Starting phenix.real_space_refine on Sat Sep 12 11:14:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6vm0_21234/09_2026/6vm0_21234.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vm0_21234/09_2026/6vm0_21234.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6vm0_21234/09_2026/6vm0_21234.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6vm0_21234/09_2026/6vm0_21234.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vm0_21234/09_2026/6vm0_21234.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vm0_21234/09_2026/6vm0_21234.map" model { file = "/net/cci-nas-00/data/ceres_data/6vm0_21234/09_2026/6vm0_21234.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vm0_21234/09_2026/6vm0_21234.cif" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians P 5 5.49 5 S 100 5.16 5 C 10020 2.51 5 N 2440 2.21 5 O 2790 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 65 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15355 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2949 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 16, 'TRANS': 345} Chain breaks: 1 Chain: "E" Number of atoms: 2949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2949 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 16, 'TRANS': 345} Chain breaks: 1 Chain: "C" Number of atoms: 2949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2949 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 16, 'TRANS': 345} Chain breaks: 1 Chain: "B" Number of atoms: 2949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2949 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 16, 'TRANS': 345} Chain breaks: 1 Chain: "D" Number of atoms: 2949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2949 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 16, 'TRANS': 345} Chain breaks: 1 Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 95 Unusual residues: {'IVM': 1, 'PIO': 1} Inner-chain residues flagged as termini: ['pdbres="GLY A 804 "'] Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 95 Unusual residues: {'IVM': 1, 'PIO': 1} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 95 Unusual residues: {'IVM': 1, 'PIO': 1} Inner-chain residues flagged as termini: ['pdbres="GLY C 804 "'] Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 90 Unusual residues: {'IVM': 1, 'PIO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 6 Chain: "D" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 95 Unusual residues: {'IVM': 1, 'PIO': 1} Inner-chain residues flagged as termini: ['pdbres="GLY D 902 "'] Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 3.46, per 1000 atoms: 0.23 Number of scatterers: 15355 At special positions: 0 Unit cell: (99.64, 97.52, 139.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 100 16.00 P 5 15.00 O 2790 8.00 N 2440 7.00 C 10020 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " Time building additional restraints: 1.25 Conformation dependent library (CDL) restraints added in 646.6 milliseconds 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3480 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 25 sheets defined 39.1% alpha, 37.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 33 through 41 removed outlier: 3.888A pdb=" N PHE A 37 " --> pdb=" O PRO A 33 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU A 41 " --> pdb=" O PHE A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 251 removed outlier: 3.508A pdb=" N LEU A 248 " --> pdb=" O MET A 244 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE A 249 " --> pdb=" O GLY A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 265 removed outlier: 3.764A pdb=" N SER A 255 " --> pdb=" O MET A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 295 removed outlier: 3.799A pdb=" N ARG A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 340 Processing helix chain 'A' and resid 395 through 444 removed outlier: 3.704A pdb=" N ASP A 411 " --> pdb=" O ALA A 407 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL A 416 " --> pdb=" O THR A 412 " (cutoff:3.500A) Proline residue: A 419 - end of helix Processing helix chain 'E' and resid 33 through 41 removed outlier: 3.888A pdb=" N PHE E 37 " --> pdb=" O PRO E 33 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU E 41 " --> pdb=" O PHE E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 251 removed outlier: 3.508A pdb=" N LEU E 248 " --> pdb=" O MET E 244 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE E 249 " --> pdb=" O GLY E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 265 removed outlier: 3.764A pdb=" N SER E 255 " --> pdb=" O MET E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 295 removed outlier: 3.798A pdb=" N ARG E 295 " --> pdb=" O SER E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 340 Processing helix chain 'E' and resid 395 through 444 removed outlier: 3.704A pdb=" N ASP E 411 " --> pdb=" O ALA E 407 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL E 416 " --> pdb=" O THR E 412 " (cutoff:3.500A) Proline residue: E 419 - end of helix Processing helix chain 'C' and resid 33 through 41 removed outlier: 3.889A pdb=" N PHE C 37 " --> pdb=" O PRO C 33 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU C 41 " --> pdb=" O PHE C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 251 removed outlier: 3.508A pdb=" N LEU C 248 " --> pdb=" O MET C 244 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE C 249 " --> pdb=" O GLY C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 265 removed outlier: 3.764A pdb=" N SER C 255 " --> pdb=" O MET C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 295 removed outlier: 3.798A pdb=" N ARG C 295 " --> pdb=" O SER C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 340 Processing helix chain 'C' and resid 395 through 444 removed outlier: 3.704A pdb=" N ASP C 411 " --> pdb=" O ALA C 407 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL C 416 " --> pdb=" O THR C 412 " (cutoff:3.500A) Proline residue: C 419 - end of helix Processing helix chain 'B' and resid 33 through 41 removed outlier: 3.888A pdb=" N PHE B 37 " --> pdb=" O PRO B 33 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU B 41 " --> pdb=" O PHE B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 251 removed outlier: 3.508A pdb=" N LEU B 248 " --> pdb=" O MET B 244 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE B 249 " --> pdb=" O GLY B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 265 removed outlier: 3.762A pdb=" N SER B 255 " --> pdb=" O MET B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 295 removed outlier: 3.799A pdb=" N ARG B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 340 Processing helix chain 'B' and resid 395 through 444 removed outlier: 3.703A pdb=" N ASP B 411 " --> pdb=" O ALA B 407 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL B 416 " --> pdb=" O THR B 412 " (cutoff:3.500A) Proline residue: B 419 - end of helix Processing helix chain 'D' and resid 33 through 41 removed outlier: 3.889A pdb=" N PHE D 37 " --> pdb=" O PRO D 33 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU D 41 " --> pdb=" O PHE D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 251 removed outlier: 3.508A pdb=" N LEU D 248 " --> pdb=" O MET D 244 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE D 249 " --> pdb=" O GLY D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 265 