Starting phenix.real_space_refine on Tue Dec 31 06:41:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qnb_14073/12_2024/7qnb_14073.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qnb_14073/12_2024/7qnb_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_14073/12_2024/7qnb_14073.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qnb_14073/12_2024/7qnb_14073.map" model { file = "/net/cci-nas-00/data/ceres_data/7qnb_14073/12_2024/7qnb_14073.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qnb_14073/12_2024/7qnb_14073.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 82 5.16 5 C 9639 2.51 5 N 2383 2.21 5 O 2689 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 14793 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2701 Classifications: {'peptide': 328} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 314} Chain breaks: 1 Chain: "B" Number of atoms: 2714 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 330, 2709 Classifications: {'peptide': 330} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 315} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 330, 2709 Classifications: {'peptide': 330} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 315} Chain breaks: 1 bond proxies already assigned to first conformer: 2775 Chain: "C" Number of atoms: 2701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2701 Classifications: {'peptide': 328} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 314} Chain breaks: 1 Chain: "D" Number of atoms: 2721 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 330, 2709 Classifications: {'peptide': 330} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 315} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 330, 2709 Classifications: {'peptide': 330} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 315} Chain breaks: 1 bond proxies already assigned to first conformer: 2767 Chain: "E" Number of atoms: 2714 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 330, 2709 Classifications: {'peptide': 330} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 315} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 330, 2709 Classifications: {'peptide': 330} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 315} Chain breaks: 1 bond proxies already assigned to first conformer: 2775 Chain: "N" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATYR D 66 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR D 66 " occ=0.50 Time building chain proxies: 12.52, per 1000 atoms: 0.85 Number of scatterers: 14793 At special positions: 0 Unit cell: (119.168, 92.288, 128.128, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 82 16.00 O 2689 8.00 N 2383 7.00 C 9639 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 151 " - pdb=" SG CYS A 165 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 150 " distance=2.03 Simple disulfide: pdb=" SG CYS C 151 " - pdb=" SG CYS C 165 " distance=2.03 Simple disulfide: pdb=" SG CYS D 136 " - pdb=" SG CYS D 150 " distance=2.03 Simple disulfide: pdb=" SG CYS E 136 " - pdb=" SG CYS E 150 " distance=2.03 Simple disulfide: pdb=" SG CYS N 409 " - pdb=" SG CYS N 483 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA F 3 " - " MAN F 4 " " BMA G 3 " - " MAN G 4 " " BMA H 3 " - " MAN H 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " " BMA G 3 " - " MAN G 5 " " BMA H 3 " - " MAN H 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG b 1 " - " NAG b 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " NAG-ASN " NAG A 501 " - " ASN A 208 " " NAG C 501 " - " ASN C 208 " " NAG F 1 " - " ASN B 149 " " NAG G 1 " - " ASN D 149 " " NAG H 1 " - " ASN E 149 " " NAG b 1 " - " ASN B 80 " " NAG d 1 " - " ASN D 80 " " NAG e 1 " - " ASN E 80 " Time building additional restraints: 4.22 Conformation dependent library (CDL) restraints added in 3.2 seconds 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3360 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 20 sheets defined 39.1% alpha, 40.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.93 Creating SS restraints... Processing helix chain 'A' and resid 27 through 36 Processing helix chain 'A' and resid 85 through 88 Processing helix chain 'A' and resid 99 through 106 removed outlier: 3.532A pdb=" N GLY A 104 " --> pdb=" O ASN A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 240 Processing helix chain 'A' and resid 240 through 257 removed outlier: 3.956A pdb=" N SER A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N PHE A 255 " --> pdb=" O SER A 251 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N TRP A 256 " --> pdb=" O TRP A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 284 removed outlier: 3.568A pdb=" N ILE A 282 " --> pdb=" O THR A 278 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ARG A 284 " --> pdb=" O SER A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 323 removed outlier: 3.503A pdb=" N LEU A 311 " --> pdb=" O VAL A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 435 removed outlier: 3.600A pdb=" N ILE A 416 " --> pdb=" O SER A 412 " (cutoff:3.500A) Proline residue: A 419 - end of helix Processing helix chain 'B' and resid 8 through 21 Processing helix chain 'B' and resid 70 through 73 Processing helix chain 'B' and resid 84 through 91 removed outlier: 3.542A pdb=" N ASP B 89 " --> pdb=" O ARG B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 173 Processing helix chain 'B' and resid 218 through 225 Processing helix chain 'B' and resid 225 through 242 removed outlier: 3.502A pdb=" N VAL B 238 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N SER B 239 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N PHE B 240 " --> pdb=" O SER B 236 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N TRP B 241 " --> pdb=" O TRP B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 269 Processing helix chain 'B' and resid 270 through 272 No H-bonds generated for 'chain 'B' and resid 270 through 272' Processing helix chain 'B' and resid 279 through 307 Processing helix chain 'B' and resid 313 through 447 Proline residue: B 432 - end of helix Processing helix chain 'C' and resid 28 through 36 Processing helix chain 'C' and resid 85 through 88 Processing helix chain 'C' and resid 99 through 106 removed outlier: 3.533A pdb=" N GLY C 104 " --> pdb=" O ASN C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 240 Processing helix chain 'C' and resid 240 through 257 removed outlier: 3.955A pdb=" N SER C 254 " --> pdb=" O LEU C 250 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N PHE C 255 " --> pdb=" O SER C 251 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N TRP C 256 " --> pdb=" O TRP C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 284 removed outlier: 3.568A pdb=" N ILE C 282 " --> pdb=" O THR C 278 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG C 284 " --> pdb=" O SER C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 323 removed outlier: 3.504A pdb=" N LEU C 311 " --> pdb=" O