Starting phenix.real_space_refine on Thu Feb 5 03:57:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qnb_14073/02_2026/7qnb_14073.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qnb_14073/02_2026/7qnb_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_14073/02_2026/7qnb_14073.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qnb_14073/02_2026/7qnb_14073.map" model { file = "/net/cci-nas-00/data/ceres_data/7qnb_14073/02_2026/7qnb_14073.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qnb_14073/02_2026/7qnb_14073.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/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: 4.67, per 1000 atoms: 0.32 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: 1.34 Conformation dependent library (CDL) restraints added in 767.2 milliseconds 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: 0.41 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: 2.27 Time building geometry restraints manager: 1.71 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: 2.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.630 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.040 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (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 ARG 0.002 0.000 ARG D 196 TYR 0.015 0.001 TYR B 299 PHE 0.006 0.001 PHE E 293 TRP 0.006 0.001 TRP B 241 HIS 0.002 0.000 HIS A 122 Details of bonding type rmsd covalent geometry : bond 0.00252 (15183) covalent geometry : angle 0.45740 (20662) SS BOND : bond 0.00066 ( 6) SS BOND : angle 0.57433 ( 12) hydrogen bonds : bond 0.21911 ( 752) hydrogen bonds : angle 7.07904 ( 2427) link_ALPHA1-3 : bond 0.00146 ( 3) link_ALPHA1-3 : angle 0.75068 ( 9) 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_NAG-ASN : bond 0.00586 ( 8) link_NAG-ASN : angle 1.69353 ( 24) *********************** 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 : 0.359 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: 0.7276 (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: 0.8477 (tppt) REVERT: B 306 PHE cc_start: 0.7000 (t80) cc_final: 0.6686 (t80) REVERT: C 42 LEU cc_start: 0.9038 (mt) cc_final: 0.8828 (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: 0.7426 (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: 0.7392 (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: 0.7677 (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: 0.7878 (t80) cc_final: 0.7664 (t80) REVERT: E 426 TRP cc_start: 0.7966 (t60) cc_final: 0.7718 (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: 0.1462 time to fit residues: 72.7004 Evaluate side-chains 210 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 206 time to evaluate : 0.570 ------------------------------------------------------------------------------- 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 98 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 C 152 GLN E 267 HIS N 507 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.088513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.059588 restraints weight = 75112.387| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 4.69 r_work: 0.2734 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2738 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2738 r_free = 0.2738 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2738 r_free = 0.2738 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2738 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 15212 Z= 0.252 Angle : 0.722 10.948 20743 Z= 0.375 Chirality : 0.048 0.221 2391 Planarity : 0.005 0.050 2520 Dihedral : 7.960 77.176 2462 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.63 % Allowed : 8.02 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.46 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.20), residues: 1748 helix: 1.88 (0.21), residues: 559 sheet: 0.79 (0.24), residues: 491 loop : 0.25 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 185 TYR 0.029 0.002 TYR D 299 PHE 0.024 0.002 PHE B 306 TRP 0.040 0.002 TRP C 123 HIS 0.004 0.001 HIS C 318 Details of bonding type rmsd covalent geometry : bond 0.00582 (15183) covalent geometry : angle 0.71194 (20662) SS BOND : bond 0.00283 ( 6) SS BOND : angle 0.74676 ( 12) hydrogen bonds : bond 0.05065 ( 752) hydrogen bonds : angle 4.95080 ( 2427) link_ALPHA1-3 : bond 0.00660 ( 3) link_ALPHA1-3 : angle 2.74536 ( 9) link_ALPHA1-6 : bond 0.00748 ( 3) link_ALPHA1-6 : angle 1.86645 ( 9) link_BETA1-4 : bond 0.00435 ( 9) link_BETA1-4 : angle 2.34871 ( 27) link_NAG-ASN : bond 0.00327 ( 8) link_NAG-ASN : angle 2.04554 ( 24) *********************** 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 251 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 209 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 GLU cc_start: 0.8921 (pt0) cc_final: 0.8315 (pt0) REVERT: A 105 LYS cc_start: 0.8949 (mmtt) cc_final: 0.8391 (mmtp) REVERT: A 130 MET cc_start: 0.7904 (ttm) cc_final: 0.7077 (tpp) REVERT: A 197 ARG cc_start: 0.8640 (ttp-110) cc_final: 0.8260 (mtt90) REVERT: A 285 LYS cc_start: 0.9097 (OUTLIER) cc_final: 0.8759 (mmmm) REVERT: A 320 PHE cc_start: 0.9173 (m-80) cc_final: 0.8966 (m-80) REVERT: B 9 MET cc_start: 0.8880 (mtp) cc_final: 0.8395 (pmm) REVERT: B 115 MET cc_start: 0.7232 (ttp) cc_final: 0.6908 (ttp) REVERT: B 268 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7681 (mp) REVERT: C 42 LEU cc_start: 0.9075 (mt) cc_final: 0.8852 (mt) REVERT: C 70 MET cc_start: 0.9373 (mtt) cc_final: 0.9155 (mtm) REVERT: C 71 GLU cc_start: 0.8499 (pm20) cc_final: 0.8136 (pm20) REVERT: C 123 TRP cc_start: 0.8014 (m100) cc_final: 0.7775 (m100) REVERT: C 130 MET cc_start: 0.6871 (ttp) cc_final: 0.6345 (tmm) REVERT: C 150 GLU cc_start: 0.8523 (tm-30) cc_final: 0.8158 (tm-30) REVERT: C 152 GLN cc_start: 0.8645 (mm-40) cc_final: 0.8318 (mm110) REVERT: C 177 GLU cc_start: 0.9146 (mt-10) cc_final: 0.8820 (mp0) REVERT: C 178 GLU cc_start: 0.8283 (mt-10) cc_final: 0.7571 (mt-10) REVERT: C 189 GLU cc_start: 0.8600 (tp30) cc_final: 0.8332 (tm-30) REVERT: C 223 MET cc_start: 0.8912 (mmm) cc_final: 0.7915 (mmm) REVERT: C 239 GLN cc_start: 0.8665 (mm110) cc_final: 0.8390 (mm110) REVERT: D 9 MET cc_start: 0.8715 (mpp) cc_final: 0.8493 (mpp) REVERT: D 18 LYS cc_start: 0.9329 (pttp) cc_final: 0.8620 (pptt) REVERT: D 49 MET cc_start: 0.8982 (ttp) cc_final: 0.8734 (ttp) REVERT: D 79 LEU cc_start: 0.9067 (mt) cc_final: 0.8783 (mp) REVERT: D 215 LYS cc_start: 0.9101 (tttt) cc_final: 0.8800 (tptp) REVERT: D 224 GLN cc_start: 0.8672 (tp40) cc_final: 0.8289 (tp40) REVERT: D 274 LYS cc_start: 0.8338 (mmtt) cc_final: 0.8049 (mmtm) REVERT: N 3 GLN cc_start: 0.8395 (mp10) cc_final: 0.8163 (mp10) REVERT: N 421 MET cc_start: 0.8206 (mmm) cc_final: 0.7784 (mmm) REVERT: N 426 GLN cc_start: 0.8650 (tt0) cc_final: 0.8004 (tp-100) REVERT: N 432 ARG cc_start: 0.8046 (ttm170) cc_final: 0.7522 (ttm110) REVERT: N 433 GLU cc_start: 0.9188 (tt0) cc_final: 0.8918 (pt0) REVERT: N 472 ASN cc_start: 0.8416 (t0) cc_final: 0.8174 (t0) outliers start: 42 outliers final: 23 residues processed: 232 average time/residue: 0.1273 time to fit residues: 42.5355 Evaluate side-chains 211 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 186 time to evaluate : 0.559 ------------------------------------------------------------------------------- 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 96 LEU 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 222 ILE 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 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 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 235 LEU Chi-restraints excluded: chain D residue 444 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 Chi-restraints excluded: chain E residue 437 LEU 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 3 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 33 optimal weight: 9.9990 chunk 150 optimal weight: 0.8980 chunk 6 optimal weight: 0.2980 chunk 91 optimal weight: 7.9990 chunk 168 optimal weight: 9.9990 chunk 43 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 146 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 156 HIS ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 267 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.088193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.059242 restraints weight = 85314.063| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 4.97 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2904 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2904 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15212 Z= 0.144 Angle : 0.571 8.608 20743 Z= 0.294 Chirality : 0.044 0.208 2391 Planarity : 0.004 0.029 2520 Dihedral : 7.207 73.065 2457 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.63 % Allowed : 10.14 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.46 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.20), residues: 1748 helix: 2.07 (0.21), residues: 564 sheet: 0.97 (0.24), residues: 465 loop : 0.12 (0.24), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 86 TYR 0.025 0.001 TYR D 299 PHE 0.024 0.001 PHE D 306 TRP 0.017 0.001 TRP E 241 HIS 0.003 0.001 HIS C 122 Details of bonding type rmsd covalent geometry : bond 0.00320 (15183) covalent geometry : angle 0.56363 (20662) SS BOND : bond 0.00078 ( 6) SS BOND : angle 0.53593 ( 12) hydrogen bonds : bond 0.04629 ( 752) hydrogen bonds : angle 4.48380 ( 2427) link_ALPHA1-3 : bond 0.00992 ( 3) link_ALPHA1-3 : angle 1.44310 ( 9) link_ALPHA1-6 : bond 0.00716 ( 3) link_ALPHA1-6 : angle 1.83329 ( 9) link_BETA1-4 : bond 0.00409 ( 9) link_BETA1-4 : angle 1.62967 ( 27) link_NAG-ASN : bond 0.00230 ( 8) link_NAG-ASN : angle 1.62998 ( 24) *********************** 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 218 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 192 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 LYS cc_start: 0.8933 (mmtt) cc_final: 0.8395 (mmtp) REVERT: A 130 MET cc_start: 0.7873 (ttm) cc_final: 0.6777 (tpp) REVERT: A 197 ARG cc_start: 0.8452 (ttp-110) cc_final: 0.8215 (mpt-90) REVERT: A 223 MET cc_start: 0.8738 (mmm) cc_final: 0.8511 (mmm) REVERT: A 239 GLN cc_start: 0.8703 (tp40) cc_final: 0.8490 (tp40) REVERT: A 276 MET cc_start: 0.9359 (mmm) cc_final: 0.9110 (tpp) REVERT: B 9 MET cc_start: 0.8832 (mtp) cc_final: 0.8490 (pmm) REVERT: B 115 MET cc_start: 0.7223 (ttp) cc_final: 0.6899 (ttp) REVERT: C 42 LEU cc_start: 0.9018 (mt) cc_final: 0.8809 (mt) REVERT: C 71 GLU cc_start: 0.8089 (pm20) cc_final: 0.7612 (pm20) REVERT: C 130 MET cc_start: 0.6722 (ttp) cc_final: 0.6292 (tmm) REVERT: C 150 GLU cc_start: 0.8252 (tm-30) cc_final: 0.7784 (tm-30) REVERT: C 152 GLN cc_start: 0.8361 (mm-40) cc_final: 0.7990 (mm110) REVERT: C 177 GLU cc_start: 0.9026 (mt-10) cc_final: 0.8717 (mp0) REVERT: C 189 GLU cc_start: 0.8430 (tp30) cc_final: 0.8187 (tm-30) REVERT: C 223 MET cc_start: 0.8470 (mmm) cc_final: 0.7349 (mtp) REVERT: C 423 CYS cc_start: 0.9131 (t) cc_final: 0.8901 (m) REVERT: D 9 MET cc_start: 0.8815 (mpp) cc_final: 0.8581 (mpp) REVERT: D 49 MET cc_start: 0.8710 (ttp) cc_final: 0.8413 (ttp) REVERT: D 215 LYS cc_start: 0.9045 (tttt) cc_final: 0.8749 (tptp) REVERT: D 224 GLN cc_start: 0.8316 (tp40) cc_final: 0.8008 (tp40) REVERT: E 17 ASP cc_start: 0.9343 (t0) cc_final: 0.8747 (t0) REVERT: E 