Starting phenix.real_space_refine on Thu Sep 26 10:31:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jad_6344/09_2024/3jad_6344.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jad_6344/09_2024/3jad_6344.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jad_6344/09_2024/3jad_6344.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jad_6344/09_2024/3jad_6344.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jad_6344/09_2024/3jad_6344.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jad_6344/09_2024/3jad_6344.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 65 5.16 5 C 8305 2.51 5 N 2090 2.21 5 O 2245 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 12705 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2488 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 15, 'TRANS': 321} Chain breaks: 1 Unresolved non-hydrogen bonds: 241 Unresolved non-hydrogen angles: 294 Unresolved non-hydrogen dihedrals: 194 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 8, 'PHE:plan': 3, 'GLU:plan': 11, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 121 Chain: "B" Number of atoms: 2488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2488 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 15, 'TRANS': 321} Chain breaks: 1 Unresolved non-hydrogen bonds: 241 Unresolved non-hydrogen angles: 294 Unresolved non-hydrogen dihedrals: 194 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 8, 'PHE:plan': 3, 'GLU:plan': 11, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 121 Chain: "C" Number of atoms: 2488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2488 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 15, 'TRANS': 321} Chain breaks: 1 Unresolved non-hydrogen bonds: 241 Unresolved non-hydrogen angles: 294 Unresolved non-hydrogen dihedrals: 194 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 8, 'PHE:plan': 3, 'GLU:plan': 11, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 121 Chain: "D" Number of atoms: 2488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2488 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 15, 'TRANS': 321} Chain breaks: 1 Unresolved non-hydrogen bonds: 241 Unresolved non-hydrogen angles: 294 Unresolved non-hydrogen dihedrals: 194 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 8, 'PHE:plan': 3, 'GLU:plan': 11, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 121 Chain: "E" Number of atoms: 2488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2488 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 15, 'TRANS': 321} Chain breaks: 1 Unresolved non-hydrogen bonds: 241 Unresolved non-hydrogen angles: 294 Unresolved non-hydrogen dihedrals: 194 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 8, 'PHE:plan': 3, 'GLU:plan': 11, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 121 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'SY9': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'SY9': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'SY9': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'SY9': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'SY9': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.99, per 1000 atoms: 0.63 Number of scatterers: 12705 At special positions: 0 Unit cell: (98.98, 97.97, 126.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 65 16.00 O 2245 8.00 N 2090 7.00 C 8305 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 225 " distance=2.04 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 225 " distance=2.04 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 225 " distance=2.04 Simple disulfide: pdb=" SG CYS D 214 " - pdb=" SG CYS D 225 " distance=2.04 Simple disulfide: pdb=" SG CYS E 214 " - pdb=" SG CYS E 225 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " Time building additional restraints: 3.27 Conformation dependent library (CDL) restraints added in 1.7 seconds 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3230 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 15 sheets defined 37.4% alpha, 38.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'A' and resid 25 through 35 removed outlier: 3.513A pdb=" N LEU A 33 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 108 removed outlier: 4.053A pdb=" N ASP A 107 " --> pdb=" O SER A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 243 Processing helix chain 'A' and resid 243 through 259 removed outlier: 3.674A pdb=" N SER A 247 " --> pdb=" O MET A 243 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TRP A 259 " --> pdb=" O TRP A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 290 Processing helix chain 'A' and resid 297 through 325 removed outlier: 3.959A pdb=" N LEU A 314 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG A 325 " --> pdb=" O ASN A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 362 Proline residue: A 347 - end of helix removed outlier: 3.841A pdb=" N ILE A 359 " --> pdb=" O ILE A 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 35 removed outlier: 3.514A pdb=" N LEU B 33 " --> pdb=" O PHE B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 108 removed outlier: 4.053A pdb=" N ASP B 107 " --> pdb=" O SER B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 243 Processing helix chain 'B' and resid 243 through 259 removed outlier: 3.673A pdb=" N SER B 247 " --> pdb=" O MET B 243 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TRP B 259 " --> pdb=" O TRP B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 290 Processing helix chain 'B' and resid 297 through 325 removed