Starting phenix.real_space_refine on Fri Jul 3 15:30:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7m6s_23706/07_2026/7m6s_23706.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m6s_23706/07_2026/7m6s_23706.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7m6s_23706/07_2026/7m6s_23706.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m6s_23706/07_2026/7m6s_23706.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7m6s_23706/07_2026/7m6s_23706.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7m6s_23706/07_2026/7m6s_23706.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7m6s_23706/07_2026/7m6s_23706.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m6s_23706/07_2026/7m6s_23706.map" } resolution = 3.61 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 9510 2.51 5 N 2390 2.21 5 O 2625 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14625 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2906 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 16, 'TRANS': 340} Chain breaks: 1 Chain: "B" Number of atoms: 2906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2906 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 16, 'TRANS': 340} Chain breaks: 1 Chain: "C" Number of atoms: 2906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2906 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 16, 'TRANS': 340} Chain breaks: 1 Chain: "D" Number of atoms: 2906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2906 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 16, 'TRANS': 340} Chain breaks: 1 Chain: "E" Number of atoms: 2906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2906 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 16, 'TRANS': 340} Chain breaks: 1 Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 19 Unusual residues: {'NAG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.65, per 1000 atoms: 0.25 Number of scatterers: 14625 At special positions: 0 Unit cell: (93.5, 92.4, 140.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 100 16.00 O 2625 8.00 N 2390 7.00 C 9510 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 176 " distance=2.06 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 176 " distance=2.06 Simple disulfide: pdb=" SG CYS C 162 " - pdb=" SG CYS C 176 " distance=2.06 Simple disulfide: pdb=" SG CYS D 162 " - pdb=" SG CYS D 176 " distance=2.06 Simple disulfide: pdb=" SG CYS E 162 " - pdb=" SG CYS E 176 " distance=2.06 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 NAG-ASN " NAG A 501 " - " ASN A 62 " " NAG B 802 " - " ASN B 62 " " NAG C 802 " - " ASN C 62 " " NAG D 802 " - " ASN D 62 " " NAG E 802 " - " ASN E 62 " Time building additional restraints: 1.00 Conformation dependent library (CDL) restraints added in 657.1 milliseconds 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3430 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 25 sheets defined 41.3% alpha, 38.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 33 through 42 removed outlier: 3.637A pdb=" N PHE A 37 " --> pdb=" O PRO A 33 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N MET A 42 " --> pdb=" O LEU A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 117 removed outlier: 4.417A pdb=" N SER A 116 " --> pdb=" O SER A 112 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE A 117 " --> pdb=" O MET A 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 112 through 117' Processing helix chain 'A' and resid 244 through 251 removed outlier: 3.554A pdb=" N LEU A 248 " --> pdb=" O MET A 244 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE A 249 " --> pdb=" O GLY A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 268 Processing helix chain 'A' and resid 272 through 295 Processing helix chain 'A' and resid 305 through 341 removed outlier: 3.877A pdb=" N LEU A 322 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 323 " --> pdb=" O PHE A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 440 removed outlier: 4.153A pdb=" N LYS A 401 " --> pdb=" O GLU A 397 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N LEU A 402 " --> pdb=" O GLU A 398 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL A 416 " --> pdb=" O THR A 412 " (cutoff:3.500A) Proline residue: A 419 - end of helix removed outlier: 4.442A pdb=" N PHE A 425 " --> pdb=" O VAL A 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 42 removed outlier: 3.637A pdb=" N PHE B 37 " --> pdb=" O PRO B 33 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N MET B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 117 removed outlier: 4.417A pdb=" N SER B 116 " --> pdb=" O SER B 112 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE B 117 " --> pdb=" O MET B 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 112 through 117' Processing helix chain 'B' and resid 244 through 251 removed outlier: 3.553A pdb=" N LEU B 248 " --> pdb=" O MET B 244 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE B 249 " --> pdb=" O GLY B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 268 Processing helix chain 'B' and resid 272 through 295 Processing helix chain 'B' and resid 305 through 341 removed outlier: 3.877A pdb=" N LEU B 322 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU B 323 " --> pdb=" O PHE B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 440 removed outlier: 4.152A pdb=" N LYS B 401 " --> pdb=" O GLU B 397 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LEU B 402 " --> pdb=" O GLU B 398 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL B 416 " --> pdb=" O THR B 412 " (cutoff:3.500A) Proline residue: B 419 - end of helix removed outlier: 4.443A pdb=" N PHE B 425 " --> pdb=" O VAL B 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 42 removed outlier: 3.637A pdb=" N PHE C 37 " --> pdb=" O PRO C 33 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N MET C 42 " --> pdb=" O LEU C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 117 removed outlier: 4.417A pdb=" N SER C 116 " --> pdb=" O SER C 112 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE C 117 " --> pdb=" O MET C 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 112 through 117' Processing helix chain 'C' and resid 244 through 251 removed outlier: 3.554A pdb=" N LEU C 248 " --> pdb=" O MET C 244 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE C 249 " --> pdb=" O GLY C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 268 Processing helix chain 'C' and resid 272 through 295 Processing helix chain 'C' and resid 305 through 341 removed outlier: 3.877A pdb=" N LEU C 322 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU C 323 " --> pdb=" O PHE C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 440 removed outlier: 4.152A pdb=" N LYS C 401 " --> pdb=" O GLU C 397 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LEU C 402 " --> pdb=" O GLU C 398 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL C 416 " --> pdb=" O THR C 412 " (cutoff:3.500A) Proline residue: C 419 - end of helix removed outlier: 4.443A pdb=" N PHE C 425 " --> pdb=" O VAL C 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 42 removed outlier: 3.637A pdb=" N PHE D 37 " --> pdb=" O PRO D 33 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N MET D 42 " --> pdb=" O LEU D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 117 removed outlier: 4.418A pdb=" N SER D 116 " --> pdb=" O SER D 112 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE D 117 " --> pdb=" O MET D 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 112 through 117' Processing helix chain 'D' and resid 244 through 251 removed outlier: 3.554A pdb=" N LEU D 248 " --> pdb=" O MET D 244 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE D 249 " --> pdb=" O GLY D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 268 Processing helix chain 'D' and resid 272 through 295 Processing helix chain 'D' and resid 305 through 341 removed outlier: 3.876A pdb=" N LEU D 322 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU D 323 " --> pdb=" O PHE