIER) cc_final: 0.8516 (ptt) REVERT: B 90 GLN cc_start: 0.8458 (mp10) cc_final: 0.8035 (mp10) REVERT: B 274 LYS cc_start: 0.8549 (mmtt) cc_final: 0.8188 (mmpt) REVERT: C 71 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7712 (mm-30) REVERT: C 239 GLN cc_start: 0.8921 (tp40) cc_final: 0.8686 (tp40) REVERT: D 23 TYR cc_start: 0.7690 (OUTLIER) cc_final: 0.7488 (t80) REVERT: D 55 MET cc_start: 0.8987 (mtt) cc_final: 0.8560 (mmm) REVERT: D 86 ARG cc_start: 0.7610 (ttp80) cc_final: 0.7258 (tmt-80) REVERT: D 90 GLN cc_start: 0.8473 (pm20) cc_final: 0.7991 (pm20) REVERT: D 95 ASP cc_start: 0.8475 (p0) cc_final: 0.8084 (p0) REVERT: D 147 GLU cc_start: 0.7853 (tt0) cc_final: 0.7432 (tm-30) REVERT: D 185 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7732 (pm20) REVERT: D 224 GLN cc_start: 0.7933 (tp40) cc_final: 0.7571 (tp40) REVERT: E 90 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.8534 (pm20) REVERT: E 155 GLU cc_start: 0.8051 (tt0) cc_final: 0.7689 (mt-10) REVERT: E 190 GLU cc_start: 0.8409 (tt0) cc_final: 0.8204 (pt0) REVERT: E 298 GLU cc_start: 0.9334 (tm-30) cc_final: 0.9111 (tm-30) REVERT: N 421 MET cc_start: 0.8200 (tpp) cc_final: 0.7963 (mpp) REVERT: N 452 LYS cc_start: 0.8694 (ttmt) cc_final: 0.8402 (tppp) REVERT: N 463 LYS cc_start: 0.9347 (OUTLIER) cc_final: 0.9130 (tppp) REVERT: N 469 GLU cc_start: 0.8528 (mp0) cc_final: 0.8127 (mm-30) REVERT: N 472 ASN cc_start: 0.8328 (t0) cc_final: 0.7757 (t0) REVERT: N 480 VAL cc_start: 0.9007 (t) cc_final: 0.8452 (p) REVERT: N 482 TYR cc_start: 0.8292 (m-80) cc_final: 0.8033 (m-80) REVERT: N 504 GLN cc_start: 0.8692 (mp10) cc_final: 0.8371 (pm20) outliers start: 35 outliers final: 8 residues processed: 235 average time/residue: 1.4300 time to fit residues: 367.6659 Evaluate side-chains 207 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 194 time to evaluate : 1.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL 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 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 23 TYR Chi-restraints excluded: chain D residue 185 GLN Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain N residue 463 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 155 optimal weight: 1.9990 chunk 118 optimal weight: 7.9990 chunk 81 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 75 optimal weight: 6.9990 chunk 105 optimal weight: 0.9990 chunk 157 optimal weight: 1.9990 chunk 167 optimal weight: 10.0000 chunk 82 optimal weight: 7.9990 chunk 149 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15164 Z= 0.198 Angle : 0.612 9.515 20619 Z= 0.312 Chirality : 0.044 0.243 2398 Planarity : 0.004 0.049 2505 Dihedral : 7.123 63.460 2544 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 2.90 % Allowed : 15.56 % Favored : 81.54 % 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: 1.60 (0.21), residues: 1744 helix: 2.02 (0.21), residues: 568 sheet: 0.85 (0.24), residues: 463 loop : 0.55 (0.25), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D 241 HIS 0.003 0.001 HIS A 184 PHE 0.015 0.001 PHE A 337 TYR 0.024 0.001 TYR D 299 ARG 0.006 0.000 ARG E 180 *********************** 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 250 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 204 time to evaluate : 1.