outlier: 3.959A pdb=" N LEU B 314 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG B 325 " --> pdb=" O ASN B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 362 Proline residue: B 347 - end of helix removed outlier: 3.841A pdb=" N ILE B 359 " --> pdb=" O ILE B 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 35 removed outlier: 3.513A pdb=" N LEU C 33 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 108 removed outlier: 4.053A pdb=" N ASP C 107 " --> pdb=" O SER C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 243 Processing helix chain 'C' and resid 243 through 259 removed outlier: 3.674A pdb=" N SER C 247 " --> pdb=" O MET C 243 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TRP C 259 " --> pdb=" O TRP C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 290 Processing helix chain 'C' and resid 297 through 325 removed outlier: 3.960A pdb=" N LEU C 314 " --> pdb=" O VAL C 310 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG C 325 " --> pdb=" O ASN C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 362 Proline residue: C 347 - end of helix removed outlier: 3.841A pdb=" N ILE C 359 " --> pdb=" O ILE C 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 35 removed outlier: 3.514A pdb=" N LEU D 33 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 108 removed outlier: 4.053A pdb=" N ASP D 107 " --> pdb=" O SER D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 243 Processing helix chain 'D' and resid 243 through 259 removed outlier: 3.673A pdb=" N SER D 247 " --> pdb=" O MET D 243 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TRP D 259 " --> pdb=" O TRP D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 290 Processing helix chain 'D' and resid 297 through 325 removed outlier: 3.960A pdb=" N LEU D 314 " --> pdb=" O VAL D 310 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG D 325 " --> pdb=" O ASN D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 362 Proline residue: D 347 - end of helix removed outlier: 3.841A pdb=" N ILE D 359 " --> pdb=" O ILE D 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 35 removed outlier: 3.514A pdb=" N LEU E 33 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 108 removed outlier: 4.052A pdb=" N ASP E 107 " --> pdb=" O SER E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 243 Processing helix chain 'E' and resid 243 through 259 removed outlier: 3.674A pdb=" N SER E 247 " --> pdb=" O MET E 243 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TRP E 259 " --> pdb=" O TRP E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 290 Processing helix chain 'E' and resid 297 through 325 removed outlier: 3.959A pdb=" N LEU E 314 " --> pdb=" O VAL E 310 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG E 325 " --> pdb=" O ASN E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 362 Proline residue: E 347 - end of helix removed outlier: 3.841A pdb=" N ILE E 359 " --> pdb=" O ILE E 355 " (cutoff:3.500A) Processing sheet with id=A, first strand: chain 'A' and resid 119 through 124 removed outlier: 3.825A pdb=" N GLY A 121 " --> pdb=" O VAL A 151 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ASP A 73 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N SER A 66 " --> pdb=" O ASP A 73 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL A 53 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N GLU A 185 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL A 55 " --> pdb=" O GLU A 185 " (cutoff:3.500A) Processing sheet with id=B, first strand: chain 'A' and resid 133 through 136 removed outlier: 5.990A pdb=" N ASP A 73 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N SER A 66 " --> pdb=" O ASP A 73 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N GLN A 193 " --> pdb=" O CYS A 57 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE A 59 " --> pdb=" O GLN A 193 " (cutoff:3.500A) Processing sheet with id=C, first strand: chain 'A' and resid 114 through 116 removed outlier: 5.713A pdb=" N THR A 224 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N HIS A 231 " --> pdb=" O GLU A 208 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLU A 208 " --> pdb=" O HIS A 231 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N GLU A 233 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LYS A 206 " --> pdb=" O GLU A 233 " (cutoff:3.500A) Processing sheet with id=D, first strand: chain 'B' and resid 119 through 124 removed outlier: 3.824A pdb=" N GLY B 121 " --> pdb=" O VAL B 151 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ASP B 73 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N SER B 66 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL B 53 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N GLU B 185 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL B 55 " --> pdb=" O GLU B 185 " (cutoff:3.500A) Processing sheet with id=E, first strand: chain 'B' and resid 133 through 136 removed outlier: 5.991A pdb=" N ASP B 73 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N SER B 66 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N GLN B 193 " --> pdb=" O CYS B 57 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE B 59 " --> pdb=" O GLN B 193 " (cutoff:3.500A) Processing sheet with id=F, first strand: chain 'B' and resid 114 through 116 removed outlier: 5.712A pdb=" N THR B 224 " --> pdb=" O SER B 174 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N HIS B 231 " --> pdb=" O GLU B 208 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLU B 208 " --> pdb=" O HIS B 231 