Starting phenix.real_space_refine on Fri Jun 13 13:19:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qnb_14073/06_2025/7qnb_14073.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qnb_14073/06_2025/7qnb_14073.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qnb_14073/06_2025/7qnb_14073.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qnb_14073/06_2025/7qnb_14073.map" model { file = "/net/cci-nas-00/data/ceres_data/7qnb_14073/06_2025/7qnb_14073.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qnb_14073/06_2025/7qnb_14073.cif" } resolution = 3.1 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 82 5.16 5 C 9639 2.51 5 N 2383 2.21 5 O 2689 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 14793 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" 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: "B" Number of atoms: 2714 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 330, 2709 Classifications: {'peptide': 330} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 315} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 330, 2709 Classifications: {'peptide': 330} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 315} Chain breaks: 1 bond proxies already assigned to first conformer: 2775 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: 2721 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 330, 2709 Classifications: {'peptide': 330} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 315} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 330, 2709 Classifications: {'peptide': 330} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 315} Chain breaks: 1 bond proxies already assigned to first conformer: 2767 Chain: "E" Number of atoms: 2714 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 330, 2709 Classifications: {'peptide': 330} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 315} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 330, 2709 Classifications: {'peptide': 330} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 315} Chain breaks: 1 bond proxies already assigned to first conformer: 2775 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: "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: 13.30, per 1000 atoms: 0.90 Number of scatterers: 14793 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 82 16.00 O 2689 8.00 N 2383 7.00 C 9639 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 151 " - pdb=" SG CYS A 165 " 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 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " " BMA G 3 " - " MAN G 5 " " BMA H 3 " - " MAN H 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 b 1 " - " NAG b 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " NAG-ASN " NAG A 501 " - " ASN A 208 " " 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 b 1 " - " ASN B 80 " " NAG d 1 " - " ASN D 80 " " NAG e 1 " - " ASN E 80 " Time building additional restraints: 4.06 Conformation dependent library (CDL) restraints added in 3.0 seconds 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3360 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 20 sheets defined 39.1% alpha, 40.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'A' and resid 27 through 36 Processing helix chain 'A' and resid 85 through 88 Processing helix chain 'A' and resid 99 through 106 removed outlier: 3.532A pdb=" N GLY A 104 " --> pdb=" O ASN A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 240 Processing helix chain 'A' and resid 240 through 257 removed outlier: 3.956A pdb=" N SER A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N PHE A 255 " --> pdb=" O SER A 251 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N TRP A 256 " --> pdb=" O TRP A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 284 removed outlier: 3.568A pdb=" N ILE A 282 " --> pdb=" O THR A 278 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ARG A 284 " --> pdb=" O SER A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 323 removed outlier: 3.503A pdb=" N LEU A 311 " --> pdb=" O VAL A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 435 removed outlier: 3.600A pdb=" N ILE A 416 " --> pdb=" O SER A 412 " (cutoff:3.500A) Proline residue: A 419 - 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 removed outlier: 3.542A pdb=" N ASP B 89 " --> pdb=" O ARG B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 173 Processing helix chain 'B' and resid 218 through 225 Processing helix chain 'B' and resid 225 through 242 removed outlier: 3.502A pdb=" N VAL B 238 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N SER B 239 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N PHE B 240 " --> pdb=" O SER B 236 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N TRP B 241 " --> pdb=" O TRP B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 269 Processing helix chain 'B' and resid 270 through 272 No H-bonds generated for 'chain 'B' and resid 270 through 272' Processing helix chain 'B' and resid 279 through 307 Processing helix chain 'B' and resid 313 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: 3.533A pdb=" N GLY C 104 " --> pdb=" O ASN C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 240 Processing helix chain 'C' and resid 240 through 257 removed outlier: 3.955A pdb=" N SER C 254 " --> pdb=" O LEU C 250 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N PHE C 255 " --> pdb=" O SER C 251 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N TRP C 256 " --> pdb=" O TRP C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 284 removed outlier: 3.568A pdb=" N ILE C 282 " --> pdb=" O THR C 278 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG C 284 " --> pdb=" O SER C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 323 removed outlier: 3.504A pdb=" N LEU C 311 " --> pdb=" O VAL C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 435 removed outlier: 3.600A pdb=" N ILE C 416 " --> pdb=" O SER C 412 " (cutoff:3.500A) Proline residue: C 419 - end of helix 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 removed outlier: 3.542A pdb=" N ASP D 89 " --> pdb=" O ARG D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 173 Processing helix chain 'D' and resid 218 through 225 Processing helix chain 'D' and resid 225 through 242 removed outlier: 4.359A pdb=" N SER D 239 " --> pdb=" O LEU D 235 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N PHE D 240 " --> pdb=" O SER D 236 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N TRP D 241 " --> pdb=" O TRP D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 269 Processing helix chain 'D' and resid 270 through 272 No H-bonds generated for 'chain 'D' and resid 270 through 272' Processing helix chain 'D' and resid 279 through 307 Processing helix chain 'D' and resid 313 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 removed outlier: 3.542A pdb=" N ASP E 89 " --> pdb=" O ARG E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 173 Processing helix chain 'E' and resid 218 through 225 Processing helix chain 'E' and resid 225 through 242 removed outlier: 3.501A pdb=" N VAL E 238 " --> pdb=" O ILE E 234 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N SER E 239 " --> pdb=" O LEU E 235 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N PHE E 240 " --> pdb=" O SER E 236 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N TRP E 241 " --> pdb=" O TRP E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 269 Processing helix chain 'E' and resid 270 through 272 No H-bonds generated for 'chain 'E' and resid 270 through 272' Processing helix chain 'E' and resid 279 through 307 Processing helix chain 'E' and resid 313 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: 3.643A pdb=" N THR N 478 " --> pdb=" O PRO N 475 " (cutoff:3.500A) Processing helix chain 'N' and resid 495 through 499 Processing sheet with id=AA1, first strand: chain 'A' and resid 95 through 98 removed outlier: 4.262A pdb=" N LEU A 131 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ARG A 138 " --> pdb=" O TRP A 134 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS A 118 " --> pdb=" O ASP A 148 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N GLU A 150 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N SER A 116 " --> pdb=" O GLU A 150 