Starting phenix.real_space_refine on Thu Sep 18 01:16:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3jad_6344/09_2025/3jad_6344.cif Found real_map, /net/cci-nas-00/data/ceres_data/3jad_6344/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/3jad_6344/09_2025/3jad_6344.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3jad_6344/09_2025/3jad_6344.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/3jad_6344/09_2025/3jad_6344.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3jad_6344/09_2025/3jad_6344.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 65 5.16 5 C 8305 2.51 5 N 2090 2.21 5 O 2245 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12705 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2488 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 15, 'TRANS': 321} Chain breaks: 1 Unresolved non-hydrogen bonds: 241 Unresolved non-hydrogen angles: 294 Unresolved non-hydrogen dihedrals: 194 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLU:plan': 11, 'ASP:plan': 8, 'ARG:plan': 5, 'GLN:plan1': 1, 'PHE:plan': 3, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 121 Chain: "B" Number of atoms: 2488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2488 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 15, 'TRANS': 321} Chain breaks: 1 Unresolved non-hydrogen bonds: 241 Unresolved non-hydrogen angles: 294 Unresolved non-hydrogen dihedrals: 194 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLU:plan': 11, 'ASP:plan': 8, 'ARG:plan': 5, 'GLN:plan1': 1, 'PHE:plan': 3, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 121 Chain: "C" Number of atoms: 2488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2488 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 15, 'TRANS': 321} Chain breaks: 1 Unresolved non-hydrogen bonds: 241 Unresolved non-hydrogen angles: 294 Unresolved non-hydrogen dihedrals: 194 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLU:plan': 11, 'ASP:plan': 8, 'ARG:plan': 5, 'GLN:plan1': 1, 'PHE:plan': 3, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 121 Chain: "D" Number of atoms: 2488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2488 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 15, 'TRANS': 321} Chain breaks: 1 Unresolved non-hydrogen bonds: 241 Unresolved non-hydrogen angles: 294 Unresolved non-hydrogen dihedrals: 194 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLU:plan': 11, 'ASP:plan': 8, 'ARG:plan': 5, 'GLN:plan1': 1, 'PHE:plan': 3, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 121 Chain: "E" Number of atoms: 2488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2488 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 15, 'TRANS': 321} Chain breaks: 1 Unresolved non-hydrogen bonds: 241 Unresolved non-hydrogen angles: 294 Unresolved non-hydrogen dihedrals: 194 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLU:plan': 11, 'ASP:plan': 8, 'ARG:plan': 5, 'GLN:plan1': 1, 'PHE:plan': 3, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 121 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: 3.26, per 1000 atoms: 0.26 Number of scatterers: 12705 At special positions: 0 Unit cell: (98.98, 97.97, 126.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 65 16.00 O 2245 8.00 N 2090 7.00 C 8305 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 225 " distance=2.04 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 225 " distance=2.04 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 225 " distance=2.04 Simple disulfide: pdb=" SG CYS D 214 " - pdb=" SG CYS D 225 " distance=2.04 Simple disulfide: pdb=" SG CYS E 214 " - pdb=" SG CYS E 225 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " Time building additional restraints: 1.00 Conformation dependent library (CDL) restraints added in 576.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3230 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 15 sheets defined 37.4% alpha, 38.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 25 through 35 removed outlier: 3.513A pdb=" N LEU A 33 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 108 removed outlier: 4.053A pdb=" N ASP A 107 " --> pdb=" O SER A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 243 Processing helix chain 'A' and resid 243 through 259 removed outlier: 3.674A pdb=" N SER A 247 " --> pdb=" O MET A 243 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TRP A 259 " --> pdb=" O TRP A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 290 Processing helix chain 'A' and resid 297 through 325 removed outlier: 3.959A pdb=" N LEU A 314 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG A 325 " --> pdb=" O ASN A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 362 Proline residue: A 347 - end of helix removed outlier: 3.841A pdb=" N ILE A 359 " --> pdb=" O ILE A 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 35 removed outlier: 3.514A pdb=" N LEU B 33 " --> pdb=" O PHE B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 108 removed outlier: 4.053A pdb=" N ASP B 107 " --> pdb=" O SER B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 243 Processing helix chain 'B' and resid 243 through 259 removed outlier: 3.673A pdb=" N SER B 247 " --> pdb=" O MET B 243 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TRP B 259 " --> pdb=" O TRP B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 290 Processing helix chain 'B' and resid 297 through 325 removed outlier: 3.959A pdb=" N LEU B 314 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG B 325 " --> pdb=" O ASN B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 362 Proline residue: B 347 - end of helix removed outlier: 3.841A pdb=" N ILE B 359 " --> pdb=" O ILE B 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 35 removed outlier: 3.513A pdb=" N LEU C 33 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 108 removed outlier: 4.053A pdb=" N ASP C 107 " --> pdb=" O SER C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 243 Processing helix chain 'C' and resid 243 through 259 removed outlier: 3.674A pdb=" N SER C 247 " --> pdb=" O MET C 243 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TRP C 259 " --> pdb=" O TRP C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 290 Processing helix chain 'C' and resid 297 through 325 removed outlier: 3.960A pdb=" N LEU C 314 " --> pdb=" O VAL C 310 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG C 325 " --> pdb=" O ASN C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 362 Proline residue: C 347 - end of helix removed outlier: 3.841A pdb=" N ILE C 359 " --> pdb=" O ILE C 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 35 removed outlier: 3.514A pdb=" N LEU D 33 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 108 removed outlier: 4.053A pdb=" N ASP D 107 " --> pdb=" O SER D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 243 Processing helix chain 'D' and resid 243 through 259 removed outlier: 3.673A pdb=" N SER D 247 " --> pdb=" O MET D 243 