removed outlier: 3.763A pdb=" N SER D 255 " --> pdb=" O MET D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 295 removed outlier: 3.798A pdb=" N ARG D 295 " --> pdb=" O SER D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 340 Processing helix chain 'D' and resid 395 through 444 removed outlier: 3.704A pdb=" N ASP D 411 " --> pdb=" O ALA D 407 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL D 416 " --> pdb=" O THR D 412 " (cutoff:3.500A) Proline residue: D 419 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 108 through 109 removed outlier: 4.425A pdb=" N LEU A 142 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ASP A 81 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N SER A 74 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ARG A 83 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N PHE A 72 " --> pdb=" O ARG A 83 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ASN A 85 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ASN A 93 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASN A 62 " --> pdb=" O ASN A 93 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N VAL A 61 " --> pdb=" O ILE A 191 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N GLU A 193 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N VAL A 63 " --> pdb=" O GLU A 193 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 127 through 132 removed outlier: 3.553A pdb=" N ALA A 130 " --> pdb=" O THR A 157 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N THR A 157 " --> pdb=" O ALA A 130 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N PHE A 132 " --> pdb=" O ARG A 155 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N ARG A 155 " --> pdb=" O PHE A 132 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ASP A 81 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N SER A 74 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ARG A 83 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N PHE A 72 " --> pdb=" O ARG A 83 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ASN A 85 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ASN A 93 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASN A 62 " --> pdb=" O ASN A 93 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 123 through 124 Processing sheet with id=AA4, first strand: chain 'A' and resid 123 through 124 Processing sheet with id=AA5, first strand: chain 'A' and resid 224 through 225 removed outlier: 3.610A pdb=" N LYS A 224 " --> pdb=" O PHE A 231 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 108 through 109 removed outlier: 4.425A pdb=" N LEU E 142 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ASP E 81 " --> pdb=" O SER E 74 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N SER E 74 " --> pdb=" O ASP E 81 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ARG E 83 " --> pdb=" O PHE E 72 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N PHE E 72 " --> pdb=" O ARG E 83 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ASN E 85 " --> pdb=" O ASN E 70 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ASN E 93 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ASN E 62 " --> pdb=" O ASN E 93 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N VAL E 61 " --> pdb=" O ILE E 191 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N GLU E 193 " --> pdb=" O VAL E 61 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N VAL E 63 " --> pdb=" O GLU E 193 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 127 through 132 removed outlier: 3.553A pdb=" N ALA E 130 " --> pdb=" O THR E 157 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N THR E 157 " --> pdb=" O ALA E 130 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N PHE E 132 " --> pdb=" O ARG E 155 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N ARG E 155 " --> pdb=" O PHE E 132 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ASP E 81 " --> pdb=" O SER E 74 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N SER E 74 " --> pdb=" O ASP E 81 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ARG E 83 " --> pdb=" O PHE E 72 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N PHE E 72 " --> pdb=" O ARG E 83 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ASN E 85 " --> pdb=" O ASN E 70 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ASN E 93 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ASN E 62 " --> pdb=" O ASN E 93 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 123 through 124 Processing sheet with id=AA9, first strand: chain 'E' and resid 123 through 124 Processing sheet with id=AB1, first strand: chain 'E' and resid 224 through 225 removed outlier: 3.609A pdb=" N LYS E 224 " --> pdb=" O PHE E 231 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 108 through 109 removed outlier: 4.425A pdb=" N LEU C 142 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ASP C 81 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N SER C 74 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ARG C 83 " --> pdb=" O PHE C 72 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N PHE C 72 " --> pdb=" O ARG C 83 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ASN C 85 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ASN C 93 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASN C 62 " --> pdb=" O ASN C 93 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N VAL C 61 " --> pdb=" O ILE C 191 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N GLU C 193 " --> pdb=" O VAL C 61 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N VAL C 63 " --> pdb=" O GLU C 193 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 127 through 132 removed outlier: 3.552A pdb=" N ALA C 130 " --> pdb=" O THR C 157 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N THR C 157 " --> pdb=" O ALA C 130 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N PHE C 132 " --> pdb=" O ARG C 155 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N ARG C 155 " --> pdb=" O PHE C 132 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ASP C 81 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N SER C 74 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ARG C 83 " --> pdb=" O PHE C 72 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N PHE C 72 " --> pdb=" O ARG C 83 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ASN C 85 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ASN C 93 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASN C 62 " --> pdb=" O ASN C 93 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 123 through 124 Processing sheet with id=AB5, first strand: chain 'C' and resid 123 through 124 Processing sheet with id=AB6, first strand: chain 'C' and resid 224 through 225 removed outlier: 3.609A pdb=" N LYS C 224 " --> pdb=" O PHE C 231 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 108 through 109 removed outlier: 4.424A pdb=" N LEU B 142 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ASP B 81 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N SER B 74 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ARG B 83 " --> pdb=" O PHE B 72 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N PHE B 72 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ASN B 85 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ASN B 93 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ASN