D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 440 removed outlier: 4.152A pdb=" N LYS D 401 " --> pdb=" O GLU D 397 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LEU D 402 " --> pdb=" O GLU D 398 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL D 416 " --> pdb=" O THR D 412 " (cutoff:3.500A) Proline residue: D 419 - end of helix removed outlier: 4.442A pdb=" N PHE D 425 " --> pdb=" O VAL D 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 42 removed outlier: 3.637A pdb=" N PHE E 37 " --> pdb=" O PRO E 33 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N MET E 42 " --> pdb=" O LEU E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 117 removed outlier: 4.417A pdb=" N SER E 116 " --> pdb=" O SER E 112 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE E 117 " --> pdb=" O MET E 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 112 through 117' Processing helix chain 'E' and resid 244 through 251 removed outlier: 3.554A pdb=" N LEU E 248 " --> pdb=" O MET E 244 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE E 249 " --> pdb=" O GLY E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 268 Processing helix chain 'E' and resid 272 through 295 Processing helix chain 'E' and resid 305 through 341 removed outlier: 3.877A pdb=" N LEU E 322 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU E 323 " --> pdb=" O PHE E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 440 removed outlier: 4.153A pdb=" N LYS E 401 " --> pdb=" O GLU E 397 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LEU E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL E 416 " --> pdb=" O THR E 412 " (cutoff:3.500A) Proline residue: E 419 - end of helix removed outlier: 4.441A pdb=" N PHE E 425 " --> pdb=" O VAL E 421 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 106 through 109 removed outlier: 3.885A pdb=" N LEU A 142 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ASN A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ASP A 81 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N SER A 74 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ARG A 83 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N PHE A 72 " --> pdb=" O ARG A 83 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ASN A 85 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ASN A 93 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASN A 62 " --> pdb=" O ASN A 93 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N VAL A 61 " --> pdb=" O ILE A 191 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N GLU A 193 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL A 63 " --> pdb=" O GLU A 193 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 132 removed outlier: 3.575A pdb=" N VAL A 159 " --> pdb=" O LYS A 128 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA A 130 " --> pdb=" O THR A 157 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N THR A 157 " --> pdb=" O ALA A 130 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N PHE A 132 " --> pdb=" O ARG A 155 " (cutoff:3.500A) removed outlier: 8.917A pdb=" N ARG A 155 " --> pdb=" O PHE A 132 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ASP A 81 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N SER A 74 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ARG A 83 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N PHE A 72 " --> pdb=" O ARG A 83 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ASN A 85 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ASN A 93 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 6.785A 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 Processing sheet with id=AA6, first strand: chain 'B' and resid 106 through 109 removed outlier: 3.885A pdb=" N LEU B 142 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ASN B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ASP B 81 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N SER B 74 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N ARG B 83 " --> pdb=" O PHE B 72 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N PHE B 72 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ASN B 85 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ASN B 93 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASN B 62 " --> pdb=" O ASN B 93 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N VAL B 61 " --> pdb=" O ILE B 191 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N GLU B 193 " --> pdb=" O VAL B 61 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL B 63 " --> pdb=" O GLU B 193 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 128 through 132 removed outlier: 3.576A pdb=" N VAL B 159 " --> pdb=" O LYS B 128 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA B 130 " --> pdb=" O THR B 157 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N THR B 157 " --> pdb=" O ALA B 130 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N PHE B 132 " --> pdb=" O ARG B 155 " (cutoff:3.500A) removed outlier: 8.917A pdb=" N ARG B 155 " --> pdb=" O PHE B 132 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ASP B 81 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N SER B 74 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N ARG B 83 " --> pdb=" O PHE B 72 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N PHE B 72 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ASN B 85 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ASN B 93 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASN B 62 " --> pdb=" O ASN B 93 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 123 through 124 Processing sheet with id=AA9, first strand: chain 'B' and resid 123 through 124 Processing sheet with id=AB1, first strand: chain 'B' and resid 224 through 225 Processing sheet with id=AB2, first strand: chain 'C' and resid 106 through 109 removed outlier: 3.885A pdb=" N LEU C 142 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ASN C 149 " --> pdb=" O SER C 145 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ASP C 81 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N SER C 74 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ARG C 83 " --> pdb=" O PHE C 72 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N PHE C 72 " --> pdb=" O ARG C 83 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ASN C 85 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ASN C 93 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASN C 62 " --> pdb=" O ASN C 93 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N VAL C 61 " --> pdb=" O ILE C 191 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N GLU C 193 " --> pdb=" O VAL C 61 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL C 63 " --> pdb=" O GLU C 193 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 128 through 132 removed outlier: 3.575A pdb=" N VAL C 159 " --> pdb=" O LYS C 128 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA C 130 " --> pdb=" O THR C 157 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N THR C 157 " --> pdb=" O ALA C 130 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N PHE C 132 " --> pdb=" O ARG C 155 " (cutoff:3.500A) removed outlier: 8.917A pdb=" N ARG C 155 " --> pdb=" O PHE C 132 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ASP C 81 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N SER C 74 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ARG C 83 " --> pdb=" O PHE C 72 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N PHE C 72 " --> pdb=" O ARG C 83 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ASN C 85 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ASN C 93 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 6.786A 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 Processing sheet with id=AB7, first strand: chain 'D' and resid 106 through 109 removed outlier: 3.885A pdb=" N LEU D 142 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ASN D 149 " --> pdb=" O SER D 145 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N ASP D 81 