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 95 through 98 removed outlier: 4.262A pdb=" N LEU A 131 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ARG A 138 " --> pdb=" O TRP A 134 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLU A 71 " --> pdb=" O PRO A 64 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N THR A 73 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ILE A 62 " --> pdb=" O THR A 73 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ASP A 75 " --> pdb=" O ASN A 60 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR A 58 " --> pdb=" O PHE A 77 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N TYR A 83 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU A 52 " --> pdb=" O TYR A 83 " (cutoff:3.500A) removed outlier: 9.686A pdb=" N THR A 51 " --> pdb=" O TYR A 181 " (cutoff:3.500A) removed outlier: 10.840A pdb=" N TRP A 183 " --> pdb=" O THR A 51 " (cutoff:3.500A) removed outlier: 9.036A pdb=" N ILE A 53 " --> pdb=" O TRP A 183 " (cutoff:3.500A) removed outlier: 10.114A pdb=" N ARG A 185 " --> pdb=" O ILE A 53 " (cutoff:3.500A) removed outlier: 10.731A pdb=" N THR A 55 " --> pdb=" O ARG A 185 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N SER A 187 " --> pdb=" O THR A 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 111 through 113 removed outlier: 4.644A pdb=" N SER A 171 " --> pdb=" O VAL A 221 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL A 221 " --> pdb=" O SER A 171 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 111 through 113 removed outlier: 4.644A pdb=" N SER A 171 " --> pdb=" O VAL A 221 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL A 221 " --> pdb=" O SER A 171 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY A 205 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N SER A 230 " --> pdb=" O PHE A 203 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N PHE A 203 " --> pdb=" O SER A 230 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 82 through 83 removed outlier: 4.469A pdb=" N ILE B 116 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ASP B 56 " --> pdb=" O MET B 49 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N MET B 49 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.612A 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: 6.679A pdb=" N THR B 133 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N SER B 104 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N THR B 131 " --> pdb=" O SER B 104 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N VAL B 106 " --> pdb=" O ARG B 129 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N ARG B 129 " --> pdb=" O VAL B 106 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ASP B 56 " --> pdb=" O MET B 49 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N MET B 49 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.612A 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: 3.952A pdb=" N SER B 156 " --> pdb=" O PRO B 206 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU B 190 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LYS B 215 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 5.711A 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: 4.262A pdb=" N LEU C 131 " --> pdb=" O LEU C 98 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ARG C 138 " --> pdb=" O TRP C 134 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS C 118 " --> pdb=" O ASP C 148 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLU C 150 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N SER C 116 " --> pdb=" O GLU C 150 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 95 through 98 removed outlier: 4.262A pdb=" N LEU C 131 " --> pdb=" O LEU C 98 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ARG C 138 " --> pdb=" O TRP C 134 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N GLU C 71 " --> pdb=" O PRO C 64 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N THR C 73 " --> pdb=" O ILE C 62 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ILE C 62 " --> pdb=" O THR C 73 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ASP C 75 " --> pdb=" O ASN C 60 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR C 58 " --> pdb=" O PHE C 77 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N TYR C 83 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU C 52 " --> pdb=" O TYR C 83 " (cutoff:3.500A) removed outlier: 9.686A pdb=" N THR C 51 " --> pdb=" O TYR C 181 " (cutoff:3.500A) removed outlier: 10.841A pdb=" N TRP C 183 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 9.036A pdb=" N ILE C 53 " --> pdb=" O TRP C 183 " (cutoff:3.500A) removed outlier: 10.114A pdb=" N ARG C 185 " --> pdb=" O ILE C 53 " (cutoff:3.500A) removed outlier: 10.731A pdb=" N THR C 55 " --> pdb=" O ARG C 185 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N SER C 187 " --> pdb=" O THR C 55 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 111 through 113 removed outlier: 4.644A pdb=" N SER C 171 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL C 221 " --> pdb=" O SER C 171 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 111 through 113 removed outlier: 4.644A pdb=" N SER C 171 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL C 221 " --> pdb=" O SER C 171 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY C 205 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N SER C 230 " --> pdb=" O PHE C 203 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N PHE C 203 " --> pdb=" O SER C 230 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 82 through 83 removed outlier: 4.468A pdb=" N ILE D 116 " --> pdb=" O LEU D 83 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ASP D 56 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N MET D 49 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N THR D 58 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ILE D 47 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.880A 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: 6.612A pdb=" N CYS D 37 " --> pdb=" O ARG D 68 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 101 through 106 removed outlier: 6.680A pdb=" N THR D 133 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N SER D 104 " --> pdb=" O THR D 131 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N THR D 131 " --> pdb=" O SER D 104 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N VAL D 106 " --> pdb=" O ARG D 129 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N ARG D 129 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ASP D 56 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N MET D 49 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N THR D 58 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ILE D 47 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.880A 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: 6.612A pdb=" N CYS D 37 " --> pdb=" O ARG D 68 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 96 through 98 removed outlier: 3.952A pdb=" N SER D 156 " --> pdb=" O PRO D 206 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU D 190 " --> pdb=" O ARG D 213 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LYS D 215 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ILE D 188 " --> pdb=" O LYS D 215 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 82 through 83 removed outlier: 4.468A pdb=" N ILE E 116 " --> pdb=" O LEU E 83 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ASP E 56 " --> pdb=" O MET E 49 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N MET E 49 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N THR E 58 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ILE E 47 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.879A 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: 6.612A pdb=" N CYS E 37 " --> pdb=" O ARG E 68 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 101 through 106 removed outlier: 6.679A pdb=" N THR E 133 " --> pdb=" O LYS E 102 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N SER E 104 " --> pdb=" O THR E 131 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N THR E 131 " --> pdb=" O SER E 104 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N VAL E 106 " --> pdb=" O ARG E 129 