Starting phenix.real_space_refine on Wed Mar 4 16:23:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m6s_23706/03_2026/7m6s_23706.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m6s_23706/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7m6s_23706/03_2026/7m6s_23706.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m6s_23706/03_2026/7m6s_23706.map" model { file = "/net/cci-nas-00/data/ceres_data/7m6s_23706/03_2026/7m6s_23706.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m6s_23706/03_2026/7m6s_23706.cif" } 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-5986/lib/python3.9/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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.95, per 1000 atoms: 0.20 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: 1.01 Conformation dependent library (CDL) restraints added in 541.4 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: 0.41 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: 2.80 Time building geometry restraints manager: 1.42 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: 8185 14.22 - 28.44: 584 28.44 - 42.67: 181 42.67 - 56.89: 65 56.89 - 71.11: 20 Dihedral angle restraints: 9035 sinusoidal: 3755 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 9032 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: 0.02 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: 2.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 13.400 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 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 : 12.299 71.110 5590 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 covalent geometry : bond 0.00827 (14975) covalent geometry : angle 1.48688 (20285) SS BOND : bond 0.02548 ( 5) SS BOND : angle 3.86164 ( 10) hydrogen bonds : bond 0.11318 ( 755) hydrogen bonds : angle 5.15944 ( 2640) link_NAG-ASN : bond 0.00620 ( 5) link_NAG-ASN : angle 3.60619 ( 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 : 0.413 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: 0.0871 time to fit residues: 41.2848 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 : 0.606 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 GLN ** C 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 329 ASN ** E 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 329 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.061227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.049114 restraints weight = 89334.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.050445 restraints weight = 54086.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.051368 restraints weight = 38356.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.051999 restraints weight = 30007.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.052407 restraints weight = 25180.045| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2484 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= 0.176 Angle : 0.760 11.977 20310 Z= 0.379 Chirality : 0.046 0.162 2285 Planarity : 0.004 0.035 2535 Dihedral : 4.399 18.297 2055 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.61 % Allowed : 15.40 % Favored : 82.98 % 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: 1.52 (0.19), residues: 1765 helix: 2.63 (0.19), residues: 680 sheet: 1.73 (0.25), residues: 420 loop : -1.33 (0.21), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 333 TYR 0.026 0.002 TYR A 325 PHE 0.023 0.002 PHE C 422 TRP 0.045 0.002 TRP C 267 HIS 0.002 0.001 HIS A 133 Details of bonding type rmsd covalent geometry : bond 0.00380 (14975) covalent geometry : angle 0.75938 (20285) SS BOND : bond 0.00392 ( 5) SS BOND : angle 0.63587 ( 10) hydrogen bonds : bond 0.06041 ( 755) hydrogen bonds : angle 4.47019 ( 2640) link_NAG-ASN : bond 0.00059 ( 5) link_NAG-ASN : angle 1.52131 ( 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 197 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 171 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 MET cc_start: 0.8695 (ptm) cc_final: 0.8397 (ttp) REVERT: A 90 GLN cc_start: 0.7871 (mp10) cc_final: 0.7544 (mp10) REVERT: A 250 GLN cc_start: 0.9219 (tp40) cc_final: 0.8873 (tp40) REVERT: A 266 PHE cc_start: 0.8522 (m-80) cc_final: 0.8068 (m-80) REVERT: A 287 MET cc_start: 0.9226 (ttm) cc_final: 0.8971 (ttm) REVERT: A 290 GLN cc_start: 0.9485 (tt0) cc_final: 0.9118 (tm-30) REVERT: A 314 CYS cc_start: 0.9547 (m) cc_final: 0.9161 (p) REVERT: B 187 MET cc_start: 0.9050 (tpp) cc_final: 0.8811 (mmm) REVERT: B 266 PHE cc_start: 0.8556 (m-80) cc_final: 0.8170 (m-80) REVERT: C 113 MET cc_start: 0.8659 (mmm) cc_final: 0.8356 (mmt) REVERT: C 266 PHE cc_start: 0.8402 (m-80) cc_final: 0.7930 (m-80) REVERT: D 109 LEU cc_start: 0.8722 (mt) cc_final: 0.8422 (mp) REVERT: D 113 MET cc_start: 0.8523 (mmm) cc_final: 0.8151 (mmt) REVERT: D 187 MET cc_start: 0.9094 (tpp) cc_final: 0.8749 (mmm) REVERT: D 266 PHE cc_start: 0.8694 (m-80) cc_final: 0.8213 (m-80) REVERT: D 267 TRP cc_start: 0.6885 (m100) cc_final: 0.6383 (m100) REVERT: D 314 CYS cc_start: 0.9690 (m) cc_final: 0.9473 (m) REVERT: E 266 PHE cc_start: 0.8581 (m-80) cc_final: 0.8231 (m-80) outliers start: 26 outliers final: 13 residues processed: 191 average time/residue: 0.0904 time to fit residues: 28.1484 Evaluate side-chains 168 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 155 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 0.1980 chunk 70 optimal weight: 6.9990 chunk 121 optimal weight: 4.9990 chunk 104 optimal weight: 7.9990 chunk 164 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 61 optimal weight: 7.9990 chunk 40 optimal weight: 8.9990 chunk 36 optimal weight: 0.9980 chunk 165 optimal weight: 2.9990 chunk 168 optimal weight: 0.9980 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 243 GLN ** B 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 GLN B 250 GLN B 329 ASN C 243 GLN D 243 GLN E 243 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.059521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.047393 restraints weight = 91819.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.048687 restraints weight = 55597.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.049556 restraints weight = 39565.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.050179 restraints weight = 31229.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.050606 restraints weight = 26326.020| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14985 Z= 0.160 Angle : 0.715 11.301 20310 Z= 0.346 Chirality : 0.045 0.195 2285 Planarity : 0.004 0.030 2535 Dihedral : 4.109 16.107 2055 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.17 % Allowed : 15.96 % Favored : 81.86 % 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: 1.37 (0.19), residues: 1765 helix: 2.52 (0.18), residues: 680 sheet: 1.72 (0.27), residues: 390 loop : -1.34 (0.20), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 333 TYR 0.020 0.002 TYR B 325 PHE 0.024 0.002 PHE C 422 TRP 0.027 0.002 TRP C 267 HIS 0.003 0.001 HIS A 133 Details of bonding type rmsd covalent geometry : bond 0.00350 (14975) covalent geometry : angle 0.71404 (20285) SS BOND : bond 0.00325 ( 5) SS BOND : angle 0.42493 ( 10) hydrogen bonds : bond 0.05026 ( 755) hydrogen bonds : angle 4.10511 ( 2640) link_NAG-ASN : bond 0.00090 ( 5) link_NAG-ASN : angle 1.27459 ( 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 186 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 151 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 MET cc_start: 0.8756 (ptm) cc_final: 0.8508 (ttp) REVERT: A 90 GLN cc_start: 0.8140 (mp10) cc_final: 0.7751 (mp10) REVERT: A 113 MET cc_start: 0.8857 (mmm) cc_final: 0.8657 (mmm) REVERT: A 266 PHE cc_start: 0.8624 (m-80) cc_final: 0.8091 (m-80) REVERT: A 290 GLN cc_start: 0.9555 (tt0) cc_final: 0.9129 (tm-30) REVERT: A 311 MET cc_start: 0.9337 (mmm) cc_final: 0.9131 (ptp) REVERT: B 102 TYR cc_start: 0.6592 (OUTLIER) cc_final: 0.6239 (t80) REVERT: B 113 MET cc_start: 0.8650 (mmm) cc_final: 0.8372 (mmt) REVERT: B 263 TRP cc_start: 0.7953 (m-10) cc_final: 0.7354 (m-10) REVERT: B 266 PHE cc_start: 0.8612 (m-80) cc_final: 0.8147 (m-80) REVERT: B 267 TRP cc_start: 0.6952 (m100) cc_final: 0.6707 (m100) REVERT: C 113 MET cc_start: 0.8755 (mmm) cc_final: 0.8442 (mmt) REVERT: C 263 TRP cc_start: 0.8346 (m-10) cc_final: 0.8105 (m-10) REVERT: D 109 LEU cc_start: 0.8755 (mt) cc_final: 0.8436 (mp) REVERT: D 113 MET cc_start: 0.8700 (mmm) cc_final: 0.8425 (mmt) REVERT: D 187 MET cc_start: 0.9018 (tpp) cc_final: 0.8672 (mmm) REVERT: D 263 TRP cc_start: 0.7968 (m-10) cc_final: 0.7741 (m-10) REVERT: D 266 PHE cc_start: 0.8751 (m-80) cc_final: 0.8215 (m-80) REVERT: D 267 TRP cc_start: 0.6854 (m100) cc_final: 0.6294 (m100) REVERT: D 314 CYS cc_start: 0.9714 (m) cc_final: 0.9506 (m) REVERT: E 102 TYR cc_start: 0.6814 (OUTLIER) cc_final: 0.6266 (t80) REVERT: E 187 MET cc_start: 0.8996 (tpp) cc_final: 0.8685 (mmm) REVERT: E 266 PHE cc_start: 0.8667 (m-80) cc_final: 0.8222 (m-80) REVERT: E 267 TRP cc_start: 0.6180 (m100) cc_final: 0.5813 (m100) outliers start: 35 outliers final: 14 residues processed: 173 average time/residue: 0.0898 time to fit residues: 25.5376 Evaluate side-chains 155 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 137 THR 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 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 204 ASP Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain E residue 102 TYR Chi-restraints excluded: chain E residue 204 ASP 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: 9.9990 chunk 82 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 86 optimal weight: 6.9990 chunk 83 optimal weight: 0.6980 chunk 78 optimal weight: 0.6980 chunk 81 optimal weight: 0.7980 chunk 116 optimal weight: 1.9990 chunk 64 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 95 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 329 ASN B 210 GLN C 329 ASN E 174 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.060226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.048014 restraints weight = 91259.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.049326 restraints weight = 55310.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.050227 restraints weight = 39300.