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TRP D 259 " --> pdb=" O TRP D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 290 Processing helix chain 'D' and resid 297 through 325 removed outlier: 3.960A pdb=" N LEU D 314 " --> pdb=" O VAL D 310 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG D 325 " --> pdb=" O ASN D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 362 Proline residue: D 347 - end of helix removed outlier: 3.841A pdb=" N ILE D 359 " --> pdb=" O ILE D 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 35 removed outlier: 3.514A pdb=" N LEU E 33 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 108 removed outlier: 4.052A pdb=" N ASP E 107 " --> pdb=" O SER E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 243 Processing helix chain 'E' and resid 243 through 259 removed outlier: 3.674A pdb=" N SER E 247 " --> pdb=" O MET E 243 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TRP E 259 " --> pdb=" O TRP E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 290 Processing helix chain 'E' and resid 297 through 325 removed outlier: 3.959A pdb=" N LEU E 314 " --> pdb=" O VAL E 310 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG E 325 " --> pdb=" O ASN E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 362 Proline residue: E 347 - end of helix removed outlier: 3.841A pdb=" N ILE E 359 " --> pdb=" O ILE E 355 " (cutoff:3.500A) Processing sheet with id=A, first strand: chain 'A' and resid 119 through 124 removed outlier: 3.825A pdb=" N GLY A 121 " --> pdb=" O VAL A 151 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ASP A 73 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N SER A 66 " --> pdb=" O ASP A 73 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL A 53 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N GLU A 185 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL A 55 " --> pdb=" O GLU A 185 " (cutoff:3.500A) Processing sheet with id=B, first strand: chain 'A' and resid 133 through 136 removed outlier: 5.990A pdb=" N ASP A 73 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N SER A 66 " --> pdb=" O ASP A 73 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N GLN A 193 " --> pdb=" O CYS A 57 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE A 59 " --> pdb=" O GLN A 193 " (cutoff:3.500A) Processing sheet with id=C, first strand: chain 'A' and resid 114 through 116 removed outlier: 5.713A pdb=" N THR A 224 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N HIS A 231 " --> pdb=" O GLU A 208 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLU A 208 " --> pdb=" O HIS A 231 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N GLU A 233 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LYS A 206 " --> pdb=" O GLU A 233 " (cutoff:3.500A) Processing sheet with id=D, first strand: chain 'B' and resid 119 through 124 removed outlier: 3.824A pdb=" N GLY B 121 " --> pdb=" O VAL B 151 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ASP B 73 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N SER B 66 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL B 53 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N GLU B 185 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL B 55 " --> pdb=" O GLU B 185 " (cutoff:3.500A) Processing sheet with id=E, first strand: chain 'B' and resid 133 through 136 removed outlier: 5.991A pdb=" N ASP B 73 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N SER B 66 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N GLN B 193 " --> pdb=" O CYS B 57 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE B 59 " --> pdb=" O GLN B 193 " (cutoff:3.500A) Processing sheet with id=F, first strand: chain 'B' and resid 114 through 116 removed outlier: 5.712A pdb=" N THR B 224 " --> pdb=" O SER B 174 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N HIS B 231 " --> pdb=" O GLU B 208 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLU B 208 " --> pdb=" O HIS B 231 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N GLU B 233 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LYS B 206 " --> pdb=" O GLU B 233 " (cutoff:3.500A) Processing sheet with id=G, first strand: chain 'C' and resid 119 through 124 removed outlier: 3.824A pdb=" N GLY C 121 " --> pdb=" O VAL C 151 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ASP C 73 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N SER C 66 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL C 53 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N GLU C 185 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL C 55 " --> pdb=" O GLU C 185 " (cutoff:3.500A) Processing sheet with id=H, first strand: chain 'C' and resid 133 through 136 removed outlier: 5.991A pdb=" N ASP C 73 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N SER C 66 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 8.962A pdb=" N GLN C 193 " --> pdb=" O CYS C 57 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ILE C 59 " --> pdb=" O GLN C 193 " (cutoff:3.500A) Processing sheet with id=I, first strand: chain 'C' and resid 114 through 116 removed outlier: 5.713A pdb=" N THR C 224 " --> pdb=" O SER C 174 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N HIS C 231 " --> pdb=" O GLU C 208 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLU C 208 " --> pdb=" O HIS C 231 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N GLU C 233 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LYS C 206 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing sheet with id=J, first strand: chain 'D' and resid 119 through 124 removed outlier: 3.824A pdb=" N GLY D 121 " --> pdb=" O VAL D 151 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ASP D 73 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N SER D 66 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL D 53 " --> pdb=" O ILE D 183 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N GLU D 185 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL D 55 " --> pdb=" O GLU D 185 " (cutoff:3.500A) Processing sheet with id=K, first strand: chain 'D' and resid 133 through 136 removed outlier: 5.990A pdb=" N ASP D 73 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N SER D 66 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 8.962A pdb=" N GLN D 193 " --> pdb=" O CYS D 57 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE D 59 " --> pdb=" O GLN D 193 " (cutoff:3.500A) Processing sheet with id=L, first strand: chain 'D' and resid 114 through 116 removed outlier: 5.713A pdb=" N THR D 224 " --> pdb=" O SER D 174 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N HIS D 231 " --> pdb=" O GLU D 208 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLU D 208 " --> pdb=" O HIS D 231 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N GLU D 233 " --> pdb=" O LYS D 206 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LYS D 206 " --> pdb=" O GLU D 233 " (cutoff:3.500A) Processing sheet with id=M, first strand: chain 'E' and