Starting phenix.real_space_refine on Sat Sep 12 01:35:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/3jad_6344/09_2026/3jad_6344.cif Found real_map, /net/cci-nas-00/data/ceres_data/3jad_6344/09_2026/3jad_6344.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/3jad_6344/09_2026/3jad_6344.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3jad_6344/09_2026/3jad_6344.map" restraint_files = "/net/cci-nas-00/data/ceres_data/3jad_6344/09_2026/3jad_6344.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/3jad_6344/09_2026/3jad_6344.cif" model { file = "/net/cci-nas-00/data/ceres_data/3jad_6344/09_2026/3jad_6344.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3jad_6344/09_2026/3jad_6344.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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 65 5.16 5 C 8305 2.51 5 N 2090 2.21 5 O 2245 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12705 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2488 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 15, 'TRANS': 321} Chain breaks: 1 Unresolved non-hydrogen bonds: 241 Unresolved non-hydrogen angles: 294 Unresolved non-hydrogen dihedrals: 194 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLU:plan': 11, 'ASP:plan': 8, 'ARG:plan': 5, 'GLN:plan1': 1, 'PHE:plan': 3, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 121 Chain: "B" Number of atoms: 2488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2488 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 15, 'TRANS': 321} Chain breaks: 1 Unresolved non-hydrogen bonds: 241 Unresolved non-hydrogen angles: 294 Unresolved non-hydrogen dihedrals: 194 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLU:plan': 11, 'ASP:plan': 8, 'ARG:plan': 5, 'GLN:plan1': 1, 'PHE:plan': 3, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 121 Chain: "C" Number of atoms: 2488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2488 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 15, 'TRANS': 321} Chain breaks: 1 Unresolved non-hydrogen bonds: 241 Unresolved non-hydrogen angles: 294 Unresolved non-hydrogen dihedrals: 194 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLU:plan': 11, 'ASP:plan': 8, 'ARG:plan': 5, 'GLN:plan1': 1, 'PHE:plan': 3, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 121 Chain: "D" Number of atoms: 2488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2488 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 15, 'TRANS': 321} Chain breaks: 1 Unresolved non-hydrogen bonds: 241 Unresolved non-hydrogen angles: 294 Unresolved non-hydrogen dihedrals: 194 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLU:plan': 11, 'ASP:plan': 8, 'ARG:plan': 5, 'GLN:plan1': 1, 'PHE:plan': 3, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 121 Chain: "E" Number of atoms: 2488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2488 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 15, 'TRANS': 321} Chain breaks: 1 Unresolved non-hydrogen bonds: 241 Unresolved non-hydrogen angles: 294 Unresolved non-hydrogen dihedrals: 194 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLU:plan': 11, 'ASP:plan': 8, 'ARG:plan': 5, 'GLN:plan1': 1, 'PHE:plan': 3, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 121 Chain: "F" 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 chiralities: 2 Chain: "G" 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 chiralities: 2 Chain: "H" 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 chiralities: 2 Chain: "I" 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 chiralities: 2 Chain: "J" 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 chiralities: 2 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'SY9': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'SY9': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'SY9': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'SY9': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'SY9': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.49, per 1000 atoms: 0.20 Number of scatterers: 12705 At special positions: 0 Unit cell: (98.98, 97.97, 126.25, 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 65 16.00 O 2245 8.00 N 2090 7.00 C 8305 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 225 " distance=2.04 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 225 " distance=2.04 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 225 " distance=2.04 Simple disulfide: pdb=" SG CYS D 214 " - pdb=" SG CYS D 225 " distance=2.04 Simple disulfide: pdb=" SG CYS E 214 " - pdb=" SG CYS E 225 " distance=2.04 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 BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 572.8 milliseconds 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3230 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 15 sheets defined 37.4% alpha, 38.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 25 through 35 removed outlier: 3.513A pdb=" N LEU A 33 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 108 removed outlier: 4.053A pdb=" N ASP A 107 " --> pdb=" O SER A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 243 Processing helix chain 'A' and resid 243 through 259 removed outlier: 3.674A pdb=" N SER A 247 " --> pdb=" O MET A 243 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TRP A 259 " --> pdb=" O TRP A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 290 Processing helix chain 'A' and resid 297 through 325 removed outlier: 3.959A pdb=" N LEU A 314 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG A 325 " --> pdb=" O ASN A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 362 Proline residue: A 347 - end of helix removed outlier: 3.841A pdb=" N ILE A 359 " --> pdb=" O ILE A 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 35 removed outlier: 3.514A pdb=" N LEU B 33 " --> pdb=" O PHE B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 108 removed outlier: 4.053A pdb=" N ASP B 107 " --> pdb=" O SER B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 243 Processing helix chain 'B' and resid 243 through 259 removed outlier: 3.673A pdb=" N SER B 247 " --> pdb=" O MET B 243 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TRP B 259 " --> pdb=" O TRP B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 290 Processing helix chain 'B' and resid 297 through 325 removed outlier: 3.959A pdb=" N LEU B 314 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG B 325 " --> pdb=" O ASN B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 362 Proline residue: B 347 - end of helix removed outlier: 3.841A pdb=" N ILE B 359 " --> pdb=" O ILE B 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 35 removed outlier: 3.513A pdb=" N LEU C 33 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 108 removed outlier: 4.053A pdb=" N ASP C 107 " --> pdb=" O SER C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 243 Processing helix chain 'C' and resid 243 through 259 removed outlier: 3.674A pdb=" N SER C 247 " --> pdb=" O MET C 243 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TRP C 259 " --> pdb=" O TRP C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 290 Processing helix chain 'C' and resid 297 through 325 removed outlier: 3.960A pdb=" N LEU C 314 " --> pdb=" O VAL C 310 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG C 325 " --> pdb=" O ASN C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 362 Proline residue: C 347 - end of helix removed outlier: 3.841A pdb=" N ILE C 359 " --> pdb=" O ILE C 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 35 removed outlier: 3.514A pdb=" N LEU D 33 