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N ARG E 129 " --> pdb=" O VAL E 106 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ASP E 56 " --> pdb=" O MET E 49 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N MET E 49 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N THR E 58 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ILE E 47 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.879A 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: 6.612A pdb=" N CYS E 37 " --> pdb=" O ARG E 68 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 96 through 98 removed outlier: 3.951A pdb=" N SER E 156 " --> pdb=" O PRO E 206 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU E 190 " --> pdb=" O ARG E 213 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LYS E 215 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ILE E 188 " --> pdb=" O LYS E 215 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 2 through 7 removed outlier: 3.557A pdb=" N THR N 465 " --> pdb=" O ASP N 460 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 445 through 447 removed outlier: 6.551A pdb=" N TRP N 423 " --> pdb=" O VAL N 435 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ALA N 437 " --> pdb=" O MET N 421 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N MET N 421 " --> pdb=" O ALA N 437 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TYR N 501 " --> pdb=" O ALA N 485 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 445 through 447 removed outlier: 6.551A pdb=" N TRP N 423 " --> pdb=" O VAL N 435 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ALA N 437 " --> pdb=" O MET N 421 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N MET N 421 " --> pdb=" O ALA N 437 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL N 508 " --> pdb=" O ALA N 479 " (cutoff:3.500A) 848 hydrogen bonds defined for protein. 2427 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: 5.85 Time building geometry restraints manager: 4.78 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: 4481 1.34 - 1.46: 3821 1.46 - 1.58: 6741 1.58 - 1.69: 0 1.69 - 1.81: 140 Bond restraints: 15183 Sorted by residual: bond pdb=" CG ABU B 501 " pdb=" CD ABU B 501 " ideal model delta sigma weight residual 1.540 1.500 0.040 2.00e-02 2.50e+03 3.91e+00 bond pdb=" C1 MAN F 4 " pdb=" O5 MAN F 4 " 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 2.15e+00 bond pdb=" C1 MAN H 5 " pdb=" O5 MAN H 5 " ideal model delta sigma weight residual 1.399 1.428 -0.029 2.00e-02 2.50e+03 2.13e+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 2.05e+00 ... (remaining 15178 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 20333 1.46 - 2.91: 255 2.91 - 4.37: 47 4.37 - 5.83: 23 5.83 - 7.28: 4 Bond angle restraints: 20662 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 115.90 123.18 -7.28 3.00e+00 1.11e-01 5.89e+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 F 3 " pdb=" C2 BMA F 3 " pdb=" O2 BMA F 3 " ideal model delta sigma weight residual 112.95 106.69 6.26 3.00e+00 1.11e-01 4.35e+00 angle pdb=" C3 BMA G 3 " pdb=" C2 BMA G 3 " pdb=" O2 BMA G 3 " ideal model delta sigma weight residual 112.95 106.71 6.24 3.00e+00 1.11e-01 4.33e+00 angle pdb=" CA TYR E 299 " pdb=" CB TYR E 299 " pdb=" CG TYR E 299 " ideal model delta sigma weight residual 113.90 110.22 3.68 1.80e+00 3.09e-01 4.17e+00 ... (remaining 20657 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.76: 8891 21.76 - 43.52: 205 43.52 - 65.28: 28 65.28 - 87.04: 22 87.04 - 108.80: 14 Dihedral angle restraints: 9160 sinusoidal: 3922 harmonic: 5238 Sorted by residual: 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 288.71 179.91 108.80 1 3.00e+01 1.11e-03 1.41e+01 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 288.71 179.93 108.78 1 3.00e+01 1.11e-03 1.41e+01 dihedral pdb=" O4 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C5 BMA F 3 " pdb=" O5 BMA F 3 " ideal model delta sinusoidal sigma weight residual -71.29 -178.52 107.23 1 3.00e+01 1.11e-03 1.38e+01 ... (remaining 9157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2049 0.056 - 0.113: 315 0.113 - 0.169: 18 0.169 - 0.225: 5 0.225 - 0.282: 4 Chirality restraints: 2391 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 -2.21 -0.19 2.00e-02 2.50e+03 9.00e+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 6.25e+01 chirality pdb=" C1 BMA H 3 " pdb=" O4 NAG H 2 " pdb=" C2 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.19e+01 ... (remaining 2388 not shown) Planarity restraints: 2528 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN D 65 " -0.006 2.00e-02 2.50e+03 1.12e-02 1.25e+00 pdb=" C GLN D 65 " 0.019 2.00e-02 2.50e+03 pdb=" O GLN D 65 " -0.007 2.00e-02 2.50e+03 pdb=" N BTYR D 66 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR D 143 " -0.018 5.00e-02 4.00e+02 2.65e-02 1.13e+00 pdb=" N PRO D 144 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO D 144 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 144 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR E 143 " -0.017 5.00e-02 4.00e+02 2.64e-02 1.11e+00 pdb=" N PRO E 144 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO E 144 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO E 144 " -0.014 5.00e-02 4.00e+02 ... (remaining 2525 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2576 2.77 - 3.30: 14013 3.30 - 3.84: 25223 3.84 - 4.37: 30662 4.37 - 4.90: 52258 Nonbonded interactions: 124732 Sorted by model distance: nonbonded pdb=" O VAL A 248 " pdb=" OG SER A 251 " model vdw 2.241 3.040 nonbonded pdb=" O VAL C 248 " pdb=" OG SER C 251 " model vdw 2.242 3.040 nonbonded pdb=" O ALA D 252 " pdb=" OG1 THR D 256 " model vdw 2.270 3.040 nonbonded pdb=" O ALA B 252 " pdb=" OG1 THR B 256 " model vdw 2.270 3.040 nonbonded pdb=" O ALA E 252 " pdb=" OG1 THR E 256 " model vdw 2.271 3.040 ... (remaining 124727 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } 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' } 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: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 43.440 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.100 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:3.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 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 0.040 15212 Z= 0.120 Angle : 0.464 7.284 20743 Z= 0.214 Chirality : 0.042 0.282 2391 Planarity : 0.003 0.027 2520 Dihedral : 11.197 108.803 5782 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.56 % Allowed : 3.32 % Favored : 96.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.46 % Cis-general : 0.30 % 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: 1.87 (0.21), residues: 1748 helix: 2.34 (0.22), residues: 559 sheet: 1.18 (0.25), residues: 468 loop : 0.51 (0.25), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 241 HIS 0.002 0.000 HIS A 122 PHE 0.006 0.001 PHE E 293 TYR 0.015 0.001 TYR B 299 ARG 0.002 0.000 ARG D 196 Details of bonding type rmsd link_NAG-ASN : bond 0.00586 ( 8) link_NAG-ASN : angle 1.69353 ( 24) link_ALPHA1-6 : bond 0.00069 ( 3) link_ALPHA1-6 : angle 0.35949 ( 9) link_BETA1-4 : bond 0.00290 ( 9) link_BETA1-4 : angle 1.48748 ( 27) link_ALPHA1-3 : bond 0.00146 ( 3) link_ALPHA1-3 : angle 0.75068 ( 9) hydrogen bonds : bond 0.21911 ( 752) hydrogen bonds : angle 7.07904 ( 2427) SS BOND : bond 0.00066 ( 6) SS BOND : angle 0.57433 ( 12) covalent geometry : bond 0.00252 (15183) covalent geometry : angle 0.45740 (20662) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 356 time to evaluate : 1.