VAL C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 435 removed outlier: 3.600A pdb=" N ILE C 416 " --> pdb=" O SER C 412 " (cutoff:3.500A) Proline residue: C 419 - end of helix Processing helix chain 'D' and resid 8 through 21 Processing helix chain 'D' and resid 70 through 73 Processing helix chain 'D' and resid 84 through 91 removed outlier: 3.542A pdb=" N ASP D 89 " --> pdb=" O ARG D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 173 Processing helix chain 'D' and resid 218 through 225 Processing helix chain 'D' and resid 225 through 242 removed outlier: 4.359A pdb=" N SER D 239 " --> pdb=" O LEU D 235 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N PHE D 240 " --> pdb=" O SER D 236 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N TRP D 241 " --> pdb=" O TRP D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 269 Processing helix chain 'D' and resid 270 through 272 No H-bonds generated for 'chain 'D' and resid 270 through 272' Processing helix chain 'D' and resid 279 through 307 Processing helix chain 'D' and resid 313 through 447 Proline residue: D 432 - end of helix Processing helix chain 'E' and resid 8 through 21 Processing helix chain 'E' and resid 70 through 73 Processing helix chain 'E' and resid 84 through 91 removed outlier: 3.542A pdb=" N ASP E 89 " --> pdb=" O ARG E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 173 Processing helix chain 'E' and resid 218 through 225 Processing helix chain 'E' and resid 225 through 242 removed outlier: 3.501A pdb=" N VAL E 238 " --> pdb=" O ILE E 234 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N SER E 239 " --> pdb=" O LEU E 235 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N PHE E 240 " --> pdb=" O SER E 236 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N TRP E 241 " --> pdb=" O TRP E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 269 Processing helix chain 'E' and resid 270 through 272 No H-bonds generated for 'chain 'E' and resid 270 through 272' Processing helix chain 'E' and resid 279 through 307 Processing helix chain 'E' and resid 313 through 447 Proline residue: E 432 - end of helix Processing helix chain 'N' and resid 415 through 418 Processing helix chain 'N' and resid 474 through 478 removed outlier: 3.643A pdb=" N THR N 478 " --> pdb=" O PRO N 475 " (cutoff:3.500A) Processing helix chain 'N' and resid 495 through 499 Processing sheet with id=AA1, first strand: chain 'A' and resid 95 through 98 removed outlier: 4.262A pdb=" N LEU A 131 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ARG A 138 " --> pdb=" O TRP A 134 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS A 118 " --> pdb=" O ASP A 148 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N GLU A 150 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N SER A 116 " --> pdb=" O GLU A 150 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 95 through 98 removed outlier: 4.262A pdb=" N LEU A 131 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ARG A 138 " --> pdb=" O TRP A 134 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLU A 71 " --> pdb=" O PRO A 64 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N THR A 73 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ILE A 62 " --> pdb=" O THR A 73 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ASP A 75 " --> pdb=" O ASN A 60 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR A 58 " --> pdb=" O PHE A 77 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N TYR A 83 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU A 52 " --> pdb=" O TYR A 83 " (cutoff:3.500A) removed outlier: 9.686A pdb=" N THR A 51 " --> pdb=" O TYR A 181 " (cutoff:3.500A) removed outlier: 10.840A pdb=" N TRP A 183 " --> pdb=" O THR A 51 " (cutoff:3.500A) removed outlier: 9.036A pdb=" N ILE A 53 " --> pdb=" O TRP A 183 " (cutoff:3.500A) removed outlier: 10.114A pdb=" N ARG A 185 " --> pdb=" O ILE A 53 " (cutoff:3.500A) removed outlier: 10.731A pdb=" N THR A 55 " --> pdb=" O ARG A 185 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N SER A 187 " --> pdb=" O THR A 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 111 through 113 removed outlier: 4.644A pdb=" N SER A 171 " --> pdb=" O VAL A 221 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL A 221 " --> pdb=" O SER A 171 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 111 through 113 removed outlier: 4.644A pdb=" N SER A 171 " --> pdb=" O VAL A 221 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL A 221 " --> pdb=" O SER A 171 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY A 205 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N SER A 230 " --> pdb=" O PHE A 203 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N PHE A 203 " --> pdb=" O SER A 230 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 82 through 83 removed outlier: 4.469A pdb=" N ILE B 116 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ASP B 56 " --> pdb=" O MET B 49 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N MET B 49 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N CYS B 37 " --> pdb=" O ARG B 68 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 101 through 106 removed outlier: 6.679A pdb=" N THR B 133 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N SER B 104 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N THR B 131 " --> pdb=" O SER B 104 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N VAL B 106 " --> pdb=" O ARG B 129 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N ARG B 129 " --> pdb=" O VAL B 106 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ASP B 56 " --> pdb=" O MET B 49 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N MET B 49 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N CYS B 37 " --> pdb=" O ARG B 68 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.952A pdb=" N SER B 156 " --> pdb=" O PRO B 206 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU B 190 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LYS B 215 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N ILE B 188 " --> pdb=" O LYS B 215 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 95 through 98 removed outlier: 4.262A pdb=" N LEU C 131 " --> pdb=" O LEU C 98 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ARG C 138 " --> pdb=" O TRP C 134 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS C 118 " --> pdb=" O ASP C 148 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLU C 150 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N SER C 116 " --> pdb=" O GLU C 150 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 95 through 98 removed outlier: 4.262A pdb=" N LEU C 131 " --> pdb=" O LEU C 98 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ARG C 138 " --> pdb=" O TRP C 134 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N GLU C 71 " --> pdb=" O PRO C 64 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N THR C 73 " --> pdb=" O ILE C 62 