B 62 " --> pdb=" O ASN B 93 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N VAL B 61 " --> pdb=" O ILE B 191 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N GLU B 193 " --> pdb=" O VAL B 61 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N VAL B 63 " --> pdb=" O GLU B 193 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 127 through 132 removed outlier: 3.553A pdb=" N ALA B 130 " --> pdb=" O THR B 157 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N THR B 157 " --> pdb=" O ALA B 130 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N PHE B 132 " --> pdb=" O ARG B 155 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N ARG B 155 " --> pdb=" O PHE B 132 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ASP B 81 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N SER B 74 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ARG B 83 " --> pdb=" O PHE B 72 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N PHE B 72 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ASN B 85 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ASN B 93 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ASN B 62 " --> pdb=" O ASN B 93 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 123 through 124 Processing sheet with id=AC1, first strand: chain 'B' and resid 123 through 124 Processing sheet with id=AC2, first strand: chain 'B' and resid 224 through 225 removed outlier: 3.610A pdb=" N LYS B 224 " --> pdb=" O PHE B 231 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 108 through 109 removed outlier: 4.425A pdb=" N LEU D 142 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ASP D 81 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N SER D 74 " --> pdb=" O ASP D 81 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ARG D 83 " --> pdb=" O PHE D 72 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N PHE D 72 " --> pdb=" O ARG D 83 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ASN D 85 " --> pdb=" O ASN D 70 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ASN D 93 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASN D 62 " --> pdb=" O ASN D 93 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N VAL D 61 " --> pdb=" O ILE D 191 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N GLU D 193 " --> pdb=" O VAL D 61 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N VAL D 63 " --> pdb=" O GLU D 193 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 127 through 132 removed outlier: 3.552A pdb=" N ALA D 130 " --> pdb=" O THR D 157 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N THR D 157 " --> pdb=" O ALA D 130 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N PHE D 132 " --> pdb=" O ARG D 155 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N ARG D 155 " --> pdb=" O PHE D 132 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ASP D 81 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N SER D 74 " --> pdb=" O ASP D 81 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ARG D 83 " --> pdb=" O PHE D 72 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N PHE D 72 " --> pdb=" O ARG D 83 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ASN D 85 " --> pdb=" O ASN D 70 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ASN D 93 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASN D 62 " --> pdb=" O ASN D 93 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 123 through 124 Processing sheet with id=AC6, first strand: chain 'D' and resid 123 through 124 Processing sheet with id=AC7, first strand: chain 'D' and resid 224 through 225 removed outlier: 3.610A pdb=" N LYS D 224 " --> pdb=" O PHE D 231 " (cutoff:3.500A) 895 hydrogen bonds defined for protein. 2640 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.13 Time building geometry restraints manager: 1.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 2370 1.30 - 1.43: 4291 1.43 - 1.56: 8834 1.56 - 1.69: 70 1.69 - 1.82: 175 Bond restraints: 15740 Sorted by residual: bond pdb=" C43 IVM E 901 " pdb=" C44 IVM E 901 " ideal model delta sigma weight residual 1.330 1.694 -0.364 2.00e-02 2.50e+03 3.31e+02 bond pdb=" C43 IVM C 805 " pdb=" C44 IVM C 805 " ideal model delta sigma weight residual 1.330 1.693 -0.363 2.00e-02 2.50e+03 3.30e+02 bond pdb=" C43 IVM B 602 " pdb=" C44 IVM B 602 " ideal model delta sigma weight residual 1.330 1.693 -0.363 2.00e-02 2.50e+03 3.30e+02 bond pdb=" C43 IVM D 901 " pdb=" C44 IVM D 901 " ideal model delta sigma weight residual 1.330 1.693 -0.363 2.00e-02 2.50e+03 3.30e+02 bond pdb=" C43 IVM A 805 " pdb=" C44 IVM A 805 " ideal model delta sigma weight residual 1.330 1.693 -0.363 2.00e-02 2.50e+03 3.29e+02 ... (remaining 15735 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.92: 21197 7.92 - 15.85: 118 15.85 - 23.77: 5 23.77 - 31.70: 5 31.70 - 39.62: 15 Bond angle restraints: 21340 Sorted by residual: angle pdb=" C7 IVM E 901 " pdb=" C6 IVM E 901 " pdb=" O14 IVM E 901 " ideal model delta sigma weight residual 106.56 66.94 39.62 3.00e+00 1.11e-01 1.74e+02 angle pdb=" C7 IVM B 602 " pdb=" C6 IVM B 602 " pdb=" O14 IVM B 602 " ideal model delta sigma weight residual 106.56 66.94 39.62 3.00e+00 1.11e-01 1.74e+02 angle pdb=" C7 IVM C 805 " pdb=" C6 IVM C 805 " pdb=" O14 IVM C 805 " ideal model delta sigma weight residual 106.56 66.96 39.60 3.00e+00 1.11e-01 1.74e+02 angle pdb=" C7 IVM D 901 " pdb=" C6 IVM D 901 " pdb=" O14 IVM D 901 " ideal model delta sigma weight residual 106.56 66.98 39.58 3.00e+00 1.11e-01 1.74e+02 angle pdb=" C7 IVM A 805 " pdb=" C6 IVM A 805 " pdb=" O14 IVM A 805 " ideal model delta sigma weight residual 106.56 66.99 39.57 3.00e+00 1.11e-01 1.74e+02 ... (remaining 21335 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.79: 8555 21.79 - 43.59: 880 43.59 - 65.38: 225 65.38 - 87.17: 35 87.17 - 108.96: 115 Dihedral angle restraints: 9810 sinusoidal: 4455 harmonic: 5355 Sorted by residual: dihedral pdb=" C26 IVM D 901 " pdb=" C25 IVM D 901 " pdb=" O7 IVM D 901 " pdb=" C30 IVM D 901 " ideal model delta sinusoidal sigma weight residual 56.57 -52.39 108.96 1 3.00e+01 1.11e-03 1.41e+01 dihedral pdb=" C26 IVM E 901 " pdb=" C25 IVM E 901 " pdb=" O7 IVM E 901 " pdb=" C30 IVM E 901 " ideal model delta sinusoidal sigma weight residual 56.57 -52.37 108.94 1 3.00e+01 1.11e-03 1.41e+01 dihedral pdb=" C26 IVM C 805 " pdb=" C25 IVM C 805 " pdb=" O7 IVM C 805 " pdb=" C30 IVM C 805 " ideal model delta sinusoidal sigma weight residual 56.57 -52.37 108.94 1 3.00e+01 1.11e-03 1.41e+01 ... (remaining 9807 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.213: 2370 0.213 - 0.426: 60 0.426 - 0.639: 5 0.639 - 0.852: 0 0.852 - 1.065: 5 Chirality restraints: 2440 Sorted by residual: chirality pdb=" C6 IVM A 805 " pdb=" C11 IVM A 805 " pdb=" C7 IVM A 805 " pdb=" O14 IVM A 805 " both_signs ideal model delta sigma weight residual False 2.53 1.46 1.07 2.00e-01 2.50e+01 2.84e+01 chirality pdb=" C6 IVM B 602 " pdb=" C11 IVM B 602 " pdb=" C7 IVM B 602 " pdb=" O14 IVM B 602 " both_signs ideal model delta sigma weight residual False 2.53 1.47 1.06 2.00e-01 2.50e+01 2.83e+01 chirality pdb=" C6 IVM C 805 " pdb=" C11 IVM C 805 " pdb=" C7 IVM C 805 " pdb=" O14 IVM C 805 " both_signs ideal model delta sigma weight residual False 2.53 1.47 1.06 2.00e-01 2.50e+01 2.83e+01 ... (remaining 2437 not shown) Planarity restraints: 2605 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C37 