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N SER D 74 " --> pdb=" O ASP D 81 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ARG D 83 " --> pdb=" O PHE D 72 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N PHE D 72 " --> pdb=" O ARG D 83 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ASN D 85 " --> pdb=" O ASN D 70 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ASN D 93 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASN D 62 " --> pdb=" O ASN D 93 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N VAL D 61 " --> pdb=" O ILE D 191 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N GLU D 193 " --> pdb=" O VAL D 61 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL D 63 " --> pdb=" O GLU D 193 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 128 through 132 removed outlier: 3.575A pdb=" N VAL D 159 " --> pdb=" O LYS D 128 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA D 130 " --> pdb=" O THR D 157 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N THR D 157 " --> pdb=" O ALA D 130 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N PHE D 132 " --> pdb=" O ARG D 155 " (cutoff:3.500A) removed outlier: 8.916A pdb=" N ARG D 155 " --> pdb=" O PHE D 132 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N ASP D 81 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N SER D 74 " --> pdb=" O ASP D 81 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ARG D 83 " --> pdb=" O PHE D 72 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N PHE D 72 " --> pdb=" O ARG D 83 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ASN D 85 " --> pdb=" O ASN D 70 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ASN D 93 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASN D 62 " --> pdb=" O ASN D 93 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 123 through 124 Processing sheet with id=AC1, first strand: chain 'D' and resid 123 through 124 Processing sheet with id=AC2, first strand: chain 'D' and resid 224 through 225 Processing sheet with id=AC3, first strand: chain 'E' and resid 106 through 109 removed outlier: 3.884A pdb=" N LEU E 142 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ASN E 149 " --> pdb=" O SER E 145 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ASP E 81 " --> pdb=" O SER E 74 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N SER E 74 " --> pdb=" O ASP E 81 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ARG E 83 " --> pdb=" O PHE E 72 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N PHE E 72 " --> pdb=" O ARG E 83 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ASN E 85 " --> pdb=" O ASN E 70 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ASN E 93 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASN E 62 " --> pdb=" O ASN E 93 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N VAL E 61 " --> pdb=" O ILE E 191 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N GLU E 193 " --> pdb=" O VAL E 61 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N VAL E 63 " --> pdb=" O GLU E 193 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 128 through 132 removed outlier: 3.575A pdb=" N VAL E 159 " --> pdb=" O LYS E 128 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA E 130 " --> pdb=" O THR E 157 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N THR E 157 " --> pdb=" O ALA E 130 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N PHE E 132 " --> pdb=" O ARG E 155 " (cutoff:3.500A) removed outlier: 8.917A pdb=" N ARG E 155 " --> pdb=" O PHE E 132 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ASP E 81 " --> pdb=" O SER E 74 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N SER E 74 " --> pdb=" O ASP E 81 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ARG E 83 " --> pdb=" O PHE E 72 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N PHE E 72 " --> pdb=" O ARG E 83 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ASN E 85 " --> pdb=" O ASN E 70 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ASN E 93 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASN E 62 " --> pdb=" O ASN E 93 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 123 through 124 Processing sheet with id=AC6, first strand: chain 'E' and resid 123 through 124 Processing sheet with id=AC7, first strand: chain 'E' and resid 224 through 225 900 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: 2.28 Time building geometry restraints manager: 1.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4516 1.35 - 1.47: 3901 1.47 - 1.60: 6388 1.60 - 1.73: 0 1.73 - 1.85: 170 Bond restraints: 14975 Sorted by residual: bond pdb=" C ALA D 273 " pdb=" N PRO D 274 " ideal model delta sigma weight residual 1.335 1.366 -0.030 1.36e-02 5.41e+03 4.95e+00 bond pdb=" C ALA C 273 " pdb=" N PRO C 274 " ideal model delta sigma weight residual 1.335 1.365 -0.030 1.36e-02 5.41e+03 4.85e+00 bond pdb=" C ALA A 273 " pdb=" N PRO A 274 " ideal model delta sigma weight residual 1.335 1.365 -0.030 1.36e-02 5.41e+03 4.77e+00 bond pdb=" C ILE B 253 " pdb=" N PRO B 254 " ideal model delta sigma weight residual 1.335 1.365 -0.030 1.36e-02 5.41e+03 4.73e+00 bond pdb=" C ILE C 253 " pdb=" N PRO C 254 " ideal model delta sigma weight residual 1.335 1.365 -0.029 1.36e-02 5.41e+03 4.66e+00 ... (remaining 14970 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.08: 19383 3.08 - 6.16: 752 6.16 - 9.24: 95 9.24 - 12.32: 30 12.32 - 15.40: 25 Bond angle restraints: 20285 Sorted by residual: angle pdb=" N LEU B 190 " pdb=" CA LEU B 190 " pdb=" CB LEU B 190 " ideal model delta sigma weight residual 110.49 118.63 -8.14 1.69e+00 3.50e-01 2.32e+01 angle pdb=" N LEU A 190 " pdb=" CA LEU A 190 " pdb=" CB LEU A 190 " ideal model delta sigma weight residual 110.49 118.63 -8.14 1.69e+00 3.50e-01 2.32e+01 angle pdb=" N LEU E 190 " pdb=" CA LEU E 190 " pdb=" CB LEU E 190 " ideal model delta sigma weight residual 110.49 118.60 -8.11 1.69e+00 3.50e-01 2.30e+01 angle pdb=" N LEU C 190 " pdb=" CA LEU C 190 " pdb=" CB LEU C 190 " ideal model delta sigma weight residual 110.49 118.59 -8.10 1.69e+00 3.50e-01 2.30e+01 angle pdb=" N LEU D 190 " pdb=" CA LEU D 190 " pdb=" CB LEU D 190 " ideal model delta sigma weight residual 110.49 118.59 -8.10 1.69e+00 3.50e-01 2.29e+01 ... (remaining 20280 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.22: 8100 14.22 - 28.44: 565 28.44 - 42.67: 180 42.67 - 56.89: 65 56.89 - 71.11: 20 Dihedral angle restraints: 8930 sinusoidal: 3650 harmonic: 5280 Sorted by residual: dihedral pdb=" N LEU B 190 " pdb=" C LEU B 190 " pdb=" CA LEU B 190 " pdb=" CB LEU B 190 " ideal model delta harmonic sigma weight residual 122.80 131.30 -8.50 0 2.50e+00 1.60e-01 1.15e+01 dihedral pdb=" N LEU A 190 " pdb=" C LEU A 190 " pdb=" CA LEU A 190 " pdb=" CB LEU A 190 " ideal model delta harmonic sigma weight residual 122.80 131.29 -8.49 0 2.50e+00 1.60e-01 1.15e+01 dihedral pdb=" N LEU D 190 " pdb=" C LEU D 190 " pdb=" CA LEU D 190 " pdb=" CB LEU D 190 " ideal model delta harmonic sigma weight residual 122.80 131.28 -8.48 0 2.50e+00 1.60e-01 1.15e+01 ... (remaining 8927 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.145: 2105 0.145 - 0.291: 155 0.291 - 0.436: 20 0.436 - 0.581: 0 0.581 - 0.727: 5 Chirality restraints: 2285 Sorted by residual: chirality pdb=" CG LEU C 279 " pdb=" CB LEU C 279 " pdb=" CD1 LEU C 279 " pdb=" CD2 LEU C 279 " both_signs ideal model delta sigma weight residual False -2.59 -1.86 -0.73 2.00e-01 2.50e+01 1.32e+01 chirality pdb=" CG LEU E 279 " pdb=" CB LEU E 279 " pdb=" CD1 LEU E 279 " pdb=" CD2 LEU E 279 " both_signs ideal model delta sigma weight residual False -2.59 -1.86 -0.73 2.00e-01 2.50e+01 1.32e+01 chirality pdb=" CG LEU A 279 " pdb=" CB LEU A 279 " pdb=" CD1 LEU A 279 " pdb=" CD2 LEU A 279 " both_signs ideal model delta sigma weight residual False -2.59 -1.86 -0.73 2.00e-01 2.50e+01 1.32e+01 ... (remaining 2282 not shown) Planarity restraints: 2540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY C 148 " 0.022 2.00e-02 2.50e+03 4.33e-02 1.88e+01 