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.050805 restraints weight = 30875.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.051248 restraints weight = 26122.813| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3617 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= 0.123 Angle : 0.697 11.655 20310 Z= 0.329 Chirality : 0.044 0.206 2285 Planarity : 0.003 0.021 2535 Dihedral : 3.873 15.733 2055 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.86 % Allowed : 16.09 % Favored : 82.05 % 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: 1.33 (0.19), residues: 1765 helix: 2.53 (0.19), residues: 680 sheet: 1.64 (0.26), residues: 390 loop : -1.38 (0.20), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 333 TYR 0.027 0.001 TYR E 325 PHE 0.029 0.001 PHE B 422 TRP 0.024 0.001 TRP C 263 HIS 0.002 0.001 HIS C 225 Details of bonding type rmsd covalent geometry : bond 0.00263 (14975) covalent geometry : angle 0.69652 (20285) SS BOND : bond 0.00283 ( 5) SS BOND : angle 0.30246 ( 10) hydrogen bonds : bond 0.04564 ( 755) hydrogen bonds : angle 3.85490 ( 2640) link_NAG-ASN : bond 0.00132 ( 5) link_NAG-ASN : angle 0.85577 ( 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 188 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 158 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 MET cc_start: 0.8693 (ptm) cc_final: 0.8466 (ttp) REVERT: A 113 MET cc_start: 0.8869 (mmm) cc_final: 0.8369 (mmt) REVERT: A 266 PHE cc_start: 0.8612 (m-80) cc_final: 0.8103 (m-80) REVERT: A 287 MET cc_start: 0.9289 (ttm) cc_final: 0.9070 (ttp) REVERT: A 290 GLN cc_start: 0.9551 (tt0) cc_final: 0.9133 (tm-30) REVERT: A 311 MET cc_start: 0.9398 (mmm) cc_final: 0.9176 (mmm) REVERT: A 314 CYS cc_start: 0.9538 (m) cc_final: 0.9319 (p) REVERT: B 102 TYR cc_start: 0.6629 (OUTLIER) cc_final: 0.6350 (t80) REVERT: B 113 MET cc_start: 0.8700 (mmm) cc_final: 0.8426 (mmt) REVERT: B 263 TRP cc_start: 0.7902 (m-10) cc_final: 0.7261 (m-10) REVERT: B 266 PHE cc_start: 0.8657 (m-80) cc_final: 0.8116 (m-80) REVERT: B 267 TRP cc_start: 0.6850 (m100) cc_final: 0.6617 (m100) REVERT: B 322 LEU cc_start: 0.9710 (OUTLIER) cc_final: 0.9430 (mm) REVERT: C 113 MET cc_start: 0.8783 (mmm) cc_final: 0.8508 (mmt) REVERT: D 113 MET cc_start: 0.8682 (mmm) cc_final: 0.8293 (mmt) REVERT: D 187 MET cc_start: 0.9092 (tpp) cc_final: 0.8829 (mmm) REVERT: D 263 TRP cc_start: 0.7946 (m-10) cc_final: 0.7725 (m-10) REVERT: D 266 PHE cc_start: 0.8723 (m-80) cc_final: 0.8212 (m-80) REVERT: D 267 TRP cc_start: 0.6875 (m100) cc_final: 0.6197 (m100) REVERT: D 287 MET cc_start: 0.9199 (ttm) cc_final: 0.8911 (ttm) REVERT: D 314 CYS cc_start: 0.9719 (m) cc_final: 0.9479 (m) REVERT: E 102 TYR cc_start: 0.6584 (OUTLIER) cc_final: 0.6106 (t80) REVERT: E 187 MET cc_start: 0.8951 (tpp) cc_final: 0.8623 (mmm) REVERT: E 266 PHE cc_start: 0.8704 (m-80) cc_final: 0.8203 (m-80) REVERT: E 267 TRP cc_start: 0.6348 (m100) cc_final: 0.5788 (m100) outliers start: 30 outliers final: 17 residues processed: 177 average time/residue: 0.0877 time to fit residues: 25.5497 Evaluate side-chains 168 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain B residue 102 TYR 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 204 ASP 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 204 ASP Chi-restraints excluded: chain E residue 102 TYR Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain E residue 204 ASP 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: 3.9990 chunk 136 optimal weight: 0.0030 chunk 89 optimal weight: 6.9990 chunk 112 optimal weight: 10.0000 chunk 129 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 123 optimal weight: 0.4980 chunk 66 optimal weight: 0.0870 chunk 15 optimal weight: 0.8980 chunk 80 optimal weight: 6.9990 overall best weight: 0.8970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.060056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.047855 restraints weight = 91696.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.049177 restraints weight = 55394.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.050064 restraints weight = 39279.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.050686 restraints weight = 30860.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.051126 restraints weight = 25982.954| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14985 Z= 0.119 Angle : 0.690 12.246 20310 Z= 0.324 Chirality : 0.044 0.198 2285 Planarity : 0.003 0.028 2535 Dihedral : 3.786 17.138 2055 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.11 % Allowed : 16.96 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.19), residues: 1765 helix: 2.63 (0.19), residues: 675 sheet: 1.57 (0.26), residues: 390 loop : -1.42 (0.20), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 333 TYR 0.025 0.001 TYR D 325 PHE 0.035 0.001 PHE C 422 TRP 0.021 0.001 TRP A 263 HIS 0.002 0.000 HIS C 133 Details of bonding type rmsd covalent geometry : bond 0.00257 (14975) covalent geometry : angle 0.69026 (20285) SS BOND : bond 0.00233 ( 5) SS BOND : angle 0.36846 ( 10) hydrogen bonds : bond 0.04308 ( 755) hydrogen bonds : angle 3.78679 ( 2640) link_NAG-ASN : bond 0.00103 ( 5) link_NAG-ASN : angle 0.87081 ( 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 186 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 152 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 MET cc_start: 0.8660 (ptm) cc_final: 0.8409 (ttm) REVERT: A 113 MET cc_start: 0.8891 (mmm) cc_final: 0.8368 (mmt) REVERT: A 266 PHE cc_start: 0.8657 (m-80) cc_final: 0.8155 (m-80) REVERT: A 287 MET cc_start: 0.9301 (ttm) cc_final: 0.9086 (ttp) REVERT: A 290 GLN cc_start: 0.9533 (tt0) cc_final: 0.9135 (tm-30) REVERT: A 311 MET cc_start: 0.9486 (mmm) cc_final: 0.9206 (mmm) REVERT: A 314 CYS cc_start: 0.9557 (m) cc_final: 0.9344 (p) REVERT: B 102 TYR cc_start: 0.6507 (OUTLIER) cc_final: 0.6189 (t80) REVERT: B 113 MET cc_start: 0.8762 (mmm) cc_final: 0.8447 (mmt) REVERT: B 263 TRP cc_start: 0.7908 (m-10) cc_final: 0.7252 (m-10) REVERT: B 266 PHE cc_start: 0.8740 (m-80) cc_final: 0.8211 (m-80) REVERT: B 267 TRP cc_start: 0.6850 (m100) cc_final: 0.6635 (m100) REVERT: C 42 MET cc_start: 0.8715 (ttp) cc_final: 0.8467 (ttt) REVERT: C 113 MET cc_start: 0.8773 (mmm) cc_final: 0.8388 (mmt) REVERT: C 263 TRP cc_start: 0.7988 (m-10) cc_final: 0.7076 (m100) REVERT: C 422 PHE cc_start: 0.9597 (t80) cc_final: 0.9357 (t80) REVERT: D 113 MET cc_start: 0.8640 (mmm) cc_final: 0.8412 (mmt) REVERT: D 187 MET cc_start: 0.9050 (tpp) cc_final: 0.8785 (mmm) REVERT: D 263 TRP cc_start: 0.7899 (m-10) cc_final: 0.7662 (m-10) REVERT: D 266 PHE cc_start: 0.8841 (m-80) cc_final: 0.8271 (m-80) REVERT: D 267 TRP cc_start: 0.6844 (m100) cc_final: 0.6133 (m100) REVERT: D 287 MET cc_start: 0.9195 (ttm) cc_final: 0.8896 (ttm) REVERT: D 314 CYS cc_start: 0.9697 (m) cc_final: 0.9476 (m) REVERT: E 102 TYR cc_start: 0.6599 (OUTLIER) cc_final: 0.6157 (t80) REVERT: E 113 MET cc_start: 0.8527 (mmt) cc_final: 0.8019 (mpp) REVERT: E 187 MET cc_start: 0.8941 (tpp) cc_final: 0.8672 (mmm) REVERT: E 263 TRP cc_start: 0.8129 (m-10) cc_final: 0.7815 (m-10) REVERT: E 266 PHE cc_start: 0.8738 (m-80) cc_final: 0.8231 (m-80) REVERT: E 267 TRP cc_start: 0.6258 (m100) cc_final: 0.5813 (m100) outliers start: 34 outliers final: 19 residues processed: 176 average time/residue: 0.0902 time to fit residues: 25.8530 Evaluate side-chains 163 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 164 MET 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 314 CYS 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 261 LEU Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 102 TYR Chi-restraints excluded: chain E residue 204 ASP 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: 0.9990 chunk 148 optimal weight: 8.9990 chunk 81 optimal weight: 0.8980 chunk 55 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 66 optimal weight: 0.2980 chunk 129 optimal weight: 1.9990 chunk 151 optimal weight: 6.9990 chunk 100 optimal weight: 6.9990 chunk 90 optimal weight: 6.9990 chunk 71 optimal weight: 9.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.059301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.047051 restraints weight = 91608.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.048337 restraints weight = 55626.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.049228 restraints weight = 39713.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.049838 restraints weight = 31276.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.050275 restraints weight = 26354.828| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.4166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14985 Z= 0.134 Angle : 0.710 12.697 20310 Z= 0.331 Chirality : 0.044 0.207 2285 Planarity : 0.003 0.026 2535 Dihedral : 3.802 17.317 2055 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.17 % Allowed : 18.57 % Favored : 79.25 % 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: 1.10 (0.19), residues: 1765 helix: 2.48 (0.18), residues: 695 sheet: 1.50 (0.26), residues: 410 loop : -1.87 (0.19), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 400 TYR 0.016 0.001 TYR B 325 PHE 0.032 0.001 PHE B 422 TRP 0.038 0.001 TRP A 263 HIS 0.002 0.001 HIS C 133 Details of bonding type rmsd covalent geometry : bond 0.00296 (14975) covalent geometry : angle 0.70990 (20285) SS BOND : bond 0.00218 ( 5) SS BOND : angle 0.24722 ( 10) hydrogen bonds : bond 0.04171 ( 755) hydrogen bonds : angle 3.81340 ( 2640) link_NAG-ASN : bond 0.00015 ( 5) link_NAG-ASN : angle 1.03322 ( 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: 35 poor density : 143 time to evaluate : 0.563 Fit side-chains revert: symmetry clash REVERT: A 42 MET cc_start: 0.8782 (ptm) cc_final: 0.8260 (ttm) REVERT: A 113 MET cc_start: 0.8860 (mmm) cc_final: 0.8362 (mmt) REVERT: A 266 PHE cc_start: 0.8775 (m-80) cc_final: 0.8307 (m-80) REVERT: A 287 MET cc_start: 0.9326 (ttm) cc_final: 0.9087 (ttp) REVERT: A 290 GLN cc_start: 0.9525 (tt0) cc_final: 0.9133 (tm-30) REVERT: A 311 MET cc_start: 0.9502 (mmm) cc_final: 0.9240 (mmm) REVERT: A 314 CYS cc_start: 0.9573 (m) cc_final: 0.9309 (p) REVERT: B 102 TYR cc_start: 0.6672 (OUTLIER) cc_final: 0.6267 (t80) REVERT: B 113 MET cc_start: 0.8731 (mmm) cc_final: 0.8488 (mmt) REVERT: B 263 TRP cc_start: 0.7941 (m-10) cc_final: 0.7281 (m-10) REVERT: B 266 PHE cc_start: 0.8728 (m-80) cc_final: 0.8193 (m-80) REVERT: C 263 TRP cc_start: 0.7962 (m-10) cc_final: 0.7659 (m100) REVERT: C 422 PHE cc_start: 0.9601 (t80) cc_final: 0.9377 (t80) REVERT: D 42 MET cc_start: 0.8897 (ttp) cc_final: 0.8636 (mtp) REVERT: D 113 MET cc_start: 0.8684 (mmm) cc_final: 0.8436 (mmt) REVERT: D 187 MET cc_start: 0.9055 (tpp) cc_final: 0.8778 (mmm) REVERT: D 266 PHE cc_start: 0.8984 (m-80) cc_final: 0.8437 (m-80) REVERT: D 267 TRP cc_start: 0.6873 (m100) cc_final: 0.6279 (m100) REVERT: D 287 MET cc_start: 0.9192 (ttm) cc_final: 0.8936 (ttm) REVERT: D 314 CYS cc_start: 0.9686 (m) cc_final: 0.9471 (m) REVERT: E 42 MET cc_start: 0.9148 (ptm) cc_final: 0.8836 (ppp) REVERT: E 102 TYR cc_start: 0.6697 (OUTLIER) cc_final: 0.6225 (t80) REVERT: E 113 MET cc_start: 0.8549 (mmt) cc_final: 0.8129 (mpp) REVERT: E 187 MET cc_start: 0.8894 (tpp) cc_final: 0.8632 (mmm) REVERT: E 263 TRP cc_start: 0.8109 (m-10) cc_final: 0.7418 (m-10) REVERT: E 266 PHE cc_start: 0.8804 (m-80) cc_final: 0.8301 (m-80) REVERT: E 267 TRP cc_start: 0.6286 (m100) cc_final: 0.5899 (m100) outliers start: 35 outliers final: 20 residues processed: 170 average time/residue: 0.0899 time to fit residues: 25.1448 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 : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain B residue 102 TYR 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 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 395 THR Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 102 TYR Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 261 LEU 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: 9.9990 chunk 37 optimal weight: 0.3980 chunk 133 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 chunk 172 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 171 optimal weight: 10.0000 chunk 72 optimal weight: 0.5980 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 250 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 = 0.3326 r_free = 0.3326 target = 0.057515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.045384 restraints weight = 92981.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.046612 restraints weight = 57008.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.047472 restraints weight = 40946.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.048056 restraints weight = 32430.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.048452 restraints weight = 27458.621| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.4520 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= 0.178 Angle : 0.735 12.549 20310 Z= 0.350 Chirality : 0.045 0.216 2285 Planarity : 0.004 0.028 2535 Dihedral : 4.026 17.727 2055 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.11 % Allowed : 19.32 % Favored : 78.57 % 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: 0.81 (0.19), residues: 1765 helix: 2.26 (0.19), residues: 695 sheet: 1.14 (0.26), residues: 415 loop : -1.90 (0.19), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 400 TYR 0.025 0.002 TYR B 325 PHE 0.014 0.001 PHE B 319 TRP 0.045 0.002 TRP A 263 HIS 0.003 0.001 HIS A 133 Details of bonding type rmsd covalent geometry : bond 0.00391 (14975) covalent geometry : angle 0.73472 (20285) SS BOND : bond 0.00273 ( 5) SS BOND : angle 0.37119 ( 10) hydrogen bonds : bond 0.04420 ( 755) hydrogen bonds : angle 4.06125 ( 2640) link_NAG-ASN : bond 0.00211 ( 5) link_NAG-ASN : angle 1.42381 ( 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 175 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 141 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 MET cc_start: 0.8968 (ptm) cc_final: 0.8516 (ttp) REVERT: A 113 MET cc_start: 0.8921 (mmm) cc_final: 0.8482 (mmt) REVERT: A 266 PHE cc_start: 0.8947 (m-80) cc_final: 0.8468 (m-80) REVERT: A 290 GLN cc_start: 0.9516 (tt0) cc_final: 0.9124 (tm-30) REVERT: A 311 MET cc_start: 0.9524 (mmm) cc_final: 0.9305 (mmm) REVERT: B 102 TYR cc_start: 0.6895 (OUTLIER) cc_final: 0.6411 (t80) REVERT: B 263 TRP cc_start: 0.8110 (m-10) cc_final: 0.7667 (m-10) REVERT: B 266 PHE cc_start: 0.8855 (m-80) cc_final: 0.8346 (m-80) REVERT: B 322 LEU cc_start: 0.9689 (OUTLIER) cc_final: 0.9430 (mm) REVERT: C 42 MET cc_start: 0.8862 (ttp) cc_final: 0.8564 (ttt) REVERT: C 113 MET cc_start: 0.8730 (mmm) cc_final: 0.8292 (mmt) REVERT: C 187 MET cc_start: 0.9059 (mmm) cc_final: 0.8764 (mmm) REVERT: C 263 TRP cc_start: 0.7895 (m-10) cc_final: 0.7642 (m-10) REVERT: C 266 PHE cc_start: 0.8676 (m-80) cc_final: 0.8121 (m-80) REVERT: C 287 MET cc_start: 0.9573 (ttt) cc_final: 0.9353 (ppp) REVERT: D 102 TYR cc_start: 0.7206 (OUTLIER) cc_final: 0.6891 (t80) REVERT: D 113 MET cc_start: 0.8831 (mmm) cc_final: 0.8504 (mmt) REVERT: D 187 MET cc_start: 0.9044 (tpp) cc_final: 0.8776 (mmm) REVERT: D 266 PHE cc_start: 0.9079 (m-80) cc_final: 0.8572 (m-80) REVERT: D 267 TRP cc_start: 0.6989 (m100) cc_final: 0.6412 (m100) REVERT: D 287 MET cc_start: 0.9288 (ttm) cc_final: 0.9009 (ttm) REVERT: D 314 CYS cc_start: 0.9679 (m) cc_final: 0.9470 (m) REVERT: E 42 