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N GLU B 233 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LYS B 206 " --> pdb=" O GLU B 233 " (cutoff:3.500A) Processing sheet with id=G, first strand: chain 'C' and resid 119 through 124 removed outlier: 3.824A pdb=" N GLY C 121 " --> pdb=" O VAL C 151 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ASP C 73 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N SER C 66 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL C 53 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N GLU C 185 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL C 55 " --> pdb=" O GLU C 185 " (cutoff:3.500A) Processing sheet with id=H, first strand: chain 'C' and resid 133 through 136 removed outlier: 5.991A pdb=" N ASP C 73 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N SER C 66 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 8.962A pdb=" N GLN C 193 " --> pdb=" O CYS C 57 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ILE C 59 " --> pdb=" O GLN C 193 " (cutoff:3.500A) Processing sheet with id=I, first strand: chain 'C' and resid 114 through 116 removed outlier: 5.713A pdb=" N THR C 224 " --> pdb=" O SER C 174 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N HIS C 231 " --> pdb=" O GLU C 208 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLU C 208 " --> pdb=" O HIS C 231 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N GLU C 233 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LYS C 206 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing sheet with id=J, first strand: chain 'D' and resid 119 through 124 removed outlier: 3.824A pdb=" N GLY D 121 " --> pdb=" O VAL D 151 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ASP D 73 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N SER D 66 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL D 53 " --> pdb=" O ILE D 183 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N GLU D 185 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL D 55 " --> pdb=" O GLU D 185 " (cutoff:3.500A) Processing sheet with id=K, first strand: chain 'D' and resid 133 through 136 removed outlier: 5.990A pdb=" N ASP D 73 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N SER D 66 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 8.962A pdb=" N GLN D 193 " --> pdb=" O CYS D 57 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE D 59 " --> pdb=" O GLN D 193 " (cutoff:3.500A) Processing sheet with id=L, first strand: chain 'D' and resid 114 through 116 removed outlier: 5.713A pdb=" N THR D 224 " --> pdb=" O SER D 174 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N HIS D 231 " --> pdb=" O GLU D 208 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLU D 208 " --> pdb=" O HIS D 231 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N GLU D 233 " --> pdb=" O LYS D 206 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LYS D 206 " --> pdb=" O GLU D 233 " (cutoff:3.500A) Processing sheet with id=M, first strand: chain 'E' and resid 119 through 124 removed outlier: 3.824A pdb=" N GLY E 121 " --> pdb=" O VAL E 151 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ASP E 73 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N SER E 66 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL E 53 " --> pdb=" O ILE E 183 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N GLU E 185 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N VAL E 55 " --> pdb=" O GLU E 185 " (cutoff:3.500A) Processing sheet with id=N, first strand: chain 'E' and resid 133 through 136 removed outlier: 5.990A pdb=" N ASP E 73 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N SER E 66 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 8.962A pdb=" N GLN E 193 " --> pdb=" O CYS E 57 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ILE E 59 " --> pdb=" O GLN E 193 " (cutoff:3.500A) Processing sheet with id=O, first strand: chain 'E' and resid 114 through 116 removed outlier: 5.714A pdb=" N THR E 224 " --> pdb=" O SER E 174 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N HIS E 231 " --> pdb=" O GLU E 208 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLU E 208 " --> pdb=" O HIS E 231 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N GLU E 233 " --> pdb=" O LYS E 206 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LYS E 206 " --> pdb=" O GLU E 233 " (cutoff:3.500A) 776 hydrogen bonds defined for protein. 2283 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.75 Time building geometry restraints manager: 3.73 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: 0.00 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: 2.260 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: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 30.360 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.640 ------------------------------------------------------------------------------- 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 13060 Z= 0.536 Angle : 1.327 11.471 17935 Z= 0.854 Chirality : 0.062 0.728 2120 Planarity : 0.004 0.034 2235 Dihedral : 10.082 79.771 4710 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.43 % Allowed : 1.72 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.18), residues: 1665 helix: -1.20 (0.19), residues: 575 sheet: -0.41 (0.22), residues: 385 loop : -2.11 (0.20), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 259 HIS 0.002 0.001 HIS C 217 PHE 0.075 0.003 PHE C 115 TYR 0.015 0.002 TYR D 144 ARG 0.006 0.001 ARG B 234 *********************** 