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 PHE cc_start: 0.8052 (m-80) cc_final: 0.7815 (m-80) REVERT: A 155 MET cc_start: 0.8348 (mpp) cc_final: 0.8056 (mmt) REVERT: B 9 MET cc_start: 0.6965 (mtp) cc_final: 0.6712 (ttm) REVERT: B 90 GLN cc_start: 0.8490 (mp10) cc_final: 0.8052 (mp10) REVERT: D 52 GLU cc_start: 0.8985 (mp0) cc_final: 0.8681 (mp0) REVERT: D 55 MET cc_start: 0.9012 (mtt) cc_final: 0.8665 (mmm) REVERT: D 86 ARG cc_start: 0.7489 (ttp80) cc_final: 0.7142 (tmt-80) REVERT: D 90 GLN cc_start: 0.8161 (pm20) cc_final: 0.7796 (pm20) REVERT: D 95 ASP cc_start: 0.8494 (p0) cc_final: 0.8092 (p0) REVERT: D 147 GLU cc_start: 0.8002 (tt0) cc_final: 0.7671 (tm-30) REVERT: D 224 GLN cc_start: 0.8024 (tp40) cc_final: 0.7648 (tp40) REVERT: E 90 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.8340 (pm20) REVERT: E 137 MET cc_start: 0.8386 (mmm) cc_final: 0.8070 (mmp) REVERT: E 155 GLU cc_start: 0.8009 (tt0) cc_final: 0.7685 (tt0) REVERT: E 190 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.8077 (pt0) REVERT: N 421 MET cc_start: 0.8151 (tpp) cc_final: 0.7898 (mpp) REVERT: N 426 GLN cc_start: 0.7968 (tp-100) cc_final: 0.7368 (tp40) REVERT: N 433 GLU cc_start: 0.6847 (mp0) cc_final: 0.6413 (mp0) REVERT: N 452 LYS cc_start: 0.8711 (ttmt) cc_final: 0.8417 (tppp) REVERT: N 472 ASN cc_start: 0.8240 (t0) cc_final: 0.7918 (t0) REVERT: N 480 VAL cc_start: 0.9064 (t) cc_final: 0.8518 (p) REVERT: N 482 TYR cc_start: 0.8300 (m-80) cc_final: 0.7966 (m-80) REVERT: N 504 GLN cc_start: 0.8668 (mp10) cc_final: 0.8311 (pm20) outliers start: 46 outliers final: 18 residues processed: 226 average time/residue: 1.3636 time to fit residues: 338.3056 Evaluate side-chains 208 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 188 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 96 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 424 ASP Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain E residue 190 GLU 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 139 optimal weight: 5.9990 chunk 94 optimal weight: 10.0000 chunk 2 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 142 optimal weight: 0.8980 chunk 115 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 150 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 ASN ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15164 Z= 0.198 Angle : 0.611 9.729 20619 Z= 0.311 Chirality : 0.044 0.238 2398 Planarity : 0.003 0.044 2505 Dihedral : 6.651 58.671 2544 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.46 % Allowed : 16.76 % 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: 1.54 (0.20), residues: 1744 helix: 2.01 (0.21), residues: 569 sheet: 0.76 (0.24), residues: 466 loop : 0.52 (0.25), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP E 241 HIS 0.003 0.001 HIS A 184 PHE 0.031 0.001 PHE C 417 TYR 0.024 0.001 TYR D 299 ARG 0.009 0.000 ARG E 428 *********************** 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 239 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 200 time to evaluate : 1.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 PHE cc_start: 0.8061 (m-80) cc_final: 0.7780 (m-80) REVERT: A 155 MET cc_start: 0.8315 (mpp) cc_final: 0.8047 (mmt) REVERT: B 9 MET cc_start: 0.7058 (mtp) cc_final: 0.6817 (ttm) REVERT: B 55 MET cc_start: 0.8534 (mtm) cc_final: 0.8164 (mtm) REVERT: B 90 GLN cc_start: 0.8517 (mp10) cc_final: 0.7979 (mp10) REVERT: D 52 GLU cc_start: 0.9022 (mp0) cc_final: 0.8724 (mp0) REVERT: D 55 MET cc_start: 0.9056 (mtt) cc_final: 0.8698 (mmm) REVERT: D 86 ARG cc_start: 0.7608 (ttp80) cc_final: 0.7367 (tmt-80) REVERT: D 90 GLN cc_start: 0.8238 (pm20) cc_final: 0.7838 (pm20) REVERT: D 95 ASP cc_start: 0.8517 (p0) cc_final: 0.8120 (p0) REVERT: D 147 GLU cc_start: 0.8077 (tt0) cc_final: 0.7730 (tt0) REVERT: D 185 GLN cc_start: 0.8205 (mp10) cc_final: 0.7847 (pm20) REVERT: D 224 GLN cc_start: 0.7986 (tp40) cc_final: 0.7382 (tp40) REVERT: E 87 VAL cc_start: 0.9194 (OUTLIER) cc_final: 0.8403 (p) REVERT: E 90 GLN cc_start: 0.8852 (OUTLIER) cc_final: 0.8356 (pm20) REVERT: E 155 GLU cc_start: 0.7979 (tt0) cc_final: 0.7613 (mt-10) REVERT: E 180 ARG cc_start: 0.7653 (mmp80) cc_final: 0.7387 (mpp80) REVERT: E 190 GLU cc_start: 0.8356 (tt0) cc_final: 0.8115 (pt0) REVERT: N 426 GLN cc_start: 0.7950 (OUTLIER) cc_final: 0.7296 (tp40) REVERT: N 433 GLU cc_start: 0.6891 (mp0) cc_final: 0.6454 (mp0) REVERT: N 452 LYS cc_start: 0.8698 (ttmt) cc_final: 0.8395 (tppp) REVERT: N 472 ASN cc_start: 0.8238 (t0) cc_final: 0.7961 (t0) REVERT: N 480 VAL cc_start: 0.9099 (t) cc_final: 0.8566 (p) REVERT: N 482 TYR cc_start: 0.8314 (m-80) cc_final: 0.7979 (m-80) outliers start: 39 outliers final: 15 residues processed: 220 average time/residue: 1.3999 time to fit residues: 336.8669 Evaluate side-chains 202 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 184 time to evaluate : 1.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 96 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 B residue 14 GLU 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 424 LEU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 227 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 426 GLN 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 56 optimal weight: 0.6980 chunk 150 optimal weight: 0.0470 chunk 33 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 167 optimal weight: 0.9980 chunk 138 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 overall best weight: 0.7280 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15164 Z= 0.177 Angle : 0.621 10.993 20619 Z= 0.311 Chirality : 0.044 0.242 2398 Planarity : 0.003 0.032 2505 Dihedral : 6.220 53.724 2544 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.14 % Allowed : 17.39 % 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: 1.57 (0.20), residues: 1744 helix: 2.03 (0.22), residues: 570 sheet: 0.77 (0.24), residues: 460 loop : 0.55 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP E 241 HIS 0.003 0.000 HIS A 184 PHE 0.013 0.001 PHE E 31 TYR 0.023 0.001 TYR D 299 ARG 0.005 0.000 ARG D 26 *********************** 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 236 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 202 time to evaluate : 1.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 PHE cc_start: 0.8061 (m-80) cc_final: 0.7776 (m-80) REVERT: A 155 MET cc_start: 0.8332 (mpp) cc_final: 0.8045 (mmt) REVERT: B 9 MET cc_start: 0.7056 (mtp) cc_final: 0.6705 (ttm) REVERT: B 55 MET cc_start: 0.8680 (mtm) cc_final: 0.8343 (mtm) REVERT: B 90 GLN cc_start: 0.8499 (mp10) cc_final: 0.7966 (mp10) REVERT: B 137 MET cc_start: 0.7328 (mmm) cc_final: 0.6745 (ttm) REVERT: C 71 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7560 (mp0) REVERT: C 105 LYS cc_start: 0.9098 (mmtt) cc_final: 0.8710 (mppt) REVERT: D 52 GLU cc_start: 0.9045 (mp0) cc_final: 0.8793 (mp0) REVERT: D 55 MET cc_start: 0.9038 (mtt) cc_final: 0.8672 (mmm) REVERT: D 90 GLN cc_start: 0.8270 (pm20) cc_final: 0.7874 (pm20) REVERT: D 95 ASP cc_start: 0.8517 (p0) cc_final: 0.8141 (p0) REVERT: D 147 GLU cc_start: 0.8074 (tt0) cc_final: 0.7750 (tt0) REVERT: D 185 GLN cc_start: 0.8216 (mp10) cc_final: 0.7853 (pm20) REVERT: D 224 GLN cc_start: 0.8069 (tp40) cc_final: 0.7710 (tp40) REVERT: E 87 VAL cc_start: 0.9188 (OUTLIER) cc_final: 0.8372 (p) REVERT: E 90 GLN cc_start: 0.8850 (OUTLIER) cc_final: 0.8335 (pm20) REVERT: E 137 MET cc_start: 0.8463 (mpp) cc_final: 0.7973 (tpp) REVERT: E 155 GLU cc_start: 0.7979 (tt0) cc_final: 0.7624 (mt-10) REVERT: E 190 GLU cc_start: 0.8336 (tt0) cc_final: 0.8077 (pt0) REVERT: N 426 GLN cc_start: 0.7928 (tp-100) cc_final: 0.7307 (tp40) REVERT: N 433 GLU cc_start: 0.6913 (mp0) cc_final: 0.6495 (mp0) REVERT: N 452 LYS cc_start: 0.8722 (ttmt) cc_final: 0.8481 (tppp) REVERT: N 469 GLU cc_start: 0.8421 (mp0) cc_final: 0.8044 (mm-30) REVERT: N 480 VAL cc_start: 0.9102 (t) cc_final: 0.8589 (p) REVERT: N 482 TYR cc_start: 0.8302 (m-80) cc_final: 0.7985 (m-80) REVERT: N 504 GLN cc_start: 0.8715 (mp10) cc_final: 0.8366 (pm20) outliers start: 34 outliers final: 18 residues processed: 220 average time/residue: 1.3804 time to fit residues: 334.1735 Evaluate side-chains 207 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 187 time to evaluate : 1.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 96 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 239 ILE 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 87 VAL 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 53 VAL Chi-restraints excluded: chain D residue 227 MET 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 407 LEU Chi-restraints excluded: chain N residue 464 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 161 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 chunk 95 optimal weight: 0.7980 chunk 122 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 140 optimal weight: 8.9990 chunk 93 optimal weight: 3.9990 chunk 166 optimal weight: 1.9990 chunk 104 optimal weight: 9.9990 chunk 101 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 ASN D 303 ASN E 303 ASN N 507 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.4524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 15164 Z= 0.415 Angle : 0.721 13.478 20619 Z= 0.370 Chirality : 0.048 0.236 2398 Planarity : 0.004 0.034 2505 Dihedral : 6.286 53.166 2544 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.39 % Allowed : 17.45 % Favored : 80.15 % 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: 1.13 (0.20), residues: 1744 helix: 1.76 (0.21), residues: 575 sheet: 0.75 (0.24), residues: 445 loop : 0.02 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP E 241 HIS 0.005 0.001 HIS C 318 PHE 0.033 0.002 PHE C 417 TYR 0.042 0.002 TYR D 299 ARG 0.010 0.001 ARG A 253 *********************** 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 218 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 180 time to evaluate : 1.