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 GLU cc_start: 0.8401 (pt0) cc_final: 0.7747 (pt0) REVERT: A 105 LYS cc_start: 0.9029 (mmtt) cc_final: 0.8565 (mmmm) REVERT: A 197 ARG cc_start: 0.8040 (ttp-110) cc_final: 0.7730 (mpt-90) REVERT: B 9 MET cc_start: 0.8364 (mtp) cc_final: 0.7483 (pmm) REVERT: B 115 MET cc_start: 0.7671 (ttp) cc_final: 0.7123 (ttp) REVERT: B 215 LYS cc_start: 0.8773 (tttt) cc_final: 0.8476 (tppt) REVERT: B 306 PHE cc_start: 0.7000 (t80) cc_final: 0.6685 (t80) REVERT: C 42 LEU cc_start: 0.9037 (mt) cc_final: 0.8744 (mt) REVERT: C 177 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8532 (mp0) REVERT: C 223 MET cc_start: 0.7852 (mmm) cc_final: 0.7425 (mmm) REVERT: D 55 MET cc_start: 0.8908 (mtt) cc_final: 0.8602 (mmm) REVERT: D 153 GLU cc_start: 0.8895 (mm-30) cc_final: 0.8626 (mm-30) REVERT: D 190 GLU cc_start: 0.7689 (tt0) cc_final: 0.7393 (tt0) REVERT: D 215 LYS cc_start: 0.8855 (tttt) cc_final: 0.8613 (tmmt) REVERT: D 224 GLN cc_start: 0.8172 (tp40) cc_final: 0.7678 (tp40) REVERT: D 268 LEU cc_start: 0.7808 (mp) cc_final: 0.7504 (mp) REVERT: D 306 PHE cc_start: 0.7852 (t80) cc_final: 0.7607 (t80) REVERT: E 306 PHE cc_start: 0.7877 (t80) cc_final: 0.7664 (t80) REVERT: E 426 TRP cc_start: 0.7966 (t60) cc_final: 0.7720 (t60) REVERT: N 426 GLN cc_start: 0.7868 (tt0) cc_final: 0.7565 (tp-100) REVERT: N 432 ARG cc_start: 0.8024 (ttm170) cc_final: 0.7185 (ttm110) REVERT: N 472 ASN cc_start: 0.7958 (t0) cc_final: 0.7722 (t0) outliers start: 9 outliers final: 4 residues processed: 360 average time/residue: 0.3307 time to fit residues: 163.1624 Evaluate side-chains 211 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 207 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain E residue 255 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 0.9990 chunk 132 optimal weight: 0.0570 chunk 73 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 137 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 83 optimal weight: 9.9990 chunk 102 optimal weight: 1.9990 chunk 158 optimal weight: 4.9990 overall best weight: 0.9702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 267 HIS C 152 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.094047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.066029 restraints weight = 72566.758| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 4.74 r_work: 0.2895 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2899 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2898 r_free = 0.2898 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2898 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15212 Z= 0.154 Angle : 0.617 8.324 20743 Z= 0.325 Chirality : 0.044 0.224 2391 Planarity : 0.004 0.035 2520 Dihedral : 8.314 79.658 2462 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.94 % Allowed : 8.95 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.46 % Cis-general : 0.30 % 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: 1.72 (0.20), residues: 1748 helix: 2.23 (0.21), residues: 566 sheet: 1.08 (0.24), residues: 471 loop : 0.38 (0.24), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 123 HIS 0.005 0.001 HIS D 267 PHE 0.016 0.001 PHE B 307 TYR 0.022 0.001 TYR D 299 ARG 0.007 0.001 ARG C 197 Details of bonding type rmsd link_NAG-ASN : bond 0.00246 ( 8) link_NAG-ASN : angle 1.46043 ( 24) link_ALPHA1-6 : bond 0.00639 ( 3) link_ALPHA1-6 : angle 1.48976 ( 9) link_BETA1-4 : bond 0.00366 ( 9) link_BETA1-4 : angle 1.70227 ( 27) link_ALPHA1-3 : bond 0.00828 ( 3) link_ALPHA1-3 : angle 2.25128 ( 9) hydrogen bonds : bond 0.05255 ( 752) hydrogen bonds : angle 4.97390 ( 2427) SS BOND : bond 0.00130 ( 6) SS BOND : angle 0.76169 ( 12) covalent geometry : bond 0.00342 (15183) covalent geometry : angle 0.61073 (20662) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 218 time to evaluate : 1.828 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 197 ARG cc_start: 0.8477 (ttp-110) cc_final: 0.8124 (mpt-90) REVERT: A 285 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8604 (mmmm) REVERT: B 9 MET cc_start: 0.8695 (mtp) cc_final: 0.8285 (pmm) REVERT: B 115 MET cc_start: 0.7257 (ttp) cc_final: 0.6714 (ttp) REVERT: C 70 MET cc_start: 0.9317 (mtt) cc_final: 0.9090 (mtm) REVERT: C 71 GLU cc_start: 0.8127 (pm20) cc_final: 0.7660 (pm20) REVERT: C 123 TRP cc_start: 0.7983 (m100) cc_final: 0.7759 (m100) REVERT: C 130 MET cc_start: 0.6681 (ttp) cc_final: 0.6239 (tmm) REVERT: C 177 GLU cc_start: 0.9108 (mt-10) cc_final: 0.8764 (mp0) REVERT: C 189 GLU cc_start: 0.8547 (tp30) cc_final: 0.8286 (tm-30) REVERT: C 223 MET cc_start: 0.8716 (mmm) cc_final: 0.7883 (mtp) REVERT: D 9 MET cc_start: 0.8644 (mpp) cc_final: 0.8419 (mpp) REVERT: D 18 LYS cc_start: 0.9319 (pttp) cc_final: 0.8589 (pptt) REVERT: D 49 MET cc_start: 0.8970 (ttp) cc_final: 0.8704 (ttp) REVERT: D 215 LYS cc_start: 0.9042 (tttt) cc_final: 0.8693 (tptp) REVERT: D 224 GLN cc_start: 0.8627 (tp40) cc_final: 0.8134 (tp40) REVERT: D 268 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7748 (mp) REVERT: D 274 LYS cc_start: 0.7993 (mmtt) cc_final: 0.7737 (mmtm) REVERT: D 306 PHE cc_start: 0.8381 (t80) cc_final: 0.8147 (t80) REVERT: E 17 ASP cc_start: 0.9165 (t0) cc_final: 0.8782 (t0) REVERT: E 55 MET cc_start: 0.8918 (mtp) cc_final: 0.8645 (mtp) REVERT: N 405 LEU cc_start: 0.8021 (tp) cc_final: 0.7817 (tp) REVERT: N 421 MET cc_start: 0.7363 (mmm) cc_final: 0.6972 (mmm) REVERT: N 426 GLN cc_start: 0.8504 (tt0) cc_final: 0.8029 (tp-100) REVERT: N 433 GLU cc_start: 0.9124 (tt0) cc_final: 0.8810 (pt0) REVERT: N 472 ASN cc_start: 0.8214 (t0) cc_final: 0.7972 (t0) outliers start: 31 outliers final: 20 residues processed: 238 average time/residue: 0.2965 time to fit residues: 102.4502 Evaluate side-chains 211 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 189 time to evaluate : 1.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 426 TRP Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 423 CYS Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 437 LEU Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 493 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 157 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 26 optimal weight: 0.0870 chunk 30 optimal weight: 3.9990 chunk 75 optimal weight: 8.9990 chunk 120 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 131 optimal weight: 0.9990 chunk 11 optimal weight: 7.9990 chunk 133 optimal weight: 0.9990 chunk 47 optimal weight: 10.0000 overall best weight: 0.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 ASN B 267 HIS C 152 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.093731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.065823 restraints weight = 67602.964| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 4.50 r_work: 0.2891 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2896 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2896 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15212 Z= 0.126 Angle : 0.568 9.273 20743 Z= 0.292 Chirality : 0.043 0.221 2391 Planarity : 0.004 0.038 2520 Dihedral : 7.276 72.213 2457 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.07 % Allowed : 9.96 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.46 % Cis-general : 0.30 % 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: 1.62 (0.20), residues: 1748 helix: 2.15 (0.21), residues: 566 sheet: 1.04 (0.24), residues: 465 loop : 0.32 (0.24), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 241 HIS 0.002 0.000 HIS B 267 PHE 0.019 0.001 PHE E 306 TYR 0.023 0.001 TYR D 299 ARG 0.010 0.000 ARG D 86 Details of bonding type rmsd link_NAG-ASN : bond 0.00222 ( 8) link_NAG-ASN : angle 1.49547 ( 24) link_ALPHA1-6 : bond 0.00875 ( 3) link_ALPHA1-6 : angle 1.94557 ( 9) link_BETA1-4 : bond 0.00431 ( 9) link_BETA1-4 : angle 1.54162 ( 27) link_ALPHA1-3 : bond 0.01038 ( 3) link_ALPHA1-3 : angle 1.66594 ( 9) hydrogen bonds : bond 0.04399 ( 752) hydrogen bonds : angle 4.48880 ( 2427) SS BOND : bond 0.00054 ( 6) SS BOND : angle 0.59401 ( 12) covalent geometry : bond 0.00275 (15183) covalent geometry : angle 0.56140 (20662) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 194 time to evaluate : 1.