IVM C 805 " 0.301 2.00e-02 2.50e+03 3.23e-01 1.31e+03 pdb=" C38 IVM C 805 " -0.593 2.00e-02 2.50e+03 pdb=" C39 IVM C 805 " 0.279 2.00e-02 2.50e+03 pdb=" C40 IVM C 805 " -0.024 2.00e-02 2.50e+03 pdb=" C47 IVM C 805 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C37 IVM A 805 " 0.301 2.00e-02 2.50e+03 3.23e-01 1.31e+03 pdb=" C38 IVM A 805 " -0.593 2.00e-02 2.50e+03 pdb=" C39 IVM A 805 " 0.280 2.00e-02 2.50e+03 pdb=" C40 IVM A 805 " -0.024 2.00e-02 2.50e+03 pdb=" C47 IVM A 805 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C37 IVM D 901 " 0.301 2.00e-02 2.50e+03 3.23e-01 1.31e+03 pdb=" C38 IVM D 901 " -0.593 2.00e-02 2.50e+03 pdb=" C39 IVM D 901 " 0.279 2.00e-02 2.50e+03 pdb=" C40 IVM D 901 " -0.024 2.00e-02 2.50e+03 pdb=" C47 IVM D 901 " 0.037 2.00e-02 2.50e+03 ... (remaining 2602 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 4374 2.82 - 3.34: 13523 3.34 - 3.86: 24987 3.86 - 4.38: 28151 4.38 - 4.90: 49652 Nonbonded interactions: 120687 Sorted by model distance: nonbonded pdb=" O GLY C 43 " pdb=" OG SER C 46 " model vdw 2.295 3.040 nonbonded pdb=" O GLY A 43 " pdb=" OG SER A 46 " model vdw 2.296 3.040 nonbonded pdb=" O GLY B 43 " pdb=" OG SER B 46 " model vdw 2.297 3.040 nonbonded pdb=" O GLY E 43 " pdb=" OG SER E 46 " model vdw 2.297 3.040 nonbonded pdb=" O GLY D 43 " pdb=" OG SER D 46 " model vdw 2.297 3.040 ... (remaining 120682 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and resid 31 through 444) selection = (chain 'B' and resid 31 through 444) selection = (chain 'C' and resid 31 through 444) selection = (chain 'D' and resid 31 through 444) selection = (chain 'E' and resid 31 through 444) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.310 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.460 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 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 : 0.017 0.364 15745 Z= 0.783 Angle : 1.863 39.624 21355 Z= 0.805 Chirality : 0.096 1.065 2440 Planarity : 0.025 0.323 2605 Dihedral : 22.187 108.964 6330 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.00 % Allowed : 14.68 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.33 (0.16), residues: 1790 helix: -1.66 (0.15), residues: 665 sheet: -0.13 (0.23), residues: 375 loop : -2.09 (0.18), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 89 TYR 0.040 0.004 TYR C 325 PHE 0.023 0.003 PHE C 169 TRP 0.028 0.004 TRP E 118 HIS 0.026 0.005 HIS A 335 Details of bonding type rmsd/Z covalent geometry : bond 0.01670 / 0.78 (15740) covalent geometry : angle 1.86323 / 0.80 (21340) hydrogen bonds : bond 0.15257 / 9.90 ( 750) hydrogen bonds : angle 7.35817 / 4.99 ( 2640) link_BETA1-4 : bond 0.00383 / 0.22 ( 5) link_BETA1-4 : angle 2.06038 / 1.07 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.614 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: C 263 TRP cc_start: 0.8784 (m-10) cc_final: 0.8450 (m-10) REVERT: B 262 SER cc_start: 0.9354 (m) cc_final: 0.9152 (p) REVERT: D 221 TYR cc_start: 0.8227 (p90) cc_final: 0.8013 (p90) REVERT: D 262 SER cc_start: 0.9325 (m) cc_final: 0.9085 (p) REVERT: D 263 TRP cc_start: 0.8861 (m-10) cc_final: 0.8598 (m-10) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.1419 time to fit residues: 38.3494 Evaluate side-chains 134 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.0370 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.0970 chunk 149 optimal weight: 0.8980 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 133 HIS A 168 ASN A 201 GLN A 225 HIS A 269 ASN A 290 GLN ** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 133 HIS E 168 ASN E 201 GLN E 225 HIS E 269 ASN E 290 GLN ** E 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 ASN C 133 HIS C 168 ASN C 201 GLN C 225 HIS C 269 ASN C 290 GLN ** C 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 HIS B 168 ASN B 201 GLN B 225 HIS B 269 ASN B 290 GLN ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 ASN D 133 HIS D 168 ASN D 201 GLN D 225 HIS D 290 GLN ** D 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.079377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.060224 restraints weight = 43144.965| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 3.98 r_work: 0.2814 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15745 Z= 0.147 Angle : 0.819 9.955 21355 Z= 0.378 Chirality : 0.051 0.359 2440 Planarity : 0.004 0.031 2605 Dihedral : 14.519 75.676 2725 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.77 % Allowed : 16.21 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.18), residues: 1790 helix: 0.91 (0.18), residues: 645 sheet: 0.32 (0.24), residues: 395 loop : -1.76 (0.19), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 220 TYR 0.024 0.002 TYR C 221 PHE 0.015 0.001 PHE C 319 TRP 0.013 0.001 TRP A 118 HIS 0.005 0.001 HIS A 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.15 (15740) covalent geometry : angle 0.81823 / 0.38 (21340) hydrogen bonds : bond 0.04939 / 3.12 ( 750) hydrogen bonds : angle 5.04185 / 3.46 ( 2640) link_BETA1-4 : bond 0.00891 / 0.48 ( 5) link_BETA1-4 : angle 1.31571 / 0.81 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 159 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 MET cc_start: 0.8945 (mpp) cc_final: 0.8735 (mpp) REVERT: A 80 MET cc_start: 0.9409 (mtt) cc_final: 0.9131 (mmm) REVERT: A 113 MET cc_start: 0.8788 (ppp) cc_final: 0.8450 (ppp) REVERT: A 263 TRP cc_start: 0.8817 (m-10) cc_final: 0.8569 (m-10) REVERT: E 80 MET cc_start: 0.9346 (mtt) cc_final: 0.9041 (mmm) REVERT: E 113 MET cc_start: 0.8883 (ppp) cc_final: 0.8577 (ppp) REVERT: E 176 CYS cc_start: 0.9000 (m) cc_final: 0.8708 (m) REVERT: E 187 MET cc_start: 0.8617 (tpt) cc_final: 0.8163 (mmm) REVERT: E 221 TYR cc_start: 0.8482 (p90) cc_final: 0.8272 (p90) REVERT: E 262 SER cc_start: 0.9584 (m) cc_final: 0.9277 (p) REVERT: E 263 TRP cc_start: 0.8741 (m-10) cc_final: 0.8471 (m-10) REVERT: C 113 MET cc_start: 0.8929 (ppp) cc_final: 0.8567 (ppp) REVERT: C 187 MET cc_start: 0.8814 (mmm) cc_final: 0.8588 (tpt) REVERT: C 235 GLU cc_start: 0.8992 (OUTLIER) cc_final: 0.8738 (pt0) REVERT: C 244 MET cc_start: 0.8961 (tpp) cc_final: 0.8497 (tpp) REVERT: C 263 TRP cc_start: 0.8895 (m-10) cc_final: 0.8584 (m-10) REVERT: B 113 MET cc_start: 0.8976 (ppp) cc_final: 0.8724 (ppp) REVERT: D 113 MET cc_start: 0.8863 (ppp) cc_final: 0.8500 (ppp) REVERT: D 187 MET cc_start: 0.8504 (tpt) cc_final: 0.7821 (tpp) REVERT: D 221 TYR cc_start: 0.8509 (p90) cc_final: 0.8180 (p90) REVERT: D 263 TRP cc_start: 0.8910 (m-10) cc_final: 0.8640 (m-10) REVERT: D 411 ASP cc_start: 0.9085 (m-30) cc_final: 0.8851 (t0) outliers start: 29 outliers final: 3 residues processed: 180 average time/residue: 0.1078 time to fit residues: 29.6966 Evaluate side-chains 137 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 133 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 235 GLU Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain D residue 264 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 13 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 chunk 163 optimal weight: 4.9990 chunk 53 optimal weight: 0.4980 chunk 78 optimal weight: 4.