Starting phenix.real_space_refine on Wed Jun 11 14:03:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3jad_6344/06_2025/3jad_6344.cif Found real_map, /net/cci-nas-00/data/ceres_data/3jad_6344/06_2025/3jad_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_6344/06_2025/3jad_6344.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3jad_6344/06_2025/3jad_6344.map" model { file = "/net/cci-nas-00/data/ceres_data/3jad_6344/06_2025/3jad_6344.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3jad_6344/06_2025/3jad_6344.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 8, 'PHE:plan': 3, 'GLU:plan': 11, 'ARG:plan': 5} 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: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 8, 'PHE:plan': 3, 'GLU:plan': 11, 'ARG:plan': 5} 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: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 8, 'PHE:plan': 3, 'GLU:plan': 11, 'ARG:plan': 5} 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: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 8, 'PHE:plan': 3, 'GLU:plan': 11, 'ARG:plan': 5} 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: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 8, 'PHE:plan': 3, 'GLU:plan': 11, 'ARG:plan': 5} 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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: 7.86, per 1000 atoms: 0.62 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: 3.49 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.30 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: 3.81 Time building geometry restraints manager: 4.07 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: 7664 15.95 - 31.91: 187 31.91 - 47.86: 54 47.86 - 63.82: 40 63.82 - 79.77: 10 Dihedral angle restraints: 7955 sinusoidal: 2975 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 7952 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } ncs_group { reference = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' 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: 1.420 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: 0.480 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 31.560 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 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 : 10.082 79.771 4710 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.012 0.002 TRP B 259 HIS 0.002 0.001 HIS C 217 PHE 0.075 0.003 PHE C 115 TYR 0.015 0.002 TYR D 144 ARG 0.006 0.001 ARG B 234 Details of bonding type rmsd link_BETA1-4 : bond 0.02360 ( 5) link_BETA1-4 : angle 0.61971 ( 15) hydrogen bonds : bond 0.08182 ( 681) hydrogen bonds : angle 9.47842 ( 2283) SS BOND : bond 0.01190 ( 5) SS BOND : angle 0.74740 ( 10) covalent geometry : bond 0.00803 (13060) covalent geometry : angle 1.32661 (17935) *********************** 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 : 1.368 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: 0.7837 (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: 0.8399 (tp) REVERT: D 255 TRP cc_start: 0.8072 (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: 0.2759 time to fit residues: 114.8730 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 : 1.498 ------------------------------------------------------------------------------- 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 139 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 84 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 78 optimal weight: 8.9990 chunk 96 optimal weight: 0.0770 chunk 149 optimal weight: 2.9990 overall best weight: 2.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 GLN B 83 GLN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 GLN D 123 ASN D 235 GLN E 83 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.040069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.033347 restraints weight = 94324.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.034050 restraints weight = 61182.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.034457 restraints weight = 44260.470| |-----------------------------------------------------------------------------| r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 13070 Z= 0.174 Angle : 0.724 9.158 17960 Z= 0.365 Chirality : 0.045 0.174 2120 Planarity : 0.004 0.057 2235 Dihedral : 8.146 59.884 2337 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.76 % Allowed : 6.47 % Favored : 90.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.19), residues: 1665 helix: 0.95 (0.20), residues: 580 sheet: -0.35 (0.22), residues: 410 loop : -1.59 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 259 HIS 0.004 0.001 HIS E 125 PHE 0.028 0.002 PHE E 115 TYR 0.020 0.002 TYR A 144 ARG 0.005 0.001 ARG D 229 Details of bonding type rmsd link_BETA1-4 : bond 0.01290 ( 5) link_BETA1-4 : angle 0.48929 ( 15) hydrogen bonds : bond 0.04039 ( 681) hydrogen bonds : angle 6.54705 ( 2283) SS BOND : bond 0.00100 ( 5) SS BOND : angle 0.85425 ( 10) covalent geometry : bond 0.00375 (13060) covalent geometry : angle 0.72380 (17935) *********************** 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: 32 poor density : 184 time to evaluate : 1.467 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: 0.8928 (OUTLIER) cc_final: 0.8398 (p90) REVERT: A 119 GLU cc_start: 0.8059 (pm20) cc_final: 0.7628 (pm20) REVERT: A 219 ASN cc_start: 0.8635 (m-40) cc_final: 0.8291 (p0) REVERT: A 255 TRP cc_start: 0.8694 (m-10) cc_final: 0.8455 (m-10) REVERT: A 274 THR cc_start: 0.9077 (m) cc_final: 0.8461 (t) REVERT: A 303 MET cc_start: 0.9049 (mmm) cc_final: 