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.8242 (ttm) cc_final: 0.7556 (tpp) REVERT: A 150 GLU cc_start: 0.8950 (tm-30) cc_final: 0.8722 (tm-30) REVERT: A 197 ARG cc_start: 0.8513 (ttp-110) cc_final: 0.8222 (mpt-90) REVERT: A 285 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8461 (mmmm) REVERT: B 9 MET cc_start: 0.8846 (mtp) cc_final: 0.8377 (pmm) REVERT: B 115 MET cc_start: 0.7410 (ttp) cc_final: 0.7049 (ttp) REVERT: C 71 GLU cc_start: 0.8202 (pm20) cc_final: 0.7712 (pm20) REVERT: C 130 MET cc_start: 0.7027 (ttp) cc_final: 0.6616 (tmm) REVERT: C 150 GLU cc_start: 0.8491 (tm-30) cc_final: 0.8165 (tm-30) REVERT: C 152 GLN cc_start: 0.8602 (mm-40) cc_final: 0.8289 (mm110) REVERT: C 177 GLU cc_start: 0.9093 (mt-10) cc_final: 0.8780 (mp0) REVERT: C 223 MET cc_start: 0.8713 (mmm) cc_final: 0.7904 (mtp) REVERT: C 239 GLN cc_start: 0.8773 (mm110) cc_final: 0.8439 (mm110) REVERT: C 423 CYS cc_start: 0.9351 (t) cc_final: 0.9001 (m) REVERT: D 9 MET cc_start: 0.8715 (mpp) cc_final: 0.8473 (mpp) REVERT: D 49 MET cc_start: 0.8989 (ttp) cc_final: 0.8787 (ttp) REVERT: D 55 MET cc_start: 0.9328 (mtp) cc_final: 0.8748 (mmm) REVERT: D 215 LYS cc_start: 0.9145 (tttt) cc_final: 0.8870 (tptp) REVERT: D 224 GLN cc_start: 0.8627 (tp40) cc_final: 0.8289 (tp40) REVERT: N 3 GLN cc_start: 0.8190 (mp10) cc_final: 0.7977 (mp10) REVERT: N 426 GLN cc_start: 0.8442 (tt0) cc_final: 0.8025 (tp-100) REVERT: N 433 GLU cc_start: 0.9049 (tt0) cc_final: 0.8824 (pt0) REVERT: N 447 TYR cc_start: 0.8945 (m-80) cc_final: 0.8676 (m-80) REVERT: N 452 LYS cc_start: 0.8903 (tptm) cc_final: 0.8684 (tptp) REVERT: N 472 ASN cc_start: 0.8471 (t0) cc_final: 0.8125 (t0) REVERT: N 482 TYR cc_start: 0.8392 (m-10) cc_final: 0.8155 (m-10) outliers start: 33 outliers final: 15 residues processed: 217 average time/residue: 0.2887 time to fit residues: 92.4881 Evaluate side-chains 192 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 176 time to evaluate : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 426 TRP Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 268 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 87 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 153 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 157 optimal weight: 0.9980 chunk 11 optimal weight: 8.9990 chunk 100 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 HIS B 267 HIS B 303 ASN C 156 HIS ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 267 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.089627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.060799 restraints weight = 72388.485| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 4.64 r_work: 0.2774 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2779 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2779 r_free = 0.2779 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2779 r_free = 0.2779 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2779 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15212 Z= 0.162 Angle : 0.594 9.870 20743 Z= 0.305 Chirality : 0.044 0.251 2391 Planarity : 0.005 0.122 2520 Dihedral : 6.677 66.996 2457 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.00 % Allowed : 10.27 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.46 % Cis-general : 0.30 % 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: 1.45 (0.20), residues: 1748 helix: 2.17 (0.21), residues: 562 sheet: 0.88 (0.24), residues: 468 loop : 0.11 (0.24), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 241 HIS 0.003 0.001 HIS B 267 PHE 0.023 0.002 PHE D 306 TYR 0.029 0.002 TYR D 299 ARG 0.016 0.001 ARG E 68 Details of bonding type rmsd link_NAG-ASN : bond 0.00221 ( 8) link_NAG-ASN : angle 1.68695 ( 24) link_ALPHA1-6 : bond 0.00946 ( 3) link_ALPHA1-6 : angle 1.72092 ( 9) link_BETA1-4 : bond 0.00380 ( 9) link_BETA1-4 : angle 1.68790 ( 27) link_ALPHA1-3 : bond 0.00935 ( 3) link_ALPHA1-3 : angle 1.83629 ( 9) hydrogen bonds : bond 0.04144 ( 752) hydrogen bonds : angle 4.36093 ( 2427) SS BOND : bond 0.00122 ( 6) SS BOND : angle 0.54937 ( 12) covalent geometry : bond 0.00371 (15183) covalent geometry : angle 0.58665 (20662) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 181 time to evaluate : 1.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.8221 (ttm) cc_final: 0.7432 (tpp) REVERT: A 150 GLU cc_start: 0.9015 (tm-30) cc_final: 0.8510 (tm-30) REVERT: A 197 ARG cc_start: 0.8632 (ttp-110) cc_final: 0.8348 (mpt-90) REVERT: A 259 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8289 (pttm) REVERT: A 285 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8510 (mmmm) REVERT: B 9 MET cc_start: 0.8928 (mtp) cc_final: 0.8408 (pmm) REVERT: B 115 MET cc_start: 0.7359 (ttp) cc_final: 0.7051 (ttp) REVERT: C 71 GLU cc_start: 0.8261 (pm20) cc_final: 0.7716 (pm20) REVERT: C 130 MET cc_start: 0.7047 (ttp) cc_final: 0.6595 (tmm) REVERT: C 150 GLU cc_start: 0.8563 (tm-30) cc_final: 0.8132 (tm-30) REVERT: C 152 GLN cc_start: 0.8836 (mm-40) cc_final: 0.8343 (mm-40) REVERT: C 177 GLU cc_start: 0.9141 (mt-10) cc_final: 0.8816 (mp0) REVERT: C 178 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7555 (mt-10) REVERT: C 182 GLN cc_start: 0.8616 (tt0) cc_final: 0.8105 (tt0) REVERT: C 223 MET cc_start: 0.8792 (mmm) cc_final: 0.8120 (mtt) REVERT: C 423 CYS cc_start: 0.9338 (OUTLIER) cc_final: 0.9025 (m) REVERT: D 9 MET cc_start: 0.8787 (mpp) cc_final: 0.8541 (mpp) REVERT: D 49 MET cc_start: 0.9132 (ttp) cc_final: 0.8811 (ttp) REVERT: D 215 LYS cc_start: 0.9183 (tttt) cc_final: 0.8884 (tptp) REVERT: D 224 GLN cc_start: 0.8636 (tp40) cc_final: 0.8431 (tp40) REVERT: E 9 MET cc_start: 0.7430 (ttp) cc_final: 0.6989 (mtp) REVERT: N 3 GLN cc_start: 0.8033 (mp10) cc_final: 0.7663 (mp10) REVERT: N 4 LEU cc_start: 0.8122 (mt) cc_final: 0.7897 (tp) REVERT: N 426 GLN cc_start: 0.8551 (tt0) cc_final: 0.8086 (tp-100) REVERT: N 432 ARG cc_start: 0.8188 (tpp80) cc_final: 0.7605 (tpp80) REVERT: N 433 GLU cc_start: 0.9172 (tt0) cc_final: 0.8840 (pt0) REVERT: N 449 ASP cc_start: 0.8966 (m-30) cc_final: 0.8522 (p0) REVERT: N 452 LYS cc_start: 0.8971 (tptm) cc_final: 0.8746 (tptp) REVERT: N 474 LYS cc_start: 0.8364 (mmmm) cc_final: 0.7848 (ttpp) REVERT: N 482 TYR cc_start: 0.8468 (m-10) cc_final: 0.7899 (m-10) outliers start: 32 outliers final: 20 residues processed: 200 average time/residue: 0.2814 time to fit residues: 82.4252 Evaluate side-chains 197 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 174 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 423 CYS Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 437 LEU Chi-restraints excluded: chain N residue 493 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 34 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 154 optimal weight: 0.8980 chunk 83 optimal weight: 20.0000 chunk 11 optimal weight: 3.9990 chunk 52 optimal weight: 10.0000 chunk 159 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 267 HIS E 267 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.089063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.060252 restraints weight = 76532.976| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 4.74 r_work: 0.2757 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2758 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2758 r_free = 0.2758 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2758 r_free = 0.2758 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2758 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15212 Z= 0.137 Angle : 0.566 10.276 20743 Z= 0.288 Chirality : 0.043 0.249 2391 Planarity : 0.004 0.041 2520 Dihedral : 6.253 61.364 2457 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.75 % Allowed : 10.71 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.46 % Cis-general : 0.30 % 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: 1.42 (0.20), residues: 1748 helix: 2.15 (0.21), residues: 566 sheet: 0.83 (0.24), residues: 468 loop : 0.11 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 241 HIS 0.002 0.000 HIS C 122 PHE 0.020 0.001 PHE B 31 TYR 0.026 0.001 TYR D 299 ARG 0.009 0.000 ARG D 86 Details of bonding type rmsd link_NAG-ASN : bond 0.00199 ( 8) link_NAG-ASN : angle 1.53077 ( 24) link_ALPHA1-6 : bond 0.00918 ( 3) link_ALPHA1-6 : angle 1.65743 ( 9) link_BETA1-4 : bond 0.00354 ( 9) link_BETA1-4 : angle 1.50503 ( 27) link_ALPHA1-3 : bond 0.00969 ( 3) link_ALPHA1-3 : angle 1.61475 ( 9) hydrogen bonds : bond 0.03821 ( 752) hydrogen bonds : angle 4.22578 ( 2427) SS BOND : bond 0.00124 ( 6) SS BOND : angle 0.39891 ( 12) covalent geometry : bond 0.00311 (15183) covalent geometry : angle 0.56036 (20662) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 178 time to evaluate : 1.