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 fitting. rotamer outliers: 5 poor density : 295 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 PHE cc_start: 0.8106 (OUTLIER) cc_final: 0.7837 (p90) REVERT: A 239 TYR cc_start: 0.7194 (m-80) cc_final: 0.6984 (m-80) REVERT: A 255 TRP cc_start: 0.8111 (m-10) cc_final: 0.7412 (m-10) REVERT: A 262 MET cc_start: 0.7608 (mtm) cc_final: 0.7233 (mtm) REVERT: A 277 LEU cc_start: 0.8917 (tp) cc_final: 0.8686 (tp) REVERT: B 72 MET cc_start: 0.7714 (tpp) cc_final: 0.7499 (tpp) REVERT: B 255 TRP cc_start: 0.8038 (m-10) cc_final: 0.7314 (m-10) REVERT: B 302 TRP cc_start: 0.7996 (t60) cc_final: 0.7655 (t60) REVERT: C 255 TRP cc_start: 0.8073 (m-10) cc_final: 0.7462 (m-10) REVERT: D 80 LEU cc_start: 0.8622 (tp) cc_final: 0.8399 (tp) REVERT: D 255 TRP cc_start: 0.8072 (m-10) cc_final: 0.7500 (m-10) REVERT: D 277 LEU cc_start: 0.9028 (tp) cc_final: 0.8787 (tp) REVERT: E 255 TRP cc_start: 0.8029 (m-10) cc_final: 0.7476 (m-10) REVERT: E 302 TRP cc_start: 0.8033 (t60) cc_final: 0.7777 (t60) outliers start: 5 outliers final: 0 residues processed: 300 average time/residue: 0.2710 time to fit residues: 113.2613 Evaluate side-chains 157 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 156 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 84 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 78 optimal weight: 8.9990 chunk 96 optimal weight: 0.0770 chunk 149 optimal weight: 2.9990 overall best weight: 2.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 GLN B 83 GLN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 GLN D 123 ASN D 235 GLN E 83 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 13060 Z= 0.254 Angle : 0.724 9.158 17935 Z= 0.365 Chirality : 0.045 0.174 2120 Planarity : 0.004 0.057 2235 Dihedral : 8.146 59.884 2337 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.76 % Allowed : 6.47 % Favored : 90.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.19), residues: 1665 helix: 0.95 (0.20), residues: 580 sheet: -0.35 (0.22), residues: 410 loop : -1.59 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 259 HIS 0.004 0.001 HIS E 125 PHE 0.028 0.002 PHE E 115 TYR 0.020 0.002 TYR A 144 ARG 0.005 0.001 ARG D 229 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 184 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 TYR cc_start: 0.7283 (m-80) cc_final: 0.7024 (m-80) REVERT: A 255 TRP cc_start: 0.8064 (m-10) cc_final: 0.7720 (m-10) REVERT: A 274 THR cc_start: 0.8570 (m) cc_final: 0.7874 (t) REVERT: B 72 MET cc_start: 0.7669 (tpp) cc_final: 0.7427 (tpp) REVERT: B 132 LYS cc_start: 0.7967 (mmtt) cc_final: 0.7641 (mmtm) REVERT: B 239 TYR cc_start: 0.7256 (m-80) cc_final: 0.6986 (m-80) REVERT: B 255 TRP cc_start: 0.8123 (m-10) cc_final: 0.7692 (m-10) REVERT: B 302 TRP cc_start: 0.7885 (t60) cc_final: 0.7432 (t60) REVERT: B 311 PHE cc_start: 0.8169 (t80) cc_final: 0.7799 (t80) REVERT: C 239 TYR cc_start: 0.7442 (m-80) cc_final: 0.7052 (m-80) REVERT: C 255 TRP cc_start: 0.8011 (m-10) cc_final: 0.7521 (m-10) REVERT: D 255 TRP cc_start: 0.8046 (m-10) cc_final: 0.7635 (m-10) REVERT: E 72 MET cc_start: 0.7054 (mmm) cc_final: 0.6734 (tpp) REVERT: E 132 LYS cc_start: 0.8014 (mmtm) cc_final: 0.7783 (mmtm) REVERT: E 255 TRP cc_start: 0.8022 (m-10) cc_final: 0.7557 (m-10) outliers start: 32 outliers final: 21 residues processed: 205 average time/residue: 0.2060 time to fit residues: 63.6477 Evaluate side-chains 171 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 150 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain D residue 57 CYS Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 115 PHE Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 198 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 102 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 150 optimal weight: 0.0270 chunk 162 optimal weight: 10.0000 chunk 133 optimal weight: 3.9990 chunk 148 optimal weight: 7.9990 chunk 51 optimal weight: 10.0000 chunk 120 optimal weight: 9.9990 overall best weight: 1.7442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13060 Z= 0.206 Angle : 0.686 14.204 17935 Z= 0.335 Chirality : 0.043 0.157 2120 Planarity : 0.003 0.029 2235 Dihedral : 7.437 59.225 2335 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.02 % Allowed : 9.14 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.20), residues: 1665 helix: 1.69 (0.20), residues: 585 sheet: -0.41 (0.23), residues: 410 loop : -1.49 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP E 302 HIS 0.002 0.001 HIS E 231 PHE 0.031 0.001 PHE A 115 TYR 0.020 0.002 TYR E 144 ARG 0.004 0.001 ARG D 229 *********************** 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 197 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 162 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 239 TYR cc_start: 0.7303 (m-80) cc_final: 0.6977 (m-80) REVERT: A 255 TRP cc_start: 0.8098 (m-10) cc_final: 0.7680 (m-10) REVERT: B 72 MET cc_start: 0.7587 (tpp) cc_final: 0.7356 (tpp) REVERT: B 132 LYS cc_start: 0.7902 (mmtt) cc_final: 0.7564 (mptt) REVERT: B 255 TRP cc_start: 0.8091 (m-10) cc_final: 0.7752 (m-10) REVERT: B 302 TRP cc_start: 0.7929 (t60) cc_final: 0.7457 (t60) REVERT: C 255 TRP cc_start: 0.8009 (m-10) cc_final: 0.7630 (m-10) REVERT: D 255 TRP cc_start: 0.8046 (m-10) cc_final: 0.7583 (m-10) REVERT: D 303 MET cc_start: 0.7867 (mmm) cc_final: 0.7653 (mmm) REVERT: E 255 TRP cc_start: 0.7951 (m-10) cc_final: 0.7466 (m-10) outliers start: 35 outliers final: 26 residues processed: 185 average time/residue: 0.2379 time to fit residues: 67.6078 Evaluate side-chains 169 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 143 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 64 PHE Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain D residue 57 CYS Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 115 PHE Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 198 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 9.9990 chunk 112 optimal weight: 8.9990 chunk 77 optimal weight: 8.9990 chunk 16 optimal weight: 9.9990 chunk 71 optimal weight: 6.9990 chunk 100 optimal weight: 0.9980 chunk 150 optimal weight: 5.9990 chunk 159 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 142 optimal weight: 0.3980 chunk 42 optimal weight: 4.