MET cc_start: 0.9187 (ptm) cc_final: 0.8842 (ppp) REVERT: E 102 TYR cc_start: 0.6971 (OUTLIER) cc_final: 0.6364 (t80) REVERT: E 263 TRP cc_start: 0.8137 (m-10) cc_final: 0.7454 (m-10) REVERT: E 266 PHE cc_start: 0.8884 (m-80) cc_final: 0.8417 (m-80) REVERT: E 267 TRP cc_start: 0.6470 (m100) cc_final: 0.6236 (m100) outliers start: 34 outliers final: 18 residues processed: 171 average time/residue: 0.0942 time to fit residues: 26.4193 Evaluate side-chains 159 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 0.506 ------------------------------------------------------------------------------- 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 249 ILE Chi-restraints excluded: chain B residue 102 TYR 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 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 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 E residue 65 CYS Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 102 TYR Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 144 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 113 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 93 optimal weight: 0.8980 chunk 21 optimal weight: 7.9990 chunk 12 optimal weight: 0.9980 chunk 77 optimal weight: 9.9990 chunk 118 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 63 optimal weight: 0.0370 chunk 83 optimal weight: 0.0010 overall best weight: 0.5864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 250 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.058955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.046675 restraints weight = 91572.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.047970 restraints weight = 55348.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.048868 restraints weight = 39308.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.049476 restraints weight = 30839.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.049896 restraints weight = 26000.182| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.4639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14985 Z= 0.120 Angle : 0.739 12.767 20310 Z= 0.342 Chirality : 0.045 0.198 2285 Planarity : 0.003 0.028 2535 Dihedral : 3.848 19.788 2055 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.18 % Allowed : 20.75 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.22 (0.18), residues: 695 sheet: 1.19 (0.26), residues: 410 loop : -1.90 (0.19), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 400 TYR 0.020 0.001 TYR B 325 PHE 0.036 0.001 PHE B 422 TRP 0.061 0.002 TRP A 263 HIS 0.001 0.000 HIS E 133 Details of bonding type rmsd covalent geometry : bond 0.00257 (14975) covalent geometry : angle 0.73927 (20285) SS BOND : bond 0.00225 ( 5) SS BOND : angle 0.20444 ( 10) hydrogen bonds : bond 0.04012 ( 755) hydrogen bonds : angle 3.83196 ( 2640) link_NAG-ASN : bond 0.00182 ( 5) link_NAG-ASN : angle 0.81760 ( 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: 19 poor density : 149 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 MET cc_start: 0.8786 (ptm) cc_final: 0.8330 (ttp) REVERT: A 113 MET cc_start: 0.8855 (mmm) cc_final: 0.8418 (mmt) REVERT: A 266 PHE cc_start: 0.8920 (m-80) cc_final: 0.8456 (m-80) REVERT: A 290 GLN cc_start: 0.9511 (tt0) cc_final: 0.9142 (tm-30) REVERT: A 311 MET cc_start: 0.9539 (mmm) cc_final: 0.9319 (mmm) REVERT: B 102 TYR cc_start: 0.6852 (OUTLIER) cc_final: 0.6375 (t80) REVERT: B 187 MET cc_start: 0.8924 (mmm) cc_final: 0.8554 (mmm) REVERT: B 263 TRP cc_start: 0.7972 (m-10) cc_final: 0.7426 (m-10) REVERT: B 266 PHE cc_start: 0.8751 (m-80) cc_final: 0.8282 (m-80) REVERT: B 322 LEU cc_start: 0.9696 (OUTLIER) cc_final: 0.9398 (mm) REVERT: C 113 MET cc_start: 0.8665 (mmm) cc_final: 0.8400 (mmt) REVERT: C 187 MET cc_start: 0.9070 (mmm) cc_final: 0.8834 (mmm) REVERT: C 263 TRP cc_start: 0.7835 (m-10) cc_final: 0.7141 (m100) REVERT: C 266 PHE cc_start: 0.8686 (m-80) cc_final: 0.8064 (m-80) REVERT: C 267 TRP cc_start: 0.6413 (m100) cc_final: 0.5704 (m100) REVERT: D 102 TYR cc_start: 0.7069 (OUTLIER) cc_final: 0.6794 (t80) REVERT: D 266 PHE cc_start: 0.9022 (m-80) cc_final: 0.8515 (m-80) REVERT: D 267 TRP cc_start: 0.6742 (m100) cc_final: 0.6125 (m100) REVERT: D 287 MET cc_start: 0.9210 (ttm) cc_final: 0.8908 (ttm) REVERT: D 314 CYS cc_start: 0.9686 (m) cc_final: 0.9475 (m) REVERT: E 42 MET cc_start: 0.9162 (ptm) cc_final: 0.8893 (ppp) REVERT: E 102 TYR cc_start: 0.6966 (OUTLIER) cc_final: 0.6315 (t80) REVERT: E 187 MET cc_start: 0.9047 (mmm) cc_final: 0.8789 (mmm) REVERT: E 263 TRP cc_start: 0.8044 (m-10) cc_final: 0.7338 (m-10) REVERT: E 266 PHE cc_start: 0.8835 (m-80) cc_final: 0.8373 (m-80) outliers start: 19 outliers final: 9 residues processed: 167 average time/residue: 0.0875 time to fit residues: 23.9920 Evaluate side-chains 153 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 140 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 322 LEU 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 402 LEU Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain E residue 65 CYS Chi-restraints excluded: chain E residue 102 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 18 optimal weight: 4.9990 chunk 22 optimal weight: 0.4980 chunk 122 optimal weight: 0.0980 chunk 170 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 126 optimal weight: 3.9990 chunk 118 optimal weight: 0.9980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.059287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.046967 restraints weight = 91427.