0.8626 (mmm) REVERT: B 72 MET cc_start: 0.8723 (tpp) cc_final: 0.8103 (tpp) REVERT: B 119 GLU cc_start: 0.8378 (pm20) cc_final: 0.7969 (pm20) REVERT: B 255 TRP cc_start: 0.8652 (m-10) cc_final: 0.8353 (m-10) REVERT: B 302 TRP cc_start: 0.8415 (t60) cc_final: 0.8196 (t60) REVERT: B 311 PHE cc_start: 0.9183 (t80) cc_final: 0.8602 (t80) REVERT: C 119 GLU cc_start: 0.8275 (pm20) cc_final: 0.7935 (pm20) REVERT: C 171 GLN cc_start: 0.8996 (pt0) cc_final: 0.8558 (pm20) REVERT: C 239 TYR cc_start: 0.8774 (m-80) cc_final: 0.8487 (m-80) REVERT: C 253 LEU cc_start: 0.9558 (mt) cc_final: 0.9334 (mt) REVERT: C 255 TRP cc_start: 0.8594 (m-10) cc_final: 0.8265 (m-10) REVERT: D 255 TRP cc_start: 0.8706 (m-10) cc_final: 0.8425 (m-10) REVERT: E 72 MET cc_start: 0.8316 (mmm) cc_final: 0.7637 (tpp) REVERT: E 255 TRP cc_start: 0.8625 (m-10) cc_final: 0.8315 (m-10) outliers start: 32 outliers final: 21 residues processed: 205 average time/residue: 0.2201 time to fit residues: 67.6514 Evaluate side-chains 177 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 155 time to evaluate : 1.475 ------------------------------------------------------------------------------- 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 168 CYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain B residue 57 CYS 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 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 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 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 151 optimal weight: 0.8980 chunk 90 optimal weight: 0.8980 chunk 132 optimal weight: 8.9990 chunk 114 optimal weight: 4.9990 chunk 109 optimal weight: 0.0970 chunk 154 optimal weight: 8.9990 chunk 122 optimal weight: 9.9990 chunk 75 optimal weight: 6.9990 chunk 77 optimal weight: 8.9990 chunk 130 optimal weight: 10.0000 chunk 139 optimal weight: 20.0000 overall best weight: 2.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 83 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 = 0.2810 r_free = 0.2810 target = 0.038726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.032269 restraints weight = 103481.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.033062 restraints weight = 63428.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.033462 restraints weight = 45305.660| |-----------------------------------------------------------------------------| r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 13070 Z= 0.175 Angle : 0.694 13.407 17960 Z= 0.343 Chirality : 0.044 0.168 2120 Planarity : 0.004 0.033 2235 Dihedral : 7.431 59.659 2337 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.36 % Allowed : 9.57 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.20), residues: 1665 helix: 1.72 (0.20), residues: 585 sheet: -0.37 (0.24), residues: 385 loop : -1.55 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 302 HIS 0.003 0.001 HIS E 217 PHE 0.017 0.002 PHE E 115 TYR 0.024 0.002 TYR E 144 ARG 0.004 0.001 ARG D 229 Details of bonding type rmsd link_BETA1-4 : bond 0.00768 ( 5) link_BETA1-4 : angle 0.56818 ( 15) hydrogen bonds : bond 0.03789 ( 681) hydrogen bonds : angle 5.81873 ( 2283) SS BOND : bond 0.00082 ( 5) SS BOND : angle 0.98625 ( 10) covalent geometry : bond 0.00376 (13060) covalent geometry : angle 0.69363 (17935) *********************** 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: 39 poor density : 166 time to evaluate : 1.408 Fit side-chains revert: symmetry clash REVERT: A 72 MET cc_start: 0.8586 (tpp) cc_final: 0.7765 (tpp) REVERT: A 170 MET cc_start: 0.8304 (tmm) cc_final: 0.7830 (tmm) REVERT: A 219 ASN cc_start: 0.8543 (m-40) cc_final: 0.8223 (p0) REVERT: A 255 TRP cc_start: 0.8670 (m-10) cc_final: 0.8431 (m-10) REVERT: A 303 MET cc_start: 0.9107 (mmm) cc_final: 0.8673 (mmm) REVERT: B 64 PHE cc_start: 0.8773 (OUTLIER) cc_final: 0.8327 (t80) REVERT: B 72 MET cc_start: 0.8628 (tpp) cc_final: 0.7926 (tpp) REVERT: B 255 TRP cc_start: 0.8688 (m-10) cc_final: 0.8459 (m-10) REVERT: B 302 TRP cc_start: 0.8544 (t60) cc_final: 0.8169 (t60) REVERT: B 303 MET cc_start: 0.9129 (mmm) cc_final: 0.8754 (mmm) REVERT: C 72 MET cc_start: 0.8548 (tpp) cc_final: 0.8236 (tpp) REVERT: C 119 GLU cc_start: 0.7979 (pm20) cc_final: 0.7454 (pm20) REVERT: C 171 GLN cc_start: 0.8895 (pt0) cc_final: 0.8503 (pm20) REVERT: C 255 TRP cc_start: 0.8587 (m-10) cc_final: 0.8322 (m-10) REVERT: C 274 THR cc_start: 0.8960 (p) cc_final: 0.8590 (t) REVERT: D 72 MET cc_start: 0.8695 (tpp) cc_final: 0.8275 (tpp) REVERT: D 82 GLN cc_start: 0.8979 (mp10) cc_final: 0.8769 (mp10) REVERT: D 255 TRP cc_start: 0.8779 (m-10) cc_final: 0.8499 (m-10) REVERT: D 303 MET cc_start: 0.9152 (mmm) cc_final: 0.8816 (mmm) REVERT: E 170 MET cc_start: 0.8658 (tmm) cc_final: 0.8271 (tmm) REVERT: E 255 TRP cc_start: 0.8602 (m-10) cc_final: 0.8287 (m-10) outliers start: 39 outliers final: 28 residues processed: 192 average time/residue: 0.2311 time to fit residues: 66.5082 Evaluate side-chains 175 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 146 time to evaluate : 1.597 ------------------------------------------------------------------------------- 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 172 LEU Chi-restraints excluded: chain A residue 198 LEU 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 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 123 optimal weight: 0.0980 chunk 13 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 44 optimal weight: 7.9990 chunk 134 optimal weight: 2.9990 chunk 125 optimal weight: 6.9990 chunk 147 optimal weight: 6.9990 chunk 142 optimal weight: 10.0000 chunk 121 optimal weight: 0.9980 chunk 50 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 ASN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 ASN ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 235 GLN ** 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 = 0.2819 r_free = 0.2819 target = 0.039883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.033335 restraints weight = 97310.