190 GLU cc_start: 0.8349 (tt0) cc_final: 0.8122 (tt0) REVERT: N 3 GLN cc_start: 0.8139 (mp10) cc_final: 0.7791 (mp10) REVERT: N 426 GLN cc_start: 0.8784 (tt0) cc_final: 0.8141 (tp-100) REVERT: N 433 GLU cc_start: 0.9061 (tt0) cc_final: 0.8761 (pt0) REVERT: N 472 ASN cc_start: 0.8559 (t0) cc_final: 0.8211 (t0) outliers start: 26 outliers final: 13 residues processed: 211 average time/residue: 0.1139 time to fit residues: 35.8075 Evaluate side-chains 189 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 176 time to evaluate : 0.563 ------------------------------------------------------------------------------- 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 275 ILE 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 427 LEU Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain N residue 493 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 128 optimal weight: 0.7980 chunk 81 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 chunk 112 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 102 optimal weight: 7.9990 chunk 125 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 71 optimal weight: 8.9990 chunk 146 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- 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 = 0.3504 r_free = 0.3504 target = 0.085173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.056318 restraints weight = 77021.139| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 4.62 r_work: 0.2661 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2664 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2664 r_free = 0.2664 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 = 0.2664 r_free = 0.2664 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2664 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.4414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 15212 Z= 0.238 Angle : 0.637 9.266 20743 Z= 0.328 Chirality : 0.046 0.251 2391 Planarity : 0.004 0.041 2520 Dihedral : 6.843 68.795 2457 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.50 % Allowed : 9.58 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.46 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.20), residues: 1748 helix: 1.93 (0.21), residues: 562 sheet: 0.57 (0.24), residues: 487 loop : -0.02 (0.24), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 86 TYR 0.031 0.002 TYR D 299 PHE 0.032 0.002 PHE E 307 TRP 0.018 0.001 TRP E 241 HIS 0.005 0.001 HIS E 267 Details of bonding type rmsd covalent geometry : bond 0.00546 (15183) covalent geometry : angle 0.62735 (20662) SS BOND : bond 0.00125 ( 6) SS BOND : angle 0.45841 ( 12) hydrogen bonds : bond 0.04482 ( 752) hydrogen bonds : angle 4.47004 ( 2427) link_ALPHA1-3 : bond 0.00849 ( 3) link_ALPHA1-3 : angle 1.87352 ( 9) link_ALPHA1-6 : bond 0.00752 ( 3) link_ALPHA1-6 : angle 1.66748 ( 9) link_BETA1-4 : bond 0.00418 ( 9) link_BETA1-4 : angle 1.93526 ( 27) link_NAG-ASN : bond 0.00320 ( 8) link_NAG-ASN : angle 2.22584 ( 24) *********************** 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 219 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 179 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 LYS cc_start: 0.9142 (mmtt) cc_final: 0.8651 (mmtp) REVERT: A 130 MET cc_start: 0.8122 (ttm) cc_final: 0.7273 (tpp) REVERT: A 150 GLU cc_start: 0.9053 (tm-30) cc_final: 0.8784 (tm-30) REVERT: A 197 ARG cc_start: 0.8668 (ttp-110) cc_final: 0.8343 (mpt-90) REVERT: A 239 GLN cc_start: 0.9018 (tp40) cc_final: 0.8794 (tp40) REVERT: B 9 MET cc_start: 0.8770 (mtp) cc_final: 0.8546 (pmm) REVERT: C 70 MET cc_start: 0.9314 (mtm) cc_final: 0.9105 (mtp) REVERT: C 71 GLU cc_start: 0.8362 (pm20) cc_final: 0.7898 (pm20) REVERT: C 130 MET cc_start: 0.7243 (ttp) cc_final: 0.6764 (tmm) REVERT: C 152 GLN cc_start: 0.8849 (mm-40) cc_final: 0.8597 (mm-40) REVERT: C 177 GLU cc_start: 0.9146 (mt-10) cc_final: 0.8869 (mp0) REVERT: C 223 MET cc_start: 0.8959 (mmm) cc_final: 0.8002 (mmm) REVERT: C 423 CYS cc_start: 0.9235 (OUTLIER) cc_final: 0.9019 (m) REVERT: D 9 MET cc_start: 0.8796 (mpp) cc_final: 0.8584 (mpp) REVERT: D 55 MET cc_start: 0.9347 (mtp) cc_final: 0.9056 (mmm) REVERT: D 165 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7295 (pp20) REVERT: D 215 LYS cc_start: 0.9232 (tttt) cc_final: 0.8947 (tptp) REVERT: D 224 GLN cc_start: 0.8610 (tp40) cc_final: 0.8338 (tp40) REVERT: E 141 ARG cc_start: 0.8875 (mpt-90) cc_final: 0.8577 (mpt-90) REVERT: E 182 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7627 (mp0) REVERT: N 3 GLN cc_start: 0.8287 (mp10) cc_final: 0.7960 (mp10) REVERT: N 426 GLN cc_start: 0.8640 (tt0) cc_final: 0.8042 (tp-100) REVERT: N 433 GLU cc_start: 0.9044 (tt0) cc_final: 0.8844 (pt0) REVERT: N 449 ASP cc_start: 0.8987 (m-30) cc_final: 0.8596 (p0) REVERT: N 472 ASN cc_start: 0.8788 (t0) cc_final: 0.8547 (t0) REVERT: N 482 TYR cc_start: 0.8745 (m-10) cc_final: 0.8470 (m-10) outliers start: 40 outliers final: 25 residues processed: 205 average time/residue: 0.1220 time to fit residues: 36.6747 Evaluate side-chains 191 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 164 time to evaluate : 0.560 ------------------------------------------------------------------------------- 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 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 222 ILE Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 444 LEU 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 165 GLU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 165 GLU Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 437 LEU Chi-restraints excluded: chain N residue 445 THR 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 120 