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.048279 restraints weight = 55658.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.049186 restraints weight = 39632.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.049791 restraints weight = 31134.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.050225 restraints weight = 26229.097| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.4782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14985 Z= 0.121 Angle : 0.759 13.309 20310 Z= 0.348 Chirality : 0.045 0.205 2285 Planarity : 0.003 0.028 2535 Dihedral : 3.776 17.184 2055 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.87 % Allowed : 21.80 % Favored : 77.33 % 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: 2.13 (0.18), residues: 695 sheet: 1.15 (0.26), residues: 410 loop : -1.87 (0.20), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 400 TYR 0.020 0.001 TYR B 325 PHE 0.043 0.001 PHE C 422 TRP 0.062 0.002 TRP D 263 HIS 0.002 0.000 HIS D 225 Details of bonding type rmsd covalent geometry : bond 0.00265 (14975) covalent geometry : angle 0.75879 (20285) SS BOND : bond 0.00186 ( 5) SS BOND : angle 0.21771 ( 10) hydrogen bonds : bond 0.04001 ( 755) hydrogen bonds : angle 3.82250 ( 2640) link_NAG-ASN : bond 0.00147 ( 5) link_NAG-ASN : angle 0.83699 ( 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 157 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 143 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 MET cc_start: 0.8774 (ptm) cc_final: 0.8335 (ttp) REVERT: A 113 MET cc_start: 0.8832 (mmm) cc_final: 0.8438 (mmt) REVERT: A 187 MET cc_start: 0.8714 (mmm) cc_final: 0.8437 (mmm) REVERT: A 266 PHE cc_start: 0.8977 (m-80) cc_final: 0.8479 (m-80) REVERT: A 290 GLN cc_start: 0.9579 (tt0) cc_final: 0.9191 (tm-30) REVERT: A 311 MET cc_start: 0.9528 (mmm) cc_final: 0.9322 (mmm) REVERT: B 102 TYR cc_start: 0.6838 (OUTLIER) cc_final: 0.6526 (t80) REVERT: B 187 MET cc_start: 0.8950 (mmm) cc_final: 0.8614 (mmm) REVERT: B 263 TRP cc_start: 0.7983 (m-10) cc_final: 0.7543 (m-10) REVERT: B 266 PHE cc_start: 0.8821 (m-80) cc_final: 0.8343 (m-80) REVERT: B 322 LEU cc_start: 0.9702 (OUTLIER) cc_final: 0.9403 (mm) REVERT: C 113 MET cc_start: 0.8728 (mmm) cc_final: 0.8379 (mmt) REVERT: C 187 MET cc_start: 0.9113 (mmm) cc_final: 0.8890 (mmm) REVERT: C 263 TRP cc_start: 0.7842 (m-10) cc_final: 0.7240 (m-10) REVERT: C 266 PHE cc_start: 0.8700 (m-80) cc_final: 0.8086 (m-80) REVERT: C 267 TRP cc_start: 0.6418 (m100) cc_final: 0.5756 (m100) REVERT: D 102 TYR cc_start: 0.7091 (OUTLIER) cc_final: 0.6811 (t80) REVERT: D 113 MET cc_start: 0.8463 (mmt) cc_final: 0.8000 (mpp) REVERT: D 263 TRP cc_start: 0.7955 (m100) cc_final: 0.7623 (m100) REVERT: D 266 PHE cc_start: 0.9039 (m-80) cc_final: 0.8548 (m-80) REVERT: D 267 TRP cc_start: 0.6764 (m100) cc_final: 0.6347 (m100) REVERT: D 287 MET cc_start: 0.9240 (ttm) cc_final: 0.8923 (ttm) REVERT: D 314 CYS cc_start: 0.9670 (m) cc_final: 0.9462 (m) REVERT: E 42 MET cc_start: 0.9106 (ptm) cc_final: 0.8875 (ppp) REVERT: E 102 TYR cc_start: 0.6895 (OUTLIER) cc_final: 0.6365 (t80) REVERT: E 263 TRP cc_start: 0.8147 (m-10) cc_final: 0.7606 (m-10) REVERT: E 266 PHE cc_start: 0.8927 (m-80) cc_final: 0.8445 (m-80) outliers start: 14 outliers final: 9 residues processed: 156 average time/residue: 0.0965 time to fit residues: 24.6644 Evaluate side-chains 154 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 141 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 322 LEU 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 402 LEU Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain E residue 65 CYS Chi-restraints excluded: chain E residue 102 TYR Chi-restraints excluded: chain E residue 251 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 76 optimal weight: 0.9980 chunk 125 optimal weight: 8.9990 chunk 142 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 92 optimal weight: 0.0980 chunk 57 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 171 optimal weight: 0.0570 chunk 74 optimal weight: 7.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 201 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.059777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.047446 restraints weight = 91325.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.048771 restraints weight = 55481.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.049664 restraints weight = 39462.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.050298 restraints weight = 31080.