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 108 removed outlier: 4.053A pdb=" N ASP D 107 " --> pdb=" O SER D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 243 Processing helix chain 'D' and resid 243 through 259 removed outlier: 3.673A pdb=" N SER D 247 " --> pdb=" O MET D 243 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TRP D 259 " --> pdb=" O TRP D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 290 Processing helix chain 'D' and resid 297 through 325 removed outlier: 3.960A pdb=" N LEU D 314 " --> pdb=" O VAL D 310 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG D 325 " --> pdb=" O ASN D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 362 Proline residue: D 347 - end of helix removed outlier: 3.841A pdb=" N ILE D 359 " --> pdb=" O ILE D 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 35 removed outlier: 3.514A pdb=" N LEU E 33 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 108 removed outlier: 4.052A pdb=" N ASP E 107 " --> pdb=" O SER E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 243 Processing helix chain 'E' and resid 243 through 259 removed outlier: 3.674A pdb=" N SER E 247 " --> pdb=" O MET E 243 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TRP E 259 " --> pdb=" O TRP E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 290 Processing helix chain 'E' and resid 297 through 325 removed outlier: 3.959A pdb=" N LEU E 314 " --> pdb=" O VAL E 310 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG E 325 " --> pdb=" O ASN E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 362 Proline residue: E 347 - end of helix removed outlier: 3.841A pdb=" N ILE E 359 " --> pdb=" O ILE E 355 " (cutoff:3.500A) Processing sheet with id=A, first strand: chain 'A' and resid 119 through 124 removed outlier: 3.825A pdb=" N GLY A 121 " --> pdb=" O VAL A 151 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ASP A 73 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N SER A 66 " --> pdb=" O ASP A 73 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL A 53 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N GLU A 185 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL A 55 " --> pdb=" O GLU A 185 " (cutoff:3.500A) Processing sheet with id=B, first strand: chain 'A' and resid 133 through 136 removed outlier: 5.990A pdb=" N ASP A 73 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N SER A 66 " --> pdb=" O ASP A 73 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N GLN A 193 " --> pdb=" O CYS A 57 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE A 59 " --> pdb=" O GLN A 193 " (cutoff:3.500A) Processing sheet with id=C, first strand: chain 'A' and resid 114 through 116 removed outlier: 5.713A pdb=" N THR A 224 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N HIS A 231 " --> pdb=" O GLU A 208 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLU A 208 " --> pdb=" O HIS A 231 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N GLU A 233 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LYS A 206 " --> pdb=" O GLU A 233 " (cutoff:3.500A) Processing sheet with id=D, first strand: chain 'B' and resid 119 through 124 removed outlier: 3.824A pdb=" N GLY B 121 " --> pdb=" O VAL B 151 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ASP B 73 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N SER B 66 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL B 53 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N GLU B 185 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL B 55 " --> pdb=" O GLU B 185 " (cutoff:3.500A) Processing sheet with id=E, first strand: chain 'B' and resid 133 through 136 removed outlier: 5.991A pdb=" N ASP B 73 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N SER B 66 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N GLN B 193 " --> pdb=" O CYS B 57 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE B 59 " --> pdb=" O GLN B 193 " (cutoff:3.500A) Processing sheet with id=F, first strand: chain 'B' and resid 114 through 116 removed outlier: 5.712A pdb=" N THR B 224 " --> pdb=" O SER B 174 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N HIS B 231 " --> pdb=" O GLU B 208 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLU B 208 " --> pdb=" O HIS B 231 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N GLU B 233 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LYS B 206 " --> pdb=" O GLU B 233 " (cutoff:3.500A) Processing sheet with id=G, first strand: chain 'C' and resid 119 through 124 removed outlier: 3.824A pdb=" N GLY C 121 " --> pdb=" O VAL C 151 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ASP C 73 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N SER C 66 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL C 53 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N GLU C 185 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL C 55 " --> pdb=" O GLU C 185 " (cutoff:3.500A) Processing sheet with id=H, first strand: chain 'C' and resid 133 through 136 removed outlier: 5.991A pdb=" N ASP C 73 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N SER C 66 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 8.962A pdb=" N GLN C 193 " --> pdb=" O CYS C 57 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ILE C 59 " --> pdb=" O GLN C 193 " (cutoff:3.500A) Processing sheet with id=I, first strand: chain 'C' and resid 114 through 116 removed outlier: 5.713A pdb=" N THR C 224 " --> pdb=" O SER C 174 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N HIS C 231 " --> pdb=" O GLU C 208 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLU C 208 " --> pdb=" O HIS C 231 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N GLU C 233 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LYS C 206 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing sheet with id=J, first strand: chain 'D' and resid 119 through 124 removed outlier: 3.824A pdb=" N GLY D 121 " --> pdb=" O VAL D 151 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ASP D 73 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N SER D 66 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL D 53 " --> pdb=" O ILE D 183 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N GLU D 185 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL D 55 " --> pdb=" O GLU D 185 " (cutoff:3.500A) Processing sheet with id=K, first strand: chain 'D' and resid 133 through 136 removed outlier: 5.990A pdb=" N ASP D 73 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N SER D 66 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 8.962A pdb=" N GLN D 193 " --> pdb=" O CYS D 57 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE D 59 " --> pdb=" O GLN D 193 " (cutoff:3.500A) Processing sheet with id=L, first strand: chain 'D' and resid 114 through 116 removed outlier: 5.713A pdb=" N THR D 224 " --> pdb=" O SER D 174 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N HIS D 231 " --> pdb=" O GLU D 208 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLU D 208 " --> pdb=" O HIS D 231 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N GLU D 233 " --> pdb=" O LYS D 206 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LYS D 206 " --> pdb=" O GLU D 233 " (cutoff:3.500A) Processing sheet with id=M, first strand: chain 'E' and resid 119 through 124 removed outlier: 3.824A pdb=" N GLY E 121 " --> pdb=" O VAL E 151 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ASP E 73 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N SER E 66 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL E 53 " --> pdb=" O ILE E 183 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N GLU E 185 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N VAL E 55 " --> pdb=" O GLU E 185 " (cutoff:3.500A) Processing sheet with id=N, first strand: chain 'E' and resid 133 through 136 removed outlier: 5.990A pdb=" N ASP E 73 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N SER E 66 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 8.962A pdb=" N GLN E 193 " --> pdb=" O CYS E 57 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ILE E 59 " --> pdb=" O GLN E 193 " (cutoff:3.500A) Processing sheet with id=O, first strand: chain 'E' and resid 114 through 116 removed outlier: 5.714A pdb=" N THR E 224 " --> pdb=" O SER E 174 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N HIS E 231 " --> pdb=" O GLU E 208 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLU E 208 " --> pdb=" O HIS E 231 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N GLU E 233 " --> pdb=" O LYS E 206 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LYS E 206 " --> pdb=" O GLU E 233 " (cutoff:3.500A) 776 hydrogen bonds defined for protein. 