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ILE C 62 " --> pdb=" O THR C 73 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ASP C 75 " --> pdb=" O ASN C 60 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR C 58 " --> pdb=" O PHE C 77 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N TYR C 83 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU C 52 " --> pdb=" O TYR C 83 " (cutoff:3.500A) removed outlier: 9.686A pdb=" N THR C 51 " --> pdb=" O TYR C 181 " (cutoff:3.500A) removed outlier: 10.841A pdb=" N TRP C 183 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 9.036A pdb=" N ILE C 53 " --> pdb=" O TRP C 183 " (cutoff:3.500A) removed outlier: 10.114A pdb=" N ARG C 185 " --> pdb=" O ILE C 53 " (cutoff:3.500A) removed outlier: 10.731A pdb=" N THR C 55 " --> pdb=" O ARG C 185 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N SER C 187 " --> pdb=" O THR C 55 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 111 through 113 removed outlier: 4.644A pdb=" N SER C 171 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL C 221 " --> pdb=" O SER C 171 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 111 through 113 removed outlier: 4.644A pdb=" N SER C 171 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL C 221 " --> pdb=" O SER C 171 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY C 205 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N SER C 230 " --> pdb=" O PHE C 203 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N PHE C 203 " --> pdb=" O SER C 230 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 82 through 83 removed outlier: 4.468A pdb=" N ILE D 116 " --> pdb=" O LEU D 83 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ASP D 56 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N MET D 49 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N THR D 58 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ILE D 47 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N THR D 60 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ARG D 68 " --> pdb=" O CYS D 37 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N CYS D 37 " --> pdb=" O ARG D 68 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 101 through 106 removed outlier: 6.680A pdb=" N THR D 133 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N SER D 104 " --> pdb=" O THR D 131 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N THR D 131 " --> pdb=" O SER D 104 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N VAL D 106 " --> pdb=" O ARG D 129 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N ARG D 129 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ASP D 56 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N MET D 49 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N THR D 58 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ILE D 47 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N THR D 60 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ARG D 68 " --> pdb=" O CYS D 37 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N CYS D 37 " --> pdb=" O ARG D 68 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 96 through 98 removed outlier: 3.952A pdb=" N SER D 156 " --> pdb=" O PRO D 206 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU D 190 " --> pdb=" O ARG D 213 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LYS D 215 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ILE D 188 " --> pdb=" O LYS D 215 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 82 through 83 removed outlier: 4.468A pdb=" N ILE E 116 " --> pdb=" O LEU E 83 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ASP E 56 " --> pdb=" O MET E 49 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N MET E 49 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N THR E 58 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ILE E 47 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THR E 60 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ARG E 68 " --> pdb=" O CYS E 37 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N CYS E 37 " --> pdb=" O ARG E 68 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 101 through 106 removed outlier: 6.679A pdb=" N THR E 133 " --> pdb=" O LYS E 102 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N SER E 104 " --> pdb=" O THR E 131 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N THR E 131 " --> pdb=" O SER E 104 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N VAL E 106 " --> pdb=" O ARG E 129 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N ARG E 129 " --> pdb=" O VAL E 106 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ASP E 56 " --> pdb=" O MET E 49 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N MET E 49 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N THR E 58 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ILE E 47 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THR E 60 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ARG E 68 " --> pdb=" O CYS E 37 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N CYS E 37 " --> pdb=" O ARG E 68 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 96 through 98 removed outlier: 3.951A pdb=" N SER E 156 " --> pdb=" O PRO E 206 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU E 190 " --> pdb=" O ARG E 213 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LYS E 215 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ILE E 188 " --> pdb=" O LYS E 215 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 2 through 7 removed outlier: 3.557A pdb=" N THR N 465 " --> pdb=" O ASP N 460 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 445 through 447 removed outlier: 6.551A pdb=" N TRP N 423 " --> pdb=" O VAL N 435 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ALA N 437 " --> pdb=" O MET N 421 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N MET N 421 " --> pdb=" O ALA N 437 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TYR N 501 " --> pdb=" O ALA N 485 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 445 through 447 removed outlier: 6.551A pdb=" N TRP N 423 " --> pdb=" O VAL N 435 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ALA N 437 " --> pdb=" O MET N 421 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N MET N 421 " --> pdb=" O ALA N 437 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL N 508 " --> pdb=" O ALA N 479 " (cutoff:3.500A) 848 hydrogen bonds defined for protein. 2427 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.55 Time building geometry restraints manager: 4.