resid 119 through 124 removed outlier: 3.824A pdb=" N GLY E 121 " --> pdb=" O VAL E 151 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ASP E 73 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N SER E 66 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL E 53 " --> pdb=" O ILE E 183 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N GLU E 185 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N VAL E 55 " --> pdb=" O GLU E 185 " (cutoff:3.500A) Processing sheet with id=N, first strand: chain 'E' and resid 133 through 136 removed outlier: 5.990A pdb=" N ASP E 73 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N SER E 66 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 8.962A pdb=" N GLN E 193 " --> pdb=" O CYS E 57 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ILE E 59 " --> pdb=" O GLN E 193 " (cutoff:3.500A) Processing sheet with id=O, first strand: chain 'E' and resid 114 through 116 removed outlier: 5.714A pdb=" N THR E 224 " --> pdb=" O SER E 174 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N HIS E 231 " --> pdb=" O GLU E 208 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLU E 208 " --> pdb=" O HIS E 231 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N GLU E 233 " --> pdb=" O LYS E 206 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LYS E 206 " --> pdb=" O GLU E 233 " (cutoff:3.500A) 776 hydrogen bonds defined for protein. 2283 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.17 Time building geometry restraints manager: 1.32 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.670 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.230 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.13 (0.18), residues: 1665 helix: -1.20 (0.19), residues: 575 sheet: -0.41 (0.22), residues: 385 loop : -2.11 (0.20), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 234 TYR 0.015 0.002 TYR D 144 PHE 0.075 0.003 PHE C 115 TRP 0.012 0.002 TRP B 259 HIS 0.002 0.001 HIS C 217 Details of bonding type rmsd covalent geometry : bond 0.00803 (13060) covalent geometry : angle 1.32661 (17935) SS BOND : bond 0.01190 ( 5) SS BOND : angle 0.74740 ( 10) hydrogen bonds : bond 0.08182 ( 681) hydrogen bonds : angle 9.47842 ( 2283) link_BETA1-4 : bond 0.02360 ( 5) link_BETA1-4 : angle 0.61971 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 295 time to evaluate : 0.368 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: 0.7836 (p90) REVERT: A 239 TYR cc_start: 0.7194 (m-80) cc_final: 0.6984 (m-80) REVERT: A 255 TRP cc_start: 0.8111 (m-10) cc_final: 0.7412 (m-10) REVERT: A 262 MET cc_start: 0.7608 (mtm) cc_final: 0.7233 (mtm) REVERT: A 277 LEU cc_start: 0.8917 (tp) cc_final: 0.8686 (tp) REVERT: B 72 MET cc_start: 0.7714 (tpp) cc_final: 0.7499 (tpp) REVERT: B 255 TRP cc_start: 0.8038 (m-10) cc_final: 0.7314 (m-10) REVERT: B 302 TRP cc_start: 0.7996 (t60) cc_final: 0.7655 (t60) REVERT: C 255 TRP cc_start: 0.8073 (m-10) cc_final: 0.7462 (m-10) REVERT: D 80 LEU cc_start: 0.8622 (tp) cc_final: 0.8398 (tp) REVERT: D 255 TRP cc_start: 0.8072 (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: 0.1192 time to fit residues: 50.3177 Evaluate side-chains 157 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 156 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 9.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 GLN A 235 GLN B 83 GLN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 GLN C 85 ASN D 85 ASN D 123 ASN E 83 GLN E 85 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.039702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.033032 restraints weight = 95575.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.033770 restraints weight = 61524.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.034139 restraints weight = 44081.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.034492 restraints weight = 36818.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.034748 restraints weight = 31587.287| |-----------------------------------------------------------------------------| r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13070 Z= 0.195 Angle : 0.737 8.635 17960 Z= 0.376 Chirality : 0.045 0.177 2120 Planarity : 0.005 0.060 2235 Dihedral : 8.101 59.231 2337 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.36 % Allowed : 6.21 % Favored : 90.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.19), residues: 1665 helix: 0.81 (0.20), residues: 585 sheet: -0.35 (0.23), residues: 410 loop : -1.72 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 229 TYR 0.021 0.002 TYR A 144 PHE 0.029 0.002 PHE E 115 TRP 0.010 0.001 TRP A 259 HIS 0.004 0.002 HIS A 231 Details of bonding type rmsd covalent geometry : bond 0.00415 (13060) covalent geometry : angle 0.73734 (17935) SS BOND : bond 0.00146 ( 5) SS BOND : angle 0.95150 ( 10) hydrogen bonds : bond 0.04085 ( 681) hydrogen bonds : angle 6.56272 ( 2283) link_BETA1-4 : bond 0.01014 ( 5) link_BETA1-4 : angle 0.62336 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 175 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 PHE cc_start: 0.8931 (OUTLIER) cc_final: 0.8386 (p90) REVERT: A 255 TRP cc_start: 0.8690 (m-10) cc_final: 0.8452 (m-10) REVERT: A 274 THR cc_start: 0.9069 (m) cc_final: 0.8453 (t) REVERT: A 303 MET cc_start: 0.9035 (mmm) cc_final: 0.8624 (mmm) REVERT: B 72 MET cc_start: 0.8720 (tpp) cc_final: 0.7538 (tpp) REVERT: B 171 GLN cc_start: 0.8935 (pt0) cc_final: 0.8524 (pm20) REVERT: B 255 TRP cc_start: 0.8677 (m-10) cc_final: 0.8374 (m-10) REVERT: B 302 TRP cc_start: 0.8374 (t60) cc_final: 0.8124 (t60) REVERT: B 311 PHE cc_start: 0.9166 (t80) cc_final: 0.8612 (t80) REVERT: C 119 GLU cc_start: 0.8221 (pm20) cc_final: 0.7943 (pm20) REVERT: C 171 GLN cc_start: 0.9001 (pt0) cc_final: 0.8580 (pm20) REVERT: C 192 VAL cc_start: 0.9104 (OUTLIER) cc_final: 0.8861 (t) REVERT: C 253 LEU cc_start: 0.9556 (mt) cc_final: 0.9345 (mt) REVERT: C 255 TRP cc_start: 0.8617 (m-10) cc_final: 0.8296 (m-10) REVERT: C 306 CYS cc_start: 0.8856 (m) cc_final: 0.8652 (m) REVERT: D 171 GLN cc_start: 0.8762 (OUTLIER) cc_final: 0.8513 (pm20) REVERT: D 255 TRP cc_start: 0.8774 (m-10) cc_final: 0.8484 (m-10) REVERT: E 72 MET cc_start: 0.8342 (mmm) cc_final: 0.7600 (tpp) REVERT: E 120 LYS cc_start: 0.8797 (mttm) cc_final: 0.8507 (mtmm) REVERT: E 255 TRP cc_start: 0.8655 (m-10) cc_final: 0.8342 (m-10) outliers start: 39 outliers final: 27 residues processed: 203 average time/residue: 0.0931 time to fit residues: 28.6780 Evaluate side-chains 185 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 155 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 64 PHE Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain D residue 57 CYS Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 115 PHE Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 198 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 96 optimal weight: 20.0000 chunk 132 optimal weight: 1.9990 chunk 149 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 146 optimal weight: 8.9990 chunk 85 optimal weight: 5.9990 chunk 109 optimal weight: 10.0000 chunk 116 optimal weight: 9.9990 chunk 87 optimal weight: 9.9990 chunk 68 optimal weight: 0.0870 chunk 101 optimal weight: 9.9990 overall best weight: 3.8166 ------------------------------------------------------------------------------- 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** D 83 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.039502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.033039 restraints weight = 99381.