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 133 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 171 optimal weight: 20.0000 chunk 146 optimal weight: 0.6980 chunk 157 optimal weight: 0.7980 chunk 150 optimal weight: 1.9990 chunk 80 optimal weight: 9.9990 chunk 101 optimal weight: 6.9990 chunk 87 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 HIS C 258 ASN D 267 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.087295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.058806 restraints weight = 67971.414| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 4.42 r_work: 0.2724 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2727 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2727 r_free = 0.2727 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2727 r_free = 0.2727 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2727 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.4552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15212 Z= 0.114 Angle : 0.557 10.133 20743 Z= 0.285 Chirality : 0.043 0.248 2391 Planarity : 0.003 0.040 2520 Dihedral : 6.356 61.992 2457 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.88 % Allowed : 10.83 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.46 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.20), residues: 1748 helix: 2.09 (0.21), residues: 566 sheet: 0.85 (0.24), residues: 465 loop : -0.01 (0.24), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 86 TYR 0.024 0.001 TYR B 299 PHE 0.020 0.001 PHE E 307 TRP 0.010 0.001 TRP D 241 HIS 0.003 0.001 HIS D 267 Details of bonding type rmsd covalent geometry : bond 0.00248 (15183) covalent geometry : angle 0.55045 (20662) SS BOND : bond 0.00085 ( 6) SS BOND : angle 0.40598 ( 12) hydrogen bonds : bond 0.03867 ( 752) hydrogen bonds : angle 4.23072 ( 2427) link_ALPHA1-3 : bond 0.00961 ( 3) link_ALPHA1-3 : angle 1.57204 ( 9) link_ALPHA1-6 : bond 0.00938 ( 3) link_ALPHA1-6 : angle 1.64053 ( 9) link_BETA1-4 : bond 0.00340 ( 9) link_BETA1-4 : angle 1.44651 ( 27) link_NAG-ASN : bond 0.00248 ( 8) link_NAG-ASN : angle 1.56848 ( 24) *********************** 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 204 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 174 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 LYS cc_start: 0.9137 (mmtt) cc_final: 0.8644 (mmtp) REVERT: A 150 GLU cc_start: 0.9005 (tm-30) cc_final: 0.8734 (tm-30) REVERT: A 197 ARG cc_start: 0.8658 (ttp-110) cc_final: 0.8387 (mpt-90) REVERT: B 9 MET cc_start: 0.8761 (mtp) cc_final: 0.8533 (pmm) REVERT: C 71 GLU cc_start: 0.8446 (pm20) cc_final: 0.7950 (pm20) REVERT: C 130 MET cc_start: 0.7131 (ttp) cc_final: 0.6582 (tmm) REVERT: C 150 GLU cc_start: 0.8553 (tm-30) cc_final: 0.8288 (tm-30) REVERT: C 177 GLU cc_start: 0.9129 (mt-10) cc_final: 0.8836 (mp0) REVERT: C 182 GLN cc_start: 0.8720 (tt0) cc_final: 0.8243 (tt0) REVERT: C 189 GLU cc_start: 0.8621 (tm-30) cc_final: 0.8187 (tm-30) REVERT: C 223 MET cc_start: 0.8890 (mmm) cc_final: 0.8061 (mtt) REVERT: D 9 MET cc_start: 0.8788 (mpp) cc_final: 0.8567 (mpp) REVERT: D 55 MET cc_start: 0.9296 (mtp) cc_final: 0.9038 (mmm) REVERT: D 215 LYS cc_start: 0.9220 (tttt) cc_final: 0.8922 (tptp) REVERT: D 224 GLN cc_start: 0.8556 (tp40) cc_final: 0.8334 (tp40) REVERT: E 141 ARG cc_start: 0.8762 (mpt-90) cc_final: 0.8422 (mmt90) REVERT: E 182 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7608 (mp0) REVERT: N 3 GLN cc_start: 0.8304 (mp10) cc_final: 0.7992 (mp10) REVERT: N 4 LEU cc_start: 0.8306 (tp) cc_final: 0.7869 (tt) REVERT: N 426 GLN cc_start: 0.8603 (tt0) cc_final: 0.8005 (tp-100) REVERT: N 433 GLU cc_start: 0.9089 (tt0) cc_final: 0.8865 (pt0) REVERT: N 449 ASP cc_start: 0.9023 (m-30) cc_final: 0.8580 (p0) REVERT: N 472 ASN cc_start: 0.8789 (t0) cc_final: 0.8513 (t0) outliers start: 30 outliers final: 18 residues processed: 195 average time/residue: 0.1111 time to fit residues: 32.6398 Evaluate side-chains 187 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 169 time to evaluate : 0.617 ------------------------------------------------------------------------------- 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 B residue 36 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain C residue 42 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 145 LEU Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain E residue 165 GLU Chi-restraints excluded: chain N residue 473 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 90 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 108 optimal weight: 7.9990 chunk 128 optimal weight: 0.8980 chunk 52 optimal weight: 10.0000 chunk 77 optimal weight: 8.9990 chunk 78 optimal weight: 0.5980 chunk 110 optimal weight: 0.0970 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 0.0040 chunk 54 optimal weight: 2.9990 overall best weight: 0.