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.034059 restraints weight = 61420.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.034488 restraints weight = 43879.026| |-----------------------------------------------------------------------------| r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13070 Z= 0.155 Angle : 0.644 9.185 17960 Z= 0.317 Chirality : 0.043 0.145 2120 Planarity : 0.004 0.034 2235 Dihedral : 7.086 59.120 2337 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.71 % Allowed : 10.69 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.21), residues: 1665 helix: 2.28 (0.20), residues: 585 sheet: -0.61 (0.23), residues: 440 loop : -1.30 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 259 HIS 0.002 0.001 HIS C 217 PHE 0.018 0.002 PHE E 115 TYR 0.024 0.002 TYR C 144 ARG 0.004 0.001 ARG B 147 Details of bonding type rmsd link_BETA1-4 : bond 0.00785 ( 5) link_BETA1-4 : angle 0.58240 ( 15) hydrogen bonds : bond 0.03573 ( 681) hydrogen bonds : angle 5.43437 ( 2283) SS BOND : bond 0.00031 ( 5) SS BOND : angle 0.62355 ( 10) covalent geometry : bond 0.00328 (13060) covalent geometry : angle 0.64393 (17935) *********************** 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 197 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 154 time to evaluate : 2.101 Fit side-chains revert: symmetry clash REVERT: A 72 MET cc_start: 0.8428 (tpp) cc_final: 0.7788 (tpp) REVERT: A 156 MET cc_start: 0.7641 (OUTLIER) cc_final: 0.7380 (mpp) REVERT: A 170 MET cc_start: 0.8402 (tmm) cc_final: 0.7930 (tmm) REVERT: A 219 ASN cc_start: 0.8642 (m-40) cc_final: 0.8256 (p0) REVERT: A 255 TRP cc_start: 0.8677 (m-10) cc_final: 0.8386 (m-10) REVERT: A 274 THR cc_start: 0.8861 (p) cc_final: 0.8625 (t) REVERT: A 303 MET cc_start: 0.9046 (mmm) cc_final: 0.8545 (mmm) REVERT: B 64 PHE cc_start: 0.8768 (OUTLIER) cc_final: 0.8325 (t80) REVERT: B 171 GLN cc_start: 0.8953 (pt0) cc_final: 0.8385 (pm20) REVERT: B 219 ASN cc_start: 0.8734 (m-40) cc_final: 0.8398 (p0) REVERT: B 255 TRP cc_start: 0.8652 (m-10) cc_final: 0.8373 (m-10) REVERT: B 302 TRP cc_start: 0.8519 (t60) cc_final: 0.8032 (t60) REVERT: B 303 MET cc_start: 0.9076 (mmm) cc_final: 0.8761 (mmm) REVERT: C 72 MET cc_start: 0.8705 (tpp) cc_final: 0.8214 (tpp) REVERT: C 119 GLU cc_start: 0.8018 (pm20) cc_final: 0.7449 (pm20) REVERT: C 171 GLN cc_start: 0.8963 (pt0) cc_final: 0.8548 (pm20) REVERT: C 255 TRP cc_start: 0.8626 (m-10) cc_final: 0.8375 (m-10) REVERT: D 72 MET cc_start: 0.8698 (tpp) cc_final: 0.8328 (tpp) REVERT: D 82 GLN cc_start: 0.8971 (mp10) cc_final: 0.8696 (mp10) REVERT: D 170 MET cc_start: 0.8894 (ttp) cc_final: 0.8580 (tmm) REVERT: D 255 TRP cc_start: 0.8758 (m-10) cc_final: 0.8440 (m-10) REVERT: E 255 TRP cc_start: 0.8599 (m-10) cc_final: 0.8265 (m-10) REVERT: E 302 TRP cc_start: 0.9122 (t-100) cc_final: 0.8693 (t60) outliers start: 43 outliers final: 31 residues processed: 184 average time/residue: 0.2299 time to fit residues: 65.4451 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 : 1.408 ------------------------------------------------------------------------------- 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 136 ILE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 198 LEU 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 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 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 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 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 127 VAL 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 78 optimal weight: 10.0000 chunk 124 optimal weight: 0.9990 chunk 126 optimal weight: 7.9990 chunk 91 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 chunk 117 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 chunk 125 optimal weight: 4.9990 chunk 138 optimal weight: 0.0060 chunk 85 optimal weight: 4.9990 overall best weight: 2.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 GLN ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.040239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.033577 restraints weight = 95994.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.034435 restraints weight = 60379.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.034780 restraints weight = 42671.153| |-----------------------------------------------------------------------------| r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13070 Z= 0.139 Angle : 0.636 8.305 17960 Z= 0.310 Chirality : 0.042 0.148 2120 Planarity : 0.003 0.035 2235 Dihedral : 6.769 59.320 2335 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.45 % Allowed : 12.41 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.21), residues: 1665 helix: 2.61 (0.20), residues: 585 sheet: -0.51 (0.24), residues: 385 loop : -1.34 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 259 HIS 0.002 0.001 HIS C 217 PHE 0.022 0.001 PHE D 350 TYR 0.016 0.002 TYR E 295 ARG 0.005 0.001 ARG C 147 Details of bonding type rmsd link_BETA1-4 : bond 0.00733 ( 5) link_BETA1-4 : angle 0.55318 ( 15) hydrogen bonds : bond 0.03443 ( 681) hydrogen bonds : angle 5.14459 ( 2283) SS BOND : bond 0.00081 ( 5) SS BOND : angle 0.69314 ( 10) covalent geometry : bond 0.00295 (13060) covalent geometry : angle 0.63599 (17935) *********************** 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 197 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 157 time to evaluate : 1.