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 ASN B 171 GLN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13060 Z= 0.241 Angle : 0.657 8.706 17935 Z= 0.329 Chirality : 0.043 0.157 2120 Planarity : 0.004 0.030 2235 Dihedral : 7.131 59.975 2335 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.71 % Allowed : 10.69 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.21), residues: 1665 helix: 2.19 (0.21), residues: 585 sheet: -0.34 (0.25), residues: 385 loop : -1.47 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 302 HIS 0.003 0.001 HIS E 231 PHE 0.017 0.002 PHE E 115 TYR 0.026 0.002 TYR C 144 ARG 0.003 0.001 ARG E 81 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 154 time to evaluate : 1.428 Fit side-chains revert: symmetry clash REVERT: A 72 MET cc_start: 0.7616 (tpp) cc_final: 0.7266 (tpp) REVERT: A 170 MET cc_start: 0.6497 (tmm) cc_final: 0.6170 (tmm) REVERT: A 239 TYR cc_start: 0.7494 (m-80) cc_final: 0.7192 (m-80) REVERT: A 255 TRP cc_start: 0.8113 (m-10) cc_final: 0.7707 (m-10) REVERT: A 274 THR cc_start: 0.8452 (p) cc_final: 0.8182 (t) REVERT: B 132 LYS cc_start: 0.7923 (mmtt) cc_final: 0.7706 (mptt) REVERT: B 255 TRP cc_start: 0.8142 (m-10) cc_final: 0.7703 (m-10) REVERT: C 132 LYS cc_start: 0.8187 (mmpt) cc_final: 0.7816 (mmtm) REVERT: C 255 TRP cc_start: 0.8080 (m-10) cc_final: 0.7694 (m-10) REVERT: C 274 THR cc_start: 0.8511 (p) cc_final: 0.8261 (t) REVERT: D 255 TRP cc_start: 0.8167 (m-10) cc_final: 0.7745 (m-10) REVERT: E 255 TRP cc_start: 0.8000 (m-10) cc_final: 0.7526 (m-10) outliers start: 43 outliers final: 32 residues processed: 185 average time/residue: 0.2030 time to fit residues: 57.7810 Evaluate side-chains 173 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 141 time to evaluate : 1.295 ------------------------------------------------------------------------------- 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 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 262 MET Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain D residue 57 CYS Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 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 115 PHE Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 198 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 2 optimal weight: 0.0050 chunk 118 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 136 optimal weight: 0.0570 chunk 110 optimal weight: 0.1980 chunk 0 optimal weight: 20.0000 chunk 81 optimal weight: 9.9990 chunk 143 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 overall best weight: 1.6516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 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 123 ASN ** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 GLN ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13060 Z= 0.193 Angle : 0.647 8.978 17935 Z= 0.315 Chirality : 0.042 0.154 2120 Planarity : 0.003 0.033 2235 Dihedral : 6.704 56.475 2335 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.19 % Allowed : 12.67 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.21), residues: 1665 helix: 2.46 (0.20), residues: 590 sheet: -0.37 (0.25), residues: 385 loop : -1.32 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 302 HIS 0.002 0.001 HIS B 217 PHE 0.018 0.001 PHE A 223 TYR 0.017 0.002 TYR C 144 ARG 0.003 0.000 ARG E 81 *********************** 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 194 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 157 time to evaluate : 1.474 Fit side-chains revert: symmetry clash REVERT: A 72 MET cc_start: 0.7589 (tpp) cc_final: 0.7257 (tpp) REVERT: A 239 TYR cc_start: 0.7442 (m-80) cc_final: 0.7154 (m-80) REVERT: A 255 TRP cc_start: 0.8051 (m-10) cc_final: 0.7575 (m-10) REVERT: A 274 THR cc_start: 0.8507 (p) cc_final: 0.8253 (t) REVERT: B 72 MET cc_start: 0.7805 (tpp) cc_final: 0.7491 (tpp) REVERT: B 255 TRP cc_start: 0.8129 (m-10) cc_final: 0.7645 (m-10) REVERT: C 132 LYS cc_start: 0.8143 (mmpt) cc_final: 0.7703 (mmtt) REVERT: C 255 TRP cc_start: 0.8073 (m-10) cc_final: 0.7674 (m-10) REVERT: C 274 THR cc_start: 0.8414 (p) cc_final: 0.8189 (t) REVERT: D 255 TRP cc_start: 0.8124 (m-10) cc_final: 0.7669 (m-10) REVERT: D 302 TRP cc_start: 0.8030 (t60) cc_final: 0.7393 (t60) REVERT: D 303 MET cc_start: 0.7795 (mmm) cc_final: 0.7378 (mmt) REVERT: E 72 MET cc_start: 0.7551 (tpp) cc_final: 0.7283 (tpp) REVERT: E 132 LYS cc_start: 0.8250 (mmtm) cc_final: 0.7812 (mmtp) REVERT: E 255 TRP cc_start: 0.7987 (m-10) cc_final: 0.7517 (m-10) REVERT: E 274 THR cc_start: 0.8745 (m) cc_final: 0.8334 (t) outliers start: 37 outliers final: 27 residues processed: 180 average time/residue: 0.1991 time to fit residues: 55.3678 Evaluate side-chains 176 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 149 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain D residue 57 