2283 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.01 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3870 1.34 - 1.46: 3345 1.46 - 1.59: 5730 1.59 - 1.71: 15 1.71 - 1.84: 100 Bond restraints: 13060 Sorted by residual: bond pdb=" CAR SY9 E 401 " pdb=" CAS SY9 E 401 " ideal model delta sigma weight residual 1.509 1.623 -0.114 2.00e-02 2.50e+03 3.24e+01 bond pdb=" CAR SY9 B 401 " pdb=" CAS SY9 B 401 " ideal model delta sigma weight residual 1.509 1.623 -0.114 2.00e-02 2.50e+03 3.23e+01 bond pdb=" CAR SY9 C 401 " pdb=" CAS SY9 C 401 " ideal model delta sigma weight residual 1.509 1.623 -0.114 2.00e-02 2.50e+03 3.23e+01 bond pdb=" CAR SY9 A 503 " pdb=" CAS SY9 A 503 " ideal model delta sigma weight residual 1.509 1.623 -0.114 2.00e-02 2.50e+03 3.23e+01 bond pdb=" CAR SY9 D 401 " pdb=" CAS SY9 D 401 " ideal model delta sigma weight residual 1.509 1.622 -0.113 2.00e-02 2.50e+03 3.21e+01 ... (remaining 13055 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 16592 2.29 - 4.59: 1120 4.59 - 6.88: 178 6.88 - 9.18: 25 9.18 - 11.47: 20 Bond angle restraints: 17935 Sorted by residual: angle pdb=" C TYR B 94 " pdb=" N PRO B 95 " pdb=" CA PRO B 95 " ideal model delta sigma weight residual 119.32 125.78 -6.46 1.14e+00 7.69e-01 3.21e+01 angle pdb=" C TYR C 94 " pdb=" N PRO C 95 " pdb=" CA PRO C 95 " ideal model delta sigma weight residual 119.32 125.78 -6.46 1.14e+00 7.69e-01 3.21e+01 angle pdb=" C TYR D 94 " pdb=" N PRO D 95 " pdb=" CA PRO D 95 " ideal model delta sigma weight residual 119.32 125.76 -6.44 1.14e+00 7.69e-01 3.20e+01 angle pdb=" C TYR A 94 " pdb=" N PRO A 95 " pdb=" CA PRO A 95 " ideal model delta sigma weight residual 119.32 125.76 -6.44 1.14e+00 7.69e-01 3.19e+01 angle pdb=" C TYR E 94 " pdb=" N PRO E 95 " pdb=" CA PRO E 95 " ideal model delta sigma weight residual 119.32 125.69 -6.37 1.14e+00 7.69e-01 3.13e+01 ... (remaining 17930 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.95: 7249 15.95 - 31.91: 142 31.91 - 47.86: 39 47.86 - 63.82: 0 63.82 - 79.77: 10 Dihedral angle restraints: 7440 sinusoidal: 2460 harmonic: 4980 Sorted by residual: dihedral pdb=" CB CYS E 214 " pdb=" SG CYS E 214 " pdb=" SG CYS E 225 " pdb=" CB CYS E 225 " ideal model delta sinusoidal sigma weight residual -86.00 -152.09 66.09 1 1.00e+01 1.00e-02 5.71e+01 dihedral pdb=" CB CYS A 214 " pdb=" SG CYS A 214 " pdb=" SG CYS A 225 " pdb=" CB CYS A 225 " ideal model delta sinusoidal sigma weight residual -86.00 -152.09 66.09 1 1.00e+01 1.00e-02 5.71e+01 dihedral pdb=" CB CYS C 214 " pdb=" SG CYS C 214 " pdb=" SG CYS C 225 " pdb=" CB CYS C 225 " ideal model delta sinusoidal sigma weight residual -86.00 -152.09 66.09 1 1.00e+01 1.00e-02 5.71e+01 ... (remaining 7437 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.146: 2086 0.146 - 0.291: 19 0.291 - 0.437: 10 0.437 - 0.583: 0 0.583 - 0.728: 5 Chirality restraints: 2120 Sorted by residual: chirality pdb=" CAG SY9 D 401 " pdb=" CAB SY9 D 401 " pdb=" CAK SY9 D 401 " pdb=" CAV SY9 D 401 " both_signs ideal model delta sigma weight residual False -2.68 -1.96 -0.73 2.00e-01 2.50e+01 1.33e+01 chirality pdb=" CAG SY9 A 503 " pdb=" CAB SY9 A 503 " pdb=" CAK SY9 A 503 " pdb=" CAV SY9 A 503 " both_signs ideal model delta sigma weight residual False -2.68 -1.96 -0.73 2.00e-01 2.50e+01 1.32e+01 chirality pdb=" CAG SY9 C 401 " pdb=" CAB SY9 C 401 " pdb=" CAK SY9 C 401 " pdb=" CAV SY9 C 401 " both_signs ideal model delta sigma weight residual False -2.68 -1.96 -0.72 2.00e-01 2.50e+01 1.31e+01 ... (remaining 2117 not shown) Planarity restraints: 2235 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 115 " -0.030 2.00e-02 2.50e+03 3.40e-02 2.02e+01 pdb=" CG PHE C 115 " 0.075 2.00e-02 2.50e+03 pdb=" CD1 PHE C 115 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 PHE C 115 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE C 115 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE C 115 " -0.023 2.00e-02 2.50e+03 pdb=" CZ PHE C 115 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 115 " -0.030 2.00e-02 2.50e+03 3.40e-02 2.02e+01 pdb=" CG PHE E 115 " 0.075 2.00e-02 2.50e+03 pdb=" CD1 PHE E 115 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 PHE E 115 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE E 115 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE E 115 " -0.023 2.00e-02 2.50e+03 pdb=" CZ PHE E 115 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 115 " -0.030 2.00e-02 2.50e+03 3.39e-02 2.01e+01 pdb=" CG PHE A 115 " 0.075 2.00e-02 2.50e+03 pdb=" CD1 PHE A 115 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 PHE A 115 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 115 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 115 " -0.023 2.00e-02 2.50e+03 pdb=" CZ PHE A 115 " 0.005 2.00e-02 2.50e+03 ... (remaining 2232 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2544 2.78 - 3.31: 12841 3.31 - 3.84: 21184 3.84 - 4.37: 24091 4.37 - 4.90: 40606 Nonbonded interactions: 101266 Sorted by model distance: nonbonded pdb=" OH TYR E 91 " pdb=" O SER E 98 " model vdw 2.250 3.040 nonbonded pdb=" OH TYR B 91 " pdb=" O SER B 98 " model vdw 2.250 3.040 nonbonded pdb=" OH TYR D 91 " pdb=" O SER D 98 " model vdw 2.250 3.040 nonbonded pdb=" OH TYR A 91 " pdb=" O SER A 98 " model vdw 2.251 3.040 nonbonded pdb=" OH TYR C 91 " pdb=" O SER C 98 " model vdw 2.251 3.040 ... (remaining 101261 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.480 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 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 : 0.008 0.114 13070 Z= 0.479 Angle : 1.326 11.471 17960 Z= 0.853 Chirality : 0.062 0.728 2120 Planarity : 0.004 0.034 2235 Dihedral : 8.453 79.771 4195 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.43 % Allowed : 1.72 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.18), residues: 1665 helix: -1.20 (0.19), residues: 575 sheet: -0.41 (0.22), residues: 385 loop : -2.11 (0.20), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 234 TYR 0.015 0.002 TYR D 144 PHE 0.075 0.003 PHE C 115 TRP 0.012 0.002 TRP B 259 HIS 0.002 0.001 HIS C 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00803 / 0.48 (13060) covalent geometry : angle 1.32661 / 0.85 (17935) SS BOND : bond 0.01190 / 0.65 ( 5) SS BOND : angle 0.74740 / 0.54 ( 10) hydrogen bonds : bond 0.08182 / 5.55 ( 681) hydrogen bonds : angle 9.47842 / 6.63 ( 2283) link_BETA1-4 : bond 0.02360 / 1.29 ( 5) link_BETA1-4 : angle 0.61971 / 0.37 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 295 time to evaluate : 0.430 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: 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 115 PHE cc_start: 0.8106 (OUTLIER) cc_final: 0.7836 (p90) REVERT: A 239 TYR cc_start: 0.7194 (m-80) cc_final: 0.6984 (m-80) REVERT: A 255 TRP cc_start: 0.8111 (m-10) cc_final: 0.7412 (m-10) REVERT: A 262 MET cc_start: 0.7608 (mtm) cc_final: 0.7233 (mtm) REVERT: A 277 LEU cc_start: 0.8917 (tp) cc_final: 0.8686 (tp) REVERT: B 72 MET cc_start: 0.7714 (tpp) cc_final: 0.7499 (tpp) REVERT: B 255 TRP cc_start: 0.8038 (m-10) cc_final: 0.7314 (m-10) REVERT: B 302 TRP cc_start: 0.7996 (t60) cc_final: 0.7655 (t60) REVERT: C 255 TRP cc_start: 0.8073 (m-10) cc_final: 0.7462 (m-10) REVERT: D 80 LEU cc_start: 0.8622 (tp) cc_final: 0.8398 (tp) REVERT: D 255 TRP cc_start: 0.8071 (m-10) cc_final: 0.7500 (m-10) REVERT: D 277 LEU cc_start: 0.9028 (tp) cc_final: 0.8787 (tp) REVERT: E 255 TRP cc_start: 0.8029 (m-10) cc_final: 0.7476 (m-10) REVERT: E 302 TRP cc_start: 0.8033 (t60) cc_final: 0.7777 (t60) outliers start: 5 outliers final: 0 residues processed: 300 average time/residue: 0.1156 time to fit residues: 49.4780 Evaluate side-chains 157 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 156 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 9.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 83 GLN A 235 GLN B 83 GLN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 GLN C 85 ASN D 85 ASN D 123 ASN E 83 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.039705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.033034 restraints weight = 95524.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.033760 restraints weight = 61793.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.034116 restraints weight = 44099.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.034495 restraints weight = 36726.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.034751 restraints weight = 31382.119| |-----------------------------------------------------------------------------| r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13070 Z= 0.198 Angle : 0.743 8.915 17960 Z= 0.375 Chirality : 0.045 0.169 2120 Planarity : 0.005 0.057 2235 Dihedral : 5.651 26.453 1822 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.28 % Allowed : 6.21 % Favored : 90.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.19), residues: 1665 helix: 0.86 (0.20), residues: 585 sheet: -0.33 (0.23), residues: 410 loop : -1.71 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 229 TYR 0.021 0.002 TYR A 144 PHE 0.027 0.002 PHE E 115 TRP 0.011 0.001 TRP A 255 HIS 0.004 0.002 HIS A 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.20 (13060) covalent geometry : angle 0.74291 / 0.38 (17935) SS BOND : bond 0.00080 / 0.04 ( 5) SS BOND : angle 0.87475 / 0.67 ( 10) hydrogen bonds : bond 0.04121 / 2.80 ( 681) hydrogen bonds : angle 6.51718 / 4.56 ( 2283) link_BETA1-4 : bond 0.01174 / 0.64 ( 5) link_BETA1-4 : angle 0.68061 / 0.42 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 178 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 PHE cc_start: 0.8931 (OUTLIER) cc_final: 0.8382 (p90) REVERT: A 255 TRP cc_start: 0.8685 (m-10) cc_final: 0.8446 (m-10) REVERT: A 274 THR cc_start: 0.9075 (m) cc_final: 0.8456 (t) REVERT: A 303 MET cc_start: 0.9033 (mmm) cc_final: 0.8617 (mmm) REVERT: B 72 MET cc_start: 0.8710 (tpp) cc_final: 0.7522 (tpp) REVERT: B 171 GLN cc_start: 0.8915 (pt0) cc_final: 0.8521 (pm20) REVERT: B 255 TRP cc_start: 0.8673 (m-10) cc_final: 0.8368 (m-10) REVERT: B 302 TRP cc_start: 0.8369 (t60) cc_final: 0.8110 (t60) REVERT: B 311 PHE cc_start: 0.9160 (t80) cc_final: 0.8604 (t80) REVERT: C 72 MET cc_start: 0.8575 (tpp) cc_final: 0.8303 (tpp) REVERT: C 119 GLU cc_start: 0.8231 (pm20) cc_final: 0.7948 (pm20) REVERT: C 171 GLN cc_start: 0.8973 (pt0) cc_final: 0.8569 (pm20) REVERT: C 192 VAL cc_start: 0.9096 (OUTLIER) cc_final: 0.8854 (t) REVERT: C 253 LEU cc_start: 0.9557 (mt) cc_final: 0.9351 (mt) REVERT: C 255 TRP cc_start: 0.8612 (m-10) cc_final: 0.8288 (m-10) REVERT: C 306 CYS cc_start: 0.8856 (m) cc_final: 0.8652 (m) REVERT: D 255 TRP cc_start: 0.8768 (m-10) cc_final: 0.8475 (m-10) REVERT: E 72 MET cc_start: 0.8276 (mmm) cc_final: 0.7540 (tpp) REVERT: E 120 LYS cc_start: 0.8799 (mttm) cc_final: 0.8506 (mtmm) REVERT: E 255 TRP cc_start: 0.8648 (m-10) cc_final: 0.8339 (m-10) outliers start: 38 outliers final: 25 residues processed: 205 average time/residue: 0.0914 time to fit residues: 28.7858 Evaluate side-chains 181 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 154 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 64 PHE Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain D residue 57 CYS Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 115 PHE Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 198 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 96 optimal weight: 20.0000 chunk 132 optimal weight: 8.9990 chunk 149 optimal weight: 6.9990 chunk 48 optimal weight: 0.5980 chunk 146 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 109 optimal weight: 8.9990 chunk 116 optimal weight: 0.6980 chunk 87 optimal weight: 9.9990 chunk 68 optimal weight: 0.6980 chunk 101 optimal weight: 9.9990 overall best weight: 2.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.038520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.032055 restraints weight = 105250.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.032817 restraints weight = 64151.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.033386 restraints weight = 45470.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.033729 restraints weight = 35971.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.034059 restraints weight = 30530.182| |-----------------------------------------------------------------------------| r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13070 Z= 0.184 Angle : 0.706 11.962 17960 Z= 0.349 Chirality : 0.044 0.183 2120 Planarity : 0.004 0.036 2235 Dihedral : 5.236 21.545 1822 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.62 % Allowed : 9.66 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.20), residues: 1665 helix: 1.69 (0.20), residues: 585 sheet: -0.40 (0.24), residues: 385 loop : -1.57 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 229 TYR 0.023 0.002 TYR C 144 PHE 0.018 0.002 PHE A 223 TRP 0.029 0.001 TRP E 302 HIS 0.003 0.001 HIS A 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.18 (13060) covalent geometry : angle 0.70572 / 0.35 (17935) SS BOND : bond 0.00056 / 0.03 ( 5) SS BOND : angle 0.98526 / 0.70 ( 10) hydrogen bonds : bond 0.03798 / 2.60 ( 681) hydrogen bonds : angle 5.81969 / 4.08 ( 2283) link_BETA1-4 : bond 0.00790 / 0.44 ( 5) link_BETA1-4 : angle 0.53190 / 0.32 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 163 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 MET cc_start: 0.8579 (tpp) cc_final: 0.7702 (tpp) REVERT: A 120 LYS cc_start: 0.8760 (mttm) cc_final: 0.8540 (mtmm) REVERT: A 170 MET cc_start: 0.8617 (tmm) cc_final: 0.7979 (tmm) REVERT: A 255 TRP cc_start: 0.8692 (m-10) cc_final: 0.8449 (m-10) REVERT: A 303 MET cc_start: 0.9080 (mmm) cc_final: 0.8666 (mmm) REVERT: B 64 PHE cc_start: 0.8743 (OUTLIER) cc_final: 0.7927 (t80) REVERT: B 72 MET cc_start: 0.8789 (tpp) cc_final: 0.7943 (tpp) REVERT: B 171 GLN cc_start: 0.8935 (pt0) cc_final: 0.8477 (pm20) REVERT: B 255 TRP cc_start: 0.8653 (m-10) cc_final: 0.8410 (m-10) REVERT: B 274 THR cc_start: 0.9101 (m) cc_final: 0.8896 (t) REVERT: B 302 TRP cc_start: 0.8524 (t60) cc_final: 0.8095 (t60) REVERT: B 303 MET cc_start: 0.9150 (mmm) cc_final: 