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 PHE cc_start: 0.8618 (OUTLIER) cc_final: 0.8048 (t80) REVERT: A 72 MET cc_start: 0.8456 (tpp) cc_final: 0.8155 (tpp) REVERT: A 170 MET cc_start: 0.8497 (tmm) cc_final: 0.8137 (tmm) REVERT: A 171 GLN cc_start: 0.8776 (pt0) cc_final: 0.8244 (pm20) REVERT: A 219 ASN cc_start: 0.8614 (m-40) cc_final: 0.8280 (p0) REVERT: A 255 TRP cc_start: 0.8672 (m-10) cc_final: 0.8330 (m-10) REVERT: A 303 MET cc_start: 0.8996 (mmm) cc_final: 0.8558 (mmm) REVERT: B 64 PHE cc_start: 0.8660 (OUTLIER) cc_final: 0.8261 (t80) REVERT: B 72 MET cc_start: 0.8666 (tpp) cc_final: 0.8185 (tpp) REVERT: B 171 GLN cc_start: 0.8871 (pt0) cc_final: 0.8313 (pm20) REVERT: B 219 ASN cc_start: 0.8785 (m-40) cc_final: 0.8442 (p0) REVERT: B 255 TRP cc_start: 0.8692 (m-10) cc_final: 0.8375 (m-10) REVERT: B 302 TRP cc_start: 0.8555 (t60) cc_final: 0.7997 (t60) REVERT: B 303 MET cc_start: 0.9069 (mmm) cc_final: 0.8680 (mmm) REVERT: C 72 MET cc_start: 0.8724 (tpp) cc_final: 0.8271 (tpp) REVERT: C 119 GLU cc_start: 0.7957 (pm20) cc_final: 0.7466 (pm20) REVERT: C 132 LYS cc_start: 0.8378 (mmpt) cc_final: 0.8124 (mmtm) REVERT: C 171 GLN cc_start: 0.8921 (pt0) cc_final: 0.8504 (pm20) REVERT: C 255 TRP cc_start: 0.8636 (m-10) cc_final: 0.8373 (m-10) REVERT: D 72 MET cc_start: 0.8735 (tpp) cc_final: 0.8363 (tpp) REVERT: D 82 GLN cc_start: 0.9020 (mp10) cc_final: 0.8708 (mp10) REVERT: D 170 MET cc_start: 0.8828 (ttp) cc_final: 0.8591 (tmm) REVERT: D 255 TRP cc_start: 0.8761 (m-10) cc_final: 0.8466 (m-10) REVERT: D 302 TRP cc_start: 0.8531 (t60) cc_final: 0.7736 (t60) REVERT: E 72 MET cc_start: 0.8517 (mmm) cc_final: 0.8179 (tpp) REVERT: E 255 TRP cc_start: 0.8598 (m-10) cc_final: 0.8269 (m-10) outliers start: 40 outliers final: 30 residues processed: 183 average time/residue: 0.2096 time to fit residues: 59.0433 Evaluate side-chains 180 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 148 time to evaluate : 1.469 ------------------------------------------------------------------------------- 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 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 136 ILE Chi-restraints excluded: chain B residue 156 MET 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 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 71 THR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 150 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 127 VAL Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 230 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 12 optimal weight: 9.9990 chunk 48 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 117 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 101 optimal weight: 5.9990 chunk 159 optimal weight: 0.8980 chunk 82 optimal weight: 20.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 235 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 = 0.2845 r_free = 0.2845 target = 0.040801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.034138 restraints weight = 96638.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.034874 restraints weight = 60403.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.035316 restraints weight = 42838.351| |-----------------------------------------------------------------------------| r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 13070 Z= 0.113 Angle : 0.637 16.111 17960 Z= 0.302 Chirality : 0.043 0.143 2120 Planarity : 0.003 0.029 2235 Dihedral : 6.338 57.378 2335 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.28 % Allowed : 13.62 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.21), residues: 1665 helix: 2.84 (0.20), residues: 585 sheet: -0.42 (0.24), residues: 385 loop : -1.23 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 259 HIS 0.002 0.000 HIS E 125 PHE 0.016 0.001 PHE D 230 TYR 0.015 0.002 TYR C 144 ARG 0.003 0.000 ARG E 81 Details of bonding type rmsd link_BETA1-4 : bond 0.00753 ( 5) link_BETA1-4 : angle 0.49299 ( 15) hydrogen bonds : bond 0.03268 ( 681) hydrogen bonds : angle 4.85424 ( 2283) SS BOND : bond 0.00049 ( 5) SS BOND : angle 0.51181 ( 10) covalent geometry : bond 0.00238 (13060) covalent geometry : angle 0.63709 (17935) *********************** 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 207 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 169 time to evaluate : 1.421 Fit side-chains revert: symmetry clash REVERT: A 64 PHE cc_start: 0.8572 (OUTLIER) cc_final: 0.8005 (t80) REVERT: A 72 MET cc_start: 0.8822 (tpp) cc_final: 0.8556 (tpp) REVERT: A 119 GLU cc_start: 0.7977 (pm20) cc_final: 0.7471 (pm20) REVERT: A 170 MET cc_start: 0.8536 (tmm) cc_final: 0.8045 (tmm) REVERT: A 171 GLN cc_start: 0.8732 (pt0) cc_final: 0.8346 (pt0) REVERT: A 219 ASN cc_start: 0.8657 (m-40) cc_final: 0.8311 (p0) REVERT: A 255 TRP cc_start: 0.8675 (m-10) cc_final: 0.8349 (m-10) REVERT: B 64 PHE cc_start: 0.8757 (OUTLIER) cc_final: 0.8383 (t80) REVERT: B 72 MET cc_start: 0.8556 (tpp) cc_final: 0.8017 (tpp) REVERT: B 171 GLN cc_start: 0.8842 (pt0) cc_final: 0.8417 (pt0) REVERT: B 219 ASN cc_start: 0.8859 (m-40) cc_final: 0.8515 (p0) REVERT: B 255 TRP cc_start: 0.8692 (m-10) cc_final: 0.8353 (m-10) REVERT: B 303 MET cc_start: 0.9047 (mmm) cc_final: 0.8628 (mmm) REVERT: C 72 MET cc_start: 0.8714 (tpp) cc_final: 0.8360 (tpp) REVERT: C 119 GLU cc_start: 0.7814 (pm20) cc_final: 0.7410 (pm20) REVERT: C 170 MET cc_start: 0.8341 (tmm) cc_final: 0.7873 (tmm) REVERT: C 171 GLN cc_start: 0.8778 (pt0) cc_final: 0.8473 (pt0) REVERT: C 255 TRP cc_start: 0.8614 (m-10) cc_final: 0.8320 (m-10) REVERT: D 72 MET cc_start: 0.8724 (tpp) cc_final: 0.8376 (tpp) REVERT: D 82 GLN cc_start: 0.8999 (mp10) cc_final: 0.8699 (mp10) REVERT: D 170 MET cc_start: 0.8854 (ttp) cc_final: 0.8600 (tmm) REVERT: D 255 TRP cc_start: 0.8732 (m-10) cc_final: 0.8403 (m-10) REVERT: D 302 TRP cc_start: 0.8620 (t60) cc_final: 0.7792 (t60) REVERT: E 61 ILE cc_start: 0.9531 (pt) cc_final: 0.9302 (mt) REVERT: E 72 MET cc_start: 0.8399 (mmm) cc_final: 0.8043 (tpp) REVERT: E 255 TRP cc_start: 0.8614 (m-10) cc_final: 0.8247 (m-10) REVERT: E 274 THR cc_start: 0.8996 (m) cc_final: 0.8775 (t) REVERT: E 302 TRP cc_start: 0.9149 (t-100) cc_final: 0.8519 (t60) outliers start: 38 outliers final: 24 residues processed: 195 average time/residue: 0.2065 time to fit residues: 61.6622 Evaluate side-chains 180 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 1.399 ------------------------------------------------------------------------------- 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 198 LEU 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 136 ILE 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 150 LEU 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 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 Chi-restraints excluded: chain E residue 230 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 125 optimal weight: 4.9990 chunk 66 optimal weight: 0.3980 chunk 34 optimal weight: 10.0000 chunk 4 optimal weight: 0.8980 chunk 157 optimal weight: 7.9990 chunk 110 optimal weight: 7.9990 chunk 113 optimal weight: 0.6980 chunk 100 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 chunk 82 optimal weight: 0.6980 chunk 28 optimal weight: 7.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 83 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 = 0.2854 r_free = 0.2854 target = 0.040914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.034337 restraints weight = 94582.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.035022 restraints weight = 59889.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.035493 restraints weight = 43571.016| |-----------------------------------------------------------------------------| r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13070 Z= 0.111 Angle : 0.636 14.558 17960 Z= 0.299 Chirality : 0.042 0.141 2120 Planarity : 0.003 0.028 2235 Dihedral : 5.943 52.126 2335 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.02 % Allowed : 13.97 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.21), residues: 1665 helix: 2.85 (0.20), residues: 590 sheet: -0.33 (0.24), residues: 440 loop : -1.04 (0.26), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 302 HIS 0.001 0.001 HIS E 125 PHE 0.017 0.001 PHE D 230 TYR 0.015 0.001 TYR C 144 ARG 0.002 0.000 ARG A 81 Details of bonding type rmsd link_BETA1-4 : bond 0.00759 ( 5) link_BETA1-4 : angle 0.57538 ( 15) hydrogen bonds : bond 0.03241 ( 681) hydrogen bonds : angle 4.77372 ( 2283) SS BOND : bond 0.00056 ( 5) SS BOND : angle 0.47792 ( 10) covalent geometry : bond 0.00238 (13060) covalent geometry : angle 0.63660 (17935) *********************** 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 197 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 162 time to evaluate : 1.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 PHE cc_start: 0.8578 (OUTLIER) cc_final: 0.7917 (t80) REVERT: A 72 MET cc_start: 0.8679 (tpp) cc_final: 0.8440 (tpp) REVERT: A 119 GLU cc_start: 0.7950 (pm20) cc_final: 0.7414 (pm20) REVERT: A 170 MET cc_start: 0.8526 (tmm) cc_final: 0.8073 (tmm) REVERT: A 171 GLN cc_start: 0.8715 (pt0) cc_final: 0.8328 (pt0) REVERT: A 219 ASN cc_start: 0.8737 (m-40) cc_final: 0.8322 (p0) REVERT: A 255 TRP cc_start: 0.8654 (m-10) cc_final: 0.8334 (m-10) REVERT: A 292 LYS cc_start: 0.8190 (mmtp) cc_final: 0.7762 (mmtp) REVERT: A 302 TRP cc_start: 0.8562 (t60) cc_final: 0.7511 (t60) REVERT: B 64 PHE cc_start: 0.8764 (OUTLIER) cc_final: 0.8353 (t80) REVERT: B 72 MET cc_start: 0.8569 (tpp) cc_final: 0.8043 (tpp) REVERT: B 171 GLN cc_start: 0.8855 (pt0) cc_final: 0.8398 (pt0) REVERT: B 219 ASN cc_start: 0.8880 (m-40) cc_final: 0.8532 (p0) REVERT: B 255 TRP cc_start: 0.8684 (m-10) cc_final: 0.8376 (m-10) REVERT: B 302 TRP cc_start: 0.8539 (t60) cc_final: 0.7872 (t60) REVERT: B 303 MET cc_start: 0.9021 (mmm) cc_final: 0.8715 (mmm) REVERT: B 306 CYS cc_start: 0.9063 (m) cc_final: 0.8588 (m) REVERT: C 72 MET cc_start: 0.8693 (tpp) cc_final: 0.8330 (tpp) REVERT: C 119 GLU cc_start: 0.7753 (pm20) cc_final: 0.7384 (pm20) REVERT: C 170 MET cc_start: 0.8424 (tmm) cc_final: 0.7998 (tmm) REVERT: C 171 GLN cc_start: 0.8744 (pt0) cc_final: 0.8435 (pt0) REVERT: C 255 TRP cc_start: 0.8634 (m-10) cc_final: 0.8334 (m-10) REVERT: D 72 MET cc_start: 0.8727 (tpp) cc_final: 0.8394 (tpp) REVERT: D 82 GLN cc_start: 0.9002 (mp10) cc_final: 0.8699 (mp10) REVERT: D 170 MET cc_start: 0.8858 (ttp) cc_final: 0.8566 (tmm) REVERT: D 179 MET cc_start: 0.8920 (mmm) cc_final: 0.8668 (mmm) REVERT: D 241 ILE cc_start: 0.9203 (mm) cc_final: 0.8840 (tt) REVERT: D 255 TRP cc_start: 0.8757 (m-10) cc_final: 0.8410 (m-10) REVERT: D 302 TRP cc_start: 0.8589 (t60) cc_final: 0.7734 (t60) REVERT: E 61 ILE cc_start: 0.9528 (pt) cc_final: 0.9244 (mt) REVERT: E 255 TRP cc_start: 0.8650 (m-10) cc_final: 0.8302 (m-10) REVERT: E 274 THR cc_start: 0.8961 (m) cc_final: 0.8677 (t) REVERT: E 302 TRP cc_start: 0.9199 (t-100) cc_final: 0.8613 (t-100) REVERT: E 303 MET cc_start: 0.9107 (mmm) cc_final: 0.8683 (mmm) outliers start: 35 outliers final: 24 residues processed: 186 average time/residue: 0.2061 time to fit residues: 59.3105 Evaluate side-chains 185 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 159 time to evaluate : 1.378 ------------------------------------------------------------------------------- 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 198 LEU 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 136 ILE Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 262 MET 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 230 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 0.4980 chunk 73 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 93 optimal weight: 10.0000 chunk 74 optimal weight: 7.9990 chunk 4 optimal weight: 0.0270 chunk 51 optimal weight: 7.9990 chunk 164 optimal weight: 6.9990 chunk 24 optimal weight: 20.0000 chunk 19 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 overall best weight: 2.7044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 GLN ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.040405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.033816 restraints weight = 98031.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.034543 restraints weight = 61931.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.034950 restraints weight = 44870.337| |-----------------------------------------------------------------------------| r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.4334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13070 Z= 0.160 Angle : 0.637 11.560 17960 Z= 0.309 Chirality : 0.042 0.139 2120 Planarity : 0.004 0.033 2235 Dihedral : 5.776 52.631 2335 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.36 % Allowed : 14.14 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.21), residues: 1665 helix: 2.84 (0.20), residues: 590 sheet: -0.19 (0.25), residues: 425 loop : -0.99 (0.26), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 259 HIS 0.003 0.001 HIS C 217 PHE 0.015 0.001 PHE D 230 TYR 0.012 0.002 TYR E 144 ARG 0.004 0.001 ARG A 234 Details of bonding type rmsd link_BETA1-4 : bond 0.00679 ( 5) link_BETA1-4 : angle 1.00648 ( 15) hydrogen bonds : bond 0.03487 ( 681) hydrogen bonds : angle 4.91572 ( 2283) SS BOND : bond 0.00064 ( 5) SS BOND : angle 0.50386 ( 10) covalent geometry : bond 0.00342 (13060) covalent geometry : angle 0.63679 (17935) *********************** 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 195 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 156 time to evaluate : 1.554 Fit side-chains revert: symmetry clash REVERT: A 64 PHE cc_start: 0.8614 (OUTLIER) cc_final: 0.7929 (t80) REVERT: A 72 MET cc_start: 0.8623 (tpp) cc_final: 0.8403 (tpp) REVERT: A 170 MET cc_start: 0.8482 (tmm) cc_final: 0.7952 (tmm) REVERT: A 219 ASN cc_start: 0.8779 (m-40) cc_final: 0.8385 (p0) REVERT: A 255 TRP cc_start: 0.8637 (m-10) cc_final: 0.8299 (m-10) REVERT: A 290 LEU cc_start: 0.8384 (tp) cc_final: 0.8143 (tt) REVERT: B 64 PHE cc_start: 0.8790 (OUTLIER) cc_final: 0.8431 (t80) REVERT: B 72 MET cc_start: 0.8539 (tpp) cc_final: 0.8009 (tpp) REVERT: B 171 GLN cc_start: 0.8828 (pt0) cc_final: 0.8439 (pt0) REVERT: B 219 ASN cc_start: 0.8932 (m-40) cc_final: 0.8436 (p0) REVERT: B 255 TRP cc_start: 0.8669 (m-10) cc_final: 0.8367 (m-10) REVERT: B 302 TRP cc_start: 0.8509 (t60) cc_final: 0.7827 (t60) REVERT: B 303 MET cc_start: 0.8999 (mmm) cc_final: 0.8697 (mmm) REVERT: C 64 PHE cc_start: 0.8691 (OUTLIER) cc_final: 0.8321 (t80) REVERT: C 72 MET cc_start: 0.8678 (tpp) cc_final: 0.8312 (tpp) REVERT: C 171 GLN cc_start: 0.8722 (pt0) cc_final: 0.8503 (pt0) REVERT: C 255 TRP cc_start: 0.8686 (m-10) cc_final: 0.8397 (m-10) REVERT: C 296 VAL cc_start: 0.8495 (OUTLIER) cc_final: 0.8229 (p) REVERT: D 72 MET cc_start: 0.8743 (tpp) cc_final: 0.8394 (tpp) REVERT: D 82 GLN cc_start: 0.9061 (mp10) cc_final: 0.8755 (mp10) REVERT: D 170 MET cc_start: 0.8852 (ttp) cc_final: 0.8593 (tmm) REVERT: D 241 ILE cc_start: 0.9188 (mm) cc_final: 0.8816 (tt) REVERT: D 255 TRP cc_start: 0.8823 (m-10) cc_final: 0.8517 (m-10) REVERT: D 302 TRP cc_start: 0.8594 (t60) cc_final: 0.8099 (t60) REVERT: E 61 ILE cc_start: 0.9498 (pt) cc_final: 0.9180 (mt) REVERT: E 199 THR cc_start: 0.8232 (p) cc_final: 0.8032 (t) REVERT: E 255 TRP cc_start: 0.8699 (m-10) cc_final: 0.8358 (m-10) REVERT: E 274 THR cc_start: 0.9054 (m) cc_final: 0.8821 (t) REVERT: E 303 MET cc_start: 0.9125 (mmm) cc_final: 0.8699 (mmm) outliers start: 39 outliers final: 27 residues processed: 183 average time/residue: 0.1979 time to fit residues: 56.4605 Evaluate side-chains 178 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 147 time to evaluate : 1.386 ------------------------------------------------------------------------------- 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 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 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 150 LEU Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 262 MET 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 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 72 MET 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 230 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 85 optimal weight: 0.0870 chunk 71 optimal weight: 5.9990 chunk 77 optimal weight: 9.9990 chunk 8 optimal weight: 0.0030 chunk 52 optimal weight: 10.0000 chunk 102 optimal weight: 9.9990 chunk 18 optimal weight: 7.9990 chunk 118 optimal weight: 4.9990 chunk 158 optimal weight: 0.0010 chunk 125 optimal weight: 9.9990 chunk 2 optimal weight: 0.0030 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 83 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 = 0.2858 r_free = 0.2858 target = 0.041105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.034416 restraints weight = 96361.