Starting phenix.real_space_refine on Tue Nov 18 14:31:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m6s_23706/11_2025/7m6s_23706.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m6s_23706/11_2025/7m6s_23706.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7m6s_23706/11_2025/7m6s_23706.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m6s_23706/11_2025/7m6s_23706.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7m6s_23706/11_2025/7m6s_23706.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m6s_23706/11_2025/7m6s_23706.map" } resolution = 3.61 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 9510 2.51 5 N 2390 2.21 5 O 2625 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14625 Number of models: 1 Model: "" Number of chains: 10 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: "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 Restraints were copied for chains: B, C, D, E Time building chain proxies: 3.10, per 1000 atoms: 0.21 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: 1.22 Conformation dependent library (CDL) restraints added in 686.2 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: 0.57 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: 2.70 Time building geometry restraints manager: 1.71 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and resid 32 through 440) selection = (chain 'B' and resid 32 through 440) selection = (chain 'C' and resid 32 through 440) selection = (chain 'D' and resid 32 through 440) selection = (chain 'E' and resid 32 through 440) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.630 Find NCS groups from input model: 0.360 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.410 ------------------------------------------------------------------------------- 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 : 0.606 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: 0.7728 (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: 0.0992 time to fit residues: 46.6773 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 : 0.605 ------------------------------------------------------------------------------- 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 = 48)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.049112 restraints weight = 89334.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.050447 restraints weight = 54112.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.051368 restraints weight = 38344.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.051990 restraints weight = 30011.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.052424 restraints weight = 25250.049| |-----------------------------------------------------------------------------| 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 : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 MET cc_start: 0.8685 (ptm) cc_final: 0.8385 (ttp) REVERT: A 90 GLN cc_start: 0.7873 (mp10) cc_final: 0.7548 (mp10) REVERT: A 250 GLN cc_start: 0.9219 (tp40) cc_final: 0.8874 (tp40) REVERT: A 266 PHE cc_start: 0.8521 (m-80) cc_final: 0.8068 (m-80) REVERT: A 287 MET cc_start: 0.9227 (ttm) cc_final: 0.8972 (ttm) REVERT: A 290 GLN cc_start: 0.9485 (tt0) cc_final: 0.9119 (tm-30) REVERT: A 314 CYS cc_start: 0.9548 (m) cc_final: 0.9161 (p) REVERT: B 187 MET cc_start: 0.9052 (tpp) cc_final: 0.8812 (mmm) REVERT: B 266 PHE cc_start: 0.8557 (m-80) cc_final: 0.8171 (m-80) REVERT: C 113 MET cc_start: 0.8658 (mmm) cc_final: 0.8355 (mmt) REVERT: C 266 PHE cc_start: 0.8404 (m-80) cc_final: 0.7932 (m-80) REVERT: D 109 LEU cc_start: 0.8724 (mt) cc_final: 0.8425 (mp) REVERT: D 113 MET cc_start: 0.8522 (mmm) cc_final: 0.8150 (mmt) REVERT: D 187 MET cc_start: 0.9097 (tpp) cc_final: 0.8750 (mmm) REVERT: D 266 PHE cc_start: 0.8696 (m-80) cc_final: 0.8214 (m-80) REVERT: D 267 TRP cc_start: 0.6886 (m100) cc_final: 0.6383 (m100) REVERT: D 314 CYS cc_start: 0.9689 (m) cc_final: 0.9472 (m) REVERT: E 266 PHE cc_start: 0.8583 (m-80) cc_final: 0.8231 (m-80) outliers start: 26 outliers final: 13 residues processed: 191 average time/residue: 0.0999 time to fit residues: 30.9333 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 : 0.514 ------------------------------------------------------------------------------- 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: 5.9990 chunk 73 optimal weight: 4.9990 chunk 61 optimal weight: 7.9990 chunk 40 optimal weight: 8.9990 chunk 36 optimal weight: 8.9990 chunk 165 optimal weight: 3.9990 chunk 168 optimal weight: 5.9990 overall best weight: 4.0388 ------------------------------------------------------------------------------- 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 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 = 0.3299 r_free = 0.3299 target = 0.056046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.044073 restraints weight = 95926.