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.9271 (mtt) cc_final: 0.9059 (mtt) REVERT: A 130 MET cc_start: 0.8207 (ttm) cc_final: 0.7474 (tpp) REVERT: A 150 GLU cc_start: 0.9043 (tm-30) cc_final: 0.8625 (tm-30) REVERT: A 197 ARG cc_start: 0.8631 (ttp-110) cc_final: 0.8403 (mpt-90) REVERT: A 239 GLN cc_start: 0.8940 (tp40) cc_final: 0.8598 (tp40) REVERT: A 259 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8163 (pttm) REVERT: A 276 MET cc_start: 0.9480 (mmm) cc_final: 0.9264 (tpp) REVERT: A 285 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8514 (mmmm) REVERT: B 9 MET cc_start: 0.8684 (mtp) cc_final: 0.8469 (pmm) REVERT: C 71 GLU cc_start: 0.8306 (pm20) cc_final: 0.7788 (pm20) REVERT: C 85 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.8084 (mmm160) REVERT: C 130 MET cc_start: 0.7089 (ttp) cc_final: 0.6653 (tmm) REVERT: C 150 GLU cc_start: 0.8609 (tm-30) cc_final: 0.8375 (tm-30) REVERT: C 177 GLU cc_start: 0.9152 (mt-10) cc_final: 0.8842 (mp0) REVERT: C 178 GLU cc_start: 0.8270 (mt-10) cc_final: 0.8029 (mt-10) REVERT: C 182 GLN cc_start: 0.8709 (tt0) cc_final: 0.8206 (tt0) REVERT: C 189 GLU cc_start: 0.8512 (tm-30) cc_final: 0.8281 (tm-30) REVERT: C 223 MET cc_start: 0.8864 (mmm) cc_final: 0.8130 (mtt) REVERT: C 423 CYS cc_start: 0.9275 (t) cc_final: 0.9028 (m) REVERT: D 9 MET cc_start: 0.8739 (mpp) cc_final: 0.8513 (mpp) REVERT: D 49 MET cc_start: 0.9154 (ttp) cc_final: 0.8877 (ttp) REVERT: D 215 LYS cc_start: 0.9218 (tttt) cc_final: 0.8914 (tptp) REVERT: E 9 MET cc_start: 0.7498 (ttp) cc_final: 0.7053 (mtp) REVERT: N 3 GLN cc_start: 0.8045 (mp10) cc_final: 0.7762 (mp10) REVERT: N 426 GLN cc_start: 0.8563 (tt0) cc_final: 0.8047 (tp-100) REVERT: N 433 GLU cc_start: 0.9153 (tt0) cc_final: 0.8816 (pt0) REVERT: N 449 ASP cc_start: 0.8966 (m-30) cc_final: 0.8533 (p0) REVERT: N 472 ASN cc_start: 0.8276 (t0) cc_final: 0.7994 (t0) REVERT: N 482 TYR cc_start: 0.8542 (m-10) cc_final: 0.8304 (m-10) outliers start: 28 outliers final: 18 residues processed: 197 average time/residue: 0.2825 time to fit residues: 82.6079 Evaluate side-chains 192 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 171 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain C residue 85 ARG Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain N residue 493 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 33 optimal weight: 20.0000 chunk 94 optimal weight: 8.9990 chunk 37 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 171 optimal weight: 20.0000 chunk 120 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 76 optimal weight: 10.0000 chunk 119 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 267 HIS ** C 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 267 HIS N 1 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.086047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.056852 restraints weight = 98172.627| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 5.23 r_work: 0.2664 rms_B_bonded: 5.12 restraints_weight: 2.0000 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2663 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2663 r_free = 0.2663 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2663 r_free = 0.2663 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2663 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.4469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15212 Z= 0.191 Angle : 0.614 10.671 20743 Z= 0.312 Chirality : 0.045 0.256 2391 Planarity : 0.004 0.041 2520 Dihedral : 6.008 57.239 2457 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.19 % Allowed : 11.15 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.46 % Cis-general : 0.30 % 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: 1.30 (0.20), residues: 1748 helix: 2.07 (0.21), residues: 566 sheet: 0.72 (0.24), residues: 473 loop : 0.05 (0.24), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 241 HIS 0.004 0.001 HIS C 122 PHE 0.019 0.002 PHE D 306 TYR 0.029 0.002 TYR D 299 ARG 0.010 0.001 ARG D 86 Details of bonding type rmsd link_NAG-ASN : bond 0.00212 ( 8) link_NAG-ASN : angle 1.90967 ( 24) link_ALPHA1-6 : bond 0.00941 ( 3) link_ALPHA1-6 : angle 1.57132 ( 9) link_BETA1-4 : bond 0.00349 ( 9) link_BETA1-4 : angle 1.71230 ( 27) link_ALPHA1-3 : bond 0.00846 ( 3) link_ALPHA1-3 : angle 1.68346 ( 9) hydrogen bonds : bond 0.04135 ( 752) hydrogen bonds : angle 4.29261 ( 2427) SS BOND : bond 0.00122 ( 6) SS BOND : angle 0.53131 ( 12) covalent geometry : bond 0.00438 (15183) covalent geometry : angle 0.60640 (20662) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 179 time to evaluate : 1.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.9276 (mtt) cc_final: 0.9031 (mtt) REVERT: A 71 GLU cc_start: 0.8944 (pt0) cc_final: 0.8456 (pt0) REVERT: A 130 MET cc_start: 0.8220 (ttm) cc_final: 0.7463 (tpp) REVERT: A 150 GLU cc_start: 0.9124 (tm-30) cc_final: 0.8710 (tm-30) REVERT: A 197 ARG cc_start: 0.8734 (ttp-110) cc_final: 0.8447 (mpt-90) REVERT: B 9 MET cc_start: 0.8820 (mtp) cc_final: 0.8566 (pmm) REVERT: B 138 MET cc_start: 0.9243 (mtt) cc_final: 0.9024 (mtt) REVERT: C 70 MET cc_start: 0.9381 (mtp) cc_final: 0.8570 (mmm) REVERT: C 71 GLU cc_start: 0.8453 (pm20) cc_final: 0.7949 (pm20) REVERT: C 130 MET cc_start: 0.7067 (ttp) cc_final: 0.6614 (tmm) REVERT: C 150 GLU cc_start: 0.8691 (tm-30) cc_final: 0.8373 (tm-30) REVERT: C 177 GLU cc_start: 0.9163 (mt-10) cc_final: 0.8859 (mp0) REVERT: C 182 GLN cc_start: 0.8717 (tt0) cc_final: 0.8206 (tt0) REVERT: C 189 GLU cc_start: 0.8513 (tm-30) cc_final: 0.8287 (tm-30) REVERT: C 223 MET cc_start: 0.8972 (mmm) cc_final: 0.8248 (mtt) REVERT: C 239 GLN cc_start: 0.8895 (tp-100) cc_final: 0.8485 (mm110) REVERT: C 423 CYS cc_start: 0.9254 (t) cc_final: 0.9030 (m) REVERT: D 9 MET cc_start: 0.8783 (mpp) cc_final: 0.8568 (mpp) REVERT: D 49 MET cc_start: 0.9177 (ttp) cc_final: 0.8910 (ttp) REVERT: D 165 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7186 (pp20) REVERT: D 215 LYS cc_start: 0.9237 (tttt) cc_final: 0.8930 (tptp) REVERT: N 3 GLN cc_start: 0.8058 (mp10) cc_final: 0.7842 (mp10) REVERT: N 4 LEU cc_start: 0.8429 (tp) cc_final: 0.8022 (tt) REVERT: N 426 GLN cc_start: 0.8655 (tt0) cc_final: 0.8181 (tp-100) REVERT: N 449 ASP cc_start: 0.9007 (m-30) cc_final: 0.8577 (p0) REVERT: N 472 ASN cc_start: 0.8496 (t0) cc_final: 0.8272 (t0) outliers start: 35 outliers final: 25 residues processed: 201 average time/residue: 0.2640 time to fit residues: 79.5441 Evaluate side-chains 199 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 173 time to evaluate : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain N residue 405 LEU Chi-restraints excluded: chain N residue 457 ILE Chi-restraints excluded: chain N residue 493 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 59 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 chunk 121 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 113 optimal weight: 7.9990 chunk 106 optimal weight: 2.9990 chunk 69 optimal weight: 8.9990 chunk 66 optimal weight: 8.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 267 HIS D 217 ASN E 267 HIS N 507 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.084120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.055155 restraints weight = 79766.361| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 4.69 r_work: 0.2625 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2630 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2630 r_free = 0.2630 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2630 r_free = 0.2630 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2630 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 moved from start: 0.4987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 15212 Z= 0.238 Angle : 0.639 13.640 20743 Z= 0.323 Chirality : 0.046 0.257 2391 Planarity : 0.004 0.044 2520 Dihedral : 5.963 53.672 2457 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.88 % Allowed : 11.27 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.46 % Cis-general : 0.30 % 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: 1.11 (0.20), residues: 1748 helix: 1.94 (0.21), residues: 566 sheet: 0.56 (0.24), residues: 476 loop : -0.04 (0.24), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 241 HIS 0.004 0.001 HIS E 107 PHE 0.028 0.002 PHE B 11 TYR 0.029 0.002 TYR D 299 ARG 0.011 0.001 ARG D 86 Details of bonding type rmsd link_NAG-ASN : bond 0.00243 ( 8) link_NAG-ASN : angle 2.04281 ( 24) link_ALPHA1-6 : bond 0.00994 ( 3) link_ALPHA1-6 : angle 1.54120 ( 9) link_BETA1-4 : bond 0.00330 ( 9) link_BETA1-4 : angle 1.67162 ( 27) link_ALPHA1-3 : bond 0.00829 ( 3) link_ALPHA1-3 : angle 1.57555 ( 9) hydrogen bonds : bond 0.04418 ( 752) hydrogen bonds : angle 4.39726 ( 2427) SS BOND : bond 0.00091 ( 6) SS BOND : angle 0.52890 ( 12) covalent geometry : bond 0.00547 (15183) covalent geometry : angle 0.63144 (20662) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 174 time to evaluate : 1.