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.033748 restraints weight = 62124.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.034176 restraints weight = 44733.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.034539 restraints weight = 36602.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.034602 restraints weight = 31704.571| |-----------------------------------------------------------------------------| r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13070 Z= 0.215 Angle : 0.708 9.680 17960 Z= 0.356 Chirality : 0.044 0.177 2120 Planarity : 0.004 0.043 2235 Dihedral : 7.470 59.150 2337 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.88 % Allowed : 9.40 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.20), residues: 1665 helix: 1.56 (0.20), residues: 585 sheet: -0.46 (0.24), residues: 385 loop : -1.63 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 229 TYR 0.022 0.002 TYR A 144 PHE 0.017 0.002 PHE A 223 TRP 0.038 0.002 TRP E 302 HIS 0.004 0.002 HIS A 231 Details of bonding type rmsd covalent geometry : bond 0.00443 (13060) covalent geometry : angle 0.70730 (17935) SS BOND : bond 0.00041 ( 5) SS BOND : angle 0.97690 ( 10) hydrogen bonds : bond 0.03923 ( 681) hydrogen bonds : angle 5.93970 ( 2283) link_BETA1-4 : bond 0.01002 ( 5) link_BETA1-4 : angle 0.85710 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 163 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 MET cc_start: 0.8551 (tpp) cc_final: 0.7598 (tpp) REVERT: A 170 MET cc_start: 0.8684 (tmm) cc_final: 0.8056 (tmm) REVERT: A 303 MET cc_start: 0.9071 (mmm) cc_final: 0.8566 (mmm) REVERT: B 64 PHE cc_start: 0.8749 (OUTLIER) cc_final: 0.7938 (t80) REVERT: B 72 MET cc_start: 0.8821 (tpp) cc_final: 0.7629 (tpp) REVERT: B 171 GLN cc_start: 0.8935 (pt0) cc_final: 0.8459 (pm20) REVERT: B 255 TRP cc_start: 0.8637 (m-10) cc_final: 0.8411 (m-10) REVERT: B 274 THR cc_start: 0.9116 (m) cc_final: 0.8911 (t) REVERT: B 302 TRP cc_start: 0.8498 (t60) cc_final: 0.8065 (t60) REVERT: B 303 MET cc_start: 0.9139 (mmm) cc_final: 0.8755 (mmm) REVERT: C 72 MET cc_start: 0.8581 (tpp) cc_final: 0.8072 (tpp) REVERT: C 119 GLU cc_start: 0.7939 (pm20) cc_final: 0.7477 (pm20) REVERT: C 171 GLN cc_start: 0.8986 (pt0) cc_final: 0.8698 (pm20) REVERT: D 72 MET cc_start: 0.8722 (tpp) cc_final: 0.8343 (tpp) REVERT: D 82 GLN cc_start: 0.9065 (mp10) cc_final: 0.8804 (mp10) REVERT: D 255 TRP cc_start: 0.8771 (m-10) cc_final: 0.8480 (m-10) REVERT: D 303 MET cc_start: 0.9124 (mmm) cc_final: 0.8746 (mmm) REVERT: E 72 MET cc_start: 0.8293 (mmm) cc_final: 0.7974 (mmm) REVERT: E 255 TRP cc_start: 0.8630 (m-10) cc_final: 0.8319 (m-10) REVERT: E 303 MET cc_start: 0.9016 (mmm) cc_final: 0.8789 (mmm) outliers start: 45 outliers final: 33 residues processed: 194 average time/residue: 0.0987 time to fit residues: 28.7909 Evaluate side-chains 177 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 143 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain A residue 290 LEU 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 136 ILE Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain D residue 57 CYS Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 198 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 138 optimal weight: 0.9990 chunk 134 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 79 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 97 optimal weight: 10.0000 chunk 127 optimal weight: 3.9990 chunk 65 optimal weight: 20.0000 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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 123 ASN ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 ASN ** 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 = 0.2815 r_free = 0.2815 target = 0.039861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.033225 restraints weight = 96104.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.033973 restraints weight = 61678.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.034387 restraints weight = 44377.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.034670 restraints weight = 37275.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.034689 restraints weight = 31494.020| |-----------------------------------------------------------------------------| r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13070 Z= 0.137 Angle : 0.659 12.174 17960 Z= 0.318 Chirality : 0.043 0.138 2120 Planarity : 0.003 0.026 2235 Dihedral : 7.010 59.217 2337 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.53 % Allowed : 11.29 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.21), residues: 1665 helix: 2.28 (0.21), residues: 585 sheet: -0.55 (0.24), residues: 385 loop : -1.44 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 81 TYR 0.020 0.002 TYR C 144 PHE 0.018 0.001 PHE E 115 TRP 0.009 0.001 TRP C 259 HIS 0.002 0.001 HIS C 217 Details of bonding type rmsd covalent geometry : bond 0.00288 (13060) covalent geometry : angle 0.65960 (17935) SS BOND : bond 0.00035 ( 5) SS BOND : angle 0.59362 ( 10) hydrogen bonds : bond 0.03520 ( 681) hydrogen bonds : angle 5.40796 ( 2283) link_BETA1-4 : bond 0.00841 ( 5) link_BETA1-4 : angle 0.43656 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 160 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: A 72 MET cc_start: 0.8368 (tpp) cc_final: 0.7969 (tpp) REVERT: A 219 ASN cc_start: 0.8574 (m-40) cc_final: 0.8240 (p0) REVERT: A 255 TRP cc_start: 0.8701 (m-10) cc_final: 0.8411 (m-10) REVERT: A 274 THR cc_start: 0.8907 (p) cc_final: 0.8662 (t) REVERT: A 303 MET cc_start: 0.8998 (mmm) cc_final: 0.8591 (mmm) REVERT: B 64 PHE cc_start: 0.8768 (OUTLIER) cc_final: 0.8121 (t80) REVERT: B 72 MET cc_start: 0.8640 (tpp) cc_final: 0.7938 (tpp) REVERT: B 119 GLU cc_start: 0.8213 (pm20) cc_final: 0.7451 (pm20) REVERT: B 171 GLN cc_start: 0.8918 (pt0) cc_final: 0.8414 (pm20) REVERT: B 219 ASN cc_start: 0.8777 (m-40) cc_final: 0.8403 (p0) REVERT: B 255 TRP cc_start: 0.8698 (m-10) cc_final: 0.8432 (m-10) REVERT: B 303 MET cc_start: 0.9075 (mmm) cc_final: 0.8736 (mmm) REVERT: C 72 MET cc_start: 0.8669 (tpp) cc_final: 0.8169 (tpp) REVERT: C 119 GLU cc_start: 0.8117 (pm20) cc_final: 0.7508 (pm20) REVERT: C 171 GLN cc_start: 0.8957 (pt0) cc_final: 0.8539 (pm20) REVERT: C 255 TRP cc_start: 0.8652 (m-10) cc_final: 0.8402 (m-10) REVERT: D 72 MET cc_start: 0.8711 (tpp) cc_final: 0.8345 (tpp) REVERT: D 82 GLN cc_start: 0.8932 (mp10) cc_final: 0.8680 (mp10) REVERT: D 255 TRP cc_start: 0.8771 (m-10) cc_final: 0.8450 (m-10) REVERT: E 255 TRP cc_start: 0.8635 (m-10) cc_final: 0.8297 (m-10) REVERT: E 302 TRP cc_start: 0.8381 (t60) cc_final: 0.7761 (t60) REVERT: E 303 MET cc_start: 0.9008 (mmm) cc_final: 0.8794 (mmm) outliers start: 41 outliers final: 32 residues processed: 185 average time/residue: 0.0895 time to fit residues: 25.5516 Evaluate side-chains 181 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 148 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 64 PHE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 279 MET 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 198 LEU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 245 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 1 optimal weight: 9.9990 chunk 68 optimal weight: 0.0670 chunk 16 optimal weight: 0.7980 chunk 94 optimal weight: 5.9990 chunk 60 optimal weight: 20.0000 chunk 134 optimal weight: 0.0270 chunk 72 optimal weight: 0.0980 chunk 36 optimal weight: 9.9990 chunk 78 optimal weight: 9.9990 chunk 71 optimal weight: 6.9990 chunk 150 optimal weight: 7.9990 overall best weight: 1.3978 ------------------------------------------------------------------------------- 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 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 GLN ** D 118 ASN ** 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 = 0.2829 r_free = 0.2829 target = 0.040386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.033785 restraints weight = 96454.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 15)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.034519 restraints weight = 61176.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.034934 restraints weight = 43541.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.035195 restraints weight = 35562.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.035344 restraints weight = 32200.273| |-----------------------------------------------------------------------------| r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13070 Z= 0.127 Angle : 0.633 11.334 17960 Z= 0.306 Chirality : 0.042 0.138 2120 Planarity : 0.003 0.029 2235 Dihedral : 6.666 56.404 2335 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.79 % Allowed : 11.72 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.21), residues: 1665 helix: 2.59 (0.20), residues: 585 sheet: -0.57 (0.24), residues: 385 loop : -1.35 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 81 TYR 0.017 0.002 TYR B 244 PHE 0.021 0.001 PHE D 350 TRP 0.028 0.001 TRP B 302 HIS 0.002 0.001 HIS C 217 Details of bonding type rmsd covalent geometry : bond 0.00272 (13060) covalent geometry : angle 0.63327 (17935) SS BOND : bond 0.00036 ( 5) SS BOND : angle 0.56804 ( 10) hydrogen bonds : bond 0.03415 ( 681) hydrogen bonds : angle 5.19841 ( 2283) link_BETA1-4 : bond 0.00689 ( 5) link_BETA1-4 : angle 0.41220 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 159 time to evaluate : 0.487 Fit side-chains revert: symmetry clash REVERT: A 72 MET cc_start: 0.8789 (tpp) cc_final: 0.8498 (tpp) REVERT: A 170 MET cc_start: 0.8699 (tmm) cc_final: 0.7962 (tmm) REVERT: A 219 ASN cc_start: 0.8630 (m-40) cc_final: 0.8290 (p0) REVERT: A 255 TRP cc_start: 0.8698 (m-10) cc_final: 0.8380 (m-10) REVERT: B 64 PHE cc_start: 0.8799 (OUTLIER) cc_final: 0.8113 (t80) REVERT: B 72 MET cc_start: 0.8588 (tpp) cc_final: 0.7930 (tpp) REVERT: B 119 GLU cc_start: 0.8176 (pm20) cc_final: 0.7373 (pm20) REVERT: B 171 GLN cc_start: 0.8945 (pt0) cc_final: 0.8415 (pm20) REVERT: B 219 ASN cc_start: 0.8798 (m-40) cc_final: 0.8448 (p0) REVERT: B 255 TRP cc_start: 0.8697 (m-10) cc_final: 0.8390 (m-10) REVERT: B 303 MET cc_start: 0.9011 (mmm) cc_final: 0.8760 (mmm) REVERT: C 72 MET cc_start: 0.8731 (tpp) cc_final: 0.8218 (tpp) REVERT: C 119 GLU cc_start: 0.8029 (pm20) cc_final: 0.7466 (pm20) REVERT: C 171 GLN cc_start: 0.8955 (pt0) cc_final: 0.8521 (pm20) REVERT: C 255 TRP cc_start: 0.8656 (m-10) cc_final: 0.8401 (m-10) REVERT: D 72 MET cc_start: 0.8731 (tpp) cc_final: 0.8352 (tpp) REVERT: D 82 GLN cc_start: 0.9006 (mp10) cc_final: 0.8657 (mp10) REVERT: D 255 TRP cc_start: 0.8731 (m-10) cc_final: 0.8427 (m-10) REVERT: D 274 THR cc_start: 0.8952 (p) cc_final: 0.8699 (t) REVERT: D 302 TRP cc_start: 0.8512 (t60) cc_final: 0.8026 (t60) REVERT: E 255 TRP cc_start: 0.8609 (m-10) cc_final: 0.8297 (m-10) REVERT: E 274 THR cc_start: 0.8978 (m) cc_final: 0.8668 (t) REVERT: E 302 TRP cc_start: 0.8360 (t60) cc_final: 0.7609 (t60) outliers start: 44 outliers final: 30 residues processed: 190 average time/residue: 0.0843 time to fit residues: 25.1602 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 : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain 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 B residue 150 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain D residue 57 CYS Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 198 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 34 optimal weight: 20.0000 chunk 96 optimal weight: 10.0000 chunk 134 optimal weight: 0.0470 chunk 3 optimal weight: 7.9990 chunk 158 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 116 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 28 optimal weight: 7.9990 overall best weight: 3.0086 ------------------------------------------------------------------------------- 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 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.039718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.033264 restraints weight = 97835.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.033998 restraints weight = 61543.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.034395 restraints weight = 43936.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.034813 restraints weight = 35757.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.034874 restraints weight = 31365.904| |-----------------------------------------------------------------------------| r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13070 Z= 0.176 Angle : 0.658 14.363 17960 Z= 0.324 Chirality : 0.043 0.166 2120 Planarity : 0.004 0.036 2235 Dihedral : 6.514 57.360 2335 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.79 % Allowed : 13.28 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.21), residues: 1665 helix: 2.51 (0.20), residues: 590 sheet: -0.61 (0.24), residues: 405 loop : -1.27 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 234 TYR 0.017 0.002 TYR C 144 PHE 0.015 0.002 PHE D 230 TRP 0.032 0.001 TRP B 302 HIS 0.004 0.001 HIS B 217 Details of bonding type rmsd covalent geometry : bond 0.00371 (13060) covalent geometry : angle 0.65802 (17935) SS BOND : bond 0.00061 ( 5) SS BOND : angle 0.56393 ( 10) hydrogen bonds : bond 0.03619 ( 681) hydrogen bonds : angle 5.27434 ( 2283) link_BETA1-4 : bond 0.00615 ( 5) link_BETA1-4 : angle 0.79546 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 149 time to evaluate : 0.479 Fit side-chains REVERT: A 72 MET cc_start: 0.8675 (tpp) cc_final: 0.8405 (tpp) REVERT: A 255 TRP cc_start: 0.8666 (m-10) cc_final: 0.8337 (m-10) REVERT: A 303 MET cc_start: 0.9027 (mmt) cc_final: 0.8816 (mmm) REVERT: B 64 PHE cc_start: 0.8772 (OUTLIER) cc_final: 0.8184 (t80) REVERT: B 72 MET cc_start: 0.8518 (tpp) cc_final: 0.7995 (tpp) REVERT: B 119 GLU cc_start: 0.8148 (pm20) cc_final: 0.7331 (pm20) REVERT: B 171 GLN cc_start: 0.8914 (pt0) cc_final: 0.8415 (pm20) REVERT: B 219 ASN cc_start: 0.8831 (m-40) cc_final: 0.8454 (p0) REVERT: B 255 TRP cc_start: 0.8657 (m-10) cc_final: 0.8377 (m-10) REVERT: B 303 MET cc_start: 0.9064 (mmm) cc_final: 0.8643 (mmm) REVERT: C 72 MET cc_start: 0.8700 (tpp) cc_final: 0.8295 (tpp) REVERT: C 171 GLN cc_start: 0.8882 (pt0) cc_final: 0.8544 (pm20) REVERT: C 255 TRP cc_start: 0.8655 (m-10) cc_final: 0.8406 (m-10) REVERT: D 72 MET cc_start: 0.8727 (tpp) cc_final: 0.8458 (tpp) REVERT: D 82 GLN cc_start: 0.8974 (mp10) cc_final: 0.8605 (mp10) REVERT: D 241 ILE cc_start: 0.9168 (mm) cc_final: 0.8812 (tt) REVERT: D 255 TRP cc_start: 0.8815 (m-10) cc_final: 0.8530 (m-10) REVERT: D 302 TRP cc_start: 0.8538 (t60) cc_final: 0.8075 (t60) REVERT: E 170 MET cc_start: 0.8549 (tmm) cc_final: 0.8318 (tmm) REVERT: E 255 TRP cc_start: 0.8686 (m-10) cc_final: 0.8350 (m-10) REVERT: E 274 THR cc_start: 0.9043 (m) cc_final: 0.8772 (t) REVERT: E 302 TRP cc_start: 0.8493 (t60) cc_final: 0.7774 (t60) outliers start: 44 outliers final: 31 residues processed: 183 average time/residue: 0.0852 time to fit residues: 24.7561 Evaluate side-chains 179 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 147 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 64 PHE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain D residue 57 CYS Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 245 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 101 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 73 optimal weight: 0.9990 chunk 113 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 30 optimal weight: 20.0000 chunk 91 optimal weight: 3.9990 chunk 154 optimal weight: 0.6980 chunk 160 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.039910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.033374 restraints weight = 98455.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.034156 restraints weight = 62675.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.034563 restraints weight = 44475.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.034946 restraints weight = 36245.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.035180 restraints weight = 31011.566| |-----------------------------------------------------------------------------| r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.4252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13070 Z= 0.148 Angle : 0.648 15.246 17960 Z= 0.312 Chirality : 0.042 0.145 2120 Planarity : 0.003 0.039 2235 Dihedral : 6.210 57.050 2335 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.88 % Allowed : 13.36 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.21), residues: 1665 helix: 2.72 (0.20), residues: 590 sheet: -0.60 (0.24), residues: 405 loop : -1.23 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 147 TYR 0.014 0.002 TYR E 144 PHE 0.017 0.001 PHE A 223 TRP 0.022 0.001 TRP B 302 HIS 0.003 0.001 HIS C 217 Details of bonding type rmsd covalent geometry : bond 0.00316 (13060) covalent geometry : angle 0.64847 (17935) SS BOND : bond 0.00062 ( 5) SS BOND : angle 0.54565 ( 10) hydrogen bonds : bond 0.03449 ( 681) hydrogen bonds : angle 5.12829 ( 2283) link_BETA1-4 : bond 0.00720 ( 5) link_BETA1-4 : angle 0.66936 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 149 time to evaluate : 0.513 Fit side-chains REVERT: A 72 MET cc_start: 0.8651 (tpp) cc_final: 0.8402 (tpp) REVERT: A 170 MET cc_start: 0.8677 (tmm) cc_final: 0.8020 (tmm) REVERT: A 219 ASN cc_start: 0.8676 (m-40) cc_final: 0.8292 (p0) REVERT: A 255 TRP cc_start: 0.8630 (m-10) cc_final: 0.8287 (m-10) REVERT: A 277 LEU cc_start: 0.9460 (tp) cc_final: 0.9251 (mt) REVERT: A 303 MET cc_start: 0.9033 (mmt) cc_final: 0.8795 (mmm) REVERT: B 64 PHE cc_start: 0.8753 (OUTLIER) cc_final: 0.8234 (t80) REVERT: B 72 MET cc_start: 0.8521 (tpp) cc_final: 0.7881 (tpp) REVERT: B 119 GLU cc_start: 0.8112 (pm20) cc_final: 0.7291 (pm20) REVERT: B 171 GLN cc_start: 0.8842 (pt0) cc_final: 0.8298 (pm20) REVERT: B 219 ASN cc_start: 0.8834 (m-40) cc_final: 0.8380 (p0) REVERT: B 255 TRP cc_start: 0.8659 (m-10) cc_final: 0.8316 (m-10) REVERT: B 303 MET cc_start: 0.9046 (mmm) cc_final: 0.8696 (mmm) REVERT: C 72 MET cc_start: 0.8718 (tpp) cc_final: 0.8297 (tpp) REVERT: C 171 GLN cc_start: 0.8740 (pt0) cc_final: 0.8528 (pt0) REVERT: C 255 TRP cc_start: 0.8672 (m-10) cc_final: 0.8412 (m-10) REVERT: C 296 VAL cc_start: 0.8473 (OUTLIER) cc_final: 0.8223 (p) REVERT: D 72 MET cc_start: 0.8722 (tpp) cc_final: 0.8463 (tpp) REVERT: D 82 GLN cc_start: 0.8979 (mp10) cc_final: 0.8664 (mp10) REVERT: D 83 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7899 (mp10) REVERT: D 241 ILE cc_start: 0.9158 (mm) cc_final: 0.8795 (tt) REVERT: D 255 TRP cc_start: 0.8821 (m-10) cc_final: 0.8524 (m-10) REVERT: D 302 TRP cc_start: 0.8545 (t60) cc_final: 0.8087 (t60) REVERT: E 255 TRP cc_start: 0.8703 (m-10) cc_final: 0.8381 (m-10) REVERT: E 274 THR cc_start: 0.9051 (m) cc_final: 0.8779 (t) REVERT: E 302 TRP cc_start: 0.8524 (t60) cc_final: 0.7885 (t60) outliers start: 45 outliers final: 31 residues processed: 184 average time/residue: 0.0865 time to fit residues: 25.5216 Evaluate side-chains 179 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 145 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 64 PHE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain D residue 57 CYS Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 83 GLN Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 245 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 87 optimal weight: 7.9990 chunk 109 optimal weight: 10.0000 chunk 63 optimal weight: 20.0000 chunk 103 optimal weight: 7.9990 chunk 126 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 157 optimal weight: 3.9990 chunk 62 optimal weight: 20.0000 chunk 86 optimal weight: 10.0000 chunk 114 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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** ** 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 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.038855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.032418 restraints weight = 99541.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.033174 restraints weight = 63679.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.033612 restraints weight = 45362.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.034046 restraints weight = 36748.