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 PHE cc_start: 0.8107 (m-80) cc_final: 0.7792 (m-80) REVERT: B 9 MET cc_start: 0.7142 (mtp) cc_final: 0.6824 (ttm) REVERT: B 90 GLN cc_start: 0.8682 (mp10) cc_final: 0.8164 (mp10) REVERT: C 71 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7539 (mp0) REVERT: C 105 LYS cc_start: 0.9125 (mmtt) cc_final: 0.8734 (mppt) REVERT: C 239 GLN cc_start: 0.8780 (tp40) cc_final: 0.8366 (tp40) REVERT: D 55 MET cc_start: 0.9123 (mtt) cc_final: 0.8902 (mmm) REVERT: D 95 ASP cc_start: 0.8663 (p0) cc_final: 0.8357 (p0) REVERT: D 147 GLU cc_start: 0.8265 (tt0) cc_final: 0.8055 (tt0) REVERT: D 185 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.8111 (pm20) REVERT: D 190 GLU cc_start: 0.8362 (tt0) cc_final: 0.7740 (tt0) REVERT: D 224 GLN cc_start: 0.8049 (tp40) cc_final: 0.7622 (tp40) REVERT: D 282 ASP cc_start: 0.8699 (m-30) cc_final: 0.8444 (m-30) REVERT: E 87 VAL cc_start: 0.9302 (OUTLIER) cc_final: 0.8877 (p) REVERT: E 90 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.8481 (pm20) REVERT: N 426 GLN cc_start: 0.8026 (tp-100) cc_final: 0.7332 (tp40) REVERT: N 433 GLU cc_start: 0.6992 (OUTLIER) cc_final: 0.6516 (mp0) REVERT: N 452 LYS cc_start: 0.8672 (ttmt) cc_final: 0.8379 (tppp) REVERT: N 469 GLU cc_start: 0.8429 (mp0) cc_final: 0.8040 (mm-30) REVERT: N 480 VAL cc_start: 0.9137 (t) cc_final: 0.8673 (p) REVERT: N 482 TYR cc_start: 0.8247 (m-80) cc_final: 0.7905 (m-80) REVERT: N 504 GLN cc_start: 0.8577 (mp10) cc_final: 0.8239 (pm20) outliers start: 38 outliers final: 17 residues processed: 197 average time/residue: 1.4104 time to fit residues: 304.3115 Evaluate side-chains 185 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 164 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ASP 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 A residue 345 ASN Chi-restraints excluded: chain B residue 14 GLU 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 130 MET Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 185 GLN 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 E residue 222 ILE Chi-restraints excluded: chain N residue 407 LEU Chi-restraints excluded: chain N residue 433 GLU 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 103 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 99 optimal weight: 0.0070 chunk 50 optimal weight: 0.0870 chunk 32 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 131 optimal weight: 0.0870 chunk 151 optimal weight: 0.9980 overall best weight: 0.4356 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.4595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15164 Z= 0.175 Angle : 0.634 11.653 20619 Z= 0.319 Chirality : 0.044 0.240 2398 Planarity : 0.003 0.033 2505 Dihedral : 5.791 46.806 2544 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.76 % Allowed : 18.15 % 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: 1.43 (0.20), residues: 1744 helix: 1.99 (0.22), residues: 570 sheet: 0.86 (0.24), residues: 433 loop : 0.28 (0.24), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.001 TRP E 241 HIS 0.003 0.001 HIS A 184 PHE 0.015 0.001 PHE C 308 TYR 0.023 0.001 TYR E 299 ARG 0.005 0.000 ARG N 459 *********************** 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 216 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 188 time to evaluate : 1.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 PHE cc_start: 0.8056 (m-80) cc_final: 0.7766 (m-80) REVERT: A 155 MET cc_start: 0.8227 (mpp) cc_final: 0.7966 (mmt) REVERT: A 181 MET cc_start: 0.8903 (mtm) cc_final: 0.8690 (pmm) REVERT: A 262 GLN cc_start: 0.8841 (tp40) cc_final: 0.8623 (tp40) REVERT: B 9 MET cc_start: 0.7058 (mtp) cc_final: 0.6775 (ttm) REVERT: B 90 GLN cc_start: 0.8565 (mp10) cc_final: 0.8057 (mp10) REVERT: B 137 MET cc_start: 0.7642 (mmm) cc_final: 0.7302 (tpp) REVERT: C 71 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7494 (mp0) REVERT: C 102 MET cc_start: 0.8027 (tpp) cc_final: 0.7191 (tpp) REVERT: C 105 LYS cc_start: 0.9117 (mmtt) cc_final: 0.8726 (mppt) REVERT: D 55 MET cc_start: 0.9074 (mtt) cc_final: 0.8844 (mmm) REVERT: D 95 ASP cc_start: 0.8672 (p0) cc_final: 0.8322 (p0) REVERT: D 185 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.8010 (pm20) REVERT: D 224 GLN cc_start: 0.8078 (tp40) cc_final: 0.7658 (tp40) REVERT: D 282 ASP cc_start: 0.8565 (m-30) cc_final: 0.8280 (m-30) REVERT: E 87 VAL cc_start: 0.9237 (OUTLIER) cc_final: 0.8496 (p) REVERT: E 90 GLN cc_start: 0.8916 (OUTLIER) cc_final: 0.8428 (pm20) REVERT: E 282 ASP cc_start: 0.8375 (m-30) cc_final: 0.7627 (m-30) REVERT: N 426 GLN cc_start: 0.7992 (OUTLIER) cc_final: 0.7317 (tp40) REVERT: N 433 GLU cc_start: 0.6902 (OUTLIER) cc_final: 0.6433 (mp0) REVERT: N 452 LYS cc_start: 0.8712 (ttmt) cc_final: 0.8465 (tppp) REVERT: N 469 GLU cc_start: 0.8504 (mp0) cc_final: 0.8090 (mm-30) REVERT: N 480 VAL cc_start: 0.9131 (t) cc_final: 0.8586 (p) REVERT: N 482 TYR cc_start: 0.8238 (m-80) cc_final: 0.7828 (m-80) REVERT: N 486 LYS cc_start: 0.9087 (tttm) cc_final: 0.8659 (tttm) REVERT: N 504 GLN cc_start: 0.8678 (mp10) cc_final: 0.8394 (pm20) outliers start: 28 outliers final: 11 residues processed: 201 average time/residue: 1.4445 time to fit residues: 317.5781 Evaluate side-chains 195 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 179 time to evaluate : 1.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ASP 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 A residue 345 ASN Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain D residue 185 GLN 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 407 LEU Chi-restraints excluded: chain N residue 426 GLN Chi-restraints excluded: chain N residue 433 GLU 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 159 optimal weight: 0.8980 chunk 145 optimal weight: 5.9990 chunk 155 optimal weight: 9.9990 chunk 93 optimal weight: 3.9990 chunk 67 optimal weight: 8.9990 chunk 122 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 140 optimal weight: 0.4980 chunk 146 optimal weight: 0.9990 chunk 154 optimal weight: 0.6980 chunk 102 optimal weight: 7.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 148 GLN N 464 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.4708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 15164 Z= 0.233 Angle : 0.653 9.817 20619 Z= 0.331 Chirality : 0.044 0.239 2398 Planarity : 0.004 0.063 2505 Dihedral : 5.647 44.690 2544 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.45 % Allowed : 18.78 % Favored : 79.77 % 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: 1.40 (0.20), residues: 1744 helix: 1.99 (0.22), residues: 570 sheet: 0.84 (0.24), residues: 433 loop : 0.24 (0.24), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP E 241 HIS 0.003 0.001 HIS E 267 PHE 0.031 0.001 PHE C 417 TYR 0.026 0.001 TYR D 299 ARG 0.017 0.001 ARG A 62 *********************** 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 198 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 175 time to evaluate : 1.749 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: 0.8081 (m-80) cc_final: 0.7792 (m-80) REVERT: A 181 MET cc_start: 0.8906 (mtm) cc_final: 0.8639 (pmm) REVERT: A 262 GLN cc_start: 0.8835 (tp40) cc_final: 0.8589 (tp40) REVERT: B 90 GLN cc_start: 0.8581 (mp10) cc_final: 0.8067 (mp10) REVERT: B 137 MET cc_start: 0.7688 (mmm) cc_final: 