0.8790 (mmm) REVERT: C 119 GLU cc_start: 0.7904 (pm20) cc_final: 0.7491 (pm20) REVERT: C 171 GLN cc_start: 0.8909 (pt0) cc_final: 0.8633 (pm20) REVERT: C 274 THR cc_start: 0.8942 (p) cc_final: 0.8590 (t) REVERT: D 72 MET cc_start: 0.8690 (tpp) cc_final: 0.8300 (tpp) REVERT: D 255 TRP cc_start: 0.8760 (m-10) cc_final: 0.8460 (m-10) REVERT: D 303 MET cc_start: 0.9135 (mmm) cc_final: 0.8841 (mmm) REVERT: E 72 MET cc_start: 0.8262 (mmm) cc_final: 0.7997 (mmm) REVERT: E 255 TRP cc_start: 0.8616 (m-10) cc_final: 0.8304 (m-10) REVERT: E 302 TRP cc_start: 0.8093 (t60) cc_final: 0.7768 (t60) outliers start: 42 outliers final: 33 residues processed: 189 average time/residue: 0.0947 time to fit residues: 27.5247 Evaluate side-chains 178 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 144 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 64 PHE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain D residue 57 CYS Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 198 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 138 optimal weight: 3.9990 chunk 134 optimal weight: 0.0170 chunk 92 optimal weight: 9.9990 chunk 79 optimal weight: 0.9980 chunk 52 optimal weight: 6.9990 chunk 36 optimal weight: 0.8980 chunk 116 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 127 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 overall best weight: 2.3822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 123 ASN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 ASN D 83 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.039757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.033243 restraints weight = 97412.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.033953 restraints weight = 62365.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.034382 restraints weight = 44716.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.034540 restraints weight = 36831.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.034808 restraints weight = 34165.861| |-----------------------------------------------------------------------------| r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13070 Z= 0.152 Angle : 0.657 9.639 17960 Z= 0.319 Chirality : 0.043 0.162 2120 Planarity : 0.003 0.027 2235 Dihedral : 4.940 22.307 1822 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.45 % Allowed : 11.38 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.21), residues: 1665 helix: 2.25 (0.20), residues: 585 sheet: -0.50 (0.24), residues: 385 loop : -1.43 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 147 TYR 0.019 0.002 TYR D 144 PHE 0.017 0.002 PHE E 115 TRP 0.015 0.001 TRP E 302 HIS 0.002 0.001 HIS C 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 (13060) covalent geometry : angle 0.65731 / 0.32 (17935) SS BOND : bond 0.00045 / 0.03 ( 5) SS BOND : angle 0.59039 / 0.44 ( 10) hydrogen bonds : bond 0.03573 / 2.43 ( 681) hydrogen bonds : angle 5.43030 / 3.80 ( 2283) link_BETA1-4 : bond 0.00743 / 0.40 ( 5) link_BETA1-4 : angle 0.48972 / 0.29 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 153 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 MET cc_start: 0.8373 (tpp) cc_final: 0.8007 (tpp) REVERT: A 219 ASN cc_start: 0.8595 (m-40) cc_final: 0.8237 (p0) REVERT: A 255 TRP cc_start: 0.8690 (m-10) cc_final: 0.8393 (m-10) REVERT: A 274 THR cc_start: 0.8899 (p) cc_final: 0.8640 (t) REVERT: A 303 MET cc_start: 0.9021 (mmm) cc_final: 0.8599 (mmm) REVERT: B 64 PHE cc_start: 0.8816 (OUTLIER) cc_final: 0.8101 (t80) REVERT: B 72 MET cc_start: 0.8615 (tpp) cc_final: 0.8065 (tpp) REVERT: B 119 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7345 (pm20) REVERT: B 171 GLN cc_start: 0.8953 (pt0) cc_final: 0.8447 (pm20) REVERT: B 219 ASN cc_start: 0.8744 (m-40) cc_final: 0.8409 (p0) REVERT: B 255 TRP cc_start: 0.8664 (m-10) cc_final: 0.8389 (m-10) REVERT: B 274 THR cc_start: 0.9111 (m) cc_final: 0.8901 (t) REVERT: B 302 TRP cc_start: 0.8510 (t60) cc_final: 0.7967 (t60) REVERT: B 303 MET cc_start: 0.9095 (mmm) cc_final: 0.8795 (mmm) REVERT: C 119 GLU cc_start: 0.8044 (pm20) cc_final: 0.7477 (pm20) REVERT: C 171 GLN cc_start: 0.8952 (pt0) cc_final: 0.8533 (pm20) REVERT: D 72 MET cc_start: 0.8721 (tpp) cc_final: 0.8346 (tpp) REVERT: D 255 TRP cc_start: 0.8772 (m-10) cc_final: 0.8489 (m-10) REVERT: E 255 TRP cc_start: 0.8625 (m-10) cc_final: 0.8283 (m-10) REVERT: E 274 THR cc_start: 0.8919 (m) cc_final: 0.8701 (t) REVERT: E 302 TRP cc_start: 0.8243 (t60) cc_final: 0.7369 (t60) outliers start: 40 outliers final: 28 residues processed: 180 average time/residue: 0.0868 time to fit residues: 24.5127 Evaluate side-chains 175 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 145 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 64 PHE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain D residue 57 CYS Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 198 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 1 optimal weight: 7.9990 chunk 68 optimal weight: 0.9980 chunk 16 optimal weight: 8.9990 chunk 94 optimal weight: 7.9990 chunk 60 optimal weight: 6.9990 chunk 134 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.039150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.032735 restraints weight = 99232.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.033222 restraints weight = 63178.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.033880 restraints weight = 49105.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.033958 restraints weight = 38721.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.033972 restraints weight = 35523.719| |-----------------------------------------------------------------------------| r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13070 Z= 0.213 Angle : 0.682 7.948 17960 Z= 0.340 Chirality : 0.043 0.161 2120 Planarity : 0.004 0.039 2235 Dihedral : 5.154 25.477 1820 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 4.14 % Allowed : 12.16 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.21), residues: 1665 helix: 2.15 (0.20), residues: 590 sheet: -0.76 (0.23), residues: 430 loop : -1.31 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 234 TYR 0.017 0.002 TYR A 144 PHE 0.022 0.002 PHE B 79 TRP 0.010 0.001 TRP B 259 HIS 0.005 0.002 HIS B 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.21 (13060) covalent geometry : angle 0.68123 / 0.34 (17935) SS BOND : bond 0.00133 / 0.09 ( 5) SS BOND : angle 0.62438 / 0.44 ( 10) hydrogen bonds : bond 0.03832 / 2.60 ( 681) hydrogen bonds : angle 5.55070 / 3.88 ( 2283) link_BETA1-4 : bond 0.00674 / 0.35 ( 5) link_BETA1-4 : angle 1.11593 / 0.70 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 150 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: A 64 PHE cc_start: 0.8703 (OUTLIER) cc_final: 0.8072 (t80) REVERT: A 72 MET cc_start: 0.8750 (tpp) cc_final: 0.8439 (tpp) REVERT: A 255 TRP cc_start: 0.8715 (m-10) cc_final: 0.8417 (m-10) REVERT: A 303 MET cc_start: 0.8994 (mmm) cc_final: 0.8502 (mmm) REVERT: B 64 PHE cc_start: 0.8744 (OUTLIER) cc_final: 0.8132 (t80) REVERT: B 72 MET cc_start: 0.8622 (tpp) cc_final: 0.8137 (tpp) REVERT: B 119 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7376 (pm20) REVERT: B 171 GLN cc_start: 0.8969 (pt0) cc_final: 0.8411 (pm20) REVERT: B 219 ASN cc_start: 0.8854 (m-40) cc_final: 0.8466 (p0) REVERT: B 255 TRP cc_start: 0.8675 (m-10) cc_final: 0.8375 (m-10) REVERT: B 302 TRP cc_start: 0.8531 (t60) cc_final: 0.8000 (t60) REVERT: B 303 MET cc_start: 0.9081 (mmm) cc_final: 0.8774 (mmm) REVERT: C 72 MET cc_start: 0.8479 (tpp) cc_final: 0.8156 (tpp) REVERT: C 171 GLN cc_start: 0.8896 (pt0) cc_final: 