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.034095 restraints weight = 31080.524| |-----------------------------------------------------------------------------| r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.4707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 13070 Z= 0.316 Angle : 0.783 13.222 17960 Z= 0.394 Chirality : 0.045 0.163 2120 Planarity : 0.005 0.051 2235 Dihedral : 6.681 54.015 2335 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.79 % Allowed : 14.48 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.21), residues: 1665 helix: 1.87 (0.20), residues: 595 sheet: -1.06 (0.25), residues: 410 loop : -1.49 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 147 TYR 0.017 0.003 TYR E 238 PHE 0.020 0.003 PHE D 230 TRP 0.014 0.002 TRP B 259 HIS 0.008 0.003 HIS B 217 Details of bonding type rmsd covalent geometry : bond 0.00652 (13060) covalent geometry : angle 0.78239 (17935) SS BOND : bond 0.00193 ( 5) SS BOND : angle 0.68103 ( 10) hydrogen bonds : bond 0.04406 ( 681) hydrogen bonds : angle 5.72563 ( 2283) link_BETA1-4 : bond 0.00750 ( 5) link_BETA1-4 : angle 1.04083 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 145 time to evaluate : 0.541 Fit side-chains revert: symmetry clash REVERT: A 64 PHE cc_start: 0.8774 (OUTLIER) cc_final: 0.8057 (t80) REVERT: A 72 MET cc_start: 0.8520 (tpp) cc_final: 0.8070 (tpp) REVERT: A 156 MET cc_start: 0.7862 (mpp) cc_final: 0.7557 (mpp) REVERT: A 255 TRP cc_start: 0.8712 (m-10) cc_final: 0.8447 (m-10) REVERT: B 64 PHE cc_start: 0.8868 (OUTLIER) cc_final: 0.8414 (t80) REVERT: B 72 MET cc_start: 0.8470 (tpp) cc_final: 0.8046 (tpp) REVERT: B 171 GLN cc_start: 0.8919 (pt0) cc_final: 0.8329 (pm20) REVERT: B 219 ASN cc_start: 0.8845 (m-40) cc_final: 0.8391 (p0) REVERT: B 302 TRP cc_start: 0.8519 (t60) cc_final: 0.7978 (t60) REVERT: B 303 MET cc_start: 0.9041 (mmm) cc_final: 0.8746 (mmm) REVERT: C 64 PHE cc_start: 0.8716 (OUTLIER) cc_final: 0.8345 (t80) REVERT: C 72 MET cc_start: 0.8655 (tpp) cc_final: 0.8362 (tpp) REVERT: C 171 GLN cc_start: 0.8771 (pt0) cc_final: 0.8318 (pm20) REVERT: C 255 TRP cc_start: 0.8711 (m-10) cc_final: 0.8419 (m-10) REVERT: D 72 MET cc_start: 0.8704 (tpp) cc_final: 0.8345 (tpp) REVERT: D 241 ILE cc_start: 0.9148 (mm) cc_final: 0.8809 (tt) REVERT: D 255 TRP cc_start: 0.8880 (m-10) cc_final: 0.8499 (m-10) REVERT: E 199 THR cc_start: 0.8284 (p) cc_final: 0.8057 (t) REVERT: E 255 TRP cc_start: 0.8726 (m-10) cc_final: 0.8472 (m-10) REVERT: E 302 TRP cc_start: 0.8386 (t60) cc_final: 0.8056 (t60) outliers start: 44 outliers final: 29 residues processed: 180 average time/residue: 0.0934 time to fit residues: 26.5881 Evaluate side-chains 174 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 142 time to evaluate : 0.479 ------------------------------------------------------------------------------- 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 A residue 198 LEU Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 64 PHE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 64 PHE Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain D residue 57 CYS Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 80 LEU 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 71 THR Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 245 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 3 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 151 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 34 optimal weight: 0.0000 chunk 67 optimal weight: 0.2980 chunk 92 optimal weight: 0.0570 chunk 24 optimal weight: 3.9990 chunk 43 optimal weight: 9.9990 chunk 23 optimal weight: 0.8980 chunk 123 optimal weight: 30.0000 overall best weight: 0.6504 ------------------------------------------------------------------------------- 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 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.040667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.034034 restraints weight = 97853.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.034701 restraints weight = 61436.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.035185 restraints weight = 45116.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.035568 restraints weight = 36670.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.035742 restraints weight = 31901.271| |-----------------------------------------------------------------------------| r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.4634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13070 Z= 0.125 Angle : 0.694 16.160 17960 Z= 0.322 Chirality : 0.043 0.142 2120 Planarity : 0.003 0.038 2235 Dihedral : 5.955 52.574 2335 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.41 % Allowed : 16.21 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.21), residues: 1665 helix: 2.72 (0.20), residues: 595 sheet: -0.89 (0.23), residues: 430 loop : -1.15 (0.26), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 147 TYR 0.014 0.002 TYR E 144 PHE 0.017 0.001 PHE D 230 TRP 0.009 0.001 TRP A 302 HIS 0.003 0.001 HIS E 125 Details of bonding type rmsd covalent geometry : bond 0.00266 (13060) covalent geometry : angle 0.69426 (17935) SS BOND : bond 0.00075 ( 5) SS BOND : angle 0.60157 ( 10) hydrogen bonds : bond 0.03335 ( 681) hydrogen bonds : angle 5.08888 ( 2283) link_BETA1-4 : bond 0.00705 ( 5) link_BETA1-4 : angle 0.54842 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 159 time to evaluate : 0.532 Fit side-chains REVERT: A 64 PHE cc_start: 0.8764 (OUTLIER) cc_final: 0.8019 (t80) REVERT: A 72 MET cc_start: 0.8620 (tpp) cc_final: 0.8177 (tpp) REVERT: A 156 MET cc_start: 0.7901 (mpp) cc_final: 0.7440 (mpp) REVERT: A 170 MET cc_start: 0.8798 (tmm) cc_final: 0.8124 (tmm) REVERT: A 219 ASN cc_start: 0.8629 (m-40) cc_final: 0.8155 (p0) REVERT: A 241 ILE cc_start: 0.9054 (mm) cc_final: 0.8716 (tt) REVERT: A 255 TRP cc_start: 0.8667 (m-10) cc_final: 0.8387 (m-10) REVERT: A 303 MET cc_start: 0.9035 (mmt) cc_final: 0.8726 (mmm) REVERT: B 64 PHE cc_start: 0.8805 (OUTLIER) cc_final: 0.8410 (t80) REVERT: B 72 MET cc_start: 0.8483 (tpp) cc_final: 0.7932 (tpp) REVERT: B 119 GLU cc_start: 0.8228 (pm20) cc_final: 0.7505 (pm20) REVERT: B 171 GLN cc_start: 0.8769 (pt0) cc_final: 0.8377 (pt0) REVERT: B 219 ASN cc_start: 0.8817 (m-40) cc_final: 0.8383 (p0) REVERT: B 255 TRP cc_start: 0.8730 (m-10) cc_final: 0.8398 (m-10) REVERT: B 303 MET cc_start: 0.9012 (mmm) cc_final: 0.8677 (mmm) REVERT: C 72 MET cc_start: 0.8732 (tpp) cc_final: 0.8317 (tpt) REVERT: C 170 MET cc_start: 0.8420 (tmm) cc_final: 0.8184 (tmm) REVERT: C 171 GLN cc_start: 0.8730 (pt0) cc_final: 0.8516 (pt0) REVERT: C 255 TRP cc_start: 0.8697 (m-10) cc_final: 0.8381 (m-10) REVERT: C 282 GLN cc_start: 0.9057 (tp40) cc_final: 0.8658 (tp-100) REVERT: C 303 MET cc_start: 0.8936 (mmm) cc_final: 0.8601 (mmt) REVERT: D 72 MET cc_start: 0.8702 (tpp) cc_final: 0.6978 (tpp) REVERT: D 82 GLN cc_start: 0.8971 (mp10) cc_final: 0.8611 (mp10) REVERT: D 241 ILE cc_start: 0.9124 (mm) cc_final: 0.8773 (tt) REVERT: D 255 TRP cc_start: 0.8820 (m-10) cc_final: 0.8524 (m-10) REVERT: D 302 TRP cc_start: 0.8504 (t60) cc_final: 0.7586 (t60) REVERT: E 255 TRP cc_start: 0.8761 (m-10) cc_final: 0.8481 (m-10) REVERT: E 274 THR cc_start: 