pdb=" C GLY C 148 " -0.075 2.00e-02 2.50e+03 pdb=" O GLY C 148 " 0.027 2.00e-02 2.50e+03 pdb=" N ASN C 149 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 148 " -0.022 2.00e-02 2.50e+03 4.33e-02 1.87e+01 pdb=" C GLY D 148 " 0.075 2.00e-02 2.50e+03 pdb=" O GLY D 148 " -0.027 2.00e-02 2.50e+03 pdb=" N ASN D 149 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 148 " 0.022 2.00e-02 2.50e+03 4.32e-02 1.87e+01 pdb=" C GLY A 148 " -0.075 2.00e-02 2.50e+03 pdb=" O GLY A 148 " 0.027 2.00e-02 2.50e+03 pdb=" N ASN A 149 " 0.026 2.00e-02 2.50e+03 ... (remaining 2537 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 3217 2.80 - 3.32: 13425 3.32 - 3.85: 23906 3.85 - 4.37: 26093 4.37 - 4.90: 45628 Nonbonded interactions: 112269 Sorted by model distance: nonbonded pdb=" O SER A 291 " pdb=" OG SER A 294 " model vdw 2.269 3.040 nonbonded pdb=" O SER B 291 " pdb=" OG SER B 294 " model vdw 2.269 3.040 nonbonded pdb=" O SER D 291 " pdb=" OG SER D 294 " model vdw 2.269 3.040 nonbonded pdb=" O SER E 291 " pdb=" OG SER E 294 " model vdw 2.270 3.040 nonbonded pdb=" O SER C 291 " pdb=" OG SER C 294 " model vdw 2.270 3.040 ... (remaining 112264 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 32 through 440) selection = (chain 'B' and resid 32 through 440) selection = (chain 'C' and resid 32 through 440) selection = (chain 'D' and resid 32 through 440) selection = (chain 'E' and resid 32 through 440) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.670 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: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.960 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 14985 Z= 0.384 Angle : 1.492 15.404 20310 Z= 0.808 Chirality : 0.090 0.727 2285 Planarity : 0.009 0.054 2535 Dihedral : 12.336 71.110 5485 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.00 % Allowed : 13.04 % Favored : 86.96 % 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: 1.92 (0.20), residues: 1765 helix: 2.88 (0.19), residues: 680 sheet: 1.88 (0.26), residues: 410 loop : -0.93 (0.21), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG D 220 TYR 0.071 0.005 TYR A 152 PHE 0.037 0.005 PHE B 87 TRP 0.034 0.004 TRP A 263 HIS 0.005 0.002 HIS B 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00827 / 0.38 (14975) covalent geometry : angle 1.48688 / 0.81 (20285) SS BOND : bond 0.02548 / 1.49 ( 5) SS BOND : angle 3.86164 / 1.88 ( 10) hydrogen bonds : bond 0.11318 / 7.37 ( 755) hydrogen bonds : angle 5.15944 / 3.63 ( 2640) link_NAG-ASN : bond 0.00620 / 0.36 ( 5) link_NAG-ASN : angle 3.60619 / 1.97 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 290 time to evaluate : 0.520 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: 0.7849 (mmt) cc_final: 0.6873 (mmm) REVERT: A 266 PHE cc_start: 0.7702 (m-80) cc_final: 0.7252 (m-80) REVERT: A 290 GLN cc_start: 0.9027 (tt0) cc_final: 0.8813 (tm-30) REVERT: B 42 MET cc_start: 0.8294 (ptp) cc_final: 0.8075 (ttp) REVERT: B 266 PHE cc_start: 0.7857 (m-80) cc_final: 0.7397 (m-80) REVERT: C 80 MET cc_start: 0.8052 (mmt) cc_final: 0.7197 (mmm) REVERT: C 266 PHE cc_start: 0.7835 (m-80) cc_final: 0.7384 (m-80) REVERT: D 80 MET cc_start: 0.8044 (mmt) cc_final: 0.7559 (mmm) REVERT: D 266 PHE cc_start: 0.7727 (m-80) cc_final: 0.7328 (m-80) REVERT: D 314 CYS cc_start: 0.9323 (m) cc_final: 0.9047 (p) REVERT: E 266 PHE cc_start: 0.7833 (m-80) cc_final: 0.7409 (m-80) outliers start: 0 outliers final: 0 residues processed: 290 average time/residue: 0.0849 time to fit residues: 39.9582 Evaluate side-chains 171 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.0670 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 overall best weight: 1.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 GLN B 329 ASN C 174 GLN ** C 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 329 ASN D 243 GLN D 329 ASN E 243 GLN ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 329 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.061233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.048882 restraints weight = 90419.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.050200 restraints weight = 54839.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.051099 restraints weight = 39133.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.051722 restraints weight = 30897.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.052125 restraints weight = 26073.557| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14985 Z= 0.175 Angle : 0.752 11.902 20310 Z= 0.373 Chirality : 0.046 0.167 2285 Planarity : 0.004 0.035 2535 Dihedral : 4.220 13.744 1950 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.61 % Allowed : 15.65 % Favored : 82.73 % 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: 1.45 (0.19), residues: 1765 helix: 2.51 (0.19), residues: 680 sheet: 1.71 (0.25), residues: 420 loop : -1.32 (0.21), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 333 TYR 0.021 0.002 TYR A 325 PHE 0.023 0.002 PHE C 422 TRP 0.047 0.002 TRP C 267 HIS 0.003 0.001 HIS A 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 (14975) covalent geometry : angle 0.75183 / 0.37 (20285) SS BOND : bond 0.00380 / 0.23 ( 5) SS BOND : angle 0.50996 / 0.23 ( 10) hydrogen bonds : bond 0.05870 / 3.84 ( 755) hydrogen bonds : angle 4.40291 / 3.12 ( 2640) link_NAG-ASN : bond 0.00102 / 0.06 ( 5) link_NAG-ASN : angle 1.34423 / 0.76 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 170 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 MET cc_start: 0.8620 (ptm) cc_final: 0.8373 (ttp) REVERT: A 90 GLN cc_start: 0.7895 (mp10) cc_final: 0.7570 (mp10) REVERT: A 250 GLN cc_start: 0.9243 (tp40) cc_final: 0.8887 (tp40) REVERT: A 266 PHE cc_start: 0.8547 (m-80) cc_final: 0.7929 (m-80) REVERT: A 290 GLN cc_start: 0.9481 (tt0) cc_final: 0.9101 (tm-30) REVERT: B 113 MET cc_start: 0.8543 (mmt) cc_final: 0.8173 (mmt) REVERT: B 187 MET cc_start: 0.9009 (tpp) cc_final: 0.8806 (mmm) REVERT: B 266 PHE cc_start: 0.8562 (m-80) cc_final: 0.8183 (m-80) REVERT: C 113 MET cc_start: 0.8693 (mmm) cc_final: 0.8411 (mmt) REVERT: C 266 PHE cc_start: 0.8363 (m-80) cc_final: 0.7803 (m-80) REVERT: D 109 LEU cc_start: 0.8710 (mt) cc_final: 0.8407 (mp) REVERT: D 113 MET cc_start: 0.8542 (mmm) cc_final: 0.8205 (mmt) REVERT: D 187 MET cc_start: 0.9070 (tpp) cc_final: 0.8807 (mmm) REVERT: D 266 PHE cc_start: 0.8738 (m-80) cc_final: 0.8234 (m-80) REVERT: D 267 TRP cc_start: 0.6890 (m100) cc_final: 0.6366 (m100) REVERT: D 287 MET cc_start: 0.9160 (ttm) cc_final: 0.8883 (ttm) REVERT: D 314 CYS cc_start: 0.9704 (m) cc_final: 0.9483 (m) REVERT: E 266 PHE cc_start: 0.8595 (m-80) cc_final: 0.8301 (m-80) outliers start: 26 outliers final: 12 residues processed: 188 average time/residue: 0.0829 time to fit residues: 25.3312 Evaluate side-chains 162 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 150 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain E residue 65 CYS Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 261 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 27 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 104 optimal weight: 6.9990 chunk 164 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 chunk 40 optimal weight: 8.9990 chunk 36 optimal weight: 0.4980 chunk 165 optimal weight: 5.9990 chunk 168 optimal weight: 4.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 243 GLN B 210 GLN B 250 GLN C 243 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.057435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.045294 restraints weight = 94296.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.046510 restraints weight = 57950.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.047359 restraints weight = 41603.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.047939 restraints weight = 32857.