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4481 1.34 - 1.46: 3821 1.46 - 1.58: 6741 1.58 - 1.69: 0 1.69 - 1.81: 140 Bond restraints: 15183 Sorted by residual: bond pdb=" CG ABU B 501 " pdb=" CD ABU B 501 " ideal model delta sigma weight residual 1.540 1.500 0.040 2.00e-02 2.50e+03 3.91e+00 bond pdb=" C1 MAN F 4 " pdb=" O5 MAN F 4 " ideal model delta sigma weight residual 1.399 1.429 -0.030 2.00e-02 2.50e+03 2.19e+00 bond pdb=" C1 MAN G 5 " pdb=" O5 MAN G 5 " ideal model delta sigma weight residual 1.399 1.428 -0.029 2.00e-02 2.50e+03 2.15e+00 bond pdb=" C1 MAN H 5 " pdb=" O5 MAN H 5 " ideal model delta sigma weight residual 1.399 1.428 -0.029 2.00e-02 2.50e+03 2.13e+00 bond pdb=" C1 MAN F 5 " pdb=" O5 MAN F 5 " ideal model delta sigma weight residual 1.399 1.428 -0.029 2.00e-02 2.50e+03 2.05e+00 ... (remaining 15178 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 20333 1.46 - 2.91: 255 2.91 - 4.37: 47 4.37 - 5.83: 23 5.83 - 7.28: 4 Bond angle restraints: 20662 Sorted by residual: angle pdb=" CG ABU B 501 " pdb=" CD ABU B 501 " pdb=" OE2 ABU B 501 " ideal model delta sigma weight residual 115.90 123.18 -7.28 3.00e+00 1.11e-01 5.89e+00 angle pdb=" C3 BMA H 3 " pdb=" C2 BMA H 3 " pdb=" O2 BMA H 3 " ideal model delta sigma weight residual 112.95 106.61 6.34 3.00e+00 1.11e-01 4.47e+00 angle pdb=" C3 BMA F 3 " pdb=" C2 BMA F 3 " pdb=" O2 BMA F 3 " ideal model delta sigma weight residual 112.95 106.69 6.26 3.00e+00 1.11e-01 4.35e+00 angle pdb=" C3 BMA G 3 " pdb=" C2 BMA G 3 " pdb=" O2 BMA G 3 " ideal model delta sigma weight residual 112.95 106.71 6.24 3.00e+00 1.11e-01 4.33e+00 angle pdb=" CA TYR E 299 " pdb=" CB TYR E 299 " pdb=" CG TYR E 299 " ideal model delta sigma weight residual 113.90 110.22 3.68 1.80e+00 3.09e-01 4.17e+00 ... (remaining 20657 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.76: 8891 21.76 - 43.52: 205 43.52 - 65.28: 28 65.28 - 87.04: 22 87.04 - 108.80: 14 Dihedral angle restraints: 9160 sinusoidal: 3922 harmonic: 5238 Sorted by residual: dihedral pdb=" O4 BMA H 3 " pdb=" C4 BMA H 3 " pdb=" C5 BMA H 3 " pdb=" O5 BMA H 3 " ideal model delta sinusoidal sigma weight residual 288.71 179.91 108.80 1 3.00e+01 1.11e-03 1.41e+01 dihedral pdb=" O4 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C5 BMA G 3 " pdb=" O5 BMA G 3 " ideal model delta sinusoidal sigma weight residual 288.71 179.93 108.78 1 3.00e+01 1.11e-03 1.41e+01 dihedral pdb=" O4 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C5 BMA F 3 " pdb=" O5 BMA F 3 " ideal model delta sinusoidal sigma weight residual -71.29 -178.52 107.23 1 3.00e+01 1.11e-03 1.38e+01 ... (remaining 9157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2049 0.056 - 0.113: 315 0.113 - 0.169: 18 0.169 - 0.225: 5 0.225 - 0.282: 4 Chirality restraints: 2391 Sorted by residual: chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-02 2.50e+03 9.00e+01 chirality pdb=" C1 BMA G 3 " pdb=" O4 NAG G 2 " pdb=" C2 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.25e+01 chirality pdb=" C1 BMA H 3 " pdb=" O4 NAG H 2 " pdb=" C2 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.19e+01 ... (remaining 2388 not shown) Planarity restraints: 2528 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN D 65 " -0.006 2.00e-02 2.50e+03 1.12e-02 1.25e+00 pdb=" C GLN D 65 " 0.019 2.00e-02 2.50e+03 pdb=" O GLN D 65 " -0.007 2.00e-02 2.50e+03 pdb=" N BTYR D 66 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR D 143 " -0.018 5.00e-02 4.00e+02 2.65e-02 1.13e+00 pdb=" N PRO D 144 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO D 144 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 144 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR E 143 " -0.017 5.00e-02 4.00e+02 2.64e-02 1.11e+00 pdb=" N PRO E 144 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO E 144 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO E 144 " -0.014 5.00e-02 4.00e+02 ... (remaining 2525 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2576 2.77 - 3.30: 14013 3.30 - 3.84: 25223 3.84 - 4.37: 30662 4.37 - 4.90: 52258 Nonbonded interactions: 124732 Sorted by model distance: nonbonded pdb=" O VAL A 248 " pdb=" OG SER A 251 " model vdw 2.241 3.040 nonbonded pdb=" O VAL C 248 " pdb=" OG SER C 251 " model vdw 2.242 3.040 nonbonded pdb=" O ALA D 252 " pdb=" OG1 THR D 256 " model vdw 2.270 3.040 nonbonded pdb=" O ALA B 252 " pdb=" OG1 THR B 256 " model vdw 2.270 3.040 nonbonded pdb=" O ALA E 252 " pdb=" OG1 THR E 256 " model vdw 2.271 3.040 ... (remaining 124727 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = (chain 'B' and (resid 7 through 43 or resid 45 through 65 or resid 67 through 44 \ 7)) selection = (chain 'D' and (resid 7 through 43 or resid 45 through 65 or resid 67 through 44 \ 7)) selection = (chain 'E' and (resid 7 through 43 or resid 45 through 65 or resid 67 through 44 \ 7)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'b' selection = chain 'd' selection = chain 'e' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.520 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: 0.020 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 40.860 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.670 ------------------------------------------------------------------------------- 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 15183 Z= 0.161 Angle : 0.457 7.284 20662 Z= 0.213 Chirality : 0.042 0.282 2391 Planarity : 0.003 0.027 2520 Dihedral : 11.197 108.803 5782 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.56 % Allowed : 3.32 % Favored : 96.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.46 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.21), residues: 1748 helix: 2.34 (0.22), residues: 559 sheet: 1.18 (0.25), residues: 468 loop : 0.51 (0.25), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 241 HIS 0.002 0.000 HIS A 122 PHE 0.006 0.001 PHE E 293 TYR 0.015 0.001 TYR B 299 ARG 0.002 0.000 ARG D 196 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 356 time to evaluate : 1.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 GLU cc_start: 0.8401 (pt0) cc_final: 0.7747 (pt0) REVERT: A 105 LYS cc_start: 0.9029 (mmtt) cc_final: 0.8565 (mmmm) REVERT: A 197 ARG cc_start: 0.8040 (ttp-110) cc_final: 0.7730 (mpt-90) REVERT: B 9 MET cc_start: 0.8364 (mtp) cc_final: 0.7483 (pmm) REVERT: B 115 MET cc_start: 0.7671 (ttp) cc_final: 0.7123 (ttp) REVERT: B 215 LYS cc_start: 0.8773 (tttt) cc_final: 0.8476 (tppt) REVERT: B 306 PHE cc_start: 0.7000 (t80) cc_final: 0.6685 (t80) REVERT: C 42 LEU cc_start: 0.9037 (mt) cc_final: 0.8744 (mt) REVERT: C 177 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8532 (mp0) REVERT: C 223 MET cc_start: 0.7852 (mmm) cc_final: 0.7425 (mmm) REVERT: D 55 MET cc_start: 0.8908 (mtt) cc_final: 0.8602 (mmm) REVERT: D 153 GLU cc_start: 0.8895 (mm-30) cc_final: 0.8626 (mm-30) REVERT: D 190 GLU cc_start: 0.7689 (tt0) cc_final: 0.7393 (tt0) REVERT: D 215 LYS cc_start: 0.8855 (tttt) cc_final: 0.8613 (tmmt) REVERT: D 224 GLN cc_start: 0.8172 (tp40) cc_final: 0.7678 (tp40) REVERT: D 268 LEU cc_start: 0.7808 (mp) cc_final: 0.7504 (mp) REVERT: D 306 PHE cc_start: 0.7852 (t80) cc_final: 0.7607 (t80) REVERT: E 306 PHE cc_start: 0.7877 (t80) cc_final: 0.7664 (t80) REVERT: E 426 TRP cc_start: 0.7966 (t60) cc_final: 0.7720 (t60) REVERT: N 426 GLN cc_start: 0.7868 (tt0) cc_final: 0.7565 (tp-100) REVERT: N 432 ARG cc_start: 0.8024 (ttm170) cc_final: 0.7185 (ttm110) REVERT: N 472 ASN cc_start: 0.7958 (t0) cc_final: 0.7722 (t0) outliers start: 9 outliers final: 4 residues processed: 360 average time/residue: 0.3475 time to fit residues: 170.6067 Evaluate side-chains 211 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 207 time to evaluate : 1.