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 HIS D 267 HIS E 90 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.087222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.058662 restraints weight = 78896.469| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 4.69 r_work: 0.2714 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2715 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2715 r_free = 0.2715 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2715 r_free = 0.2715 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2715 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.4695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15212 Z= 0.119 Angle : 0.559 11.143 20743 Z= 0.284 Chirality : 0.043 0.250 2391 Planarity : 0.003 0.037 2520 Dihedral : 6.035 57.540 2457 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.82 % Allowed : 10.83 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.46 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.20), residues: 1748 helix: 2.10 (0.21), residues: 566 sheet: 0.71 (0.24), residues: 483 loop : 0.08 (0.24), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 86 TYR 0.025 0.001 TYR D 299 PHE 0.026 0.001 PHE D 307 TRP 0.012 0.001 TRP D 67 HIS 0.002 0.001 HIS D 267 Details of bonding type rmsd covalent geometry : bond 0.00268 (15183) covalent geometry : angle 0.55269 (20662) SS BOND : bond 0.00070 ( 6) SS BOND : angle 0.38628 ( 12) hydrogen bonds : bond 0.03692 ( 752) hydrogen bonds : angle 4.11365 ( 2427) link_ALPHA1-3 : bond 0.00915 ( 3) link_ALPHA1-3 : angle 1.64637 ( 9) link_ALPHA1-6 : bond 0.00977 ( 3) link_ALPHA1-6 : angle 1.57463 ( 9) link_BETA1-4 : bond 0.00396 ( 9) link_BETA1-4 : angle 1.46777 ( 27) link_NAG-ASN : bond 0.00179 ( 8) link_NAG-ASN : angle 1.58265 ( 24) *********************** 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 202 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 173 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 LYS cc_start: 0.9127 (mmtt) cc_final: 0.8633 (mmtp) REVERT: A 150 GLU cc_start: 0.9072 (tm-30) cc_final: 0.8801 (tm-30) REVERT: A 197 ARG cc_start: 0.8690 (ttp-110) cc_final: 0.8451 (mpt-90) REVERT: A 239 GLN cc_start: 0.8967 (tp40) cc_final: 0.8738 (tp40) REVERT: C 71 GLU cc_start: 0.8530 (pm20) cc_final: 0.8016 (pm20) REVERT: C 130 MET cc_start: 0.7147 (ttp) cc_final: 0.6573 (tmm) REVERT: C 177 GLU cc_start: 0.9141 (mt-10) cc_final: 0.8853 (mp0) REVERT: C 182 GLN cc_start: 0.8745 (tt0) cc_final: 0.8274 (tt0) REVERT: C 223 MET cc_start: 0.8897 (mmm) cc_final: 0.8116 (mtt) REVERT: D 9 MET cc_start: 0.8725 (mpp) cc_final: 0.8519 (mpp) REVERT: D 55 MET cc_start: 0.9297 (mtp) cc_final: 0.9046 (mmm) REVERT: D 215 LYS cc_start: 0.9244 (tttt) cc_final: 0.8955 (tptp) REVERT: E 141 ARG cc_start: 0.8740 (mpt-90) cc_final: 0.8370 (mmt90) REVERT: E 182 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7621 (mp0) REVERT: N 1 GLN cc_start: 0.9112 (pm20) cc_final: 0.8845 (pm20) REVERT: N 3 GLN cc_start: 0.8274 (mp10) cc_final: 0.7998 (mp10) REVERT: N 4 LEU cc_start: 0.8264 (tp) cc_final: 0.7847 (tt) REVERT: N 426 GLN cc_start: 0.8650 (tt0) cc_final: 0.8043 (tp-100) REVERT: N 433 GLU cc_start: 0.9060 (tt0) cc_final: 0.8770 (pt0) REVERT: N 449 ASP cc_start: 0.9018 (m-30) cc_final: 0.8575 (p0) REVERT: N 472 ASN cc_start: 0.8741 (t0) cc_final: 0.8482 (t0) outliers start: 29 outliers final: 20 residues processed: 191 average time/residue: 0.1155 time to fit residues: 32.7787 Evaluate side-chains 183 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 163 time to evaluate : 0.562 ------------------------------------------------------------------------------- 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 B residue 36 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain C residue 162 GLU Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 258 ASN Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain E residue 165 GLU Chi-restraints excluded: chain N residue 473 LEU 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 145 optimal weight: 8.9990 chunk 163 optimal weight: 5.9990 chunk 167 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 42 optimal weight: 0.4980 chunk 147 optimal weight: 0.3980 chunk 93 optimal weight: 0.8980 chunk 166 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 170 optimal weight: 20.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 HIS D 267 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.087221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.058388 restraints weight = 105056.566| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 5.30 r_work: 0.2696 rms_B_bonded: 5.16 restraints_weight: 2.0000 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2694 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2694 r_free = 0.2694 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2694 r_free = 0.2694 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2694 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.4818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15212 Z= 0.116 Angle : 0.559 11.547 20743 Z= 0.281 Chirality : 0.043 0.248 2391 Planarity : 0.003 0.043 2520 Dihedral : 5.768 53.153 2457 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.63 % Allowed : 11.65 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.46 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.20), residues: 1748 helix: 2.14 (0.21), residues: 566 sheet: 0.75 (0.24), residues: 481 loop : 0.08 (0.24), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 86 TYR 0.025 0.001 TYR D 299 PHE 0.022 0.001 PHE D 307 TRP 0.012 0.001 TRP D 67 HIS 0.003 0.001 HIS E 267 Details of bonding type rmsd covalent geometry : bond 0.00260 (15183) covalent geometry : angle 0.55297 (20662) SS BOND : bond 0.00063 ( 6) SS BOND : angle 0.35574 ( 12) hydrogen bonds : bond 0.03573 ( 752) hydrogen bonds : angle 4.06805 ( 2427) link_ALPHA1-3 : bond 0.00935 ( 3) link_ALPHA1-3 : angle 1.66109 ( 9) link_ALPHA1-6 : bond 0.01002 ( 3) link_ALPHA1-6 : angle 1.52190 ( 9) link_BETA1-4 : bond 0.00382 ( 9) link_BETA1-4 : angle 1.41857 ( 27) link_NAG-ASN : bond 0.00194 ( 8) link_NAG-ASN : angle 1.50718 ( 24) *********************** 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 196 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 170 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 GLU cc_start: 0.9095 (tm-30) cc_final: 0.8837 (tm-30) REVERT: A 197 ARG cc_start: 0.8726 (ttp-110) cc_final: 0.8455 (mpt-90) REVERT: A 239 GLN cc_start: 0.8962 (tp40) cc_final: 0.8723 (tp40) REVERT: C 71 GLU cc_start: 0.8529 (pm20) cc_final: 0.7939 (pm20) REVERT: C 130 MET cc_start: 0.7058 (ttp) cc_final: 0.6433 (tmm) REVERT: C 177 GLU cc_start: 0.9161 (mt-10) cc_final: 0.8864 (mp0) REVERT: C 182 GLN cc_start: 0.8747 (tt0) cc_final: 0.8262 (tt0) REVERT: C 223 MET cc_start: 0.8966 (mmm) cc_final: 0.8166 (mtt) REVERT: D 55 MET cc_start: 0.9270 (mtp) cc_final: 0.9044 (mmm) REVERT: D 215 LYS cc_start: 0.9239 (tttt) cc_final: 0.8926 (tptp) REVERT: E 141 ARG cc_start: 0.8763 (mpt-90) cc_final: 0.8378 (mmt90) REVERT: E 182 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7675 (mp0) REVERT: N 1 GLN cc_start: 0.9096 (pm20) cc_final: 0.8759 (pm20) REVERT: N 3 GLN cc_start: 0.8183 (mp10) cc_final: 0.7950 (mp10) REVERT: N 4 LEU cc_start: 0.8233 (tp) cc_final: 0.7890 (tt) REVERT: N 426 GLN cc_start: 0.8610 (tt0) cc_final: 0.8038 (tp-100) REVERT: N 433 GLU cc_start: 0.9028 (tt0) cc_final: 0.8740 (pt0) REVERT: N 449 ASP cc_start: 0.9027 (m-30) cc_final: 0.8592 (p0) REVERT: N 465 THR cc_start: 0.8795 (m) cc_final: 0.8328 (p) REVERT: N 474 LYS cc_start: 0.8564 (mmmm) cc_final: 0.8161 (tmtt) outliers start: 26 outliers final: 22 residues processed: 186 average time/residue: 0.1057 time to fit residues: 29.8244 Evaluate side-chains 184 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 233 MET 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 B residue 36 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 253 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 42 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 145 LEU Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain E residue 165 GLU 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 28 optimal weight: 3.9990 chunk 144 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 160 optimal weight: 0.7980 chunk 18 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 98 optimal weight: 0.2980 chunk 113 optimal weight: 6.9990 chunk 81 optimal weight: 8.9990 chunk 44 optimal weight: 20.0000 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.086246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.058146 restraints weight = 70720.377| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 4.41 r_work: 0.2714 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2714 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2714 r_free = 0.2714 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2714 r_free = 0.2714 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2714 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 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 : 0.003 0.036 15212 Z= 0.136 Angle : 0.565 11.706 20743 Z= 0.285 Chirality : 0.043 0.250 2391 Planarity : 0.003 0.040 2520 Dihedral : 5.548 48.762 2457 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.75 % Allowed : 11.52 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.46 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.20), residues: 1748 helix: 2.16 (0.21), residues: 566 sheet: 0.71 (0.24), residues: 488 loop : 0.07 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 86 TYR 0.027 0.001 TYR D 299 PHE 0.020 0.001 PHE D 306 TRP 0.011 0.001 TRP D 67 HIS 0.008 0.001 HIS D 191 Details of bonding type rmsd covalent geometry : bond 0.00310 (15183) covalent geometry : angle 0.55944 (20662) SS BOND : bond 0.00096 ( 6) SS BOND : angle 0.35963 ( 12) hydrogen bonds : bond 0.03639 ( 752) hydrogen bonds : angle 4.06289 ( 2427) link_ALPHA1-3 : bond 0.00830 ( 3) link_ALPHA1-3 : angle 1.62912 ( 9) link_ALPHA1-6 : bond 0.01007 ( 3) link_ALPHA1-6 : angle 1.44119 ( 9) link_BETA1-4 : bond 0.00365 ( 9) link_BETA1-4 : angle 1.47772 ( 27) link_NAG-ASN : bond 0.00139 ( 8) link_NAG-ASN : angle 1.60831 ( 24) *********************** 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: 28 poor density : 166 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 GLU cc_start: 0.9057 (tm-30) cc_final: 0.8796 (tm-30) REVERT: A 197 ARG cc_start: 0.8651 (ttp-110) cc_final: 0.8420 (mpt-90) REVERT: A 239 GLN cc_start: 0.8929 (tp40) cc_final: 0.8688 (tp40) REVERT: A 276 MET cc_start: 0.9573 (mmm) cc_final: 0.9328 (tpp) REVERT: B 26 ARG cc_start: 0.8506 (mtm180) cc_final: 0.8276 (mtm-85) REVERT: C 71 GLU cc_start: 0.8511 (pm20) cc_final: 0.7879 (pm20) REVERT: C 130 MET cc_start: 0.7131 (ttp) cc_final: 0.6476 (tmm) REVERT: C 177 GLU cc_start: 0.9121 (mt-10) cc_final: 0.8848 (mp0) REVERT: C 182 GLN cc_start: 0.8758 (tt0) cc_final: 0.8282 (tt0) REVERT: C 223 MET cc_start: 0.8902 (mmm) cc_final: 0.8147 (mtt) REVERT: D 165 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.7183 (pp20) REVERT: D 215 LYS cc_start: 0.9226 (tttt) cc_final: 0.8926 (tptp) REVERT: E 132 THR cc_start: 0.9339 (OUTLIER) cc_final: 0.9082 (t) REVERT: E 182 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7621 (mp0) REVERT: N 1 GLN cc_start: 0.9054 (pm20) cc_final: 0.8754 (pm20) REVERT: N 3 GLN cc_start: 0.8216 (mp10) cc_final: 0.8012 (mp10) REVERT: N 4 LEU cc_start: 0.8235 (tp) cc_final: 0.7877 (tt) REVERT: N 426 GLN cc_start: 0.8554 (tt0) cc_final: 0.8061 (tp-100) REVERT: N 433 GLU cc_start: 0.9052 (tt0) cc_final: 0.8774 (pt0) REVERT: N 449 ASP cc_start: 0.9015 (m-30) cc_final: 0.8603 (p0) REVERT: N 465 THR cc_start: 0.8736 (m) cc_final: 0.8198 (p) outliers start: 28 outliers final: 20 residues processed: 185 average time/residue: 0.1168 time to fit residues: 32.2988 Evaluate side-chains 184 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 0.432 ------------------------------------------------------------------------------- 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 301 SER Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 253 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 42 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 145 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 132 THR Chi-restraints excluded: chain E residue 165 GLU Chi-restraints excluded: chain N residue 405 LEU 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 26 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 81 optimal weight: 7.9990 chunk 152 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 42 optimal weight: 20.