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.050748 restraints weight = 26015.092| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.4884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14985 Z= 0.120 Angle : 0.772 13.968 20310 Z= 0.352 Chirality : 0.045 0.241 2285 Planarity : 0.003 0.030 2535 Dihedral : 3.755 15.579 2055 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.06 % Allowed : 21.74 % Favored : 77.20 % 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: 0.72 (0.19), residues: 1765 helix: 2.03 (0.19), residues: 700 sheet: 1.13 (0.26), residues: 410 loop : -1.80 (0.20), residues: 655 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 0.032 0.001 PHE C 422 TRP 0.062 0.001 TRP D 263 HIS 0.002 0.000 HIS E 225 Details of bonding type rmsd covalent geometry : bond 0.00263 (14975) covalent geometry : angle 0.77264 (20285) SS BOND : bond 0.00159 ( 5) SS BOND : angle 0.25101 ( 10) hydrogen bonds : bond 0.03891 ( 755) hydrogen bonds : angle 3.77974 ( 2640) link_NAG-ASN : bond 0.00173 ( 5) link_NAG-ASN : angle 0.79354 ( 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 165 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 148 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 MET cc_start: 0.8751 (ptm) cc_final: 0.8337 (ttp) REVERT: A 113 MET cc_start: 0.8837 (mmm) cc_final: 0.8481 (mmt) REVERT: A 187 MET cc_start: 0.8762 (mmm) cc_final: 0.8470 (mmm) REVERT: A 266 PHE cc_start: 0.8984 (m-80) cc_final: 0.8499 (m-80) REVERT: A 290 GLN cc_start: 0.9577 (tt0) cc_final: 0.9215 (tm-30) REVERT: B 42 MET cc_start: 0.8846 (ttp) cc_final: 0.8570 (ttt) REVERT: B 113 MET cc_start: 0.8542 (mpp) cc_final: 0.8278 (pmm) REVERT: B 187 MET cc_start: 0.8937 (mmm) cc_final: 0.8603 (mmm) REVERT: B 263 TRP cc_start: 0.7958 (m-10) cc_final: 0.7552 (m-10) REVERT: B 266 PHE cc_start: 0.8818 (m-80) cc_final: 0.8337 (m-80) REVERT: B 287 MET cc_start: 0.9560 (ttt) cc_final: 0.9311 (ppp) REVERT: B 322 LEU cc_start: 0.9709 (OUTLIER) cc_final: 0.9403 (mm) REVERT: C 113 MET cc_start: 0.8685 (mmm) cc_final: 0.8437 (mmt) REVERT: C 187 MET cc_start: 0.9099 (mmm) cc_final: 0.8868 (mmm) REVERT: C 201 GLN cc_start: 0.6974 (OUTLIER) cc_final: 0.6587 (mp10) REVERT: C 263 TRP cc_start: 0.7734 (m-10) cc_final: 0.7287 (m-10) REVERT: C 266 PHE cc_start: 0.8722 (m-80) cc_final: 0.8135 (m-80) REVERT: C 267 TRP cc_start: 0.6417 (m100) cc_final: 0.5711 (m100) REVERT: D 102 TYR cc_start: 0.7116 (OUTLIER) cc_final: 0.6836 (t80) REVERT: D 263 TRP cc_start: 0.8073 (m100) cc_final: 0.7763 (m100) REVERT: D 266 PHE cc_start: 0.9045 (m-80) cc_final: 0.8569 (m-80) REVERT: D 267 TRP cc_start: 0.6768 (m100) cc_final: 0.6266 (m100) REVERT: D 287 MET cc_start: 0.9227 (ttm) cc_final: 0.8823 (ttm) REVERT: D 314 CYS cc_start: 0.9671 (m) cc_final: 0.9468 (m) REVERT: E 42 MET cc_start: 0.9086 (ptm) cc_final: 0.8844 (ppp) REVERT: E 102 TYR cc_start: 0.6856 (OUTLIER) cc_final: 0.6549 (t80) REVERT: E 187 MET cc_start: 0.8719 (mmm) cc_final: 0.8456 (mmm) REVERT: E 263 TRP cc_start: 0.8067 (m-10) cc_final: 0.7665 (m-10) REVERT: E 266 PHE cc_start: 0.8937 (m-80) cc_final: 0.8279 (m-80) outliers start: 17 outliers final: 8 residues processed: 165 average time/residue: 0.0903 time to fit residues: 24.2885 Evaluate side-chains 151 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 139 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 322 LEU 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 C residue 402 LEU Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain E residue 65 CYS Chi-restraints excluded: chain E 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: 3.9990 chunk 49 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 153 optimal weight: 0.8980 chunk 106 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 21 optimal weight: 7.9990 chunk 38 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.058659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.046382 restraints weight = 91791.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.047670 restraints weight = 56118.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.048558 restraints weight = 40182.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.049160 restraints weight = 31646.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.049551 restraints weight = 26700.147| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.4984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14985 Z= 0.143 Angle : 0.781 13.537 20310 Z= 0.362 Chirality : 0.046 0.378 2285 Planarity : 0.003 0.032 2535 Dihedral : 3.825 15.392 2055 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.81 % Allowed : 22.55 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.19), residues: 1765 helix: 2.08 (0.19), residues: 695 sheet: 1.06 (0.26), residues: 410 loop : -1.89 (0.20), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 400 TYR 0.019 0.001 TYR B 325 PHE 0.032 0.001 PHE C 422 TRP 0.058 0.001 TRP D 263 HIS 0.002 0.001 HIS A 133 Details of bonding type rmsd covalent geometry : bond 0.00322 (14975) covalent geometry : angle 0.78047 (20285) SS BOND : bond 0.00161 ( 5) SS BOND : angle 0.29346 ( 10) hydrogen bonds : bond 0.04019 ( 755) hydrogen bonds : angle 3.89463 ( 2640) link_NAG-ASN : bond 0.00062 ( 5) link_NAG-ASN : angle 1.12832 ( 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 50.24 seconds (2330.24 seconds total)