CYS Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 230 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 10.0000 chunk 143 optimal weight: 0.9980 chunk 31 optimal weight: 7.9990 chunk 93 optimal weight: 1.9990 chunk 39 optimal weight: 0.0170 chunk 159 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 73 optimal weight: 7.9990 chunk 13 optimal weight: 0.0970 chunk 52 optimal weight: 6.9990 chunk 83 optimal weight: 7.9990 overall best weight: 1.8220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 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 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.3908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13060 Z= 0.201 Angle : 0.660 14.290 17935 Z= 0.316 Chirality : 0.042 0.198 2120 Planarity : 0.003 0.036 2235 Dihedral : 6.399 51.667 2335 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.36 % Allowed : 13.45 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.21), residues: 1665 helix: 2.61 (0.20), residues: 590 sheet: -0.32 (0.25), residues: 385 loop : -1.29 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.001 TRP E 302 HIS 0.002 0.001 HIS C 217 PHE 0.016 0.001 PHE D 230 TYR 0.017 0.002 TYR C 144 ARG 0.004 0.000 ARG B 147 *********************** 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 192 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 153 time to evaluate : 1.346 Fit side-chains REVERT: A 255 TRP cc_start: 0.8080 (m-10) cc_final: 0.7589 (m-10) REVERT: A 274 THR cc_start: 0.8361 (p) cc_final: 0.8115 (t) REVERT: B 72 MET cc_start: 0.7651 (tpp) cc_final: 0.7440 (tpp) REVERT: B 132 LYS cc_start: 0.8433 (mptt) cc_final: 0.8083 (mmtt) REVERT: B 255 TRP cc_start: 0.8124 (m-10) cc_final: 0.7683 (m-10) REVERT: C 132 LYS cc_start: 0.8019 (mmpt) cc_final: 0.7481 (mmtm) REVERT: C 170 MET cc_start: 0.6530 (tmm) cc_final: 0.5861 (tmm) REVERT: C 255 TRP cc_start: 0.8120 (m-10) cc_final: 0.7687 (m-10) REVERT: C 274 THR cc_start: 0.8458 (p) cc_final: 0.8216 (t) REVERT: D 255 TRP cc_start: 0.8194 (m-10) cc_final: 0.7680 (m-10) REVERT: D 274 THR cc_start: 0.8642 (p) cc_final: 0.8357 (t) REVERT: E 72 MET cc_start: 0.7416 (tpp) cc_final: 0.7138 (tpp) REVERT: E 132 LYS cc_start: 0.8218 (mmtm) cc_final: 0.7768 (mmtp) REVERT: E 255 TRP cc_start: 0.8056 (m-10) cc_final: 0.7528 (m-10) REVERT: E 274 THR cc_start: 0.8747 (m) cc_final: 0.8390 (t) outliers start: 39 outliers final: 30 residues processed: 178 average time/residue: 0.2026 time to fit residues: 55.7113 Evaluate side-chains 175 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 145 time to evaluate : 1.361 ------------------------------------------------------------------------------- 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 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 262 MET Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 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 262 MET 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 172 LEU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 230 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 chunk 90 optimal weight: 30.0000 chunk 116 optimal weight: 0.2980 chunk 134 optimal weight: 0.6980 chunk 89 optimal weight: 0.9990 chunk 159 optimal weight: 3.9990 chunk 99 optimal weight: 0.0670 chunk 96 optimal weight: 20.0000 chunk 73 optimal weight: 2.9990 chunk 98 optimal weight: 7.9990 overall best weight: 1.0122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 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 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.4082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13060 Z= 0.180 Angle : 0.689 17.437 17935 Z= 0.321 Chirality : 0.043 0.140 2120 Planarity : 0.003 0.038 2235 Dihedral : 6.055 51.815 2335 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.19 % Allowed : 14.57 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.21), residues: 1665 helix: 2.68 (0.20), residues: 590 sheet: -0.27 (0.25), residues: 385 loop : -1.28 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.087 0.002 TRP E 302 HIS 0.002 0.001 HIS E 125 PHE 0.016 0.001 PHE D 230 TYR 0.033 0.002 TYR E 244 ARG 0.004 0.000 ARG B 147 *********************** 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 195 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 158 time to evaluate : 1.525 Fit side-chains REVERT: A 170 MET cc_start: 0.6943 (tmm) cc_final: 0.6625 (tmm) REVERT: A 255 TRP cc_start: 0.8062 (m-10) cc_final: 0.7561 (m-10) REVERT: B 132 LYS cc_start: 0.8354 (mptt) cc_final: 0.8106 (mmtt) REVERT: B 170 MET cc_start: 0.6669 (tmm) cc_final: 0.5786 (tmm) REVERT: B 255 TRP cc_start: 0.8172 (m-10) cc_final: 0.7639 (m-10) REVERT: C 132 LYS cc_start: 0.8001 (mmpt) cc_final: 0.7472 (mmtt) REVERT: C 255 TRP cc_start: 0.8082 (m-10) cc_final: 0.7608 (m-10) REVERT: C 290 LEU cc_start: 0.7888 (tp) cc_final: 0.7419 (tt) REVERT: D 72 MET cc_start: 0.7496 (tpp) cc_final: 0.6620 (tpp) REVERT: D 170 MET cc_start: 0.6327 (tmm) cc_final: 0.5705 (tmm) REVERT: D 255 TRP cc_start: 0.8151 (m-10) cc_final: 0.7690 (m-10) REVERT: D 274 THR cc_start: 0.8549 (p) cc_final: 0.8259 (t) REVERT: E 132 LYS cc_start: 0.8193 (mmtm) cc_final: 0.7736 (mmtp) REVERT: E 255 TRP cc_start: 0.8032 (m-10) cc_final: 0.7481 (m-10) REVERT: E 274 THR cc_start: 0.8754 (m) cc_final: 0.8387 (t) REVERT: E 296 VAL cc_start: 0.8204 (OUTLIER) cc_final: 0.7926 (p) outliers start: 37 outliers final: 24 residues processed: 183 average time/residue: 0.2064 time to fit residues: 57.9102 Evaluate side-chains 170 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 145 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain 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 198 LEU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 230 PHE Chi-restraints excluded: chain E residue 296 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 0.9990 chunk 94 optimal weight: 7.9990 chunk 47 optimal weight: 8.9990 chunk 31 optimal weight: 8.9990 chunk 30 optimal weight: 20.0000 chunk 101 optimal weight: 6.9990 chunk 108 optimal weight: 7.9990 chunk 78 optimal weight: 10.0000 chunk 14 optimal weight: 0.0970 chunk 125 optimal weight: 0.7980 chunk 144 optimal weight: 9.9990 overall best weight: 3.