0.7163 (tpp) REVERT: C 71 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7512 (mp0) REVERT: C 102 MET cc_start: 0.8129 (tpp) cc_final: 0.7838 (tpp) REVERT: C 105 LYS cc_start: 0.9173 (mmtt) cc_final: 0.8936 (mppt) REVERT: D 55 MET cc_start: 0.9075 (mtt) cc_final: 0.8849 (mmm) REVERT: D 95 ASP cc_start: 0.8657 (p0) cc_final: 0.8281 (p0) REVERT: D 185 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.8033 (pm20) REVERT: D 224 GLN cc_start: 0.8084 (tp40) cc_final: 0.7638 (tp40) REVERT: D 282 ASP cc_start: 0.8670 (m-30) cc_final: 0.8387 (m-30) REVERT: E 87 VAL cc_start: 0.9261 (OUTLIER) cc_final: 0.8910 (p) REVERT: E 90 GLN cc_start: 0.8935 (OUTLIER) cc_final: 0.8577 (pm20) REVERT: E 282 ASP cc_start: 0.8377 (m-30) cc_final: 0.7664 (m-30) REVERT: N 426 GLN cc_start: 0.7994 (tp-100) cc_final: 0.7332 (tp40) REVERT: N 433 GLU cc_start: 0.6930 (OUTLIER) cc_final: 0.6446 (mp0) REVERT: N 452 LYS cc_start: 0.8715 (ttmt) cc_final: 0.8471 (tppp) REVERT: N 469 GLU cc_start: 0.8465 (mp0) cc_final: 0.8037 (mm-30) REVERT: N 480 VAL cc_start: 0.9128 (t) cc_final: 0.8528 (p) REVERT: N 482 TYR cc_start: 0.8230 (m-80) cc_final: 0.7691 (m-80) REVERT: N 504 GLN cc_start: 0.8636 (mp10) cc_final: 0.8325 (pm20) outliers start: 23 outliers final: 11 residues processed: 186 average time/residue: 1.4787 time to fit residues: 303.5898 Evaluate side-chains 189 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 174 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ASP 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 53 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 185 GLN 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 407 LEU Chi-restraints excluded: chain N residue 433 GLU Chi-restraints excluded: chain N residue 464 ASN Chi-restraints excluded: chain N residue 466 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 164 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 114 optimal weight: 0.2980 chunk 172 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 106 optimal weight: 3.9990 chunk 84 optimal weight: 8.9990 chunk 109 optimal weight: 4.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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** N 464 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.4790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 15164 Z= 0.259 Angle : 0.659 12.733 20619 Z= 0.333 Chirality : 0.045 0.238 2398 Planarity : 0.004 0.073 2505 Dihedral : 5.561 43.134 2544 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.51 % Allowed : 18.97 % Favored : 79.52 % 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: 1.36 (0.20), residues: 1744 helix: 1.99 (0.22), residues: 570 sheet: 0.75 (0.24), residues: 442 loop : 0.23 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP E 241 HIS 0.003 0.001 HIS A 184 PHE 0.018 0.001 PHE A 337 TYR 0.026 0.001 TYR D 299 ARG 0.015 0.000 ARG A 62 ********************** 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 197 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 173 time to evaluate : 1.