0.8580 (pm20) REVERT: D 72 MET cc_start: 0.8737 (tpp) cc_final: 0.8322 (tpp) REVERT: D 241 ILE cc_start: 0.9174 (mm) cc_final: 0.8826 (tt) REVERT: D 255 TRP cc_start: 0.8814 (m-10) cc_final: 0.8532 (m-10) REVERT: D 274 THR cc_start: 0.8947 (p) cc_final: 0.8704 (t) REVERT: E 255 TRP cc_start: 0.8696 (m-10) cc_final: 0.8385 (m-10) REVERT: E 302 TRP cc_start: 0.8317 (t60) cc_final: 0.7729 (t60) outliers start: 48 outliers final: 30 residues processed: 185 average time/residue: 0.0819 time to fit residues: 24.0558 Evaluate side-chains 171 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 138 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 64 PHE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain D residue 57 CYS Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 279 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 34 optimal weight: 7.9990 chunk 96 optimal weight: 20.0000 chunk 134 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 158 optimal weight: 0.8980 chunk 62 optimal weight: 9.9990 chunk 116 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 90 optimal weight: 20.0000 chunk 24 optimal weight: 0.0470 chunk 28 optimal weight: 6.9990 overall best weight: 1.9882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.039759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.033126 restraints weight = 95878.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.033653 restraints weight = 61704.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.034060 restraints weight = 48217.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.034385 restraints weight = 40321.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.034385 restraints weight = 34615.959| |-----------------------------------------------------------------------------| r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13070 Z= 0.142 Angle : 0.656 13.839 17960 Z= 0.314 Chirality : 0.043 0.146 2120 Planarity : 0.003 0.037 2235 Dihedral : 4.880 22.403 1820 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.05 % Allowed : 13.19 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.21), residues: 1665 helix: 2.64 (0.20), residues: 585 sheet: -0.81 (0.23), residues: 430 loop : -1.21 (0.26), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 147 TYR 0.013 0.002 TYR E 144 PHE 0.014 0.001 PHE E 115 TRP 0.008 0.001 TRP D 259 HIS 0.002 0.001 HIS B 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (13060) covalent geometry : angle 0.65582 / 0.31 (17935) SS BOND : bond 0.00052 / 0.03 ( 5) SS BOND : angle 0.54211 / 0.40 ( 10) hydrogen bonds : bond 0.03474 / 2.36 ( 681) hydrogen bonds : angle 5.29457 / 3.70 ( 2283) link_BETA1-4 : bond 0.00754 / 0.39 ( 5) link_BETA1-4 : angle 0.57749 / 0.32 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 149 time to evaluate : 0.462 Fit side-chains REVERT: A 64 PHE cc_start: 0.8711 (OUTLIER) cc_final: 0.8010 (t80) REVERT: A 72 MET cc_start: 0.8701 (tpp) cc_final: 0.8448 (tpp) REVERT: A 219 ASN cc_start: 0.8721 (m-40) cc_final: 0.8306 (p0) REVERT: A 255 TRP cc_start: 0.8651 (m-10) cc_final: 0.8340 (m-10) REVERT: B 64 PHE cc_start: 0.8803 (OUTLIER) cc_final: 0.8220 (t80) REVERT: B 72 MET cc_start: 0.8650 (tpp) cc_final: 0.8018 (tpp) REVERT: B 119 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7341 (pm20) REVERT: B 171 GLN cc_start: 0.8907 (pt0) cc_final: 0.8352 (pm20) REVERT: B 219 ASN cc_start: 0.8903 (m-40) cc_final: 0.8397 (p0) REVERT: B 255 TRP cc_start: 0.8661 (m-10) cc_final: 0.8393 (m-10) REVERT: B 302 TRP cc_start: 0.8543 (t60) cc_final: 0.7921 (t60) REVERT: B 303 MET cc_start: 0.9061 (mmm) cc_final: 0.8682 (mmm) REVERT: C 72 MET cc_start: 0.8457 (tpp) cc_final: 0.8125 (tpp) REVERT: C 171 GLN cc_start: 0.8843 (pt0) cc_final: 0.8474 (pm20) REVERT: C 255 TRP cc_start: 0.8684 (m-10) cc_final: 0.8431 (m-10) REVERT: D 72 MET cc_start: 0.8736 (tpp) cc_final: 0.8465 (tpp) REVERT: D 241 ILE cc_start: 0.9156 (mm) cc_final: 0.8801 (tt) REVERT: D 255 TRP cc_start: 0.8823 (m-10) cc_final: 0.8543 (m-10) REVERT: D 302 TRP cc_start: 0.8496 (t60) cc_final: 0.7731 (t60) REVERT: E 72 MET cc_start: 0.8426 (mmt) cc_final: 0.8002 (tpp) REVERT: E 255 TRP cc_start: 0.8711 (m-10) cc_final: 0.8405 (m-10) REVERT: E 274 THR cc_start: 0.9048 (m) cc_final: 0.8779 (t) REVERT: E 302 TRP cc_start: 0.8382 (t60) cc_final: 0.7611 (t60) outliers start: 47 outliers final: 30 residues processed: 184 average time/residue: 0.0774 time to fit residues: 22.9170 Evaluate side-chains 180 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 147 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 64 PHE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain D residue 57 CYS Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 279 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 101 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 113 optimal weight: 7.9990 chunk 33 optimal weight: 0.5980 chunk 144 optimal weight: 8.9990 chunk 30 optimal weight: 20.0000 chunk 91 optimal weight: 5.9990 chunk 154 optimal weight: 2.9990 chunk 160 optimal weight: 9.9990 chunk 51 optimal weight: 8.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.039183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.032720 restraints weight = 98412.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.033456 restraints weight = 63908.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.033804 restraints weight = 46335.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.033804 restraints weight = 37776.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.033804 restraints weight = 37776.343| |-----------------------------------------------------------------------------| r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.4414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 13070 Z= 0.225 Angle : 0.699 10.513 17960 Z= 0.343 Chirality : 0.043 0.166 2120 Planarity : 0.004 0.041 2235 Dihedral : 5.081 22.954 1820 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.97 % Allowed : 13.97 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.21), residues: 1665 helix: 2.33 (0.20), residues: 590 sheet: -0.86 (0.23), residues: 430 loop : -1.35 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 147 TYR 0.015 0.002 TYR E 144 PHE 0.015 0.002 PHE B 175 TRP 0.010 0.001 TRP B 259 HIS 0.005 0.002 HIS B 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.23 (13060) covalent geometry : angle 0.69876 / 0.34 (17935) SS BOND : bond 0.00141 / 0.09 ( 5) SS BOND : angle 0.58617 / 0.43 ( 10) hydrogen bonds : bond 0.03843 / 2.64 ( 681) hydrogen bonds : angle 5.46155 / 3.80 ( 2283) link_BETA1-4 : bond 0.00738 / 0.39 ( 5) link_BETA1-4 : angle 0.90384 / 0.53 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 148 time to evaluate : 0.457 Fit side-chains revert: symmetry clash REVERT: A 64 PHE cc_start: 0.8734 (OUTLIER) cc_final: 0.8097 (t80) REVERT: A 72 MET cc_start: 0.8638 (tpp) cc_final: 0.8280 (tpp) REVERT: A 255 TRP cc_start: 0.8709 (m-10) cc_final: 0.8429 (m-10) REVERT: A 303 MET cc_start: 0.9066 (mmt) cc_final: 0.8748 (mmm) REVERT: B 64 PHE cc_start: 0.8835 (OUTLIER) cc_final: 0.8309 (t80) REVERT: B 72 MET cc_start: 0.8555 (tpp) cc_final: 0.8121 (tpp) REVERT: B 119 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7417 (pm20) REVERT: B 171 GLN cc_start: 0.8923 (pt0) cc_final: 0.8358 (pm20) REVERT: B 219 ASN cc_start: 0.8885 (m-40) cc_final: 0.8438 (p0) REVERT: B 302 TRP cc_start: 0.8544 (t60) cc_final: 0.7915 (t60) REVERT: B 303 MET cc_start: 0.9018 (mmm) cc_final: 0.8730 (mmm) REVERT: C 64 PHE cc_start: 0.8687 (OUTLIER) cc_final: 0.8344 (t80) REVERT: C 72 MET cc_start: 0.8432 (tpp) cc_final: 