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.048349 restraints weight = 27828.902| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 14985 Z= 0.236 Angle : 0.758 11.871 20310 Z= 0.378 Chirality : 0.046 0.164 2285 Planarity : 0.004 0.032 2535 Dihedral : 4.284 18.192 1950 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.67 % Allowed : 15.84 % Favored : 81.49 % 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: 1.13 (0.19), residues: 1765 helix: 2.27 (0.19), residues: 680 sheet: 1.55 (0.26), residues: 410 loop : -1.48 (0.20), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 333 TYR 0.030 0.002 TYR E 325 PHE 0.016 0.002 PHE B 123 TRP 0.065 0.002 TRP C 267 HIS 0.005 0.001 HIS A 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.24 (14975) covalent geometry : angle 0.75698 / 0.38 (20285) SS BOND : bond 0.00368 / 0.22 ( 5) SS BOND : angle 0.64430 / 0.31 ( 10) hydrogen bonds : bond 0.05240 / 3.43 ( 755) hydrogen bonds : angle 4.38915 / 3.10 ( 2640) link_NAG-ASN : bond 0.00387 / 0.22 ( 5) link_NAG-ASN : angle 1.73306 / 1.02 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 140 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 MET cc_start: 0.8895 (ptm) cc_final: 0.8413 (ttm) REVERT: A 90 GLN cc_start: 0.8220 (mp10) cc_final: 0.7790 (mp10) REVERT: A 113 MET cc_start: 0.8946 (mmm) cc_final: 0.8698 (mmm) REVERT: A 266 PHE cc_start: 0.8830 (m-80) cc_final: 0.8355 (m-80) REVERT: A 290 GLN cc_start: 0.9562 (tt0) cc_final: 0.9134 (tm-30) REVERT: A 311 MET cc_start: 0.9375 (mmm) cc_final: 0.9141 (ptp) REVERT: B 263 TRP cc_start: 0.8211 (m-10) cc_final: 0.7547 (m-10) REVERT: B 266 PHE cc_start: 0.8819 (m-80) cc_final: 0.8287 (m-80) REVERT: B 267 TRP cc_start: 0.7172 (m100) cc_final: 0.6854 (m100) REVERT: B 322 LEU cc_start: 0.9714 (OUTLIER) cc_final: 0.9500 (mm) REVERT: C 113 MET cc_start: 0.8826 (mmm) cc_final: 0.8593 (mmt) REVERT: C 250 GLN cc_start: 0.9310 (tp40) cc_final: 0.9088 (tp40) REVERT: C 266 PHE cc_start: 0.8678 (OUTLIER) cc_final: 0.8274 (m-80) REVERT: C 402 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.8085 (pp) REVERT: D 113 MET cc_start: 0.8810 (mmm) cc_final: 0.8489 (mmt) REVERT: D 187 MET cc_start: 0.9011 (tpp) cc_final: 0.8679 (mmm) REVERT: D 266 PHE cc_start: 0.8903 (m-80) cc_final: 0.8359 (m-80) REVERT: D 267 TRP cc_start: 0.7108 (m100) cc_final: 0.6617 (m100) REVERT: D 314 CYS cc_start: 0.9712 (m) cc_final: 0.9503 (m) REVERT: E 187 MET cc_start: 0.8952 (tpp) cc_final: 0.8700 (mmm) REVERT: E 267 TRP cc_start: 0.6921 (m100) cc_final: 0.6499 (m100) outliers start: 43 outliers final: 20 residues processed: 169 average time/residue: 0.1036 time to fit residues: 28.4487 Evaluate side-chains 160 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain E residue 65 CYS Chi-restraints excluded: chain E residue 67 ILE Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 261 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 166 optimal weight: 8.9990 chunk 82 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 83 optimal weight: 8.9990 chunk 78 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 64 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 329 ASN E 174 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.058078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.045953 restraints weight = 92641.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.047215 restraints weight = 56139.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.048090 restraints weight = 39868.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.048697 restraints weight = 31375.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.049083 restraints weight = 26376.262| |-----------------------------------------------------------------------------| r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14985 Z= 0.139 Angle : 0.698 12.025 20310 Z= 0.337 Chirality : 0.045 0.257 2285 Planarity : 0.003 0.022 2535 Dihedral : 4.084 16.883 1950 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.24 % Allowed : 16.46 % Favored : 81.30 % 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: 1.07 (0.19), residues: 1765 helix: 2.31 (0.19), residues: 680 sheet: 1.44 (0.26), residues: 395 loop : -1.49 (0.20), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 333 TYR 0.019 0.002 TYR C 325 PHE 0.023 0.001 PHE C 422 TRP 0.022 0.002 TRP C 267 HIS 0.002 0.001 HIS A 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (14975) covalent geometry : angle 0.69794 / 0.34 (20285) SS BOND : bond 0.00360 / 0.22 ( 5) SS BOND : angle 0.46839 / 0.21 ( 10) hydrogen bonds : bond 0.04684 / 3.08 ( 755) hydrogen bonds : angle 4.07266 / 2.88 ( 2640) link_NAG-ASN : bond 0.00034 / 0.02 ( 5) link_NAG-ASN : angle 0.85024 / 0.53 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 140 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.8949 (mmm) cc_final: 0.8595 (mmt) REVERT: A 250 GLN cc_start: 0.9426 (tp40) cc_final: 0.9101 (tp-100) REVERT: A 266 PHE cc_start: 0.8800 (m-80) cc_final: 0.8307 (m-80) REVERT: A 290 GLN cc_start: 0.9554 (tt0) cc_final: 0.9149 (tm-30) REVERT: A 311 MET cc_start: 0.9384 (mmm) cc_final: 0.9180 (mmm) REVERT: A 314 CYS cc_start: 0.9547 (m) cc_final: 0.9286 (p) REVERT: B 263 TRP cc_start: 0.8137 (m-10) cc_final: 0.7494 (m-10) REVERT: B 266 PHE cc_start: 0.8821 (m-80) cc_final: 0.8228 (m-80) REVERT: B 267 TRP cc_start: 0.6948 (m100) cc_final: 0.6668 (m100) REVERT: C 113 MET cc_start: 0.8800 (mmm) cc_final: 0.8595 (mmt) REVERT: C 266 PHE cc_start: 0.8787 (m-80) cc_final: 0.8228 (m-80) REVERT: D 80 MET cc_start: 0.8301 (mmm) cc_final: 0.8032 (mmm) REVERT: D 113 MET cc_start: 0.8799 (mmm) cc_final: 0.8491 (mmt) REVERT: D 187 MET cc_start: 0.9093 (tpp) cc_final: 0.8858 (mmm) REVERT: D 263 TRP cc_start: 0.8023 (m-10) cc_final: 0.7273 (m100) REVERT: D 266 PHE cc_start: 0.8847 (m-80) cc_final: 0.8273 (m-80) REVERT: D 267 TRP cc_start: 0.6766 (m100) cc_final: 0.6331 (m100) REVERT: D 287 MET cc_start: 0.9273 (ttm) cc_final: 0.9015 (ttm) REVERT: D 314 CYS cc_start: 0.9711 (m) cc_final: 0.9468 (m) REVERT: E 113 MET cc_start: 0.8650 (mmt) cc_final: 0.8107 (mpp) REVERT: E 187 MET cc_start: 0.9005 (tpp) cc_final: 0.8698 (mmm) REVERT: E 263 TRP cc_start: 0.7924 (m-10) cc_final: 0.7637 (m-10) REVERT: E 266 PHE cc_start: 0.8959 (m-80) cc_final: 0.8435 (m-80) REVERT: E 267 TRP cc_start: 0.6817 (m100) cc_final: 0.6486 (m100) REVERT: E 287 MET cc_start: 0.9224 (ttm) cc_final: 0.8992 (ttm) outliers start: 36 outliers final: 22 residues processed: 165 average time/residue: 0.0945 time to fit residues: 25.5565 Evaluate side-chains 160 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 138 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 314 CYS Chi-restraints excluded: chain C residue 398 GLU Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 261 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 20 optimal weight: 6.9990 chunk 136 optimal weight: 20.0000 chunk 89 optimal weight: 6.9990 chunk 112 optimal weight: 3.9990 chunk 129 optimal weight: 0.9980 chunk 124 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 66 optimal weight: 0.2980 chunk 15 optimal weight: 6.9990 chunk 80 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 210 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.058663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.046478 restraints weight = 91791.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.047741 restraints weight = 55562.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.048612 restraints weight = 39561.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.049220 restraints weight = 31159.