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.9309 (mtt) cc_final: 0.9069 (mtt) REVERT: A 71 GLU cc_start: 0.8852 (pt0) cc_final: 0.8459 (pt0) REVERT: A 130 MET cc_start: 0.8163 (ttm) cc_final: 0.7525 (tpp) REVERT: A 150 GLU cc_start: 0.9111 (tm-30) cc_final: 0.8675 (tm-30) REVERT: A 197 ARG cc_start: 0.8696 (ttp-110) cc_final: 0.8487 (mpt-90) REVERT: A 285 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8624 (mmmm) REVERT: B 26 ARG cc_start: 0.8596 (mtm180) cc_final: 0.8355 (mtm-85) REVERT: C 70 MET cc_start: 0.9414 (mtp) cc_final: 0.8579 (mmm) REVERT: C 71 GLU cc_start: 0.8600 (pm20) cc_final: 0.8068 (pm20) REVERT: C 130 MET cc_start: 0.7167 (ttp) cc_final: 0.6710 (tmm) REVERT: C 150 GLU cc_start: 0.8637 (tm-30) cc_final: 0.8365 (tm-30) REVERT: C 177 GLU cc_start: 0.9143 (mt-10) cc_final: 0.8886 (mp0) REVERT: C 182 GLN cc_start: 0.8767 (tt0) cc_final: 0.8220 (tt0) REVERT: C 189 GLU cc_start: 0.8417 (tm-30) cc_final: 0.8173 (tm-30) REVERT: C 223 MET cc_start: 0.8975 (mmm) cc_final: 0.8067 (mmm) REVERT: D 9 MET cc_start: 0.8754 (mpp) cc_final: 0.8547 (mpp) REVERT: D 49 MET cc_start: 0.9197 (ttp) cc_final: 0.8954 (ttp) REVERT: D 215 LYS cc_start: 0.9253 (tttt) cc_final: 0.8955 (tttm) REVERT: N 4 LEU cc_start: 0.8210 (tp) cc_final: 0.7826 (tt) REVERT: N 426 GLN cc_start: 0.8714 (tt0) cc_final: 0.8187 (tp-100) REVERT: N 449 ASP cc_start: 0.9085 (m-30) cc_final: 0.8634 (p0) outliers start: 30 outliers final: 23 residues processed: 193 average time/residue: 0.2769 time to fit residues: 79.5070 Evaluate side-chains 187 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 163 time to evaluate : 1.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain B residue 11 PHE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain N residue 405 LEU Chi-restraints excluded: chain N residue 493 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 170 optimal weight: 5.9990 chunk 109 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 151 optimal weight: 0.8980 chunk 125 optimal weight: 0.7980 chunk 101 optimal weight: 8.9990 chunk 75 optimal weight: 0.5980 chunk 9 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 82 optimal weight: 8.9990 chunk 54 optimal weight: 0.6980 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 267 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.085988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.056617 restraints weight = 83293.082| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 4.93 r_work: 0.2655 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2655 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2655 r_free = 0.2655 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2655 r_free = 0.2655 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2655 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.5125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15212 Z= 0.141 Angle : 0.608 14.914 20743 Z= 0.302 Chirality : 0.043 0.253 2391 Planarity : 0.004 0.042 2520 Dihedral : 5.613 49.687 2457 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.57 % Allowed : 12.34 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.46 % Cis-general : 0.30 % 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: 1.22 (0.20), residues: 1748 helix: 2.01 (0.21), residues: 566 sheet: 0.65 (0.24), residues: 472 loop : 0.03 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 241 HIS 0.003 0.001 HIS C 156 PHE 0.023 0.001 PHE B 11 TYR 0.024 0.002 TYR D 299 ARG 0.011 0.000 ARG D 86 Details of bonding type rmsd link_NAG-ASN : bond 0.00142 ( 8) link_NAG-ASN : angle 1.75000 ( 24) link_ALPHA1-6 : bond 0.01055 ( 3) link_ALPHA1-6 : angle 1.41700 ( 9) link_BETA1-4 : bond 0.00339 ( 9) link_BETA1-4 : angle 1.50505 ( 27) link_ALPHA1-3 : bond 0.00839 ( 3) link_ALPHA1-3 : angle 1.57530 ( 9) hydrogen bonds : bond 0.03901 ( 752) hydrogen bonds : angle 4.23297 ( 2427) SS BOND : bond 0.00066 ( 6) SS BOND : angle 0.42121 ( 12) covalent geometry : bond 0.00320 (15183) covalent geometry : angle 0.60227 (20662) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 169 time to evaluate : 1.859 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.9302 (mtt) cc_final: 0.9051 (mtt) REVERT: A 71 GLU cc_start: 0.8845 (pt0) cc_final: 0.8392 (pt0) REVERT: A 130 MET cc_start: 0.8091 (ttm) cc_final: 0.7456 (tpp) REVERT: A 150 GLU cc_start: 0.9132 (tm-30) cc_final: 0.8727 (tm-30) REVERT: A 197 ARG cc_start: 0.8702 (ttp-110) cc_final: 0.8473 (mpt-90) REVERT: A 285 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8615 (mmmm) REVERT: B 26 ARG cc_start: 0.8546 (mtm180) cc_final: 0.8217 (mtm-85) REVERT: C 70 MET cc_start: 0.9382 (mtp) cc_final: 0.8588 (mmm) REVERT: C 71 GLU cc_start: 0.8621 (pm20) cc_final: 0.7986 (pm20) REVERT: C 130 MET cc_start: 0.7050 (ttp) cc_final: 0.6669 (tmm) REVERT: C 150 GLU cc_start: 0.8674 (tm-30) cc_final: 0.8370 (tm-30) REVERT: C 177 GLU cc_start: 0.9168 (mt-10) cc_final: 0.8864 (mp0) REVERT: C 182 GLN cc_start: 0.8758 (tt0) cc_final: 0.8267 (tt0) REVERT: C 189 GLU cc_start: 0.8332 (tm-30) cc_final: 0.8012 (tm-30) REVERT: C 223 MET cc_start: 0.8974 (mmm) cc_final: 0.8142 (mtt) REVERT: D 49 MET cc_start: 0.9213 (ttp) cc_final: 0.8995 (ttp) REVERT: D 215 LYS cc_start: 0.9213 (tttt) cc_final: 0.8904 (tttm) REVERT: E 9 MET cc_start: 0.7520 (OUTLIER) cc_final: 0.7095 (mtp) REVERT: N 426 GLN cc_start: 0.8674 (tt0) cc_final: 0.8125 (tp-100) REVERT: N 449 ASP cc_start: 0.9120 (m-30) cc_final: 0.8645 (p0) REVERT: N 474 LYS cc_start: 0.8469 (mmmt) cc_final: 0.8055 (ttpp) outliers start: 25 outliers final: 15 residues processed: 184 average time/residue: 0.2632 time to fit residues: 73.9045 Evaluate side-chains 178 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 161 time to evaluate : 1.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain E residue 9 MET Chi-restraints excluded: chain N residue 464 ASN Chi-restraints excluded: chain N residue 493 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 167 optimal weight: 10.0000 chunk 72 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 165 optimal weight: 10.0000 chunk 11 optimal weight: 8.9990 chunk 65 optimal weight: 10.0000 chunk 160 optimal weight: 6.9990 chunk 117 optimal weight: 9.9990 chunk 99 optimal weight: 0.8980 chunk 174 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 267 HIS C 258 ASN D 90 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.083109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.056282 restraints weight = 68474.158| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 4.17 r_work: 0.2666 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2689 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2689 r_free = 0.2689 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2689 r_free = 0.2689 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2689 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.5385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 15212 Z= 0.268 Angle : 0.692 14.492 20743 Z= 0.347 Chirality : 0.046 0.259 2391 Planarity : 0.004 0.044 2520 Dihedral : 5.827 49.479 2457 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.38 % Allowed : 12.59 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.46 % Cis-general : 0.30 % 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: 0.97 (0.20), residues: 1748 helix: 1.87 (0.21), residues: 561 sheet: 0.42 (0.24), residues: 477 loop : -0.10 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 241 HIS 0.008 0.001 HIS D 191 PHE 0.043 0.002 PHE N 455 TYR 0.030 0.002 TYR D 299 ARG 0.012 0.001 ARG D 86 Details of bonding type rmsd link_NAG-ASN : bond 0.00348 ( 8) link_NAG-ASN : angle 2.25199 ( 24) link_ALPHA1-6 : bond 0.00991 ( 3) link_ALPHA1-6 : angle 1.44888 ( 9) link_BETA1-4 : bond 0.00377 ( 9) link_BETA1-4 : angle 1.81298 ( 27) link_ALPHA1-3 : bond 0.00546 ( 3) link_ALPHA1-3 : angle 1.51995 ( 9) hydrogen bonds : bond 0.04500 ( 752) hydrogen bonds : angle 4.45796 ( 2427) SS BOND : bond 0.00339 ( 6) SS BOND : angle 0.43918 ( 12) covalent geometry : bond 0.00614 (15183) covalent geometry : angle 0.68467 (20662) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 168 time to evaluate : 1.