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.045279 restraints weight = 58713.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.046113 restraints weight = 42149.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.046688 restraints weight = 33369.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.047080 restraints weight = 28220.522| |-----------------------------------------------------------------------------| r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 14985 Z= 0.284 Angle : 0.801 10.243 20310 Z= 0.405 Chirality : 0.047 0.182 2285 Planarity : 0.005 0.039 2535 Dihedral : 4.640 20.171 2055 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.11 % Allowed : 15.78 % Favored : 81.12 % 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: 0.99 (0.19), residues: 1765 helix: 2.08 (0.19), residues: 680 sheet: 1.44 (0.25), residues: 430 loop : -1.54 (0.20), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 400 TYR 0.020 0.002 TYR B 325 PHE 0.036 0.002 PHE C 422 TRP 0.028 0.002 TRP C 263 HIS 0.005 0.001 HIS A 133 Details of bonding type rmsd covalent geometry : bond 0.00623 (14975) covalent geometry : angle 0.79949 (20285) SS BOND : bond 0.00397 ( 5) SS BOND : angle 0.71699 ( 10) hydrogen bonds : bond 0.05487 ( 755) hydrogen bonds : angle 4.61008 ( 2640) link_NAG-ASN : bond 0.00571 ( 5) link_NAG-ASN : angle 2.19159 ( 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 184 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 134 time to evaluate : 0.604 Fit side-chains REVERT: A 42 MET cc_start: 0.8997 (ptm) cc_final: 0.8611 (ttp) REVERT: A 90 GLN cc_start: 0.8288 (mp10) cc_final: 0.7833 (mp10) REVERT: A 266 PHE cc_start: 0.8803 (m-80) cc_final: 0.8260 (m-80) REVERT: A 290 GLN cc_start: 0.9546 (tt0) cc_final: 0.9077 (tm-30) REVERT: B 42 MET cc_start: 0.9058 (ttp) cc_final: 0.8801 (ttt) REVERT: B 102 TYR cc_start: 0.7030 (OUTLIER) cc_final: 0.6519 (t80) REVERT: B 113 MET cc_start: 0.8771 (mmm) cc_final: 0.8278 (mmt) REVERT: B 263 TRP cc_start: 0.7976 (m-10) cc_final: 0.7316 (m-10) REVERT: B 266 PHE cc_start: 0.8825 (m-80) cc_final: 0.8301 (m-80) REVERT: B 267 TRP cc_start: 0.7248 (m100) cc_final: 0.6962 (m100) REVERT: C 113 MET cc_start: 0.8818 (mmm) cc_final: 0.8501 (mmt) REVERT: C 263 TRP cc_start: 0.8453 (m-10) cc_final: 0.8042 (m-10) REVERT: C 402 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.8077 (pp) REVERT: D 80 MET cc_start: 0.8574 (mmm) cc_final: 0.8073 (mmm) REVERT: D 187 MET cc_start: 0.8922 (tpp) cc_final: 0.8648 (mmm) REVERT: D 263 TRP cc_start: 0.8010 (m-10) cc_final: 0.7768 (m100) REVERT: D 266 PHE cc_start: 0.8914 (m-80) cc_final: 0.8396 (m-80) REVERT: D 267 TRP cc_start: 0.7086 (m100) cc_final: 0.6629 (m100) REVERT: D 311 MET cc_start: 0.9393 (mmm) cc_final: 0.9189 (ptp) REVERT: D 314 CYS cc_start: 0.9694 (m) cc_final: 0.9476 (m) REVERT: E 102 TYR cc_start: 0.7157 (OUTLIER) cc_final: 0.6468 (t80) REVERT: E 266 PHE cc_start: 0.8740 (m-80) cc_final: 0.8375 (m-80) REVERT: E 267 TRP cc_start: 0.6542 (m100) cc_final: 0.6151 (m100) outliers start: 50 outliers final: 23 residues processed: 171 average time/residue: 0.1060 time to fit residues: 29.3093 Evaluate side-chains 152 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 0.544 ------------------------------------------------------------------------------- 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 164 MET Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 251 MET Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain E residue 65 CYS Chi-restraints excluded: chain E residue 67 ILE Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 102 TYR Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 261 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 166 optimal weight: 9.9990 chunk 82 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 86 optimal weight: 4.9990 chunk 83 optimal weight: 8.9990 chunk 78 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 95 optimal weight: 0.9980 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 A 329 ASN C 250 GLN C 329 ASN E 174 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.057719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.045501 restraints weight = 93855.