0.9007 (m) cc_final: 0.8757 (t) REVERT: E 302 TRP cc_start: 0.8463 (t60) cc_final: 0.7640 (t60) outliers start: 28 outliers final: 21 residues processed: 181 average time/residue: 0.0973 time to fit residues: 27.5694 Evaluate side-chains 168 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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 230 PHE 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 B residue 230 PHE Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 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 296 VAL Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 245 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 130 optimal weight: 9.9990 chunk 150 optimal weight: 8.9990 chunk 70 optimal weight: 8.9990 chunk 69 optimal weight: 1.9990 chunk 49 optimal weight: 0.4980 chunk 24 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 100 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 63 optimal weight: 30.0000 chunk 93 optimal weight: 8.9990 overall best weight: 5.2988 ------------------------------------------------------------------------------- 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** ** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** 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 = 0.2814 r_free = 0.2814 target = 0.039399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.032853 restraints weight = 101706.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.033600 restraints weight = 65831.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.034013 restraints weight = 49532.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.034384 restraints weight = 39972.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.034462 restraints weight = 34675.064| |-----------------------------------------------------------------------------| r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.4931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 13070 Z= 0.267 Angle : 0.765 13.223 17960 Z= 0.374 Chirality : 0.045 0.230 2120 Planarity : 0.005 0.039 2235 Dihedral : 6.391 53.910 2335 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.59 % Allowed : 16.47 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.21), residues: 1665 helix: 2.18 (0.20), residues: 580 sheet: -1.18 (0.24), residues: 420 loop : -1.39 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 147 TYR 0.016 0.003 TYR E 144 PHE 0.016 0.002 PHE D 230 TRP 0.054 0.002 TRP B 302 HIS 0.007 0.002 HIS B 217 Details of bonding type rmsd covalent geometry : bond 0.00554 (13060) covalent geometry : angle 0.76533 (17935) SS BOND : bond 0.00151 ( 5) SS BOND : angle 0.52870 ( 10) hydrogen bonds : bond 0.04181 ( 681) hydrogen bonds : angle 5.48232 ( 2283) link_BETA1-4 : bond 0.00773 ( 5) link_BETA1-4 : angle 0.95441 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 145 time to evaluate : 0.519 Fit side-chains REVERT: A 64 PHE cc_start: 0.8738 (OUTLIER) cc_final: 0.8039 (t80) REVERT: A 72 MET cc_start: 0.8525 (tpp) cc_final: 0.8255 (tpp) REVERT: A 241 ILE cc_start: 0.9101 (mm) cc_final: 0.8781 (tp) REVERT: A 255 TRP cc_start: 0.8754 (m-10) cc_final: 0.8472 (m-10) REVERT: B 64 PHE cc_start: 0.8819 (OUTLIER) cc_final: 0.8503 (t80) REVERT: B 72 MET cc_start: 0.8500 (tpp) cc_final: 0.8113 (tpp) REVERT: B 171 GLN cc_start: 0.8802 (pt0) cc_final: 0.8267 (pm20) REVERT: B 219 ASN cc_start: 0.8823 (m-40) cc_final: 0.8375 (p0) REVERT: B 255 TRP cc_start: 0.8805 (m-10) cc_final: 0.8428 (m-10) REVERT: B 303 MET cc_start: 0.8976 (mmm) cc_final: 0.8664 (mmm) REVERT: C 64 PHE cc_start: 0.8634 (OUTLIER) cc_final: 0.8279 (t80) REVERT: C 72 MET cc_start: 0.8669 (tpp) cc_final: 0.8386 (tpp) REVERT: C 255 TRP cc_start: 0.8761 (m-10) cc_final: 0.8441 (m-10) REVERT: D 72 MET cc_start: 0.8485 (tpp) cc_final: 0.7790 (tpp) REVERT: D 156 MET cc_start: 0.7602 (mpp) cc_final: 0.7157 (mpp) REVERT: D 241 ILE cc_start: 0.9082 (mm) cc_final: 0.8738 (tt) REVERT: D 255 TRP cc_start: 0.8910 (m-10) cc_final: 0.8519 (m-10) REVERT: D 302 TRP cc_start: 0.8471 (t60) cc_final: 0.8040 (t60) REVERT: E 255 TRP cc_start: 0.8735 (m-10) cc_final: 0.8450 (m-10) REVERT: E 302 TRP cc_start: 0.8493 (t60) cc_final: 0.8203 (t60) outliers start: 30 outliers final: 19 residues processed: 169 average time/residue: 0.0965 time to fit residues: 25.6787 Evaluate side-chains 162 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 0.481 ------------------------------------------------------------------------------- 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 A residue 230 PHE 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 64 PHE Chi-restraints excluded: chain C residue 127 VAL 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 E residue 57 CYS Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 245 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 91 optimal weight: 8.9990 chunk 12 optimal weight: 4.9990 chunk 132 optimal weight: 9.9990 chunk 90 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 140 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 135 optimal weight: 7.9990 chunk 93 optimal weight: 10.0000 chunk 130 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 overall best weight: 4.5388 ------------------------------------------------------------------------------- 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** ** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.039512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.033397 restraints weight = 98697.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.034119 restraints weight = 64054.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.034370 restraints weight = 45229.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.034732 restraints weight = 37819.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.034836 restraints weight = 32741.864| |-----------------------------------------------------------------------------| r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.5065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13070 Z= 0.226 Angle : 0.742 14.627 17960 Z= 0.359 Chirality : 0.044 0.219 2120 Planarity : 0.004 0.038 2235 Dihedral : 6.366 54.075 2335 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.41 % Allowed : 16.90 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.21), residues: 1665 helix: 2.29 (0.20), residues: 580 sheet: -1.24 (0.24), residues: 410 loop : -1.45 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 147 TYR 0.020 0.002 TYR B 244 PHE 0.022 0.002 PHE C 124 TRP 0.053 0.002 TRP B 302 HIS 0.006 0.002 HIS B 217 Details of bonding type rmsd covalent geometry : bond 0.00473 (13060) covalent geometry : angle 0.74232 (17935) SS BOND : bond 0.00160 ( 5) SS BOND : angle 0.58981 ( 10) hydrogen bonds : bond 0.03971 ( 681) hydrogen bonds : angle 5.44616 ( 2283) link_BETA1-4 : bond 0.00710 ( 5) link_BETA1-4 : angle 0.78256 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1630.10 seconds wall clock time: 29 minutes 14.39 seconds (1754.39 seconds total)