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.9347 (mtt) cc_final: 0.9143 (mtt) REVERT: A 130 MET cc_start: 0.8115 (ttm) cc_final: 0.7505 (tpp) REVERT: A 150 GLU cc_start: 0.9115 (tm-30) cc_final: 0.8704 (tm-30) REVERT: A 197 ARG cc_start: 0.8662 (ttp-110) cc_final: 0.8376 (mpt-90) REVERT: A 199 TYR cc_start: 0.8200 (p90) cc_final: 0.7966 (p90) REVERT: A 285 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8658 (mmmm) REVERT: B 26 ARG cc_start: 0.8679 (mtm180) cc_final: 0.8360 (mtm-85) REVERT: C 70 MET cc_start: 0.9373 (mtp) cc_final: 0.8578 (mmm) REVERT: C 71 GLU cc_start: 0.8591 (pm20) cc_final: 0.8020 (pm20) REVERT: C 130 MET cc_start: 0.7198 (ttp) cc_final: 0.6610 (tmm) REVERT: C 150 GLU cc_start: 0.8657 (tm-30) cc_final: 0.8340 (tm-30) REVERT: C 177 GLU cc_start: 0.9177 (mt-10) cc_final: 0.8915 (mp0) REVERT: C 182 GLN cc_start: 0.8807 (tt0) cc_final: 0.8277 (tt0) REVERT: C 189 GLU cc_start: 0.8291 (tm-30) cc_final: 0.8033 (tm-30) REVERT: C 223 MET cc_start: 0.9008 (mmm) cc_final: 0.8116 (mmm) REVERT: D 13 LYS cc_start: 0.9305 (tttp) cc_final: 0.9099 (tptt) REVERT: D 49 MET cc_start: 0.9141 (ttp) cc_final: 0.8940 (ttp) REVERT: D 165 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7293 (pp20) REVERT: D 215 LYS cc_start: 0.9238 (tttt) cc_final: 0.8923 (tttm) REVERT: D 274 LYS cc_start: 0.8684 (mmtt) cc_final: 0.8416 (mmtt) REVERT: N 426 GLN cc_start: 0.8594 (tt0) cc_final: 0.8181 (tp-100) REVERT: N 449 ASP cc_start: 0.9090 (m-30) cc_final: 0.8675 (p0) outliers start: 22 outliers final: 15 residues processed: 184 average time/residue: 0.2657 time to fit residues: 72.4657 Evaluate side-chains 176 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 159 time to evaluate : 1.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain N residue 493 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 5 optimal weight: 0.9990 chunk 18 optimal weight: 10.0000 chunk 113 optimal weight: 8.9990 chunk 71 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 chunk 88 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 chunk 114 optimal weight: 0.3980 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 90 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.083129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.054925 restraints weight = 80417.399| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 4.60 r_work: 0.2622 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2622 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2622 r_free = 0.2622 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2622 r_free = 0.2622 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2622 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.5502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 15212 Z= 0.209 Angle : 0.666 17.630 20743 Z= 0.330 Chirality : 0.045 0.252 2391 Planarity : 0.004 0.047 2520 Dihedral : 5.676 47.502 2457 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.44 % Allowed : 13.02 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.46 % Cis-general : 0.30 % 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: 0.93 (0.20), residues: 1748 helix: 1.79 (0.21), residues: 566 sheet: 0.37 (0.24), residues: 477 loop : -0.06 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 241 HIS 0.010 0.001 HIS D 191 PHE 0.024 0.002 PHE N 455 TYR 0.026 0.002 TYR D 299 ARG 0.011 0.000 ARG D 86 Details of bonding type rmsd link_NAG-ASN : bond 0.00154 ( 8) link_NAG-ASN : angle 1.89982 ( 24) link_ALPHA1-6 : bond 0.01031 ( 3) link_ALPHA1-6 : angle 1.39925 ( 9) link_BETA1-4 : bond 0.00302 ( 9) link_BETA1-4 : angle 1.59113 ( 27) link_ALPHA1-3 : bond 0.00750 ( 3) link_ALPHA1-3 : angle 1.52879 ( 9) hydrogen bonds : bond 0.04120 ( 752) hydrogen bonds : angle 4.36250 ( 2427) SS BOND : bond 0.00074 ( 6) SS BOND : angle 0.35867 ( 12) covalent geometry : bond 0.00480 (15183) covalent geometry : angle 0.66058 (20662) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 166 time to evaluate : 1.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.9319 (mtt) cc_final: 0.9083 (mtt) REVERT: A 130 MET cc_start: 0.8152 (ttm) cc_final: 0.7501 (tpp) REVERT: A 150 GLU cc_start: 0.9118 (tm-30) cc_final: 0.8700 (tm-30) REVERT: A 197 ARG cc_start: 0.8675 (ttp-110) cc_final: 0.8351 (mpt-90) REVERT: A 199 TYR cc_start: 0.8254 (p90) cc_final: 0.8034 (p90) REVERT: A 285 LYS cc_start: 0.8976 (OUTLIER) cc_final: 0.8704 (mmmm) REVERT: B 26 ARG cc_start: 0.8657 (mtm180) cc_final: 0.8342 (mtm-85) REVERT: C 70 MET cc_start: 0.9404 (mtp) cc_final: 0.8575 (mmm) REVERT: C 71 GLU cc_start: 0.8611 (pm20) cc_final: 0.8024 (pm20) REVERT: C 130 MET cc_start: 0.7121 (ttp) cc_final: 0.6524 (tmm) REVERT: C 150 GLU cc_start: 0.8669 (tm-30) cc_final: 0.8339 (tm-30) REVERT: C 177 GLU cc_start: 0.9215 (mt-10) cc_final: 0.8951 (mp0) REVERT: C 182 GLN cc_start: 0.8779 (tt0) cc_final: 0.8333 (tt0) REVERT: C 189 GLU cc_start: 0.8327 (tm-30) cc_final: 0.8057 (tm-30) REVERT: C 223 MET cc_start: 0.9028 (mmm) cc_final: 0.8205 (mtt) REVERT: D 165 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7258 (pp20) REVERT: D 215 LYS cc_start: 0.9226 (tttt) cc_final: 0.8888 (tttm) REVERT: D 274 LYS cc_start: 0.8673 (mmtt) cc_final: 0.8379 (mmtt) REVERT: E 9 MET cc_start: 0.7657 (OUTLIER) cc_final: 0.7193 (mtp) REVERT: N 426 GLN cc_start: 0.8576 (tt0) cc_final: 0.8185 (tp-100) REVERT: N 449 ASP cc_start: 0.9169 (m-30) cc_final: 0.8734 (p0) REVERT: N 474 LYS cc_start: 0.8341 (mmmt) cc_final: 0.7861 (tptp) outliers start: 23 outliers final: 16 residues processed: 182 average time/residue: 0.2710 time to fit residues: 73.1070 Evaluate side-chains 180 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 161 time to evaluate : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain E residue 9 MET Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain N residue 493 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 7 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 34 optimal weight: 0.0060 chunk 61 optimal weight: 0.9990 chunk 18 optimal weight: 9.9990 chunk 86 optimal weight: 0.6980 chunk 50 optimal weight: 7.9990 chunk 90 optimal weight: 0.0040 chunk 98 optimal weight: 0.7980 chunk 75 optimal weight: 10.0000 chunk 9 optimal weight: 8.9990 overall best weight: 0.5010 ------------------------------------------------------------------------------- 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 = 0.3510 r_free = 0.3510 target = 0.084971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.057630 restraints weight = 68191.379| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 4.24 r_work: 0.2697 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2700 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2700 r_free = 0.2700 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2700 r_free = 0.2700 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2700 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.5577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15212 Z= 0.117 Angle : 0.627 17.250 20743 Z= 0.309 Chirality : 0.043 0.243 2391 Planarity : 0.003 0.035 2520 Dihedral : 5.313 43.019 2457 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.06 % Allowed : 13.27 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.46 % Cis-general : 0.30 % 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: 1.12 (0.20), residues: 1748 helix: 1.94 (0.21), residues: 566 sheet: 0.50 (0.24), residues: 470 loop : 0.02 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 67 HIS 0.010 0.001 HIS D 191 PHE 0.022 0.001 PHE N 455 TYR 0.023 0.001 TYR D 299 ARG 0.010 0.000 ARG D 86 Details of bonding type rmsd link_NAG-ASN : bond 0.00156 ( 8) link_NAG-ASN : angle 1.61676 ( 24) link_ALPHA1-6 : bond 0.01097 ( 3) link_ALPHA1-6 : angle 1.32354 ( 9) link_BETA1-4 : bond 0.00372 ( 9) link_BETA1-4 : angle 1.41925 ( 27) link_ALPHA1-3 : bond 0.00787 ( 3) link_ALPHA1-3 : angle 1.47293 ( 9) hydrogen bonds : bond 0.03592 ( 752) hydrogen bonds : angle 4.14352 ( 2427) SS BOND : bond 0.00071 ( 6) SS BOND : angle 0.36735 ( 12) covalent geometry : bond 0.00255 (15183) covalent geometry : angle 0.62197 (20662) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8777.10 seconds wall clock time: 151 minutes 6.02 seconds (9066.02 seconds total)