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.046771 restraints weight = 56645.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.047641 restraints weight = 40278.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.048249 restraints weight = 31631.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.048618 restraints weight = 26671.815| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14985 Z= 0.130 Angle : 0.700 10.685 20310 Z= 0.339 Chirality : 0.045 0.207 2285 Planarity : 0.003 0.023 2535 Dihedral : 4.187 17.461 2055 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.86 % Allowed : 17.58 % Favored : 80.56 % 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: 1.08 (0.19), residues: 1765 helix: 2.34 (0.19), residues: 680 sheet: 1.29 (0.25), residues: 415 loop : -1.48 (0.20), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 333 TYR 0.016 0.002 TYR D 433 PHE 0.026 0.001 PHE A 422 TRP 0.030 0.001 TRP C 263 HIS 0.003 0.001 HIS E 225 Details of bonding type rmsd covalent geometry : bond 0.00283 (14975) covalent geometry : angle 0.69962 (20285) SS BOND : bond 0.00366 ( 5) SS BOND : angle 0.41924 ( 10) hydrogen bonds : bond 0.04669 ( 755) hydrogen bonds : angle 4.09004 ( 2640) link_NAG-ASN : bond 0.00082 ( 5) link_NAG-ASN : angle 0.97557 ( 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 167 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 137 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.8799 (mmm) cc_final: 0.8406 (mmt) REVERT: A 266 PHE cc_start: 0.8720 (m-80) cc_final: 0.8198 (m-80) REVERT: A 290 GLN cc_start: 0.9499 (tt0) cc_final: 0.9063 (tm-30) REVERT: A 314 CYS cc_start: 0.9514 (m) cc_final: 0.9311 (p) REVERT: B 102 TYR cc_start: 0.6922 (OUTLIER) cc_final: 0.6462 (t80) REVERT: B 113 MET cc_start: 0.8853 (mmm) cc_final: 0.8616 (mmt) REVERT: B 263 TRP cc_start: 0.7906 (m-10) cc_final: 0.7273 (m-10) REVERT: B 266 PHE cc_start: 0.8710 (m-80) cc_final: 0.8151 (m-80) REVERT: B 287 MET cc_start: 0.9139 (ttm) cc_final: 0.8794 (ttm) REVERT: D 113 MET cc_start: 0.8641 (mmm) cc_final: 0.8258 (mmt) REVERT: D 187 MET cc_start: 0.9033 (tpp) cc_final: 0.8819 (mmm) REVERT: D 263 TRP cc_start: 0.7919 (m-10) cc_final: 0.7679 (m-10) REVERT: D 266 PHE cc_start: 0.8830 (m-80) cc_final: 0.8265 (m-80) REVERT: D 267 TRP cc_start: 0.6826 (m100) cc_final: 0.6302 (m100) REVERT: D 287 MET cc_start: 0.9265 (ttm) cc_final: 0.8826 (ttm) REVERT: E 102 TYR cc_start: 0.6949 (OUTLIER) cc_final: 0.6349 (t80) REVERT: E 113 MET cc_start: 0.8656 (mmt) cc_final: 0.8143 (mpp) REVERT: E 266 PHE cc_start: 0.8802 (m-80) cc_final: 0.8308 (m-80) REVERT: E 267 TRP cc_start: 0.6591 (m100) cc_final: 0.6030 (m100) REVERT: E 287 MET cc_start: 0.9192 (ttm) cc_final: 0.8956 (ttm) outliers start: 30 outliers final: 13 residues processed: 159 average time/residue: 0.0996 time to fit residues: 25.8322 Evaluate side-chains 144 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain B residue 102 TYR 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 398 GLU Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain E residue 65 CYS Chi-restraints excluded: chain E residue 102 TYR 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: 7.9990 chunk 136 optimal weight: 10.0000 chunk 89 optimal weight: 0.0970 chunk 112 optimal weight: 0.9980 chunk 129 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 123 optimal weight: 7.9990 chunk 66 optimal weight: 0.1980 chunk 15 optimal weight: 0.6980 chunk 80 optimal weight: 0.0770 overall best weight: 0.4136 ------------------------------------------------------------------------------- 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 C 201 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.059355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.047094 restraints weight = 90911.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.048374 restraints weight = 55245.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.049266 restraints weight = 39210.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.049909 restraints weight = 30851.