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 ASN ** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN ** E 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 426 ASN ** C 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 426 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.078866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.059903 restraints weight = 43118.765| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 3.98 r_work: 0.2799 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 15745 Z= 0.132 Angle : 0.652 7.044 21355 Z= 0.318 Chirality : 0.045 0.197 2440 Planarity : 0.004 0.026 2605 Dihedral : 10.009 65.795 2725 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.14 % Allowed : 17.25 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.19), residues: 1790 helix: 2.00 (0.19), residues: 640 sheet: 0.61 (0.25), residues: 390 loop : -1.53 (0.19), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 437 TYR 0.021 0.002 TYR B 221 PHE 0.018 0.001 PHE C 319 TRP 0.007 0.001 TRP D 118 HIS 0.005 0.001 HIS A 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (15740) covalent geometry : angle 0.65177 / 0.32 (21340) hydrogen bonds : bond 0.04280 / 2.70 ( 750) hydrogen bonds : angle 4.54715 / 3.12 ( 2640) link_BETA1-4 : bond 0.00927 / 0.54 ( 5) link_BETA1-4 : angle 1.11826 / 0.72 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 149 time to evaluate : 0.604 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: A 80 MET cc_start: 0.9390 (mtt) cc_final: 0.9150 (mtt) REVERT: A 113 MET cc_start: 0.8821 (ppp) cc_final: 0.8419 (ppp) REVERT: E 80 MET cc_start: 0.9330 (mtt) cc_final: 0.8945 (mmm) REVERT: E 113 MET cc_start: 0.8852 (ppp) cc_final: 0.8496 (ppp) REVERT: E 164 MET cc_start: 0.9138 (ptp) cc_final: 0.8725 (ptp) REVERT: E 176 CYS cc_start: 0.8943 (m) cc_final: 0.8617 (m) REVERT: E 244 MET cc_start: 0.8984 (ttp) cc_final: 0.8739 (tpp) REVERT: E 399 MET cc_start: 0.8151 (mmm) cc_final: 0.7643 (mmp) REVERT: C 113 MET cc_start: 0.8920 (ppp) cc_final: 0.8471 (ppp) REVERT: C 187 MET cc_start: 0.8815 (mmm) cc_final: 0.8356 (mmm) REVERT: C 235 GLU cc_start: 0.9030 (OUTLIER) cc_final: 0.8765 (pt0) REVERT: C 244 MET cc_start: 0.8990 (tpp) cc_final: 0.8502 (tpp) REVERT: B 80 MET cc_start: 0.9342 (OUTLIER) cc_final: 0.8897 (mmm) REVERT: B 113 MET cc_start: 0.8937 (ppp) cc_final: 0.8620 (ppp) REVERT: B 187 MET cc_start: 0.8602 (tpt) cc_final: 0.8005 (tpt) REVERT: B 244 MET cc_start: 0.8872 (ttp) cc_final: 0.8644 (tpp) REVERT: B 399 MET cc_start: 0.8286 (mmm) cc_final: 0.7999 (mmp) REVERT: D 113 MET cc_start: 0.8797 (ppp) cc_final: 0.8404 (ppp) REVERT: D 187 MET cc_start: 0.8520 (tpt) cc_final: 0.7815 (tpp) REVERT: D 221 TYR cc_start: 0.8454 (p90) cc_final: 0.8090 (p90) REVERT: D 263 TRP cc_start: 0.8986 (m-10) cc_final: 0.8635 (m-10) REVERT: D 411 ASP cc_start: 0.9079 (m-30) cc_final: 0.8839 (t70) outliers start: 35 outliers final: 12 residues processed: 174 average time/residue: 0.1051 time to fit residues: 28.1324 Evaluate side-chains 144 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain E residue 235 GLU Chi-restraints excluded: chain E residue 431 ILE Chi-restraints excluded: chain C residue 235 GLU Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 431 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 31 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 115 optimal weight: 5.9990 chunk 152 optimal weight: 0.0970 chunk 36 optimal weight: 10.0000 chunk 57 optimal weight: 7.9990 chunk 89 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 overall best weight: 1.0980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 149 ASN A 269 ASN ** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 149 ASN ** E 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 ASN ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 149 ASN ** D 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.078051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.059251 restraints weight = 43118.387| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 3.95 r_work: 0.2785 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15745 Z= 0.138 Angle : 0.625 8.269 21355 Z= 0.307 Chirality : 0.045 0.203 2440 Planarity : 0.003 0.027 2605 Dihedral : 8.068 52.251 2725 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.02 % Allowed : 16.39 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.19), residues: 1790 helix: 2.54 (0.19), residues: 640 sheet: 0.84 (0.25), residues: 390 loop : -1.32 (0.20), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 437 TYR 0.022 0.002 TYR B 221 PHE 0.018 0.001 PHE C 319 TRP 0.006 0.001 TRP B 92 HIS 0.005 0.001 HIS A 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (15740) covalent geometry : angle 0.62425 / 0.31 (21340) hydrogen bonds : bond 0.04057 / 2.56 ( 750) hydrogen bonds : angle 4.35558 / 2.99 ( 2640) link_BETA1-4 : bond 0.00867 / 0.50 ( 5) link_BETA1-4 : angle 1.18318 / 0.76 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 134 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.9387 (mtt) cc_final: 0.9169 (mtt) REVERT: A 113 MET cc_start: 0.8819 (ppp) cc_final: 0.8368 (ppp) REVERT: A 263 TRP cc_start: 0.8963 (m-10) cc_final: 0.8596 (m-10) REVERT: A 399 MET cc_start: 0.8252 (mmm) cc_final: 0.7916 (mmp) REVERT: E 113 MET cc_start: 0.8890 (ppp) cc_final: 0.8487 (ppp) REVERT: E 187 MET cc_start: 0.8728 (mmt) cc_final: 0.8290 (mmm) REVERT: E 244 MET cc_start: 0.8954 (ttp) cc_final: 0.8727 (tpp) REVERT: E 399 MET cc_start: 0.8168 (mmm) cc_final: 0.7657 (mmp) REVERT: C 113 MET cc_start: 0.8895 (ppp) cc_final: 0.8472 (ppp) REVERT: C 187 MET cc_start: 0.8838 (mmm) cc_final: 0.8390 (mmm) REVERT: C 235 GLU cc_start: 0.9039 (OUTLIER) cc_final: 0.8764 (pt0) REVERT: C 244 MET cc_start: 0.8982 (tpp) cc_final: 0.8505 (tpp) REVERT: B 80 MET cc_start: 0.9363 (OUTLIER) cc_final: 0.8945 (mmm) REVERT: B 113 MET cc_start: 0.8911 (ppp) cc_final: 0.8587 (ppp) REVERT: B 187 MET cc_start: 0.8627 (tpt) cc_final: 0.8061 (tpt) REVERT: B 244 MET cc_start: 0.8874 (ttp) cc_final: 0.8665 (tpp) REVERT: B 399 MET cc_start: 0.8331 (mmm) cc_final: 0.8072 (mmp) REVERT: D 113 MET cc_start: 0.8788 (ppp) cc_final: 0.8396 (ppp) REVERT: D 187 MET cc_start: 0.8575 (tpt) cc_final: 0.7857 (tpp) REVERT: D 221 TYR cc_start: 0.8430 (p90) cc_final: 0.8085 (p90) REVERT: D 263 TRP cc_start: 0.9016 (m-10) cc_final: 0.8615 (m-10) REVERT: D 411 ASP cc_start: 0.9054 (m-30) cc_final: 0.8830 (t70) outliers start: 33 outliers final: 12 residues processed: 161 average time/residue: 0.1112 time to fit residues: 27.5821 Evaluate side-chains 144 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain E residue 235 GLU Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 431 ILE Chi-restraints excluded: chain C residue 235 GLU Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain D residue 235 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 24 optimal weight: 0.3980 chunk 158 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 40 optimal weight: 6.9990 chunk 62 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 122 optimal weight: 4.9990 chunk 31 optimal weight: 9.9990 chunk 138 optimal weight: 3.9990 chunk 43 optimal weight: 9.