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 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** ** D 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.4400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13060 Z= 0.262 Angle : 0.692 11.473 17935 Z= 0.337 Chirality : 0.043 0.154 2120 Planarity : 0.004 0.041 2235 Dihedral : 5.949 52.271 2335 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.02 % Allowed : 14.83 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.21), residues: 1665 helix: 2.51 (0.20), residues: 590 sheet: -0.26 (0.25), residues: 405 loop : -1.25 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP E 302 HIS 0.004 0.001 HIS C 217 PHE 0.016 0.002 PHE D 230 TYR 0.034 0.002 TYR E 244 ARG 0.005 0.001 ARG A 234 *********************** 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 179 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 144 time to evaluate : 1.356 Fit side-chains revert: symmetry clash REVERT: A 72 MET cc_start: 0.7727 (tpp) cc_final: 0.7408 (tpt) REVERT: A 255 TRP cc_start: 0.8052 (m-10) cc_final: 0.7585 (m-10) REVERT: A 274 THR cc_start: 0.8330 (p) cc_final: 0.8028 (t) REVERT: B 132 LYS cc_start: 0.8334 (mptt) cc_final: 0.8102 (mmtp) REVERT: B 170 MET cc_start: 0.6713 (tmm) cc_final: 0.6113 (tmm) REVERT: B 255 TRP cc_start: 0.8145 (m-10) cc_final: 0.7662 (m-10) REVERT: C 132 LYS cc_start: 0.7900 (mmpt) cc_final: 0.7426 (mmtm) REVERT: C 255 TRP cc_start: 0.8182 (m-10) cc_final: 0.7739 (m-10) REVERT: C 290 LEU cc_start: 0.7986 (tp) cc_final: 0.7645 (tt) REVERT: D 170 MET cc_start: 0.6618 (tmm) cc_final: 0.6129 (tmm) REVERT: D 255 TRP cc_start: 0.8258 (m-10) cc_final: 0.7861 (m-10) REVERT: D 274 THR cc_start: 0.8555 (p) cc_final: 0.8277 (t) REVERT: D 290 LEU cc_start: 0.7852 (tp) cc_final: 0.7530 (tt) REVERT: E 72 MET cc_start: 0.7584 (tpp) cc_final: 0.7243 (tpp) REVERT: E 132 LYS cc_start: 0.8044 (mmtm) cc_final: 0.7551 (mmtp) REVERT: E 255 TRP cc_start: 0.8143 (m-10) cc_final: 0.7641 (m-10) REVERT: E 274 THR cc_start: 0.8688 (m) cc_final: 0.8342 (t) REVERT: E 296 VAL cc_start: 0.8223 (OUTLIER) cc_final: 0.7946 (p) outliers start: 35 outliers final: 25 residues processed: 167 average time/residue: 0.2054 time to fit residues: 52.7678 Evaluate side-chains 167 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 141 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain D residue 57 CYS Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 230 PHE Chi-restraints excluded: chain E residue 279 MET Chi-restraints excluded: chain E residue 296 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 7.9990 chunk 139 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 chunk 89 optimal weight: 0.0010 chunk 64 optimal weight: 10.0000 chunk 116 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 133 optimal weight: 2.9990 chunk 140 optimal weight: 0.9990 chunk 147 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 overall best weight: 1.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 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** ** D 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.4478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13060 Z= 0.195 Angle : 0.682 13.039 17935 Z= 0.324 Chirality : 0.043 0.168 2120 Planarity : 0.003 0.042 2235 Dihedral : 5.682 52.774 2335 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.19 % Allowed : 14.57 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.21), residues: 1665 helix: 2.74 (0.20), residues: 590 sheet: -0.26 (0.24), residues: 425 loop : -1.15 (0.26), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP E 302 HIS 0.002 0.001 HIS E 125 PHE 0.026 0.001 PHE A 311 TYR 0.017 0.002 TYR E 244 ARG 0.002 0.000 ARG D 229 *********************** 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 184 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 147 time to evaluate : 1.533 Fit side-chains revert: symmetry clash REVERT: A 72 MET cc_start: 0.7773 (tpp) cc_final: 0.7544 (tpt) REVERT: A 255 TRP cc_start: 0.8032 (m-10) cc_final: 0.7545 (m-10) REVERT: A 274 THR cc_start: 0.8291 (p) cc_final: 0.7961 (t) REVERT: B 130 ASP cc_start: 0.7231 (t0) cc_final: 0.6955 (t0) REVERT: B 132 LYS cc_start: 0.8326 (mptt) cc_final: 0.8095 (mmtp) REVERT: B 170 MET cc_start: 0.6762 (tmm) cc_final: 0.6186 (tmm) REVERT: B 255 TRP cc_start: 0.8157 (m-10) cc_final: 0.7644 (m-10) REVERT: C 132 LYS cc_start: 0.7870 (mmpt) cc_final: 0.7379 (mmtm) REVERT: C 255 TRP cc_start: 0.8095 (m-10) cc_final: 0.7642 (m-10) REVERT: C 290 LEU cc_start: 0.8002 (tp) cc_final: 0.7654 (tt) REVERT: D 170 MET cc_start: 0.6607 (tmm) cc_final: 0.6062 (tmm) REVERT: D 255 TRP cc_start: 0.8198 (m-10) cc_final: 0.7750 (m-10) REVERT: D 274 THR cc_start: 0.8553 (p) cc_final: 0.8265 (t) REVERT: D 290 LEU cc_start: 0.7834 (tp) cc_final: 0.7528 (tt) REVERT: E 70 THR cc_start: 0.8436 (p) cc_final: 0.8036 (t) REVERT: E 72 