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.049637 restraints weight = 26257.250| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.4201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14985 Z= 0.123 Angle : 0.688 12.780 20310 Z= 0.326 Chirality : 0.044 0.219 2285 Planarity : 0.003 0.023 2535 Dihedral : 3.892 16.638 1950 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.61 % Allowed : 16.77 % Favored : 80.62 % 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: 0.83 (0.19), residues: 1765 helix: 2.20 (0.19), residues: 715 sheet: 1.24 (0.25), residues: 415 loop : -2.01 (0.19), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 400 TYR 0.015 0.001 TYR D 433 PHE 0.032 0.001 PHE B 422 TRP 0.025 0.001 TRP A 263 HIS 0.002 0.001 HIS C 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (14975) covalent geometry : angle 0.68816 / 0.33 (20285) SS BOND : bond 0.00344 / 0.21 ( 5) SS BOND : angle 0.37576 / 0.18 ( 10) hydrogen bonds : bond 0.04278 / 2.83 ( 755) hydrogen bonds : angle 3.87569 / 2.74 ( 2640) link_NAG-ASN : bond 0.00081 / 0.05 ( 5) link_NAG-ASN : angle 0.75061 / 0.51 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 142 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 MET cc_start: 0.8626 (ptm) cc_final: 0.8388 (ttp) REVERT: A 90 GLN cc_start: 0.8361 (mp10) cc_final: 0.7594 (mp10) REVERT: A 113 MET cc_start: 0.8956 (mmm) cc_final: 0.8488 (mmt) REVERT: A 266 PHE cc_start: 0.8917 (m-80) cc_final: 0.8485 (m-80) REVERT: A 290 GLN cc_start: 0.9570 (tt0) cc_final: 0.9166 (tm-30) REVERT: A 311 MET cc_start: 0.9451 (mmm) cc_final: 0.9192 (mmm) REVERT: A 314 CYS cc_start: 0.9585 (m) cc_final: 0.9309 (p) REVERT: B 113 MET cc_start: 0.8738 (mmm) cc_final: 0.8437 (mmt) REVERT: B 263 TRP cc_start: 0.8105 (m-10) cc_final: 0.7406 (m-10) REVERT: B 266 PHE cc_start: 0.8868 (m-80) cc_final: 0.8293 (m-80) REVERT: B 267 TRP cc_start: 0.6941 (m100) cc_final: 0.6690 (m100) REVERT: B 319 PHE cc_start: 0.9258 (t80) cc_final: 0.9046 (t80) REVERT: C 113 MET cc_start: 0.8861 (mmm) cc_final: 0.8594 (mmt) REVERT: C 250 GLN cc_start: 0.9370 (tp40) cc_final: 0.9106 (tp40) REVERT: C 266 PHE cc_start: 0.8713 (m-80) cc_final: 0.8191 (m-80) REVERT: D 90 GLN cc_start: 0.8522 (mp10) cc_final: 0.8262 (mp10) REVERT: D 102 TYR cc_start: 0.6968 (OUTLIER) cc_final: 0.6679 (t80) REVERT: D 113 MET cc_start: 0.8803 (mmm) cc_final: 0.8534 (mmt) REVERT: D 187 MET cc_start: 0.9097 (tpp) cc_final: 0.8850 (mmm) REVERT: D 263 TRP cc_start: 0.8007 (m-10) cc_final: 0.7246 (m-10) REVERT: D 266 PHE cc_start: 0.8874 (m-80) cc_final: 0.8357 (m-80) REVERT: D 267 TRP cc_start: 0.6728 (m100) cc_final: 0.6160 (m100) REVERT: D 314 CYS cc_start: 0.9689 (m) cc_final: 0.9447 (m) REVERT: E 42 MET cc_start: 0.9075 (ptm) cc_final: 0.8750 (ppp) REVERT: E 187 MET cc_start: 0.8957 (tpp) cc_final: 0.8712 (mmm) REVERT: E 263 TRP cc_start: 0.7957 (m-10) cc_final: 0.7616 (m-10) REVERT: E 266 PHE cc_start: 0.9003 (m-80) cc_final: 0.8463 (m-80) REVERT: E 267 TRP cc_start: 0.6609 (m100) cc_final: 0.6299 (m100) REVERT: E 287 MET cc_start: 0.9134 (ttm) cc_final: 0.8923 (ttm) outliers start: 42 outliers final: 23 residues processed: 173 average time/residue: 0.0864 time to fit residues: 24.5513 Evaluate side-chains 162 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain E residue 65 CYS Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 261 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 143 optimal weight: 8.9990 chunk 148 optimal weight: 8.9990 chunk 81 optimal weight: 8.9990 chunk 55 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 chunk 66 optimal weight: 0.0070 chunk 129 optimal weight: 0.9990 chunk 151 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 90 optimal weight: 8.9990 chunk 71 optimal weight: 0.4980 overall best weight: 0.6602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 201 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.059087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.046704 restraints weight = 91830.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.047993 restraints weight = 55967.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.048881 restraints weight = 39933.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.049491 restraints weight = 31437.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.049915 restraints weight = 26554.638| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.4353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14985 Z= 0.115 Angle : 0.695 12.929 20310 Z= 0.325 Chirality : 0.043 0.188 2285 Planarity : 0.003 0.027 2535 Dihedral : 3.793 16.133 1950 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.49 % Allowed : 18.94 % Favored : 79.57 % 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: 1765 helix: 2.37 (0.18), residues: 695 sheet: 1.21 (0.26), residues: 415 loop : -1.93 (0.19), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 333 TYR 0.021 0.001 TYR D 325 PHE 0.036 0.001 PHE C 422 TRP 0.040 0.001 TRP A 263 HIS 0.001 0.000 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (14975) covalent geometry : angle 0.69540 / 0.32 (20285) SS BOND : bond 0.00279 / 0.17 ( 5) SS BOND : angle 0.27964 / 0.15 ( 10) hydrogen bonds : bond 0.04109 / 2.72 ( 755) hydrogen bonds : angle 3.79543 / 2.68 ( 2640) link_NAG-ASN : bond 0.00152 / 0.09 ( 5) link_NAG-ASN : angle 0.65221 / 0.47 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 154 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 MET cc_start: 0.8583 (ptm) cc_final: 0.8302 (ttp) REVERT: A 113 MET cc_start: 0.8931 (mmm) cc_final: 0.8469 (mmt) REVERT: A 187 MET cc_start: 0.9057 (mmm) cc_final: 0.8839 (mmm) REVERT: A 266 PHE cc_start: 0.8896 (m-80) cc_final: 0.8450 (m-80) REVERT: A 290 GLN cc_start: 0.9584 (tt0) cc_final: 0.9176 (tm-30) REVERT: A 311 MET cc_start: 0.9534 (mmm) cc_final: 0.9290 (mmm) REVERT: A 314 CYS cc_start: 0.9521 (m) cc_final: 0.9246 (p) REVERT: B 113 MET cc_start: 0.8785 (mmm) cc_final: 0.8488 (mmt) REVERT: B 263 TRP cc_start: 0.8059 (m-10) cc_final: 0.7470 (m-10) REVERT: B 266 PHE cc_start: 0.8843 (m-80) cc_final: 0.8282 (m-80) REVERT: B 267 TRP cc_start: 0.6892 (m100) cc_final: 0.6658 (m100) REVERT: B 319 PHE cc_start: 0.9183 (t80) cc_final: 0.8977 (t80) REVERT: B 322 LEU cc_start: 0.9595 (OUTLIER) cc_final: 0.9319 (mm) REVERT: C 42 MET cc_start: 0.8818 (ttp) cc_final: 0.8587 (ttt) REVERT: C 113 MET cc_start: 0.8836 (mmm) cc_final: 0.8513 (mmt) REVERT: C 201 GLN cc_start: 0.7081 (OUTLIER) cc_final: 0.6712 (mp10) REVERT: C 250 GLN cc_start: 0.9395 (tp40) cc_final: 0.9132 (tp40) REVERT: C 266 PHE cc_start: 0.8739 (m-80) cc_final: 0.8254 (m-80) REVERT: D 102 TYR cc_start: 0.6944 (OUTLIER) cc_final: 0.6665 (t80) REVERT: D 113 MET cc_start: 0.8777 (mmm) cc_final: 0.8492 (mmt) REVERT: D 187 MET cc_start: 0.9111 (tpp) cc_final: 0.8891 (mmm) REVERT: D 263 TRP cc_start: 0.7900 (m-10) cc_final: 0.7177 (m-10) REVERT: D 266 PHE cc_start: 0.8945 (m-80) cc_final: 0.8390 (m-80) REVERT: D 267 TRP cc_start: 0.6685 (m100) cc_final: 0.6153 (m100) REVERT: D 314 CYS cc_start: 0.9688 (m) cc_final: 0.9451 (m) REVERT: E 187 MET cc_start: 0.8918 (tpp) cc_final: 0.8675 (mmm) REVERT: E 263 TRP cc_start: 0.7940 (m-10) cc_final: 0.7260 (m-10) REVERT: E 266 PHE cc_start: 0.9020 (m-80) cc_final: 0.8468 (m-80) REVERT: E 267 TRP cc_start: 0.6566 (m100) cc_final: 0.6207 (m100) outliers start: 24 outliers final: 14 residues processed: 173 average time/residue: 0.0927 time to fit residues: 26.4276 Evaluate side-chains 156 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain C residue 201 GLN Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain E residue 65 CYS Chi-restraints excluded: chain E residue 86 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 65 optimal weight: 9.9990 chunk 86 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 chunk 21 optimal weight: 8.9990 chunk 42 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 172 optimal weight: 2.9990 chunk 10 optimal weight: 0.2980 chunk 171 optimal weight: 0.0370 chunk 72 optimal weight: 0.6980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 250 GLN C 201 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.059520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.047278 restraints weight = 89610.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.048522 restraints weight = 54753.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.049403 restraints weight = 39132.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.050001 restraints weight = 30905.