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 HIS D 217 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.086216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.057130 restraints weight = 93356.672| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 5.12 r_work: 0.2675 rms_B_bonded: 5.05 restraints_weight: 2.0000 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2678 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2678 r_free = 0.2678 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2678 r_free = 0.2678 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2678 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.5106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15212 Z= 0.142 Angle : 0.593 15.730 20743 Z= 0.296 Chirality : 0.043 0.248 2391 Planarity : 0.003 0.041 2520 Dihedral : 5.411 46.191 2457 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.63 % Allowed : 12.09 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.46 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.20), residues: 1748 helix: 2.16 (0.21), residues: 564 sheet: 0.69 (0.24), residues: 490 loop : 0.10 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 86 TYR 0.026 0.001 TYR D 299 PHE 0.031 0.001 PHE N 455 TRP 0.011 0.001 TRP D 67 HIS 0.009 0.001 HIS D 191 Details of bonding type rmsd covalent geometry : bond 0.00325 (15183) covalent geometry : angle 0.58731 (20662) SS BOND : bond 0.00071 ( 6) SS BOND : angle 0.34093 ( 12) hydrogen bonds : bond 0.03670 ( 752) hydrogen bonds : angle 4.07917 ( 2427) link_ALPHA1-3 : bond 0.00830 ( 3) link_ALPHA1-3 : angle 1.61882 ( 9) link_ALPHA1-6 : bond 0.01028 ( 3) link_ALPHA1-6 : angle 1.42039 ( 9) link_BETA1-4 : bond 0.00358 ( 9) link_BETA1-4 : angle 1.46510 ( 27) link_NAG-ASN : bond 0.00138 ( 8) link_NAG-ASN : angle 1.60731 ( 24) *********************** 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: 26 poor density : 164 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 GLU cc_start: 0.9099 (tm-30) cc_final: 0.8848 (tm-30) REVERT: A 197 ARG cc_start: 0.8684 (ttp-110) cc_final: 0.8446 (mpt-90) REVERT: A 239 GLN cc_start: 0.8963 (tp40) cc_final: 0.8716 (tp40) REVERT: A 276 MET cc_start: 0.9599 (mmm) cc_final: 0.9380 (tpp) REVERT: B 26 ARG cc_start: 0.8532 (mtm180) cc_final: 0.8284 (mtm-85) REVERT: C 71 GLU cc_start: 0.8576 (pm20) cc_final: 0.7900 (pm20) REVERT: C 130 MET cc_start: 0.7122 (ttp) cc_final: 0.6478 (tmm) REVERT: C 177 GLU cc_start: 0.9149 (mt-10) cc_final: 0.8881 (mp0) REVERT: C 223 MET cc_start: 0.8982 (mmm) cc_final: 0.8230 (mtt) REVERT: D 165 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7244 (pp20) REVERT: D 215 LYS cc_start: 0.9269 (tttt) cc_final: 0.8951 (tttm) REVERT: D 224 GLN cc_start: 0.8574 (tp40) cc_final: 0.8292 (tp40) REVERT: E 132 THR cc_start: 0.9348 (OUTLIER) cc_final: 0.9092 (t) REVERT: E 155 GLU cc_start: 0.8898 (tt0) cc_final: 0.8622 (mt-10) REVERT: E 182 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7659 (mp0) REVERT: N 1 GLN cc_start: 0.9109 (pm20) cc_final: 0.8844 (pm20) REVERT: N 4 LEU cc_start: 0.8158 (tp) cc_final: 0.7864 (tt) REVERT: N 426 GLN cc_start: 0.8549 (tt0) cc_final: 0.8063 (tp-100) REVERT: N 433 GLU cc_start: 0.9074 (tt0) cc_final: 0.8795 (pt0) REVERT: N 449 ASP cc_start: 0.9062 (m-30) cc_final: 0.8623 (p0) REVERT: N 465 THR cc_start: 0.8623 (m) cc_final: 0.8021 (p) outliers start: 26 outliers final: 20 residues processed: 183 average time/residue: 0.1030 time to fit residues: 28.2726 Evaluate side-chains 183 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 161 time to evaluate : 0.503 ------------------------------------------------------------------------------- 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 301 SER 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 253 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 42 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 145 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 132 THR Chi-restraints excluded: chain E residue 165 GLU Chi-restraints excluded: chain N residue 405 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 153 optimal weight: 0.7980 chunk 160 optimal weight: 0.0870 chunk 39 optimal weight: 0.0970 chunk 14 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 146 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 chunk 167 optimal weight: 9.9990 chunk 117 optimal weight: 7.9990 overall best weight: 0.5356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.087241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.059255 restraints weight = 63835.263| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 4.28 r_work: 0.2746 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2750 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2750 r_free = 0.2750 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2750 r_free = 0.2750 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2750 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.5197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 15212 Z= 0.112 Angle : 0.596 