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 ASN C 269 ASN ** C 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.079159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.060066 restraints weight = 44371.984| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 3.98 r_work: 0.2776 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15745 Z= 0.156 Angle : 0.620 8.018 21355 Z= 0.306 Chirality : 0.045 0.207 2440 Planarity : 0.003 0.030 2605 Dihedral : 7.383 53.026 2725 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.96 % Allowed : 15.54 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.19), residues: 1790 helix: 2.63 (0.19), residues: 670 sheet: 1.04 (0.25), residues: 390 loop : -1.22 (0.21), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 437 TYR 0.024 0.002 TYR B 221 PHE 0.023 0.001 PHE E 319 TRP 0.006 0.001 TRP B 92 HIS 0.005 0.001 HIS A 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (15740) covalent geometry : angle 0.61929 / 0.31 (21340) hydrogen bonds : bond 0.04055 / 2.56 ( 750) hydrogen bonds : angle 4.31486 / 2.97 ( 2640) link_BETA1-4 : bond 0.00824 / 0.48 ( 5) link_BETA1-4 : angle 1.17984 / 0.76 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 133 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.9328 (mtt) cc_final: 0.9107 (mtt) REVERT: A 113 MET cc_start: 0.8792 (ppp) cc_final: 0.8404 (ppp) REVERT: A 399 MET cc_start: 0.8329 (mmm) cc_final: 0.7992 (mmp) REVERT: E 113 MET cc_start: 0.8845 (ppp) cc_final: 0.8493 (ppp) REVERT: E 187 MET cc_start: 0.8712 (mmt) cc_final: 0.8249 (mmm) REVERT: E 244 MET cc_start: 0.9059 (ttp) cc_final: 0.8776 (tpp) REVERT: E 262 SER cc_start: 0.9567 (m) cc_final: 0.9225 (p) REVERT: E 399 MET cc_start: 0.8284 (mmm) cc_final: 0.7882 (mmp) REVERT: C 113 MET cc_start: 0.8850 (ppp) cc_final: 0.8448 (ppp) REVERT: C 187 MET cc_start: 0.8790 (mmm) cc_final: 0.8542 (mmm) REVERT: C 235 GLU cc_start: 0.9009 (OUTLIER) cc_final: 0.8751 (pt0) REVERT: B 171 MET cc_start: 0.9071 (pmm) cc_final: 0.8780 (pmm) REVERT: B 187 MET cc_start: 0.8577 (tpt) cc_final: 0.7987 (tpt) REVERT: B 244 MET cc_start: 0.8918 (ttp) cc_final: 0.8714 (tpp) REVERT: B 399 MET cc_start: 0.8322 (mmm) cc_final: 0.8031 (mmp) REVERT: D 113 MET cc_start: 0.8815 (ppp) cc_final: 0.8464 (ppp) REVERT: D 187 MET cc_start: 0.8553 (tpt) cc_final: 0.7837 (tpp) REVERT: D 221 TYR cc_start: 0.8341 (p90) cc_final: 0.8016 (p90) REVERT: D 399 MET cc_start: 0.8241 (mmt) cc_final: 0.7932 (mmp) REVERT: D 411 ASP cc_start: 0.9021 (m-30) cc_final: 0.8809 (t70) outliers start: 32 outliers final: 17 residues processed: 156 average time/residue: 0.1080 time to fit residues: 26.0609 Evaluate side-chains 148 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain E residue 235 GLU Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain E residue 333 ARG Chi-restraints excluded: chain C residue 235 GLU Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 333 ARG Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 333 ARG Chi-restraints excluded: chain D residue 431 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 44 optimal weight: 0.8980 chunk 78 optimal weight: 0.0020 chunk 15 optimal weight: 4.9990 chunk 142 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 chunk 98 optimal weight: 9.9990 chunk 80 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 overall best weight: 1.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 269 ASN C 139 ASN ** C 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.078832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.059979 restraints weight = 44032.862| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 3.95 r_work: 0.2776 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15745 Z= 0.138 Angle : 0.603 8.465 21355 Z= 0.299 Chirality : 0.044 0.207 2440 Planarity : 0.003 0.030 2605 Dihedral : 6.980 53.228 2725 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.57 % Allowed : 15.78 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.19), residues: 1790 helix: 2.75 (0.19), residues: 670 sheet: 1.13 (0.25), residues: 390 loop : -1.14 (0.21), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 437 TYR 0.023 0.002 TYR B 221 PHE 0.021 0.001 PHE D 319 TRP 0.007 0.001 TRP C 263 HIS 0.004 0.001 HIS C 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (15740) covalent geometry : angle 0.60240 / 0.30 (21340) hydrogen bonds : bond 0.03916 / 2.47 ( 750) hydrogen bonds : angle 4.22658 / 2.91 ( 2640) link_BETA1-4 : bond 0.00793 / 0.47 ( 5) link_BETA1-4 : angle 1.18606 / 0.76 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 135 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.9289 (mtt) cc_final: 0.9059 (mtt) REVERT: A 113 MET cc_start: 0.8773 (ppp) cc_final: 0.8404 (ppp) REVERT: A 399 MET cc_start: 0.8350 (mmm) cc_final: 0.8011 (mmp) REVERT: E 113 MET cc_start: 0.8806 (ppp) cc_final: 0.8525 (ppp) REVERT: E 187 MET cc_start: 0.8643 (mmt) cc_final: 0.8212 (mmm) REVERT: E 244 MET cc_start: 0.9051 (ttp) cc_final: 0.8691 (tpp) REVERT: E 262 SER cc_start: 0.9559 (m) cc_final: 0.9213 (p) REVERT: E 279 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8149 (tp) REVERT: E 399 MET cc_start: 0.8248 (mmm) cc_final: 0.7898 (mmp) REVERT: C 113 MET cc_start: 0.8819 (ppp) cc_final: 0.8452 (ppp) REVERT: C 187 MET cc_start: 0.8791 (mmm) cc_final: 0.8529 (mmm) REVERT: C 235 GLU cc_start: 0.8974 (OUTLIER) cc_final: 0.8722 (pt0) REVERT: C 244 MET cc_start: 0.8770 (tpp) cc_final: 0.8020 (tpp) REVERT: B 80 MET cc_start: 0.9090 (mmm) cc_final: 0.8701 (mmm) REVERT: B 113 MET cc_start: 0.8843 (ppp) cc_final: 0.8566 (ppp) REVERT: B 171 MET cc_start: 0.9073 (pmm) cc_final: 0.8797 (pmm) REVERT: B 187 MET cc_start: 0.8566 (tpt) cc_final: 0.7971 (tpt) REVERT: B 244 MET cc_start: 0.8898 (ttp) cc_final: 0.8607 (tpp) REVERT: B 399 MET cc_start: 0.8446 (mmm) cc_final: 0.8131 (mmp) REVERT: D 113 MET cc_start: 0.8796 (ppp) cc_final: 0.8457 (ppp) REVERT: D 187 MET cc_start: 0.8577 (tpt) cc_final: 0.7838 (tpp) REVERT: D 221 TYR cc_start: 0.8335 (p90) cc_final: 0.7993 (p90) REVERT: D 399 MET cc_start: 0.8213 (mmt) cc_final: 0.7893 (mmp) REVERT: D 411 ASP cc_start: 0.8987 (m-30) cc_final: 0.8783 (t70) outliers start: 42 outliers final: 23 residues processed: 165 average time/residue: 0.1192 time to fit residues: 30.3249 Evaluate side-chains 155 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain E residue 235 GLU Chi-restraints excluded: chain E residue 255 SER Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 333 ARG Chi-restraints excluded: chain E residue 431 ILE Chi-restraints excluded: chain C residue 235 GLU Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 333 ARG Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 333 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 124 optimal weight: 7.9990 chunk 2 optimal weight: 0.1980 chunk 128 optimal weight: 4.9990 chunk 98 optimal weight: 10.0000 chunk 166 optimal weight: 0.9980 chunk 46 optimal weight: 6.9990 chunk 135 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 chunk 165 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 164 optimal weight: 4.