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.050424 restraints weight = 26133.000| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.4509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14985 Z= 0.117 Angle : 0.724 13.422 20310 Z= 0.332 Chirality : 0.044 0.204 2285 Planarity : 0.003 0.030 2535 Dihedral : 3.769 15.593 1950 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.24 % Allowed : 20.50 % Favored : 78.26 % 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: 0.88 (0.19), residues: 1765 helix: 2.36 (0.18), residues: 695 sheet: 1.32 (0.26), residues: 395 loop : -1.92 (0.19), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 400 TYR 0.026 0.001 TYR B 325 PHE 0.026 0.001 PHE B 422 TRP 0.055 0.001 TRP A 263 HIS 0.001 0.000 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (14975) covalent geometry : angle 0.72398 / 0.33 (20285) SS BOND : bond 0.00213 / 0.14 ( 5) SS BOND : angle 0.32374 / 0.18 ( 10) hydrogen bonds : bond 0.03999 / 2.66 ( 755) hydrogen bonds : angle 3.78678 / 2.67 ( 2640) link_NAG-ASN : bond 0.00160 / 0.09 ( 5) link_NAG-ASN : angle 0.65456 / 0.47 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 MET cc_start: 0.8517 (ptm) cc_final: 0.8271 (ttp) REVERT: A 113 MET cc_start: 0.8909 (mmm) cc_final: 0.8457 (mmt) REVERT: A 266 PHE cc_start: 0.8894 (m-80) cc_final: 0.8445 (m-80) REVERT: A 290 GLN cc_start: 0.9596 (tt0) cc_final: 0.9276 (tm-30) REVERT: B 113 MET cc_start: 0.8775 (mmm) cc_final: 0.8543 (mmt) REVERT: B 187 MET cc_start: 0.8861 (mmm) cc_final: 0.8605 (mmm) REVERT: B 263 TRP cc_start: 0.8087 (m-10) cc_final: 0.7457 (m-10) REVERT: B 266 PHE cc_start: 0.8819 (m-80) cc_final: 0.8253 (m-80) REVERT: B 322 LEU cc_start: 0.9586 (OUTLIER) cc_final: 0.9333 (mm) REVERT: C 201 GLN cc_start: 0.6908 (OUTLIER) cc_final: 0.6185 (mp10) REVERT: C 250 GLN cc_start: 0.9407 (tp40) cc_final: 0.9140 (tp40) REVERT: C 263 TRP cc_start: 0.7755 (m-10) cc_final: 0.7349 (m100) REVERT: C 266 PHE cc_start: 0.8687 (m-80) cc_final: 0.8096 (m-80) REVERT: D 102 TYR cc_start: 0.6869 (OUTLIER) cc_final: 0.6630 (t80) REVERT: D 113 MET cc_start: 0.8724 (mmm) cc_final: 0.8446 (mmt) REVERT: D 187 MET cc_start: 0.9095 (tpp) cc_final: 0.8890 (mmm) REVERT: D 263 TRP cc_start: 0.7941 (m-10) cc_final: 0.7143 (m-10) REVERT: D 266 PHE cc_start: 0.8969 (m-80) cc_final: 0.8285 (m-80) REVERT: D 267 TRP cc_start: 0.6593 (m100) cc_final: 0.6198 (m100) REVERT: D 314 CYS cc_start: 0.9679 (m) cc_final: 0.9444 (m) REVERT: E 42 MET cc_start: 0.8896 (ptm) cc_final: 0.8213 (ttt) REVERT: E 187 MET cc_start: 0.8935 (tpp) cc_final: 0.8660 (mmm) REVERT: E 263 TRP cc_start: 0.7892 (m-10) cc_final: 0.7174 (m-10) REVERT: E 266 PHE cc_start: 0.9033 (m-80) cc_final: 0.8485 (m-80) REVERT: E 267 TRP cc_start: 0.6494 (m100) cc_final: 0.6086 (m100) outliers start: 20 outliers final: 9 residues processed: 164 average time/residue: 0.0904 time to fit residues: 24.2848 Evaluate side-chains 149 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 137 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain C residue 201 GLN Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain E residue 65 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 113 optimal weight: 0.2980 chunk 40 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 21 optimal weight: 8.9990 chunk 12 optimal weight: 0.9990 chunk 77 optimal weight: 10.0000 chunk 118 optimal weight: 0.0570 chunk 0 optimal weight: 9.9990 chunk 63 optimal weight: 0.3980 chunk 83 optimal weight: 0.6980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 201 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.059711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.047391 restraints weight = 90450.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.048673 restraints weight = 55278.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.049557 restraints weight = 39502.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.050172 restraints weight = 31110.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.050597 restraints weight = 26192.853| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.4648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14985 Z= 0.118 Angle : 0.745 13.442 20310 Z= 0.343 Chirality : 0.045 0.261 2285 Planarity : 0.003 0.031 2535 Dihedral : 3.759 16.482 1950 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.30 % Allowed : 21.30 % Favored : 77.39 % 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: 0.79 (0.19), residues: 1765 helix: 2.15 (0.18), residues: 700 sheet: 1.35 (0.26), residues: 390 loop : -1.88 (0.19), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 333 TYR 0.022 0.001 TYR B 325 PHE 0.024 0.001 PHE C 422 TRP 0.076 0.002 TRP C 267 HIS 0.001 0.000 HIS C 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (14975) covalent geometry : angle 0.74531 / 0.34 (20285) SS BOND : bond 0.00206 / 0.13 ( 5) SS BOND : angle 0.20879 / 0.11 ( 10) hydrogen bonds : bond 0.03956 / 2.62 ( 755) hydrogen bonds : angle 3.75446 / 2.65 ( 2640) link_NAG-ASN : bond 0.00173 / 0.10 ( 5) link_NAG-ASN : angle 0.64451 / 0.47 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 MET cc_start: 0.8580 (ptm) cc_final: 0.8266 (ttp) REVERT: A 113 MET cc_start: 0.8827 (mmm) cc_final: 0.8567 (mmt) REVERT: A 187 MET cc_start: 0.8988 (mmm) cc_final: 0.8719 (mmm) REVERT: A 266 PHE cc_start: 0.8913 (m-80) cc_final: 0.8465 (m-80) REVERT: A 290 GLN cc_start: 0.9600 (tt0) cc_final: 0.9287 (tm-30) REVERT: A 314 CYS cc_start: 0.9164 (p) cc_final: 0.8958 (p) REVERT: B 32 MET cc_start: 0.8610 (tmm) cc_final: 0.8301 (tmm) REVERT: B 113 MET cc_start: 0.8740 (mmm) cc_final: 0.8519 (mmt) REVERT: B 187 MET cc_start: 0.8927 (mmm) cc_final: 0.8663 (mmm) REVERT: B 263 TRP cc_start: 0.8089 (m-10) cc_final: 0.7688 (m-10) REVERT: B 266 PHE cc_start: 0.8773 (m-80) cc_final: 0.8268 (m-80) REVERT: B 322 LEU cc_start: 0.9571 (OUTLIER) cc_final: 0.9335 (mm) REVERT: C 80 MET cc_start: 0.8134 (tpt) cc_final: 0.7724 (mmm) REVERT: C 187 MET cc_start: 0.8649 (mmm) cc_final: 0.8313 (mmm) REVERT: C 201 GLN cc_start: 0.6967 (OUTLIER) cc_final: 0.6276 (mp10) REVERT: C 263 TRP cc_start: 0.7697 (m-10) cc_final: 0.7421 (m100) REVERT: C 266 PHE cc_start: 0.8656 (m-80) cc_final: 0.8207 (m-80) REVERT: D 102 TYR cc_start: 0.6932 (OUTLIER) cc_final: 0.6693 (t80) REVERT: D 187 MET cc_start: 0.9065 (tpp) cc_final: 0.8862 (mmm) REVERT: D 263 TRP cc_start: 0.7880 (m-10) cc_final: 0.7116 (m-10) REVERT: D 266 PHE cc_start: 0.8905 (m-80) cc_final: 0.8320 (m-80) REVERT: D 267 TRP cc_start: 0.6515 (m100) cc_final: 0.6079 (m100) REVERT: D 314 CYS cc_start: 0.9666 (m) cc_final: 0.9422 (m) REVERT: E 42 MET cc_start: 0.8861 (ptm) cc_final: 0.8171 (ttt) REVERT: E 187 MET cc_start: 0.8908 (tpp) cc_final: 0.8651 (mmm) REVERT: E 263 TRP cc_start: 0.7912 (m-10) cc_final: 0.7201 (m-10) REVERT: E 266 PHE cc_start: 0.9028 (m-80) cc_final: 0.8494 (m-80) REVERT: E 267 TRP cc_start: 0.6473 (m100) cc_final: 0.6156 (m100) outliers start: 21 outliers final: 10 residues processed: 167 average time/residue: 0.0908 time to fit residues: 24.9260 Evaluate side-chains 151 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 138 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain C residue 201 GLN Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain E residue 65 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 18 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 122 optimal weight: 7.9990 chunk 170 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 8 optimal weight: 0.3980 chunk 67 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 126 optimal weight: 0.6980 chunk 118 optimal weight: 0.2980 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.058722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.046479 restraints weight = 92840.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.047758 restraints weight = 56252.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.048646 restraints weight = 40083.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.049243 restraints weight = 31505.