16.436 20743 Z= 0.295 Chirality : 0.043 0.243 2391 Planarity : 0.003 0.041 2520 Dihedral : 5.200 42.594 2457 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.57 % Allowed : 12.02 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.46 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.20), residues: 1748 helix: 2.16 (0.21), residues: 564 sheet: 0.73 (0.24), residues: 488 loop : 0.18 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 86 TYR 0.023 0.001 TYR D 299 PHE 0.026 0.001 PHE D 306 TRP 0.012 0.001 TRP D 67 HIS 0.009 0.001 HIS D 191 Details of bonding type rmsd covalent geometry : bond 0.00254 (15183) covalent geometry : angle 0.59116 (20662) SS BOND : bond 0.00085 ( 6) SS BOND : angle 0.36193 ( 12) hydrogen bonds : bond 0.03433 ( 752) hydrogen bonds : angle 4.02099 ( 2427) link_ALPHA1-3 : bond 0.00827 ( 3) link_ALPHA1-3 : angle 1.56966 ( 9) link_ALPHA1-6 : bond 0.01084 ( 3) link_ALPHA1-6 : angle 1.35169 ( 9) link_BETA1-4 : bond 0.00399 ( 9) link_BETA1-4 : angle 1.35645 ( 27) link_NAG-ASN : bond 0.00202 ( 8) link_NAG-ASN : angle 1.43256 ( 24) ********************** 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 194 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 169 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.8633 (tp30) cc_final: 0.8294 (mp0) REVERT: A 150 GLU cc_start: 0.9036 (tm-30) cc_final: 0.8808 (tm-30) REVERT: A 197 ARG cc_start: 0.8636 (ttp-110) cc_final: 0.8428 (mpt-90) REVERT: A 239 GLN cc_start: 0.8930 (tp40) cc_final: 0.8683 (tp40) REVERT: A 276 MET cc_start: 0.9563 (mmm) cc_final: 0.9356 (tpp) REVERT: B 26 ARG cc_start: 0.8541 (mtm180) cc_final: 0.8313 (mtm-85) REVERT: C 71 GLU cc_start: 0.8561 (pm20) cc_final: 0.7897 (pm20) REVERT: C 130 MET cc_start: 0.7047 (ttp) cc_final: 0.6489 (tmm) REVERT: C 177 GLU cc_start: 0.9114 (mt-10) cc_final: 0.8840 (mp0) REVERT: C 223 MET cc_start: 0.8861 (mmm) cc_final: 0.8052 (mtt) REVERT: D 165 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.7122 (pp20) REVERT: D 215 LYS cc_start: 0.9247 (tttt) cc_final: 0.8918 (tttm) REVERT: D 224 GLN cc_start: 0.8513 (tp40) cc_final: 0.8225 (tp40) REVERT: E 132 THR cc_start: 0.9299 (OUTLIER) cc_final: 0.9022 (t) REVERT: E 155 GLU cc_start: 0.8809 (tt0) cc_final: 0.8543 (mt-10) REVERT: E 182 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7625 (mp0) REVERT: N 1 GLN cc_start: 0.8924 (pm20) cc_final: 0.8655 (pm20) REVERT: N 4 LEU cc_start: 0.8064 (tp) cc_final: 0.7843 (tt) REVERT: N 426 GLN cc_start: 0.8458 (tt0) cc_final: 0.8051 (tp-100) REVERT: N 433 GLU cc_start: 0.9035 (tt0) cc_final: 0.8774 (pt0) REVERT: N 449 ASP cc_start: 0.9054 (m-30) cc_final: 0.8639 (p0) REVERT: N 465 THR cc_start: 0.8635 (m) cc_final: 0.8044 (p) REVERT: N 474 LYS cc_start: 0.8447 (mmmt) cc_final: 0.7986 (tptp) outliers start: 25 outliers final: 19 residues processed: 185 average time/residue: 0.1064 time to fit residues: 29.8697 Evaluate side-chains 184 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 163 time to evaluate : 0.362 ------------------------------------------------------------------------------- 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 B residue 36 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 253 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 42 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 145 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 132 THR Chi-restraints excluded: chain N residue 457 ILE 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 63 optimal weight: 1.9990 chunk 160 optimal weight: 5.9990 chunk 65 optimal weight: 20.0000 chunk 111 optimal weight: 10.0000 chunk 91 optimal weight: 0.8980 chunk 44 optimal weight: 20.0000 chunk 112 optimal weight: 0.5980 chunk 19 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 140 optimal weight: 4.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 HIS B 303 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.084570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.057207 restraints weight = 79376.700| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 4.56 r_work: 0.2694 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2694 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2694 r_free = 0.2694 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2694 r_free = 0.2694 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2694 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.5343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 15212 Z= 0.211 Angle : 0.638 14.654 20743 Z= 0.319 Chirality : 0.045 0.245 2391 Planarity : 0.004 0.040 2520 Dihedral : 5.348 42.661 2457 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.63 % Allowed : 12.34 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.20), residues: 1748 helix: 2.07 (0.21), residues: 560 sheet: 0.63 (0.24), residues: 485 loop : 0.05 (0.24), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 86 TYR 0.033 0.002 TYR B 299 PHE 0.041 0.002 PHE N 455 TRP 0.010 0.001 TRP E 67 HIS 0.009 0.001 HIS D 191 Details of bonding type rmsd covalent geometry : bond 0.00489 (15183) covalent geometry : angle 0.63133 (20662) SS BOND : bond 0.00073 ( 6) SS BOND : angle 0.37624 ( 12) hydrogen bonds : bond 0.04002 ( 752) hydrogen bonds : angle 4.19145 ( 2427) link_ALPHA1-3 : bond 0.00710 ( 3) link_ALPHA1-3 : angle 1.64272 ( 9) link_ALPHA1-6 : bond 0.00943 ( 3) link_ALPHA1-6 : angle 1.33993 ( 9) link_BETA1-4 : bond 0.00357 ( 9) link_BETA1-4 : angle 1.61827 ( 27) link_NAG-ASN : bond 0.00193 ( 8) link_NAG-ASN : angle 1.88054 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3776.64 seconds wall clock time: 65 minutes 30.92 seconds (3930.92 seconds total)