0.8122 (tpp) REVERT: C 171 GLN cc_start: 0.8795 (pt0) cc_final: 0.8403 (pm20) REVERT: C 255 TRP cc_start: 0.8683 (m-10) cc_final: 0.8419 (m-10) REVERT: C 282 GLN cc_start: 0.9172 (tp40) cc_final: 0.8537 (tp-100) REVERT: D 72 MET cc_start: 0.8753 (tpp) cc_final: 0.8478 (tpp) REVERT: D 241 ILE cc_start: 0.9142 (mm) cc_final: 0.8803 (tt) REVERT: D 255 TRP cc_start: 0.8848 (m-10) cc_final: 0.8473 (m-10) REVERT: D 302 TRP cc_start: 0.8510 (t60) cc_final: 0.8097 (t60) REVERT: E 255 TRP cc_start: 0.8704 (m-10) cc_final: 0.8421 (m-10) REVERT: E 274 THR cc_start: 0.9082 (m) cc_final: 0.8837 (t) REVERT: E 302 TRP cc_start: 0.8424 (t60) cc_final: 0.7760 (t60) outliers start: 46 outliers final: 31 residues processed: 184 average time/residue: 0.0809 time to fit residues: 23.8877 Evaluate side-chains 178 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 143 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 64 PHE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 64 PHE Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain D residue 57 CYS Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 279 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 87 optimal weight: 7.9990 chunk 109 optimal weight: 4.9990 chunk 63 optimal weight: 20.0000 chunk 103 optimal weight: 5.9990 chunk 126 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 157 optimal weight: 6.9990 chunk 62 optimal weight: 20.0000 chunk 86 optimal weight: 20.0000 chunk 114 optimal weight: 6.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 54 ASN ** A 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN ** E 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.038543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.032048 restraints weight = 98520.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.032817 restraints weight = 64775.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.033174 restraints weight = 46724.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.033174 restraints weight = 38205.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.033174 restraints weight = 38205.051| |-----------------------------------------------------------------------------| r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.4935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 13070 Z= 0.314 Angle : 0.818 19.140 17960 Z= 0.405 Chirality : 0.045 0.183 2120 Planarity : 0.006 0.057 2235 Dihedral : 5.724 24.235 1820 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 19.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 3.79 % Allowed : 15.00 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.20), residues: 1665 helix: 1.53 (0.20), residues: 595 sheet: -1.42 (0.24), residues: 405 loop : -1.66 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 147 TYR 0.023 0.003 TYR E 144 PHE 0.018 0.003 PHE C 124 TRP 0.012 0.002 TRP E 259 HIS 0.008 0.003 HIS B 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00644 / 0.31 (13060) covalent geometry : angle 0.81791 / 0.41 (17935) SS BOND : bond 0.00233 / 0.14 ( 5) SS BOND : angle 0.79438 / 0.57 ( 10) hydrogen bonds : bond 0.04633 / 3.17 ( 681) hydrogen bonds : angle 5.92710 / 4.14 ( 2283) link_BETA1-4 : bond 0.00888 / 0.49 ( 5) link_BETA1-4 : angle 1.07805 / 0.65 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 141 time to evaluate : 0.465 Fit side-chains revert: symmetry clash REVERT: A 64 PHE cc_start: 0.8778 (OUTLIER) cc_final: 0.8124 (t80) REVERT: A 72 MET cc_start: 0.8500 (tpp) cc_final: 0.8001 (tpp) REVERT: A 156 MET cc_start: 0.7812 (mpp) cc_final: 0.7333 (mpp) REVERT: A 255 TRP cc_start: 0.8738 (m-10) cc_final: 0.8506 (m-10) REVERT: B 64 PHE cc_start: 0.8863 (OUTLIER) cc_final: 0.8407 (t80) REVERT: B 119 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7399 (pm20) REVERT: B 171 GLN cc_start: 0.8884 (pt0) cc_final: 0.8234 (pm20) REVERT: B 302 TRP cc_start: 0.8470 (t60) cc_final: 0.7931 (t60) REVERT: B 303 MET cc_start: 0.9003 (mmm) cc_final: 0.8702 (mmm) REVERT: C 64 PHE cc_start: 0.8747 (OUTLIER) cc_final: 0.8405 (t80) REVERT: C 72 MET cc_start: 0.8454 (tpp) cc_final: 0.8165 (tpp) REVERT: C 282 GLN cc_start: 0.9207 (tp40) cc_final: 0.8528 (tp-100) REVERT: C 303 MET cc_start: 0.8994 (mmm) cc_final: 0.8040 (mmm) REVERT: D 72 MET cc_start: 0.8718 (tpp) cc_final: 0.8434 (tpp) REVERT: D 241 ILE cc_start: 0.9088 (mm) cc_final: 0.8752 (tt) REVERT: D 255 TRP cc_start: 0.8874 (m-10) cc_final: 0.8513 (m-10) REVERT: D 262 MET cc_start: 0.8361 (mtp) cc_final: 0.8068 (mtt) REVERT: E 255 TRP cc_start: 0.8727 (m-10) cc_final: 0.8474 (m-10) outliers start: 44 outliers final: 33 residues processed: 177 average time/residue: 0.0752 time to fit residues: 21.3391 Evaluate side-chains 172 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 135 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 64 PHE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 64 PHE Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain D residue 57 CYS Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 279 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 3 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 151 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 34 optimal weight: 0.0370 chunk 67 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 43 optimal weight: 0.8980 chunk 23 optimal weight: 7.9990 chunk 123 optimal weight: 5.9990 overall best weight: 2.3864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.039716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.033122 restraints weight = 98449.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.033885 restraints weight = 63219.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 15)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.034305 restraints weight = 45921.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.034805 restraints weight = 37034.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.034864 restraints weight = 32338.876| |-----------------------------------------------------------------------------| r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.4881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13070 Z= 0.157 Angle : 0.697 14.266 17960 Z= 0.331 Chirality : 0.043 0.138 2120 Planarity : 0.004 0.040 2235 Dihedral : 5.178 22.828 1820 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.62 % Allowed : 15.43 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.21), residues: 1665 helix: 2.29 (0.20), residues: 595 sheet: -1.21 (0.23), residues: 410 loop : -1.44 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 147 TYR 0.013 0.002 TYR E 144 PHE 0.017 0.001 PHE E 115 TRP 0.012 0.001 TRP E 302 HIS 0.003 0.001 HIS B 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.16 (13060) covalent geometry : angle 0.69697 / 0.33 (17935) SS BOND : bond 0.00135 / 0.10 ( 5) SS BOND : angle 0.70547 / 0.52 ( 10) hydrogen bonds : bond 0.03648 / 2.49 ( 681) hydrogen bonds : angle 5.36491 / 3.74 ( 2283) link_BETA1-4 : bond 0.00785 / 0.42 ( 5) link_BETA1-4 : angle 0.58661 / 0.32 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 146 time to evaluate : 0.493 Fit side-chains REVERT: A 64 PHE cc_start: 0.8736 (OUTLIER) cc_final: 0.8130 (t80) REVERT: A 72 MET cc_start: 0.8464 (tpp) cc_final: 0.8090 (tpp) REVERT: A 170 MET cc_start: 0.8750 (tmm) cc_final: 0.8127 (tmm) REVERT: A 241 ILE cc_start: 0.9058 (mm) cc_final: 0.8731 (tp) REVERT: A 255 TRP cc_start: 0.8728 (m-10) cc_final: 0.8474 (m-10) REVERT: B 64 PHE cc_start: 0.8875 (OUTLIER) cc_final: 0.8499 (t80) REVERT: B 72 MET cc_start: 0.8350 (tpp) cc_final: 0.7962 (tpp) REVERT: B 119 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7354 (pm20) REVERT: B 171 GLN cc_start: 0.8787 (pt0) cc_final: 0.8270 (pt0) REVERT: B 219 ASN cc_start: 0.8753 (m-40) cc_final: 0.8330 (p0) REVERT: B 255 TRP cc_start: 0.8781 (m-10) cc_final: 0.8439 (m-10) REVERT: B 302 TRP cc_start: 0.8513 (t60) cc_final: 0.7782 (t60) REVERT: B 303 MET cc_start: 0.9011 (mmm) cc_final: 0.8657 (mmm) REVERT: C 72 MET cc_start: 0.8567 (tpp) cc_final: 0.8212 (tpp) REVERT: C 255 TRP cc_start: 0.8702 (m-10) cc_final: 0.8411 (m-10) REVERT: C 282 GLN cc_start: 0.9165 (tp40) cc_final: 0.8508 (tp-100) REVERT: D 72 MET cc_start: 0.8699 (tpp) cc_final: 0.8433 (tpp) REVERT: D 170 MET cc_start: 0.8622 (tmm) cc_final: 0.8406 (tmm) REVERT: D 241 ILE cc_start: 0.8976 (mm) cc_final: 0.8630 (tt) REVERT: D 255 TRP cc_start: 0.8854 (m-10) cc_final: 0.8446 (m-10) REVERT: D 302 TRP cc_start: 0.8447 (t60) cc_final: 0.7571 (t60) REVERT: E 72 MET cc_start: 0.8450 (mmt) cc_final: 0.8231 (tpp) REVERT: E 255 TRP cc_start: 0.8685 (m-10) cc_final: 0.8432 (m-10) REVERT: E 274 THR cc_start: 0.9043 (m) cc_final: 0.8803 (t) REVERT: E 302 TRP cc_start: 0.8330 (t60) cc_final: 0.7779 (t60) outliers start: 42 outliers final: 30 residues processed: 180 average time/residue: 0.0802 time to fit residues: 23.2229 Evaluate side-chains 172 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 139 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 64 PHE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain D residue 57 CYS Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 279 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 130 optimal weight: 6.9990 chunk 150 optimal weight: 9.9990 chunk 70 optimal weight: 0.0030 chunk 69 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 chunk 45 optimal weight: 7.9990 chunk 100 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 63 optimal weight: 4.9990 chunk 93 optimal weight: 6.9990 overall best weight: 4.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.039420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.033056 restraints weight = 99564.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.033819 restraints weight = 65247.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.034158 restraints weight = 46554.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.034501 restraints weight = 37623.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.034714 restraints weight = 32414.030| |-----------------------------------------------------------------------------| r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.5059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13070 Z= 0.228 Angle : 0.746 13.233 17960 Z= 0.360 Chirality : 0.044 0.193 2120 Planarity : 0.005 0.042 2235 Dihedral : 5.344 23.398 1820 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.45 % Allowed : 16.21 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.21), residues: 1665 helix: 2.05 (0.20), residues: 600 sheet: -1.45 (0.23), residues: 410 loop : -1.38 (0.25), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 147 TYR 0.015 0.002 TYR E 357 PHE 0.018 0.002 PHE A 311 TRP 0.010 0.001 TRP D 259 HIS 0.006 0.002 HIS B 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.23 (13060) covalent geometry : angle 0.74614 / 0.36 (17935) SS BOND : bond 0.00199 / 0.14 ( 5) SS BOND : angle 0.72439 / 0.53 ( 10) hydrogen bonds : bond 0.04005 / 2.75 ( 681) hydrogen bonds : angle 5.51043 / 3.83 ( 2283) link_BETA1-4 : bond 0.00800 / 0.42 ( 5) link_BETA1-4 : angle 0.82210 / 0.47 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 140 time to evaluate : 0.347 Fit side-chains REVERT: A 64 PHE cc_start: 0.8727 (OUTLIER) cc_final: 0.8109 (t80) REVERT: A 72 MET cc_start: 0.8435 (tpp) cc_final: 0.8065 (tpp) REVERT: A 241 ILE cc_start: 0.9126 (mm) cc_final: 0.8805 (tp) REVERT: A 255 TRP cc_start: 0.8748 (m-10) cc_final: 0.8478 (m-10) REVERT: B 64 PHE cc_start: 0.8845 (OUTLIER) cc_final: 0.8528 (t80) REVERT: B 72 MET cc_start: 0.8310 (tpp) cc_final: 0.7925 (tpp) REVERT: B 119 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7364 (pm20) REVERT: B 171 GLN cc_start: 0.8733 (pt0) cc_final: 0.8186 (pm20) REVERT: B 219 ASN cc_start: 0.8762 (m-40) cc_final: 0.8332 (p0) REVERT: B 255 TRP cc_start: 0.8823 (m-10) cc_final: 0.8436 (m-10) REVERT: B 302 TRP cc_start: 0.8523 (t60) cc_final: 0.7852 (t60) REVERT: B 303 MET cc_start: 0.8994 (mmm) cc_final: 0.8577 (mmm) REVERT: C 64 PHE cc_start: 0.8682 (OUTLIER) cc_final: 0.8316 (t80) REVERT: C 72 MET cc_start: 0.8492 (tpp) cc_final: 0.8234 (tpp) REVERT: C 255 TRP cc_start: 0.8744 (m-10) cc_final: 0.8426 (m-10) REVERT: C 282 GLN cc_start: 0.9155 (tp40) cc_final: 0.8525 (tp-100) REVERT: D 72 MET cc_start: 0.8742 (tpp) cc_final: 0.8377 (tpp) REVERT: D 241 ILE cc_start: 0.8990 (mm) cc_final: 0.8654 (tt) REVERT: D 255 TRP cc_start: 0.8871 (m-10) cc_final: 0.8491 (m-10) REVERT: D 262 MET cc_start: 0.8243 (mtp) cc_final: 0.7931 (mtt) REVERT: E 72 MET cc_start: 0.8429 (mmt) cc_final: 0.8163 (tpp) REVERT: E 255 TRP cc_start: 0.8715 (m-10) cc_final: 0.8411 (m-10) REVERT: E 302 TRP cc_start: 0.8332 (t60) cc_final: 0.8010 (t60) outliers start: 40 outliers final: 30 residues processed: 172 average time/residue: 0.0788 time to fit residues: 22.0216 Evaluate side-chains 171 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 137 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 64 PHE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 64 PHE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain D residue 57 CYS Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 279 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 91 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 132 optimal weight: 0.0020 chunk 90 optimal weight: 7.9990 chunk 3 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 chunk 22 optimal weight: 0.0470 chunk 135 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 overall best weight: 1.0092 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.040497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.033871 restraints weight = 97144.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.034677 restraints weight = 62036.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.035097 restraints weight = 43301.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.035418 restraints weight = 34711.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.035661 restraints weight = 30324.784| |-----------------------------------------------------------------------------| r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.5022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13070 Z= 0.126 Angle : 0.697 13.322 17960 Z= 0.325 Chirality : 0.043 0.141 2120 Planarity : 0.003 0.040 2235 Dihedral : 4.889 22.016 1820 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.67 % Allowed : 16.81 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.21), residues: 1665 helix: 2.69 (0.20), residues: 600 sheet: -1.00 (0.23), residues: 435 loop : -1.24 (0.27), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 147 TYR 0.013 0.001 TYR E 144 PHE 0.015 0.001 PHE D 230 TRP 0.012 0.001 TRP D 302 HIS 0.002 0.001 HIS E 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 (13060) covalent geometry : angle 0.69676 / 0.32 (17935) SS BOND : bond 0.00104 / 0.08 ( 5) SS BOND : angle 0.64693 / 0.48 ( 10) hydrogen bonds : bond 0.03351 / 2.29 ( 681) hydrogen bonds : angle 5.05711 / 3.51 ( 2283) link_BETA1-4 : bond 0.00800 / 0.43 ( 5) link_BETA1-4 : angle 0.63009 / 0.38 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1576.20 seconds wall clock time: 28 minutes 17.91 seconds (1697.91 seconds total)