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.050348 restraints weight = 25808.688| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.4313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14985 Z= 0.115 Angle : 0.685 11.969 20310 Z= 0.328 Chirality : 0.044 0.217 2285 Planarity : 0.003 0.025 2535 Dihedral : 3.853 16.273 2055 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.17 % Allowed : 17.58 % Favored : 80.25 % 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: 0.72 (0.19), residues: 1765 helix: 2.09 (0.18), residues: 715 sheet: 1.32 (0.26), residues: 395 loop : -2.03 (0.18), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 333 TYR 0.016 0.001 TYR D 433 PHE 0.033 0.001 PHE B 422 TRP 0.027 0.001 TRP E 263 HIS 0.002 0.001 HIS E 225 Details of bonding type rmsd covalent geometry : bond 0.00240 (14975) covalent geometry : angle 0.68464 (20285) SS BOND : bond 0.00293 ( 5) SS BOND : angle 0.32210 ( 10) hydrogen bonds : bond 0.04229 ( 755) hydrogen bonds : angle 3.85901 ( 2640) link_NAG-ASN : bond 0.00221 ( 5) link_NAG-ASN : angle 0.79146 ( 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 179 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 144 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 MET cc_start: 0.8684 (ptm) cc_final: 0.8436 (ttp) REVERT: A 113 MET cc_start: 0.8911 (mmm) cc_final: 0.8387 (mmt) REVERT: A 266 PHE cc_start: 0.8834 (m-80) cc_final: 0.8364 (m-80) REVERT: A 290 GLN cc_start: 0.9564 (tt0) cc_final: 0.9171 (tm-30) REVERT: A 314 CYS cc_start: 0.9595 (m) cc_final: 0.9338 (p) REVERT: B 102 TYR cc_start: 0.6917 (OUTLIER) cc_final: 0.6458 (t80) REVERT: B 113 MET cc_start: 0.8790 (mmm) cc_final: 0.8531 (mmt) REVERT: B 263 TRP cc_start: 0.8042 (m-10) cc_final: 0.7640 (m-10) REVERT: B 266 PHE cc_start: 0.8733 (m-80) cc_final: 0.8264 (m-80) REVERT: C 201 GLN cc_start: 0.7041 (OUTLIER) cc_final: 0.6696 (mp10) REVERT: D 113 MET cc_start: 0.8669 (mmm) cc_final: 0.8314 (mmt) REVERT: D 263 TRP cc_start: 0.7851 (m-10) cc_final: 0.7526 (m-10) REVERT: D 266 PHE cc_start: 0.8845 (m-80) cc_final: 0.8319 (m-80) REVERT: D 267 TRP cc_start: 0.6792 (m100) cc_final: 0.6095 (m100) REVERT: D 314 CYS cc_start: 0.9636 (m) cc_final: 0.9181 (p) REVERT: E 42 MET cc_start: 0.9070 (ptm) cc_final: 0.8826 (ppp) REVERT: E 102 TYR cc_start: 0.6902 (OUTLIER) cc_final: 0.6365 (t80) REVERT: E 113 MET cc_start: 0.8588 (mmt) cc_final: 0.8106 (mpp) REVERT: E 266 PHE cc_start: 0.8845 (m-80) cc_final: 0.8379 (m-80) REVERT: E 267 TRP cc_start: 0.6449 (m100) cc_final: 0.5803 (m100) REVERT: E 287 MET cc_start: 0.9137 (ttm) cc_final: 0.8927 (ttm) outliers start: 35 outliers final: 18 residues processed: 167 average time/residue: 0.1005 time to fit residues: 27.1180 Evaluate side-chains 155 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain C residue 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 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 204 ASP Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain E residue 102 TYR Chi-restraints excluded: chain E residue 164 MET 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: 0.9990 chunk 81 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 66 optimal weight: 0.0970 chunk 129 optimal weight: 1.9990 chunk 151 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 90 optimal weight: 8.9990 chunk 71 optimal weight: 0.0000 overall best weight: 0.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 250 GLN C 201 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.058760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.046446 restraints weight = 91189.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.047717 restraints weight = 55614.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.048593 restraints weight = 39744.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.049187 restraints weight = 31330.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.049619 restraints weight = 26464.888| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.4463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14985 Z= 0.119 Angle : 0.707 12.785 20310 Z= 0.332 Chirality : 0.043 0.199 2285 Planarity : 0.003 0.023 2535 Dihedral : 3.800 16.250 2055 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.99 % Allowed : 18.94 % Favored : 79.07 % 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: 0.78 (0.19), residues: 1765 helix: 2.19 (0.18), residues: 710 sheet: 1.18 (0.26), residues: 415 loop : -2.01 (0.19), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 333 TYR 0.024 0.001 TYR B 325 PHE 0.034 0.001 PHE A 422 TRP 0.037 0.002 TRP E 263 HIS 0.002 0.000 