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain E residue 255 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 0.9990 chunk 132 optimal weight: 0.0570 chunk 73 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 137 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 83 optimal weight: 9.9990 chunk 102 optimal weight: 1.9990 chunk 158 optimal weight: 4.9990 overall best weight: 0.9702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 267 HIS C 152 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15183 Z= 0.226 Angle : 0.611 8.324 20662 Z= 0.324 Chirality : 0.044 0.224 2391 Planarity : 0.004 0.035 2520 Dihedral : 8.314 79.658 2462 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.94 % Allowed : 8.95 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.46 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.20), residues: 1748 helix: 2.23 (0.21), residues: 566 sheet: 1.08 (0.24), residues: 471 loop : 0.38 (0.24), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 123 HIS 0.005 0.001 HIS D 267 PHE 0.016 0.001 PHE B 307 TYR 0.022 0.001 TYR D 299 ARG 0.007 0.001 ARG C 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 218 time to evaluate : 1.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.7423 (ttm) cc_final: 0.7201 (ttm) REVERT: A 285 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8427 (mmmm) REVERT: B 9 MET cc_start: 0.8480 (mtp) cc_final: 0.8181 (pmm) REVERT: B 115 MET cc_start: 0.7468 (ttp) cc_final: 0.7013 (ttp) REVERT: C 71 GLU cc_start: 0.8001 (pm20) cc_final: 0.7626 (pm20) REVERT: C 123 TRP cc_start: 0.7230 (m100) cc_final: 0.6910 (m100) REVERT: C 130 MET cc_start: 0.6795 (ttp) cc_final: 0.6465 (tmm) REVERT: C 177 GLU cc_start: 0.8791 (mt-10) cc_final: 0.8577 (mp0) REVERT: C 223 MET cc_start: 0.8010 (mmm) cc_final: 0.7433 (mtp) REVERT: D 9 MET cc_start: 0.8429 (mpp) cc_final: 0.8175 (mpp) REVERT: D 18 LYS cc_start: 0.9187 (pttp) cc_final: 0.8403 (pptt) REVERT: D 215 LYS cc_start: 0.8944 (tttt) cc_final: 0.8673 (tptp) REVERT: D 224 GLN cc_start: 0.8125 (tp40) cc_final: 0.7698 (tp40) REVERT: D 274 LYS cc_start: 0.7920 (mmtt) cc_final: 0.7680 (mmtm) REVERT: E 17 ASP cc_start: 0.8799 (t0) cc_final: 0.8459 (t0) REVERT: E 55 MET cc_start: 0.8670 (mtp) cc_final: 0.8441 (mtp) REVERT: N 421 MET cc_start: 0.7144 (mmm) cc_final: 0.6857 (mmm) REVERT: N 426 GLN cc_start: 0.8237 (tt0) cc_final: 0.7962 (tp-100) REVERT: N 472 ASN cc_start: 0.8159 (t0) cc_final: 0.7954 (t0) outliers start: 31 outliers final: 20 residues processed: 238 average time/residue: 0.2900 time to fit residues: 99.4789 Evaluate side-chains 209 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 188 time to evaluate : 1.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 426 TRP Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 423 CYS Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 437 LEU Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 493 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 88 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 chunk 108 optimal weight: 9.9990 chunk 43 optimal weight: 10.0000 chunk 159 optimal weight: 1.9990 chunk 171 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 chunk 157 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 127 optimal weight: 0.8980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 HIS A 258 ASN B 267 HIS C 152 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 15183 Z= 0.243 Angle : 0.587 8.989 20662 Z= 0.305 Chirality : 0.044 0.222 2391 Planarity : 0.004 0.034 2520 Dihedral : 7.252 72.819 2457 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.32 % Allowed : 9.89 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.46 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.20), residues: 1748 helix: 2.17 (0.21), residues: 562 sheet: 1.01 (0.24), residues: 465 loop : 0.19 (0.24), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 241 HIS 0.002 0.001 HIS D 267 PHE 0.022 0.002 PHE E 306 TYR 0.027 0.002 TYR D 299 ARG 0.010 0.001 ARG D 86 *********************** 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 226 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 189 time to evaluate : 1.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.7451 (ttm) cc_final: 0.6710 (tpp) REVERT: A 285 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8446 (mmmm) REVERT: B 9 MET cc_start: 0.8565 (mtp) cc_final: 0.8284 (pmm) REVERT: B 115 MET cc_start: 0.7496 (ttp) cc_final: 0.7163 (ttp) REVERT: C 71 GLU cc_start: 0.8039 (pm20) cc_final: 0.7563 (pm20) REVERT: C 123 TRP cc_start: 0.7232 (m100) cc_final: 0.7022 (m100) REVERT: C 130 MET cc_start: 0.6980 (ttp) cc_final: 0.6581 (tmm) REVERT: C 177 GLU cc_start: 0.8813 (mt-10) cc_final: 0.8596 (mp0) REVERT: C 223 MET cc_start: 0.8065 (mmm) cc_final: 0.7500 (mtt) REVERT: C 239 GLN cc_start: 0.8335 (mm110) cc_final: 0.8009 (mm-40) REVERT: D 9 MET cc_start: 0.8536 (mpp) cc_final: 0.8287 (mpp) REVERT: D 40 MET cc_start: 0.8652 (mtt) cc_final: 0.8444 (mtt) REVERT: D 215 LYS cc_start: 0.9004 (tttt) cc_final: 0.8757 (tptp) REVERT: D 224 GLN cc_start: 0.8134 (tp40) cc_final: 0.7836 (tp40) REVERT: N 426 GLN cc_start: 0.8289 (tt0) cc_final: 0.7852 (tp40) REVERT: N 472 ASN cc_start: 0.8462 (t0) cc_final: 0.8190 (t0) REVERT: N 482 TYR cc_start: 0.8146 (m-10) cc_final: 0.7936 (m-10) outliers start: 37 outliers final: 18 residues processed: 211 average time/residue: 0.2798 time to fit residues: 86.8316 Evaluate side-chains 194 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 175 time to evaluate : 1.814 ------------------------------------------------------------------------------- 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 222 ILE Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 297 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 427 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E 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 157 optimal weight: 0.6980 chunk 119 optimal weight: 3.9990 chunk 82 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 chunk 159 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 83 optimal weight: 20.0000 chunk 151 optimal weight: 0.9990 chunk 45 optimal weight: 0.4980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 267 HIS C 156 HIS C 258 ASN ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15183 Z= 0.195 Angle : 0.569 9.894 20662 Z= 0.290 Chirality : 0.043 0.236 2391 Planarity : 0.004 0.044 2520 Dihedral : 6.631 65.980 2457 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.13 % Allowed : 10.14 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.46 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.20), residues: 1748 helix: 2.14 (0.21), residues: 566 sheet: 0.92 (0.24), residues: 465 loop : 0.14 (0.24), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 241 HIS 0.004 0.001 HIS D 267 PHE 0.017 0.001 PHE D 307 TYR 0.026 0.002 TYR D 299 ARG 0.012 0.001 ARG D 86 *********************** 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: 34 poor density : 185 time to evaluate : 1.