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 329 ASN ** C 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 ASN D 329 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.074907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.056387 restraints weight = 43469.412| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 3.83 r_work: 0.2749 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15745 Z= 0.196 Angle : 0.655 9.809 21355 Z= 0.321 Chirality : 0.045 0.206 2440 Planarity : 0.003 0.030 2605 Dihedral : 6.922 53.215 2725 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.45 % Allowed : 16.82 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.19), residues: 1790 helix: 2.71 (0.19), residues: 670 sheet: 0.73 (0.24), residues: 420 loop : -1.19 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 437 TYR 0.024 0.002 TYR B 221 PHE 0.023 0.001 PHE D 319 TRP 0.009 0.001 TRP D 263 HIS 0.005 0.001 HIS C 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.20 (15740) covalent geometry : angle 0.65406 / 0.32 (21340) hydrogen bonds : bond 0.04259 / 2.68 ( 750) hydrogen bonds : angle 4.36562 / 3.01 ( 2640) link_BETA1-4 : bond 0.00804 / 0.46 ( 5) link_BETA1-4 : angle 1.21524 / 0.78 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 133 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.9290 (mtt) cc_final: 0.9087 (mtt) REVERT: A 113 MET cc_start: 0.8822 (ppp) cc_final: 0.8602 (ppp) REVERT: A 399 MET cc_start: 0.8387 (mmm) cc_final: 0.8046 (mmp) REVERT: E 113 MET cc_start: 0.8875 (ppp) cc_final: 0.8538 (ppp) REVERT: E 176 CYS cc_start: 0.9100 (m) cc_final: 0.8878 (m) REVERT: E 187 MET cc_start: 0.8695 (mmt) cc_final: 0.8270 (mmm) REVERT: E 244 MET cc_start: 0.9026 (ttp) cc_final: 0.8623 (tpp) REVERT: E 262 SER cc_start: 0.9578 (m) cc_final: 0.9258 (p) REVERT: E 399 MET cc_start: 0.8293 (mmm) cc_final: 0.7970 (mmp) REVERT: C 113 MET cc_start: 0.8812 (ppp) cc_final: 0.8457 (ppp) REVERT: C 187 MET cc_start: 0.8868 (mmm) cc_final: 0.8599 (tpt) REVERT: C 235 GLU cc_start: 0.9011 (OUTLIER) cc_final: 0.8758 (pt0) REVERT: B 80 MET cc_start: 0.9075 (mmm) cc_final: 0.8776 (mmm) REVERT: B 113 MET cc_start: 0.8850 (ppp) cc_final: 0.8558 (ppp) REVERT: B 187 MET cc_start: 0.8621 (tpt) cc_final: 0.8015 (tpt) REVERT: B 244 MET cc_start: 0.8908 (ttp) cc_final: 0.8490 (tpp) REVERT: B 399 MET cc_start: 0.8467 (mmm) cc_final: 0.8133 (mmp) REVERT: D 113 MET cc_start: 0.8799 (ppp) cc_final: 0.8483 (ppp) REVERT: D 187 MET cc_start: 0.8633 (tpt) cc_final: 0.8179 (tpt) REVERT: D 221 TYR cc_start: 0.8313 (p90) cc_final: 0.7991 (p90) REVERT: D 399 MET cc_start: 0.8493 (mmt) cc_final: 0.8145 (mmp) REVERT: D 411 ASP cc_start: 0.9039 (m-30) cc_final: 0.8807 (t70) outliers start: 40 outliers final: 24 residues processed: 156 average time/residue: 0.1180 time to fit residues: 28.4999 Evaluate side-chains 151 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 255 SER Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 333 ARG Chi-restraints excluded: chain E residue 431 ILE Chi-restraints excluded: chain C residue 171 MET Chi-restraints excluded: chain C residue 235 GLU Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 333 ARG Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 333 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 127 optimal weight: 7.9990 chunk 96 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 176 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 112 optimal weight: 0.0040 chunk 91 optimal weight: 0.0470 chunk 118 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 overall best weight: 0.5894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 70 ASN ** C 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.076869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.058364 restraints weight = 43490.390| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 3.87 r_work: 0.2795 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15745 Z= 0.114 Angle : 0.613 9.248 21355 Z= 0.299 Chirality : 0.044 0.206 2440 Planarity : 0.003 0.030 2605 Dihedral : 6.701 54.090 2725 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.08 % Allowed : 17.31 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.19), residues: 1790 helix: 2.74 (0.19), residues: 670 sheet: 0.74 (0.24), residues: 420 loop : -1.17 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 437 TYR 0.022 0.002 TYR B 221 PHE 0.020 0.001 PHE D 319 TRP 0.010 0.001 TRP C 263 HIS 0.004 0.001 HIS B 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (15740) covalent geometry : angle 0.61214 / 0.30 (21340) hydrogen bonds : bond 0.03922 / 2.48 ( 750) hydrogen bonds : angle 4.10820 / 2.82 ( 2640) link_BETA1-4 : bond 0.00734 / 0.43 ( 5) link_BETA1-4 : angle 1.24168 / 0.80 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 136 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.9001 (tmm) cc_final: 0.8739 (tmm) REVERT: A 80 MET cc_start: 0.9311 (mtt) cc_final: 0.9096 (mtt) REVERT: A 263 TRP cc_start: 0.8914 (m-10) cc_final: 0.8501 (m-10) REVERT: A 399 MET cc_start: 0.8386 (mmm) cc_final: 0.8032 (mmp) REVERT: E 113 MET cc_start: 0.8807 (ppp) cc_final: 0.8559 (ppp) REVERT: E 176 CYS cc_start: 0.8982 (m) cc_final: 0.8755 (m) REVERT: E 187 MET cc_start: 0.8673 (mmt) cc_final: 0.8304 (mmm) REVERT: E 244 MET cc_start: 0.8976 (ttp) cc_final: 0.8603 (tpp) REVERT: E 262 SER cc_start: 0.9581 (m) cc_final: 0.9237 (p) REVERT: E 279 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8135 (tp) REVERT: E 311 MET cc_start: 0.9472 (mmm) cc_final: 0.9162 (mmt) REVERT: E 399 MET cc_start: 0.8314 (mmm) cc_final: 0.8000 (mmp) REVERT: C 113 MET cc_start: 0.8784 (ppp) cc_final: 0.8472 (ppp) REVERT: C 187 MET cc_start: 0.8885 (mmm) cc_final: 0.8617 (mmm) REVERT: C 311 MET cc_start: 0.9240 (mmm) cc_final: 0.8693 (mmm) REVERT: B 80 MET cc_start: 0.9086 (mmm) cc_final: 0.8776 (mmm) REVERT: B 113 MET cc_start: 0.8837 (ppp) cc_final: 0.8574 (ppp) REVERT: B 187 MET cc_start: 0.8633 (tpt) cc_final: 0.8031 (tpt) REVERT: B 221 TYR cc_start: 0.8459 (p90) cc_final: 0.8203 (p90) REVERT: B 244 MET cc_start: 0.8872 (ttp) cc_final: 0.8590 (tpp) REVERT: B 399 MET cc_start: 0.8467 (mmm) cc_final: 0.8142 (mmp) REVERT: D 113 MET cc_start: 0.8779 (ppp) cc_final: 0.8492 (ppp) REVERT: D 187 MET cc_start: 0.8630 (tpt) cc_final: 0.7880 (tpp) REVERT: D 221 TYR cc_start: 0.8299 (p90) cc_final: 0.7987 (p90) REVERT: D 399 MET cc_start: 0.8507 (mmt) cc_final: 0.8166 (mmp) REVERT: D 411 ASP cc_start: 0.9027 (m-30) cc_final: 0.8802 (t70) outliers start: 34 outliers final: 23 residues processed: 158 average time/residue: 0.1136 time to fit residues: 28.1672 Evaluate side-chains 159 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain E residue 255 SER Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 333 ARG Chi-restraints excluded: chain C residue 235 GLU Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 333 ARG Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 333 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 128 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 100 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 143 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 335 HIS ** 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 = 0.3356 r_free = 0.3356 target = 0.075740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.057311 restraints weight = 43185.147| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 3.84 r_work: 0.2782 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15745 Z= 0.149 Angle : 0.626 9.490 21355 Z= 0.305 Chirality : 0.044 0.249 2440 Planarity : 0.003 0.031 2605 Dihedral : 6.596 54.434 2725 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.71 % Allowed : 17.61 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.20), residues: 1790 helix: 2.71 (0.19), residues: 670 sheet: 0.71 (0.24), residues: 420 loop : -1.13 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 437 TYR 0.021 0.002 TYR B 221 PHE 0.019 0.001 PHE D 319 TRP 0.008 0.001 TRP C 263 HIS 0.005 0.001 HIS B 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (15740) covalent