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.049638 restraints weight = 26585.694| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.4770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14985 Z= 0.138 Angle : 0.760 13.486 20310 Z= 0.353 Chirality : 0.045 0.223 2285 Planarity : 0.003 0.041 2535 Dihedral : 3.847 18.595 1950 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.12 % Allowed : 21.93 % Favored : 76.96 % 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: 0.77 (0.19), residues: 1765 helix: 2.11 (0.19), residues: 705 sheet: 1.28 (0.26), residues: 390 loop : -1.84 (0.19), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 276 TYR 0.020 0.001 TYR B 325 PHE 0.037 0.001 PHE B 422 TRP 0.072 0.002 TRP A 263 HIS 0.002 0.001 HIS C 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (14975) covalent geometry : angle 0.76048 / 0.35 (20285) SS BOND : bond 0.00177 / 0.11 ( 5) SS BOND : angle 0.32524 / 0.14 ( 10) hydrogen bonds : bond 0.04008 / 2.65 ( 755) hydrogen bonds : angle 3.85739 / 2.72 ( 2640) link_NAG-ASN : bond 0.00024 / 0.01 ( 5) link_NAG-ASN : angle 0.92730 / 0.63 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 142 time to evaluate : 0.540 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 42 MET cc_start: 0.8598 (ptm) cc_final: 0.8215 (ttp) REVERT: A 187 MET cc_start: 0.9016 (mmm) cc_final: 0.8760 (mmm) REVERT: A 266 PHE cc_start: 0.8817 (m-80) cc_final: 0.8404 (m-80) REVERT: A 290 GLN cc_start: 0.9562 (tt0) cc_final: 0.9273 (tm-30) REVERT: B 263 TRP cc_start: 0.8111 (m-10) cc_final: 0.7671 (m-10) REVERT: B 266 PHE cc_start: 0.8796 (m-80) cc_final: 0.8293 (m-80) REVERT: B 322 LEU cc_start: 0.9602 (OUTLIER) cc_final: 0.9374 (mm) REVERT: C 266 PHE cc_start: 0.8624 (m-80) cc_final: 0.8162 (m-80) REVERT: D 102 TYR cc_start: 0.7131 (OUTLIER) cc_final: 0.6778 (t80) REVERT: D 263 TRP cc_start: 0.7853 (m-10) cc_final: 0.7051 (m-10) REVERT: D 266 PHE cc_start: 0.8939 (m-80) cc_final: 0.8386 (m-80) REVERT: D 267 TRP cc_start: 0.6607 (m100) cc_final: 0.6188 (m100) REVERT: D 314 CYS cc_start: 0.9666 (m) cc_final: 0.9442 (m) REVERT: E 42 MET cc_start: 0.8919 (ptm) cc_final: 0.8216 (ttt) REVERT: E 263 TRP cc_start: 0.7862 (m-10) cc_final: 0.7110 (m-10) REVERT: E 266 PHE cc_start: 0.9024 (m-80) cc_final: 0.8510 (m-80) REVERT: E 267 TRP cc_start: 0.6519 (m100) cc_final: 0.6181 (m100) outliers start: 18 outliers final: 14 residues processed: 156 average time/residue: 0.0934 time to fit residues: 23.8386 Evaluate side-chains 153 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 251 MET Chi-restraints excluded: chain E residue 261 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 76 optimal weight: 0.1980 chunk 125 optimal weight: 4.9990 chunk 142 optimal weight: 0.0050 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 92 optimal weight: 0.2980 chunk 57 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 171 optimal weight: 8.9990 chunk 74 optimal weight: 7.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.059689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.047360 restraints weight = 90815.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.048658 restraints weight = 55674.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.049538 restraints weight = 39827.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.050165 restraints weight = 31445.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.050560 restraints weight = 26421.780| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.4903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14985 Z= 0.123 Angle : 0.786 13.986 20310 Z= 0.359 Chirality : 0.045 0.216 2285 Planarity : 0.003 0.057 2535 Dihedral : 3.795 17.707 1950 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.06 % Allowed : 22.17 % Favored : 76.77 % 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: 0.74 (0.19), residues: 1765 helix: 2.06 (0.18), residues: 700 sheet: 1.29 (0.26), residues: 390 loop : -1.82 (0.19), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 53 TYR 0.019 0.001 TYR B 325 PHE 0.027 0.001 PHE C 422 TRP 0.048 0.001 TRP C 267 HIS 0.002 0.000 HIS E 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (14975) covalent geometry : angle 0.78663 / 0.36 (20285) SS BOND : bond 0.00180 / 0.12 ( 5) SS BOND : angle 0.23010 / 0.10 ( 10) hydrogen bonds : bond 0.03897 / 2.58 ( 755) hydrogen bonds : angle 3.77469 / 2.66 ( 2640) link_NAG-ASN : bond 0.00178 / 0.10 ( 5) link_NAG-ASN : angle 0.63400 / 0.46 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 0.571 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 42 MET cc_start: 0.8672 (ptm) cc_final: 0.8201 (ttp) REVERT: A 187 MET cc_start: 0.9083 (mmm) cc_final: 0.8816 (mmm) REVERT: A 266 PHE cc_start: 0.8942 (m-80) cc_final: 0.8481 (m-80) REVERT: A 290 GLN cc_start: 0.9603 (tt0) cc_final: 0.9312 (tm-30) REVERT: B 113 MET cc_start: 0.8382 (mmt) cc_final: 0.7957 (mpp) REVERT: B 187 MET cc_start: 0.8859 (mmm) cc_final: 0.8654 (mmm) REVERT: B 210 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8402 (tp40) REVERT: B 263 TRP cc_start: 0.8069 (m-10) cc_final: 0.7646 (m-10) REVERT: B 266 PHE cc_start: 0.8757 (m-80) cc_final: 0.8254 (m-80) REVERT: B 322 LEU cc_start: 0.9583 (OUTLIER) cc_final: 0.9353 (mm) REVERT: C 187 MET cc_start: 0.8597 (mmm) cc_final: 0.8078 (mmm) REVERT: C 263 TRP cc_start: 0.7847 (m-10) cc_final: 0.7624 (m100) REVERT: C 266 PHE cc_start: 0.8650 (m-80) cc_final: 0.8198 (m-80) REVERT: D 102 TYR cc_start: 0.7061 (OUTLIER) cc_final: 0.6723 (t80) REVERT: D 113 MET cc_start: 0.8388 (mmt) cc_final: 0.8052 (mpp) REVERT: D 263 TRP cc_start: 0.7774 (m-10) cc_final: 0.7028 (m-10) REVERT: D 266 PHE cc_start: 0.8977 (m-80) cc_final: 0.8438 (m-80) REVERT: D 267 TRP cc_start: 0.6519 (m100) cc_final: 0.6035 (m100) REVERT: D 314 CYS cc_start: 0.9662 (m) cc_final: 0.9431 (m) REVERT: E 42 MET cc_start: 0.8898 (ptm) cc_final: 0.8180 (ttt) REVERT: E 187 MET cc_start: 0.8895 (mmm) cc_final: 0.8662 (mmm) REVERT: E 263 TRP cc_start: 0.7875 (m-10) cc_final: 0.7432 (m-10) REVERT: E 266 PHE cc_start: 0.9031 (m-80) cc_final: 0.8552 (m-80) outliers start: 17 outliers final: 9 residues processed: 155 average time/residue: 0.0872 time to fit residues: 22.0352 Evaluate side-chains 148 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 136 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 102 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 173 optimal weight: 0.0970 chunk 49 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 153 optimal weight: 0.6980 chunk 106 optimal weight: 0.4980 chunk 9 optimal weight: 4.9990 chunk 98 optimal weight: 0.8980 chunk 21 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.059759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.047486 restraints weight = 91260.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.048784 restraints weight = 55782.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.049675 restraints weight = 39880.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.050247 restraints weight = 31444.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.050711 restraints weight = 26646.778| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.4998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14985 Z= 0.121 Angle : 0.792 20.335 20310 Z= 0.360 Chirality : 0.045 0.223 2285 Planarity : 0.003 0.042 2535 Dihedral : 3.772 17.521 1950 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.93 % Allowed : 22.48 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.19), residues: 1765 helix: 2.00 (0.19), residues: 715 sheet: 1.25 (0.26), residues: 390 loop : -1.91 (0.19), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 333 TYR 0.019 0.001 TYR B 325 PHE 0.042 0.001 PHE B 422 TRP 0.042 0.001 TRP C 267 HIS 0.002 0.000 HIS D 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (14975) covalent geometry : angle 0.79205 / 0.36 (20285) SS BOND : bond 0.00167 / 0.11 ( 5) SS BOND : angle 0.26738 / 0.12 ( 10) hydrogen bonds : bond 0.03805 / 2.51 ( 755) hydrogen bonds : angle 3.77096 / 2.66 ( 2640) link_NAG-ASN : bond 0.00123 / 0.07 ( 5) link_NAG-ASN : angle 0.72975 / 0.53 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2198.91 seconds wall clock time: 38 minutes 57.01 seconds (2337.01 seconds total)