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.035153 restraints weight = 62052.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.035605 restraints weight = 44384.118| |-----------------------------------------------------------------------------| r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.4426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13070 Z= 0.113 Angle : 0.638 12.290 17960 Z= 0.299 Chirality : 0.042 0.136 2120 Planarity : 0.003 0.031 2235 Dihedral : 5.487 52.816 2335 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.76 % Allowed : 14.66 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.22), residues: 1665 helix: 3.05 (0.20), residues: 590 sheet: -0.10 (0.24), residues: 455 loop : -0.91 (0.27), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 302 HIS 0.002 0.001 HIS E 125 PHE 0.016 0.001 PHE D 230 TYR 0.012 0.001 TYR C 144 ARG 0.002 0.000 ARG A 81 Details of bonding type rmsd link_BETA1-4 : bond 0.00754 ( 5) link_BETA1-4 : angle 0.75461 ( 15) hydrogen bonds : bond 0.03202 ( 681) hydrogen bonds : angle 4.69756 ( 2283) SS BOND : bond 0.00065 ( 5) SS BOND : angle 0.44542 ( 10) covalent geometry : bond 0.00243 (13060) covalent geometry : angle 0.63782 (17935) *********************** 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 190 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 158 time to evaluate : 1.503 Fit side-chains revert: symmetry clash REVERT: A 64 PHE cc_start: 0.8557 (OUTLIER) cc_final: 0.7957 (t80) REVERT: A 72 MET cc_start: 0.8562 (tpp) cc_final: 0.8327 (tpp) REVERT: A 119 GLU cc_start: 0.7935 (pm20) cc_final: 0.7382 (pm20) REVERT: A 170 MET cc_start: 0.8545 (tmm) cc_final: 0.8112 (tmm) REVERT: A 219 ASN cc_start: 0.8723 (m-40) cc_final: 0.8338 (p0) REVERT: A 255 TRP cc_start: 0.8631 (m-10) cc_final: 0.8286 (m-10) REVERT: A 290 LEU cc_start: 0.8397 (tp) cc_final: 0.8109 (tt) REVERT: A 302 TRP cc_start: 0.8583 (t60) cc_final: 0.8046 (t60) REVERT: B 64 PHE cc_start: 0.8774 (OUTLIER) cc_final: 0.8442 (t80) REVERT: B 72 MET cc_start: 0.8576 (tpp) cc_final: 0.8080 (tpp) REVERT: B 171 GLN cc_start: 0.8774 (pt0) cc_final: 0.8405 (pt0) REVERT: B 219 ASN cc_start: 0.8881 (m-40) cc_final: 0.8413 (p0) REVERT: B 255 TRP cc_start: 0.8691 (m-10) cc_final: 0.8349 (m-10) REVERT: B 302 TRP cc_start: 0.8542 (t60) cc_final: 0.8249 (t60) REVERT: B 303 MET cc_start: 0.8963 (mmm) cc_final: 0.8701 (mmm) REVERT: C 64 PHE cc_start: 0.8668 (OUTLIER) cc_final: 0.8340 (t80) REVERT: C 72 MET cc_start: 0.8702 (tpp) cc_final: 0.8373 (tpp) REVERT: C 170 MET cc_start: 0.8322 (tmm) cc_final: 0.7840 (tmm) REVERT: C 171 GLN cc_start: 0.8683 (pt0) cc_final: 0.8300 (pt0) REVERT: C 255 TRP cc_start: 0.8645 (m-10) cc_final: 0.8335 (m-10) REVERT: C 282 GLN cc_start: 0.9069 (tp40) cc_final: 0.8653 (tt0) REVERT: C 296 VAL cc_start: 0.8500 (OUTLIER) cc_final: 0.8222 (p) REVERT: D 72 MET cc_start: 0.8729 (tpp) cc_final: 0.7054 (tpp) REVERT: D 82 GLN cc_start: 0.9057 (mp10) cc_final: 0.8748 (mp10) REVERT: D 179 MET cc_start: 0.8919 (mmm) cc_final: 0.8701 (mmm) REVERT: D 241 ILE cc_start: 0.9162 (mm) cc_final: 0.8794 (tt) REVERT: D 255 TRP cc_start: 0.8794 (m-10) cc_final: 0.8458 (m-10) REVERT: D 302 TRP cc_start: 0.8591 (t60) cc_final: 0.7709 (t60) REVERT: E 61 ILE cc_start: 0.9496 (pt) cc_final: 0.9183 (mt) REVERT: E 179 MET cc_start: 0.8978 (mmm) cc_final: 0.8772 (mmm) REVERT: E 199 THR cc_start: 0.8203 (p) cc_final: 0.8000 (t) REVERT: E 255 TRP cc_start: 0.8707 (m-10) cc_final: 0.8361 (m-10) REVERT: E 274 THR cc_start: 0.9049 (m) cc_final: 0.8813 (t) REVERT: E 302 TRP cc_start: 0.9213 (t-100) cc_final: 0.8587 (t-100) REVERT: E 303 MET cc_start: 0.9096 (mmm) cc_final: 0.8653 (mmm) outliers start: 32 outliers final: 22 residues processed: 181 average time/residue: 0.2029 time to fit residues: 56.9063 Evaluate side-chains 180 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 1.495 ------------------------------------------------------------------------------- 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 B residue 57 CYS Chi-restraints excluded: chain B residue 64 PHE 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 136 ILE Chi-restraints excluded: chain C residue 150 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 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 230 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 162 optimal weight: 20.0000 chunk 157 optimal weight: 10.0000 chunk 55 optimal weight: 0.0670 chunk 59 optimal weight: 3.9990 chunk 78 optimal weight: 9.9990 chunk 83 optimal weight: 0.9990 chunk 131 optimal weight: 7.9990 chunk 104 optimal weight: 10.0000 chunk 124 optimal weight: 9.9990 chunk 76 optimal weight: 1.9990 chunk 23 optimal weight: 9.9990 overall best weight: 3.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 83 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 = 0.2837 r_free = 0.2837 target = 0.040414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.033900 restraints weight = 99586.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.034665 restraints weight = 63239.