MET cc_start: 0.7654 (tpp) cc_final: 0.7420 (tpp) REVERT: E 132 LYS cc_start: 0.8022 (mmtm) cc_final: 0.7514 (mmtp) REVERT: E 255 TRP cc_start: 0.8156 (m-10) cc_final: 0.7644 (m-10) REVERT: E 274 THR cc_start: 0.8703 (m) cc_final: 0.8391 (t) REVERT: E 296 VAL cc_start: 0.8165 (OUTLIER) cc_final: 0.7867 (p) REVERT: E 307 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8783 (tt) outliers start: 37 outliers final: 25 residues processed: 173 average time/residue: 0.2066 time to fit residues: 54.6343 Evaluate side-chains 170 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 143 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain D residue 57 CYS Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 80 LEU 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 230 PHE Chi-restraints excluded: chain E residue 279 MET Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 307 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 9.9990 chunk 95 optimal weight: 20.0000 chunk 74 optimal weight: 8.9990 chunk 108 optimal weight: 2.9990 chunk 164 optimal weight: 5.9990 chunk 151 optimal weight: 0.8980 chunk 130 optimal weight: 9.9990 chunk 13 optimal weight: 0.0030 chunk 101 optimal weight: 4.9990 chunk 80 optimal weight: 20.0000 chunk 103 optimal weight: 0.9990 overall best weight: 1.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 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** ** D 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.4638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13060 Z= 0.201 Angle : 0.690 11.844 17935 Z= 0.326 Chirality : 0.043 0.152 2120 Planarity : 0.004 0.053 2235 Dihedral : 5.613 53.164 2335 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.33 % Allowed : 15.86 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.21), residues: 1665 helix: 2.74 (0.20), residues: 590 sheet: -0.22 (0.25), residues: 425 loop : -1.14 (0.26), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.001 TRP E 302 HIS 0.003 0.001 HIS E 125 PHE 0.015 0.001 PHE D 230 TYR 0.021 0.002 TYR E 244 ARG 0.003 0.001 ARG B 147 ********************** 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 177 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 150 time to evaluate : 1.458 Fit side-chains revert: symmetry clash REVERT: A 170 MET cc_start: 0.6916 (tmm) cc_final: 0.6491 (tmm) REVERT: A 255 TRP cc_start: 0.8024 (m-10) cc_final: 0.7612 (m-10) REVERT: A 274 THR cc_start: 0.8320 (p) cc_final: 0.8038 (t) REVERT: B 130 ASP cc_start: 0.7229 (t0) cc_final: 0.6946 (t0) REVERT: B 132 LYS cc_start: 0.8330 (mptt) cc_final: 0.8098 (mmtp) REVERT: B 170 MET cc_start: 0.6745 (tmm) cc_final: 0.6174 (tmm) REVERT: B 255 TRP cc_start: 0.8119 (m-10) cc_final: 0.7608 (m-10) REVERT: C 132 LYS cc_start: 0.7906 (mmpt) cc_final: 0.7463 (mmtm) REVERT: C 255 TRP cc_start: 0.8094 (m-10) cc_final: 0.7614 (m-10) REVERT: D 72 MET cc_start: 0.7685 (tpt) cc_final: 0.7471 (tpp) REVERT: D 170 MET cc_start: 0.6658 (tmm) cc_final: 0.6081 (tmm) REVERT: D 255 TRP cc_start: 0.8198 (m-10) cc_final: 0.7795 (m-10) REVERT: D 274 THR cc_start: 0.8547 (p) cc_final: 0.8261 (t) REVERT: D 290 LEU cc_start: 0.7808 (tp) cc_final: 0.7494 (tt) REVERT: E 70 THR cc_start: 0.8397 (p) cc_final: 0.8109 (t) REVERT: E 72 MET cc_start: 0.7564 (tpp) cc_final: 0.7360 (tpp) REVERT: E 132 LYS cc_start: 0.8025 (mmtm) cc_final: 0.7518 (mmtp) REVERT: E 255 TRP cc_start: 0.8218 (m-10) cc_final: 0.7700 (m-10) REVERT: E 296 VAL cc_start: 0.8183 (OUTLIER) cc_final: 0.7903 (p) outliers start: 27 outliers final: 23 residues processed: 167 average time/residue: 0.2055 time to fit residues: 52.7894 Evaluate side-chains 168 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 144 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain D residue 57 CYS Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 156 MET 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 230 PHE Chi-restraints excluded: chain E residue 296 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 8.9990 chunk 40 optimal weight: 0.1980 chunk 120 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 131 optimal weight: 6.9990 chunk 54 optimal weight: 0.9980 chunk 134 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 115 optimal weight: 8.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 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** ** D 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.041025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.034347 restraints weight = 97722.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.035165 restraints weight = 61964.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.035582 restraints weight = 44012.018| |-----------------------------------------------------------------------------| r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.4735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13060 Z= 0.184 Angle : 0.694 13.967 17935 Z= 0.324 Chirality : 0.043 0.152 2120 Planarity : 0.003 0.050 2235 Dihedral : 5.552 53.119 2335 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.16 % Allowed : 16.03 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.22), residues: 1665 helix: 2.73 (0.20), residues: 595 sheet: -0.17 (0.25), residues: 425 loop : -1.08 (0.26), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP E 302 HIS 0.002 0.001 HIS E 125 PHE 0.016 0.001 PHE D 230 TYR 0.017 0.002 TYR E 244 ARG 0.003 0.000 ARG B 81 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2244.82 seconds wall clock time: 41 minutes 12.36 seconds (2472.36 seconds total)