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.7399 (ttm) cc_final: 0.6747 (tpp) REVERT: A 150 GLU cc_start: 0.8345 (tm-30) cc_final: 0.7835 (tm-30) REVERT: A 259 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8175 (pttm) REVERT: B 9 MET cc_start: 0.8463 (mtp) cc_final: 0.8230 (pmm) REVERT: B 115 MET cc_start: 0.7425 (ttp) cc_final: 0.7161 (ttp) REVERT: C 71 GLU cc_start: 0.8162 (pm20) cc_final: 0.7735 (pm20) REVERT: C 130 MET cc_start: 0.6965 (ttp) cc_final: 0.6543 (tmm) REVERT: C 177 GLU cc_start: 0.8822 (mt-10) cc_final: 0.8606 (mp0) REVERT: C 178 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7372 (mt-10) REVERT: C 182 GLN cc_start: 0.8520 (tt0) cc_final: 0.8051 (tt0) REVERT: C 223 MET cc_start: 0.8117 (mmm) cc_final: 0.7549 (mtt) REVERT: D 9 MET cc_start: 0.8591 (mpp) cc_final: 0.8328 (mpp) REVERT: D 215 LYS cc_start: 0.9011 (tttt) cc_final: 0.8752 (tptp) REVERT: N 4 LEU cc_start: 0.8423 (mt) cc_final: 0.7950 (tt) REVERT: N 426 GLN cc_start: 0.8263 (tt0) cc_final: 0.7916 (tp-100) REVERT: N 449 ASP cc_start: 0.8653 (m-30) cc_final: 0.8367 (p0) REVERT: N 472 ASN cc_start: 0.8555 (t0) cc_final: 0.8326 (t0) REVERT: N 482 TYR cc_start: 0.8042 (m-10) cc_final: 0.7820 (m-10) outliers start: 34 outliers final: 21 residues processed: 207 average time/residue: 0.2764 time to fit residues: 84.5142 Evaluate side-chains 193 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 171 time to evaluate : 1.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 416 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 145 LEU 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 140 optimal weight: 0.0170 chunk 96 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 125 optimal weight: 0.9990 chunk 69 optimal weight: 8.9990 chunk 144 optimal weight: 7.9990 chunk 116 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 86 optimal weight: 0.9990 chunk 151 optimal weight: 6.9990 chunk 42 optimal weight: 10.0000 overall best weight: 2.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 267 HIS ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15183 Z= 0.272 Angle : 0.592 10.458 20662 Z= 0.305 Chirality : 0.044 0.251 2391 Planarity : 0.004 0.100 2520 Dihedral : 6.376 62.688 2457 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.00 % Allowed : 10.83 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.46 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.20), residues: 1748 helix: 2.11 (0.21), residues: 566 sheet: 0.79 (0.24), residues: 473 loop : 0.00 (0.24), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 241 HIS 0.003 0.001 HIS D 267 PHE 0.019 0.002 PHE B 31 TYR 0.028 0.002 TYR D 299 ARG 0.014 0.001 ARG E 68 *********************** 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 209 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 177 time to evaluate : 1.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 GLU cc_start: 0.8233 (pt0) cc_final: 0.7881 (pt0) REVERT: A 130 MET cc_start: 0.7390 (ttm) cc_final: 0.6696 (tpp) REVERT: A 150 GLU cc_start: 0.8459 (tm-30) cc_final: 0.7987 (tm-30) REVERT: A 239 GLN cc_start: 0.8692 (tp40) cc_final: 0.8285 (tp40) REVERT: A 285 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8484 (mmmm) REVERT: B 115 MET cc_start: 0.7429 (ttp) cc_final: 0.7225 (ttp) REVERT: C 71 GLU cc_start: 0.8185 (pm20) cc_final: 0.7731 (pm20) REVERT: C 130 MET cc_start: 0.7088 (ttp) cc_final: 0.6620 (tmm) REVERT: C 177 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8612 (mp0) REVERT: C 178 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7824 (mt-10) REVERT: C 182 GLN cc_start: 0.8597 (tt0) cc_final: 0.8114 (tt0) REVERT: C 223 MET cc_start: 0.8177 (mmm) cc_final: 0.7521 (mtt) REVERT: D 9 MET cc_start: 0.8537 (mpp) cc_final: 0.8308 (mpp) REVERT: D 215 LYS cc_start: 0.9037 (tttt) cc_final: 0.8763 (tptp) REVERT: N 426 GLN cc_start: 0.8308 (tt0) cc_final: 0.7912 (tp-100) REVERT: N 449 ASP cc_start: 0.8712 (m-30) cc_final: 0.8410 (p0) REVERT: N 472 ASN cc_start: 0.8708 (t0) cc_final: 0.8480 (t0) REVERT: N 482 TYR cc_start: 0.8247 (m-10) cc_final: 0.8035 (m-10) outliers start: 32 outliers final: 25 residues processed: 196 average time/residue: 0.2805 time to fit residues: 82.6073 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 : 1.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 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 444 LEU Chi-restraints excluded: chain C residue 258 ASN Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain N residue 405 LEU Chi-restraints excluded: chain N residue 445 THR 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 56 optimal weight: 0.7980 chunk 152 optimal weight: 0.9980 chunk 33 optimal weight: 20.0000 chunk 99 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 169 optimal weight: 9.9990 chunk 140 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 14 optimal weight: 7.9990 chunk 88 optimal weight: 0.5980 chunk 163 optimal weight: 9.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 267 HIS ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.4499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15183 Z= 0.222 Angle : 0.562 10.680 20662 Z= 0.288 Chirality : 0.043 0.252 2391 Planarity : 0.004 0.037 2520 Dihedral : 5.979 56.107 2457 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.13 % Allowed : 10.83 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.46 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.20), residues: 1748 helix: 2.11 (0.21), residues: 566 sheet: 0.60 (0.24), residues: 485 loop : 0.06 (0.24), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP E 241 HIS 0.003 0.001 HIS C 122 PHE 0.014 0.001 PHE B 307 TYR 0.025 0.001 TYR D 299 ARG 0.008 0.000 ARG D 86 *********************** 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 205 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 171 time to evaluate : 1.