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 PHE cc_start: 0.8087 (m-80) cc_final: 0.7789 (m-80) REVERT: A 155 MET cc_start: 0.8204 (mpp) cc_final: 0.7959 (mmt) REVERT: A 262 GLN cc_start: 0.8837 (tp40) cc_final: 0.8588 (tp40) REVERT: B 90 GLN cc_start: 0.8603 (mp10) cc_final: 0.8089 (mp10) REVERT: B 137 MET cc_start: 0.7726 (mmm) cc_final: 0.7452 (tpp) REVERT: C 71 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7519 (mp0) REVERT: C 102 MET cc_start: 0.8121 (tpp) cc_final: 0.7870 (tpp) REVERT: C 105 LYS cc_start: 0.9166 (mmtt) cc_final: 0.8915 (mppt) REVERT: C 239 GLN cc_start: 0.8821 (tp40) cc_final: 0.8439 (tp-100) REVERT: D 14 GLU cc_start: 0.9156 (mm-30) cc_final: 0.8949 (mm-30) REVERT: D 55 MET cc_start: 0.9082 (mtt) cc_final: 0.8871 (mmm) REVERT: D 95 ASP cc_start: 0.8671 (p0) cc_final: 0.8307 (p0) REVERT: D 185 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.8014 (pm20) REVERT: D 224 GLN cc_start: 0.8087 (tp40) cc_final: 0.7670 (tp40) REVERT: D 282 ASP cc_start: 0.8702 (m-30) cc_final: 0.8418 (m-30) REVERT: E 87 VAL cc_start: 0.9272 (OUTLIER) cc_final: 0.8932 (p) REVERT: E 90 GLN cc_start: 0.8944 (OUTLIER) cc_final: 0.8591 (pm20) REVERT: E 282 ASP cc_start: 0.8439 (m-30) cc_final: 0.8144 (m-30) REVERT: N 421 MET cc_start: 0.8251 (tpp) cc_final: 0.7845 (mpp) REVERT: N 426 GLN cc_start: 0.8016 (tp-100) cc_final: 0.7376 (tp40) REVERT: N 433 GLU cc_start: 0.6937 (OUTLIER) cc_final: 0.6441 (mp0) REVERT: N 452 LYS cc_start: 0.8728 (ttmt) cc_final: 0.8486 (tppp) REVERT: N 469 GLU cc_start: 0.8508 (mp0) cc_final: 0.8060 (mm-30) REVERT: N 480 VAL cc_start: 0.9130 (t) cc_final: 0.8538 (p) REVERT: N 482 TYR cc_start: 0.8220 (m-80) cc_final: 0.7680 (m-80) REVERT: N 504 GLN cc_start: 0.8638 (mp10) cc_final: 0.8339 (pm20) outliers start: 24 outliers final: 12 residues processed: 186 average time/residue: 1.3618 time to fit residues: 278.4392 Evaluate side-chains 189 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 173 time to evaluate : 1.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 96 ASP 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 49 MET Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 185 GLN 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 433 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 146 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 137 optimal weight: 0.0270 chunk 57 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 120 optimal weight: 0.9980 overall best weight: 0.9642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.081854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.059452 restraints weight = 62051.159| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 4.23 r_work: 0.2674 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2680 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2680 r_free = 0.2680 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2680 r_free = 0.2680 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2680 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.4906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 15164 Z= 0.200 Angle : 0.651 12.631 20619 Z= 0.328 Chirality : 0.044 0.232 2398 Planarity : 0.004 0.067 2505 Dihedral : 5.371 40.013 2544 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.45 % Allowed : 18.84 % Favored : 79.71 % 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: 1.38 (0.20), residues: 1744 helix: 1.98 (0.22), residues: 570 sheet: 0.81 (0.24), residues: 434 loop : 0.25 (0.24), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP E 241 HIS 0.003 0.001 HIS E 267 PHE 0.033 0.001 PHE C 417 TYR 0.024 0.001 TYR E 299 ARG 0.015 0.000 ARG A 62 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5743.02 seconds wall clock time: 104 minutes 12.27 seconds (6252.27 seconds total)