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.035198 restraints weight = 46335.948| |-----------------------------------------------------------------------------| r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.4603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 13070 Z= 0.170 Angle : 0.669 13.125 17960 Z= 0.320 Chirality : 0.042 0.149 2120 Planarity : 0.004 0.034 2235 Dihedral : 5.622 53.691 2335 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.41 % Allowed : 15.86 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.22), residues: 1665 helix: 2.81 (0.20), residues: 595 sheet: -0.19 (0.24), residues: 455 loop : -0.93 (0.27), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 259 HIS 0.004 0.001 HIS B 217 PHE 0.016 0.001 PHE C 124 TYR 0.013 0.002 TYR C 239 ARG 0.005 0.001 ARG E 147 Details of bonding type rmsd link_BETA1-4 : bond 0.00737 ( 5) link_BETA1-4 : angle 0.95209 ( 15) hydrogen bonds : bond 0.03491 ( 681) hydrogen bonds : angle 4.90276 ( 2283) SS BOND : bond 0.00071 ( 5) SS BOND : angle 0.44867 ( 10) covalent geometry : bond 0.00363 (13060) covalent geometry : angle 0.66923 (17935) ********************** 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 178 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 150 time to evaluate : 1.583 Fit side-chains revert: symmetry clash REVERT: A 64 PHE cc_start: 0.8551 (OUTLIER) cc_final: 0.7903 (t80) REVERT: A 72 MET cc_start: 0.8536 (tpp) cc_final: 0.8290 (tpp) REVERT: A 170 MET cc_start: 0.8451 (tmm) cc_final: 0.8057 (tmm) REVERT: A 219 ASN cc_start: 0.8670 (m-40) cc_final: 0.8235 (p0) REVERT: A 255 TRP cc_start: 0.8675 (m-10) cc_final: 0.8359 (m-10) REVERT: B 64 PHE cc_start: 0.8766 (OUTLIER) cc_final: 0.8482 (t80) REVERT: B 72 MET cc_start: 0.8518 (tpp) cc_final: 0.8177 (tpp) REVERT: B 219 ASN cc_start: 0.8821 (m-40) cc_final: 0.8383 (p0) REVERT: B 255 TRP cc_start: 0.8776 (m-10) cc_final: 0.8364 (m-10) REVERT: B 302 TRP cc_start: 0.8547 (t60) cc_final: 0.7858 (t60) REVERT: B 303 MET cc_start: 0.8964 (mmm) cc_final: 0.8632 (mmm) REVERT: C 64 PHE cc_start: 0.8567 (OUTLIER) cc_final: 0.8228 (t80) REVERT: C 72 MET cc_start: 0.8607 (tpp) cc_final: 0.8344 (tpp) REVERT: C 170 MET cc_start: 0.8303 (tmm) cc_final: 0.7863 (tmm) REVERT: C 171 GLN cc_start: 0.8639 (pt0) cc_final: 0.8257 (pt0) REVERT: C 255 TRP cc_start: 0.8706 (m-10) cc_final: 0.8394 (m-10) REVERT: C 296 VAL cc_start: 0.8454 (OUTLIER) cc_final: 0.8167 (p) REVERT: D 72 MET cc_start: 0.8497 (tpp) cc_final: 0.7861 (tpp) REVERT: D 82 GLN cc_start: 0.9050 (mp10) cc_final: 0.8759 (mp10) REVERT: D 156 MET cc_start: 0.7675 (mpp) cc_final: 0.7177 (mpp) REVERT: D 241 ILE cc_start: 0.9164 (mm) cc_final: 0.8794 (tt) REVERT: D 255 TRP cc_start: 0.8870 (m-10) cc_final: 0.8535 (m-10) REVERT: D 302 TRP cc_start: 0.8587 (t60) cc_final: 0.8129 (t60) REVERT: E 255 TRP cc_start: 0.8736 (m-10) cc_final: 0.8395 (m-10) REVERT: E 303 MET cc_start: 0.9105 (mmm) cc_final: 0.8671 (mmm) outliers start: 28 outliers final: 22 residues processed: 170 average time/residue: 0.2061 time to fit residues: 54.8488 Evaluate side-chains 170 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 1.486 ------------------------------------------------------------------------------- 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 136 ILE Chi-restraints excluded: chain A residue 168 CYS 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 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 150 LEU Chi-restraints excluded: chain C residue 262 MET 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 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 72 MET 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 230 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 20.0000 chunk 11 optimal weight: 9.9990 chunk 126 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 chunk 35 optimal weight: 0.0070 chunk 24 optimal weight: 7.9990 chunk 67 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 chunk 113 optimal weight: 10.0000 chunk 151 optimal weight: 7.9990 chunk 1 optimal weight: 7.9990 overall best weight: 5.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 83 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 = 0.2818 r_free = 0.2818 target = 0.039492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.033124 restraints weight = 102499.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.033827 restraints weight = 66871.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.034359 restraints weight = 49091.799| |-----------------------------------------------------------------------------| r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.4924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 13070 Z= 0.273 Angle : 0.765 14.068 17960 Z= 0.377 Chirality : 0.045 0.157 2120 Planarity : 0.005 0.045 2235 Dihedral : 6.199 54.622 2335 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.84 % Allowed : 15.43 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.21), residues: 1665 helix: 2.14 (0.20), residues: 600 sheet: -0.63 (0.25), residues: 415 loop : -1.23 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 259 HIS 0.007 0.002 HIS B 217 PHE 0.028 0.002 PHE A 175 TYR 0.017 0.003 TYR C 239 ARG 0.008 0.001 ARG E 147 Details of bonding type rmsd link_BETA1-4 : bond 0.00744 ( 5) link_BETA1-4 : angle 0.90674 ( 15) hydrogen bonds : bond 0.04286 ( 681) hydrogen bonds : angle 5.39091 ( 2283) SS BOND : bond 0.00139 ( 5) SS BOND : angle 0.49638 ( 10) covalent geometry : bond 0.00569 (13060) covalent geometry : angle 0.76484 (17935) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3350.37 seconds wall clock time: 59 minutes 23.42 seconds (3563.42 seconds total)