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 GLU cc_start: 0.8221 (pt0) cc_final: 0.7721 (pt0) REVERT: A 130 MET cc_start: 0.7314 (OUTLIER) cc_final: 0.6634 (tpp) REVERT: A 150 GLU cc_start: 0.8402 (tm-30) cc_final: 0.7995 (tm-30) REVERT: C 71 GLU cc_start: 0.8287 (pm20) cc_final: 0.7741 (pm20) REVERT: C 130 MET cc_start: 0.7079 (ttp) cc_final: 0.6737 (tmm) REVERT: C 177 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8620 (mp0) REVERT: C 182 GLN cc_start: 0.8638 (tt0) cc_final: 0.8190 (tt0) REVERT: C 223 MET cc_start: 0.8162 (mmm) cc_final: 0.7503 (mtt) REVERT: C 239 GLN cc_start: 0.8382 (tp-100) cc_final: 0.8068 (mm-40) REVERT: D 165 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.7033 (pp20) REVERT: D 215 LYS cc_start: 0.9025 (tttt) cc_final: 0.8735 (tttm) REVERT: D 224 GLN cc_start: 0.8268 (tp40) cc_final: 0.8042 (tp40) REVERT: N 4 LEU cc_start: 0.8502 (tp) cc_final: 0.8132 (tt) REVERT: N 426 GLN cc_start: 0.8347 (tt0) cc_final: 0.7934 (tp-100) REVERT: N 449 ASP cc_start: 0.8739 (m-30) cc_final: 0.8425 (p0) REVERT: N 474 LYS cc_start: 0.8644 (mmmm) cc_final: 0.8284 (ttpp) outliers start: 34 outliers final: 22 residues processed: 193 average time/residue: 0.2759 time to fit residues: 79.3716 Evaluate side-chains 190 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 166 time to evaluate : 1.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain B residue 11 PHE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain D residue 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 268 LEU Chi-restraints excluded: chain N residue 405 LEU Chi-restraints excluded: chain N residue 457 ILE Chi-restraints excluded: chain N residue 493 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 19 optimal weight: 6.9990 chunk 96 optimal weight: 0.9980 chunk 123 optimal weight: 6.9990 chunk 95 optimal weight: 0.9980 chunk 142 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 chunk 168 optimal weight: 10.0000 chunk 105 optimal weight: 1.9990 chunk 102 optimal weight: 7.9990 chunk 77 optimal weight: 0.8980 chunk 104 optimal weight: 7.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- 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 ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.4745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15183 Z= 0.251 Angle : 0.588 14.433 20662 Z= 0.299 Chirality : 0.044 0.253 2391 Planarity : 0.003 0.040 2520 Dihedral : 5.800 52.745 2457 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.63 % Allowed : 11.33 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.46 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.20), residues: 1748 helix: 2.07 (0.21), residues: 566 sheet: 0.62 (0.24), residues: 490 loop : 0.08 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP E 241 HIS 0.004 0.001 HIS C 122 PHE 0.014 0.001 PHE N 434 TYR 0.028 0.001 TYR D 299 ARG 0.010 0.000 ARG D 86 *********************** 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 195 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 169 time to evaluate : 1.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.7276 (OUTLIER) cc_final: 0.6605 (tpp) REVERT: A 150 GLU cc_start: 0.8432 (tm-30) cc_final: 0.7988 (tm-30) REVERT: A 239 GLN cc_start: 0.8750 (tp40) cc_final: 0.8488 (tp40) REVERT: A 285 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8514 (mmmm) REVERT: C 71 GLU cc_start: 0.8309 (pm20) cc_final: 0.7733 (pm20) REVERT: C 123 TRP cc_start: 0.7259 (m100) cc_final: 0.6973 (m100) REVERT: C 130 MET cc_start: 0.7020 (ttp) cc_final: 0.6743 (tmm) REVERT: C 182 GLN cc_start: 0.8649 (tt0) cc_final: 0.8195 (tt0) REVERT: C 223 MET cc_start: 0.8213 (mmm) cc_final: 0.7532 (mtt) REVERT: D 165 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.7070 (pp20) REVERT: D 215 LYS cc_start: 0.9046 (tttt) cc_final: 0.8737 (tttm) REVERT: E 9 MET cc_start: 0.7309 (OUTLIER) cc_final: 0.6900 (mtp) REVERT: E 141 ARG cc_start: 0.8292 (mmt90) cc_final: 0.8077 (mmt90) REVERT: N 4 LEU cc_start: 0.8440 (tp) cc_final: 0.8046 (tt) REVERT: N 426 GLN cc_start: 0.8292 (tt0) cc_final: 0.7864 (tp-100) REVERT: N 449 ASP cc_start: 0.8785 (m-30) cc_final: 0.8461 (p0) outliers start: 26 outliers final: 19 residues processed: 184 average time/residue: 0.2723 time to fit residues: 74.9122 Evaluate side-chains 187 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 164 time to evaluate : 1.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 130 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 A residue 427 LEU Chi-restraints excluded: chain B residue 11 PHE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain E residue 9 MET Chi-restraints excluded: chain N residue 405 LEU Chi-restraints excluded: chain N residue 473 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 67 optimal weight: 8.9990 chunk 100 optimal weight: 0.9990 chunk 50 optimal weight: 9.9990 chunk 33 optimal weight: 20.0000 chunk 32 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 114 optimal weight: 9.9990 chunk 83 optimal weight: 20.0000 chunk 15 optimal weight: 4.9990 chunk 132 optimal weight: 0.0000 chunk 153 optimal weight: 0.7980 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 267 HIS E 267 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.4901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15183 Z= 0.197 Angle : 0.575 14.737 20662 Z= 0.290 Chirality : 0.043 0.250 2391 Planarity : 0.003 0.039 2520 Dihedral : 5.539 48.570 2457 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.38 % Allowed : 12.15 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.46 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.20), residues: 1748 helix: 2.10 (0.21), residues: 566 sheet: 0.65 (0.24), residues: 490 loop : 0.13 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP E 241 HIS 0.002 0.000 HIS D 267 PHE 0.021 0.001 PHE B 307 TYR 0.026 0.001 TYR D 299 ARG 0.011 0.000 ARG D 86 *********************** 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 193 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 171 time to evaluate : 1.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.7275 (OUTLIER) cc_final: 0.6603 (tpp) REVERT: A 150 GLU cc_start: 0.8422 (tm-30) cc_final: 0.7997 (tm-30) REVERT: A 239 GLN cc_start: 0.8769 (tp40) cc_final: 0.8513 (tp40) REVERT: A 285 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8482 (mmmm) REVERT: C 71 GLU cc_start: 0.8349 (pm20) cc_final: 0.7809 (pm20) REVERT: C 123 TRP cc_start: 0.7185 (m100) cc_final: 0.6743 (m100) REVERT: C 130 MET cc_start: 0.7048 (ttp) cc_final: 0.6789 (tmm) REVERT: C 182 GLN cc_start: 0.8684 (tt0) cc_final: 0.8269 (tt0) REVERT: C 223 MET cc_start: 0.8197 (mmm) cc_final: 0.7401 (mtt) REVERT: D 215 LYS cc_start: 0.9040 (tttt) cc_final: 0.8744 (tttm) REVERT: E 9 MET cc_start: 0.7316 (OUTLIER) cc_final: 0.6902 (mtp) REVERT: E 141 ARG cc_start: 0.8270 (mmt90) cc_final: 0.8054 (mmt90) REVERT: N 426 GLN cc_start: 0.8277 (tt0) cc_final: 0.7870 (tp-100) REVERT: N 449 ASP cc_start: 0.8783 (m-30) cc_final: 0.8460 (p0) REVERT: N 474 LYS cc_start: 0.8558 (mmmt) cc_final: 0.8137 (tptp) outliers start: 22 outliers final: 16 residues processed: 185 average time/residue: 0.2829 time to fit residues: 78.1004 Evaluate side-chains 184 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 165 time to evaluate : 1.