geometry : angle 0.62491 / 0.31 (21340) hydrogen bonds : bond 0.03975 / 2.51 ( 750) hydrogen bonds : angle 4.16100 / 2.87 ( 2640) link_BETA1-4 : bond 0.00700 / 0.40 ( 5) link_BETA1-4 : angle 1.28444 / 0.83 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.8925 (tmm) cc_final: 0.8695 (tmm) REVERT: A 80 MET cc_start: 0.9354 (mtt) cc_final: 0.9131 (mtt) REVERT: A 399 MET cc_start: 0.8396 (mmm) cc_final: 0.8042 (mmp) REVERT: E 113 MET cc_start: 0.8840 (ppp) cc_final: 0.8557 (ppp) REVERT: E 187 MET cc_start: 0.8693 (mmt) cc_final: 0.8301 (mmm) REVERT: E 244 MET cc_start: 0.8963 (ttp) cc_final: 0.8552 (tpp) REVERT: E 262 SER cc_start: 0.9582 (m) cc_final: 0.9238 (p) REVERT: E 279 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8178 (tp) REVERT: E 311 MET cc_start: 0.9478 (mmm) cc_final: 0.9167 (mmt) REVERT: E 399 MET cc_start: 0.8464 (mmm) cc_final: 0.8135 (mmp) REVERT: C 113 MET cc_start: 0.8784 (ppp) cc_final: 0.8449 (ppp) REVERT: C 187 MET cc_start: 0.8918 (mmm) cc_final: 0.8648 (mmm) REVERT: B 32 MET cc_start: 0.8863 (tmm) cc_final: 0.8546 (tmm) REVERT: B 80 MET cc_start: 0.9075 (mmm) cc_final: 0.8780 (mmm) REVERT: B 113 MET cc_start: 0.8835 (ppp) cc_final: 0.8582 (ppp) REVERT: B 187 MET cc_start: 0.8672 (tpt) cc_final: 0.8071 (tpt) REVERT: B 221 TYR cc_start: 0.8478 (p90) cc_final: 0.8219 (p90) REVERT: B 244 MET cc_start: 0.8865 (ttp) cc_final: 0.8592 (tpp) REVERT: B 399 MET cc_start: 0.8471 (mmm) cc_final: 0.8138 (mmp) REVERT: D 113 MET cc_start: 0.8784 (ppp) cc_final: 0.8519 (ppp) REVERT: D 187 MET cc_start: 0.8672 (tpt) cc_final: 0.8192 (tpt) REVERT: D 221 TYR cc_start: 0.8306 (p90) cc_final: 0.7996 (p90) REVERT: D 399 MET cc_start: 0.8510 (mmt) cc_final: 0.8158 (mmp) REVERT: D 411 ASP cc_start: 0.9038 (m-30) cc_final: 0.8813 (t70) outliers start: 28 outliers final: 24 residues processed: 149 average time/residue: 0.1106 time to fit residues: 25.6754 Evaluate side-chains 156 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain E residue 255 SER Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 333 ARG Chi-restraints excluded: chain E residue 431 ILE Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 333 ARG Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 333 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 109 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 131 optimal weight: 0.8980 chunk 16 optimal weight: 6.9990 chunk 85 optimal weight: 0.0670 chunk 152 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 70 ASN E 70 ASN ** C 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.077074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.058715 restraints weight = 43322.582| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 3.86 r_work: 0.2806 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15745 Z= 0.113 Angle : 0.615 10.247 21355 Z= 0.296 Chirality : 0.044 0.271 2440 Planarity : 0.003 0.030 2605 Dihedral : 6.465 55.169 2725 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.53 % Allowed : 18.17 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.19), residues: 1790 helix: 2.79 (0.18), residues: 665 sheet: 0.72 (0.24), residues: 420 loop : -1.12 (0.22), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 437 TYR 0.022 0.002 TYR E 221 PHE 0.019 0.001 PHE A 319 TRP 0.011 0.001 TRP C 263 HIS 0.004 0.001 HIS B 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (15740) covalent geometry : angle 0.61400 / 0.30 (21340) hydrogen bonds : bond 0.03755 / 2.38 ( 750) hydrogen bonds : angle 4.01908 / 2.76 ( 2640) link_BETA1-4 : bond 0.00722 / 0.43 ( 5) link_BETA1-4 : angle 1.32459 / 0.85 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.8866 (tmm) cc_final: 0.8632 (tmm) REVERT: A 80 MET cc_start: 0.9341 (mtt) cc_final: 0.9109 (mtt) REVERT: A 263 TRP cc_start: 0.8933 (m-10) cc_final: 0.8512 (m-10) REVERT: A 311 MET cc_start: 0.9264 (mmm) cc_final: 0.9048 (tpp) REVERT: A 399 MET cc_start: 0.8392 (mmm) cc_final: 0.8041 (mmp) REVERT: E 113 MET cc_start: 0.8771 (ppp) cc_final: 0.8447 (ppp) REVERT: E 187 MET cc_start: 0.8667 (mmt) cc_final: 0.8300 (mmm) REVERT: E 244 MET cc_start: 0.8952 (ttp) cc_final: 0.8543 (tpp) REVERT: E 262 SER cc_start: 0.9570 (m) cc_final: 0.9217 (p) REVERT: E 279 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.8063 (tp) REVERT: E 311 MET cc_start: 0.9443 (mmm) cc_final: 0.9185 (mmt) REVERT: E 399 MET cc_start: 0.8295 (mmm) cc_final: 0.7972 (mmp) REVERT: C 113 MET cc_start: 0.8696 (ppp) cc_final: 0.8387 (ppp) REVERT: C 187 MET cc_start: 0.8907 (mmm) cc_final: 0.8638 (mmm) REVERT: C 235 GLU cc_start: 0.8986 (OUTLIER) cc_final: 0.8726 (tt0) REVERT: C 244 MET cc_start: 0.8735 (tpp) cc_final: 0.8322 (tpp) REVERT: B 32 MET cc_start: 0.8790 (tmm) cc_final: 0.8509 (tmm) REVERT: B 80 MET cc_start: 0.9045 (mmm) cc_final: 0.8754 (mmm) REVERT: B 113 MET cc_start: 0.8813 (ppp) cc_final: 0.8586 (ppp) REVERT: B 187 MET cc_start: 0.8674 (tpt) cc_final: 0.8080 (tpt) REVERT: B 221 TYR cc_start: 0.8440 (p90) cc_final: 0.8184 (p90) REVERT: B 287 MET cc_start: 0.9313 (tpp) cc_final: 0.9073 (mmm) REVERT: B 399 MET cc_start: 0.8468 (mmm) cc_final: 0.8132 (mmp) REVERT: D 113 MET cc_start: 0.8754 (ppp) cc_final: 0.8539 (ppp) REVERT: D 187 MET cc_start: 0.8670 (tpt) cc_final: 0.7890 (tpp) REVERT: D 221 TYR cc_start: 0.8321 (p90) cc_final: 0.7991 (p90) REVERT: D 399 MET cc_start: 0.8505 (mmt) cc_final: 0.8160 (mmp) REVERT: D 411 ASP cc_start: 0.8990 (m-30) cc_final: 0.8777 (t0) outliers start: 25 outliers final: 22 residues processed: 156 average time/residue: 0.1213 time to fit residues: 29.7448 Evaluate side-chains 162 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain E residue 255 SER Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 333 ARG Chi-restraints excluded: chain C residue 235 GLU Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 333 ARG Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 333 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 27 optimal weight: 0.6980 chunk 41 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 10 optimal weight: 0.4980 chunk 140 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 335 HIS ** 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 = 0.3383 r_free = 0.3383 target = 0.076954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.058645 restraints weight = 42898.534| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 3.83 r_work: 0.2816 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15745 Z= 0.120 Angle : 0.617 10.600 21355 Z= 0.298 Chirality : 0.044 0.274 2440 Planarity : 0.003 0.031 2605 Dihedral : 6.385 56.700 2725 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.53 % Allowed : 18.23 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.20), residues: 1790 helix: 2.82 (0.18), residues: 665 sheet: 0.72 (0.24), residues: 420 loop : -1.08 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 437 TYR 0.021 0.002 TYR E 221 PHE 0.018 0.001 PHE A 319 TRP 0.009 0.001 TRP D 263 HIS 0.004 0.001 HIS D 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (15740) covalent geometry : angle 0.61634 / 0.30 (21340) hydrogen bonds : bond 0.03753 / 2.38 ( 750) hydrogen bonds : angle 4.00501 / 2.75 ( 2640) link_BETA1-4 : bond 0.00736 / 0.43 ( 5) link_BETA1-4 : angle 1.29086 / 0.84 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2952.62 seconds wall clock time: 51 minutes 45.28 seconds (3105.28 seconds total)