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain E residue 9 MET 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 161 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 157 optimal weight: 0.6980 chunk 94 optimal weight: 8.9990 chunk 68 optimal weight: 3.9990 chunk 123 optimal weight: 7.9990 chunk 48 optimal weight: 8.9990 chunk 142 optimal weight: 5.9990 chunk 148 optimal weight: 4.9990 chunk 156 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.5085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 15183 Z= 0.266 Angle : 0.611 16.325 20662 Z= 0.308 Chirality : 0.044 0.252 2391 Planarity : 0.004 0.041 2520 Dihedral : 5.499 46.878 2457 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.69 % Allowed : 11.90 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.20), residues: 1748 helix: 2.08 (0.21), residues: 566 sheet: 0.59 (0.24), residues: 491 loop : 0.09 (0.24), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP E 241 HIS 0.008 0.001 HIS D 191 PHE 0.036 0.001 PHE N 455 TYR 0.028 0.002 TYR D 299 ARG 0.012 0.000 ARG D 86 *********************** 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 193 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 166 time to evaluate : 1.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.7343 (OUTLIER) cc_final: 0.6644 (tpp) REVERT: A 150 GLU cc_start: 0.8429 (tm-30) cc_final: 0.8029 (tm-30) REVERT: A 239 GLN cc_start: 0.8760 (tp40) cc_final: 0.8499 (tp40) REVERT: A 276 MET cc_start: 0.9432 (mmm) cc_final: 0.9192 (tpp) REVERT: A 285 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8513 (mmmm) REVERT: B 9 MET cc_start: 0.8040 (pmm) cc_final: 0.7450 (pmm) REVERT: B 282 ASP cc_start: 0.8386 (m-30) cc_final: 0.8159 (m-30) REVERT: C 71 GLU cc_start: 0.8387 (pm20) cc_final: 0.7828 (pm20) REVERT: C 130 MET cc_start: 0.7035 (ttp) cc_final: 0.6745 (tmm) REVERT: C 182 GLN cc_start: 0.8648 (tt0) cc_final: 0.8207 (tt0) REVERT: C 223 MET cc_start: 0.8251 (mmm) cc_final: 0.7461 (mtt) REVERT: D 215 LYS cc_start: 0.9072 (tttt) cc_final: 0.8738 (tttm) REVERT: D 224 GLN cc_start: 0.8120 (tp40) cc_final: 0.7749 (tp40) REVERT: E 9 MET cc_start: 0.7397 (OUTLIER) cc_final: 0.6999 (mtp) REVERT: N 426 GLN cc_start: 0.8267 (tt0) cc_final: 0.7935 (tp-100) REVERT: N 449 ASP cc_start: 0.8819 (m-30) cc_final: 0.8484 (p0) outliers start: 27 outliers final: 19 residues processed: 183 average time/residue: 0.2779 time to fit residues: 76.0147 Evaluate side-chains 185 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 163 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 130 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 A residue 427 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 258 ASN Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain E residue 9 MET Chi-restraints excluded: chain N residue 493 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 166 optimal weight: 1.9990 chunk 101 optimal weight: 10.0000 chunk 78 optimal weight: 0.0570 chunk 115 optimal weight: 6.9990 chunk 174 optimal weight: 4.9990 chunk 160 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 overall best weight: 1.1902 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.5179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15183 Z= 0.192 Angle : 0.598 17.459 20662 Z= 0.298 Chirality : 0.043 0.244 2391 Planarity : 0.003 0.043 2520 Dihedral : 5.286 43.454 2457 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.44 % Allowed : 12.34 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.46 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.20), residues: 1748 helix: 2.12 (0.21), residues: 564 sheet: 0.61 (0.24), residues: 490 loop : 0.16 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP E 241 HIS 0.009 0.001 HIS D 191 PHE 0.030 0.001 PHE N 455 TYR 0.025 0.001 TYR D 299 ARG 0.012 0.000 ARG D 86 ********************** 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 188 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 165 time to evaluate : 1.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.7259 (OUTLIER) cc_final: 0.6612 (tpp) REVERT: A 150 GLU cc_start: 0.8430 (tm-30) cc_final: 0.8056 (tm-30) REVERT: A 239 GLN cc_start: 0.8759 (tp40) cc_final: 0.8498 (tp40) REVERT: A 276 MET cc_start: 0.9412 (mmm) cc_final: 0.9203 (tpp) REVERT: A 285 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8484 (mmmm) REVERT: B 9 MET cc_start: 0.8048 (pmm) cc_final: 0.7458 (pmm) REVERT: B 282 ASP cc_start: 0.8357 (m-30) cc_final: 0.8122 (m-30) REVERT: C 71 GLU cc_start: 0.8397 (pm20) cc_final: 0.7826 (pm20) REVERT: C 130 MET cc_start: 0.7063 (ttp) cc_final: 0.6828 (tmm) REVERT: C 182 GLN cc_start: 0.8685 (tt0) cc_final: 0.8301 (tt0) REVERT: C 223 MET cc_start: 0.8207 (mmm) cc_final: 0.7395 (mtt) REVERT: D 215 LYS cc_start: 0.9069 (tttt) cc_final: 0.8746 (tttm) REVERT: D 224 GLN cc_start: 0.8079 (tp40) cc_final: 0.7697 (tp40) REVERT: E 9 MET cc_start: 0.7432 (OUTLIER) cc_final: 0.6997 (mtp) REVERT: N 426 GLN cc_start: 0.8199 (tt0) cc_final: 0.7880 (tp-100) REVERT: N 449 ASP cc_start: 0.8843 (m-30) cc_final: 0.8487 (p0) outliers start: 23 outliers final: 18 residues processed: 178 average time/residue: 0.2807 time to fit residues: 75.3814 Evaluate side-chains 182 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 161 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 130 MET 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 268 LEU Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain E residue 9 MET Chi-restraints excluded: chain N residue 470 MET Chi-restraints excluded: chain N residue 493 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 128 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 chunk 139 optimal weight: 2.9990 chunk 58 optimal weight: 0.0060 chunk 142 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 overall best weight: 1.1798 ------------------------------------------------------------------------------- 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 = 0.3564 r_free = 0.3564 target = 0.086998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.059334 restraints weight = 72030.086| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 4.47 r_work: 0.2740 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2741 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2741 r_free = 0.2741 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2741 r_free = 0.2741 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2741 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.5263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15183 Z= 0.193 Angle : 0.601 16.538 20662 Z= 0.299 Chirality : 0.043 0.242 2391 Planarity : 0.003 0.039 2520 Dihedral : 5.152 41.021 2457 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.50 % Allowed : 12.52 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.46 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.20), residues: 1748 helix: 2.11 (0.21), residues: 564 sheet: 0.61 (0.24), residues: 490 loop : 0.17 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP E 241 HIS 0.009 0.001 HIS D 191 PHE 0.032 0.001 PHE N 455 TYR 0.026 0.001 TYR D 299 ARG 0.012 0.000 ARG D 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3142.27 seconds wall clock time: 58 minutes 29.38 seconds (3509.38 seconds total)