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00259 (14975) covalent geometry : angle 0.70664 (20285) SS BOND : bond 0.00215 ( 5) SS BOND : angle 0.27412 ( 10) hydrogen bonds : bond 0.04136 ( 755) hydrogen bonds : angle 3.85154 ( 2640) link_NAG-ASN : bond 0.00115 ( 5) link_NAG-ASN : angle 0.86630 ( 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 173 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 141 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 MET cc_start: 0.8640 (ptm) cc_final: 0.8327 (ttp) REVERT: A 113 MET cc_start: 0.8906 (mmm) cc_final: 0.8389 (mmt) REVERT: A 187 MET cc_start: 0.8930 (mmm) cc_final: 0.8642 (mmm) REVERT: A 266 PHE cc_start: 0.8893 (m-80) cc_final: 0.8408 (m-80) REVERT: A 290 GLN cc_start: 0.9580 (tt0) cc_final: 0.9187 (tm-30) REVERT: A 314 CYS cc_start: 0.9610 (m) cc_final: 0.9332 (p) REVERT: B 80 MET cc_start: 0.8730 (mmm) cc_final: 0.8499 (tpt) REVERT: B 102 TYR cc_start: 0.6836 (OUTLIER) cc_final: 0.6392 (t80) REVERT: B 113 MET cc_start: 0.8810 (mmm) cc_final: 0.8546 (mmt) REVERT: B 263 TRP cc_start: 0.8095 (m-10) cc_final: 0.7595 (m-10) REVERT: B 266 PHE cc_start: 0.8722 (m-80) cc_final: 0.8181 (m-80) REVERT: B 267 TRP cc_start: 0.6764 (m100) cc_final: 0.6397 (m100) REVERT: B 322 LEU cc_start: 0.9676 (OUTLIER) cc_final: 0.9353 (mm) REVERT: C 42 MET cc_start: 0.8758 (ttp) cc_final: 0.8491 (ttt) REVERT: C 201 GLN cc_start: 0.6937 (OUTLIER) cc_final: 0.6456 (mp10) REVERT: C 266 PHE cc_start: 0.8666 (m-80) cc_final: 0.8081 (m-80) REVERT: D 102 TYR cc_start: 0.7017 (OUTLIER) cc_final: 0.6785 (t80) REVERT: D 113 MET cc_start: 0.8711 (mmm) cc_final: 0.8355 (mmt) REVERT: D 266 PHE cc_start: 0.8951 (m-80) cc_final: 0.8397 (m-80) REVERT: D 267 TRP cc_start: 0.6815 (m100) cc_final: 0.6234 (m100) REVERT: D 314 CYS cc_start: 0.9588 (m) cc_final: 0.9097 (p) REVERT: E 42 MET cc_start: 0.9119 (ptm) cc_final: 0.8781 (ppp) REVERT: E 102 TYR cc_start: 0.6852 (OUTLIER) cc_final: 0.6310 (t80) REVERT: E 187 MET cc_start: 0.8853 (mmm) cc_final: 0.8406 (mmm) REVERT: E 266 PHE cc_start: 0.8773 (m-80) cc_final: 0.8334 (m-80) REVERT: E 267 TRP cc_start: 0.6477 (m100) cc_final: 0.6044 (m100) outliers start: 32 outliers final: 15 residues processed: 167 average time/residue: 0.1009 time to fit residues: 27.4309 Evaluate side-chains 154 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain C residue 201 GLN Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 102 TYR 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: 10.0000 chunk 86 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 21 optimal weight: 8.9990 chunk 42 optimal weight: 6.9990 chunk 105 optimal weight: 0.8980 chunk 172 optimal weight: 8.9990 chunk 10 optimal weight: 0.7980 chunk 171 optimal weight: 8.9990 chunk 72 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.058364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.046109 restraints weight = 91169.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.047372 restraints weight = 55950.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.048230 restraints weight = 40074.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.048830 restraints weight = 31665.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.049238 restraints weight = 26752.065| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.4608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14985 Z= 0.131 Angle : 0.715 12.921 20310 Z= 0.337 Chirality : 0.043 0.193 2285 Planarity : 0.003 0.028 2535 Dihedral : 3.823 16.506 2055 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.93 % Allowed : 19.57 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.19), residues: 1765 helix: 2.23 (0.19), residues: 710 sheet: 1.13 (0.26), residues: 415 loop : -2.03 (0.19), residues: 640 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 0.034 0.001 PHE C 422 TRP 0.053 0.002 TRP C 263 HIS 0.003 0.001 HIS E 133 Details of bonding type rmsd covalent geometry : bond 0.00291 (14975) covalent geometry : angle 0.71486 (20285) SS BOND : bond 0.00196 ( 5) SS BOND : angle 0.22487 ( 10) hydrogen bonds : bond 0.04102 ( 755) hydrogen bonds : angle 3.93473 ( 2640) link_NAG-ASN : bond 0.00021 ( 5) link_NAG-ASN : angle 0.99666 ( 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 171 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 MET cc_start: 0.8655 (ptm) cc_final: 0.8258 (ttp) REVERT: A 113 MET cc_start: 0.8926 (mmm) cc_final: 0.8433 (mmt) REVERT: A 266 PHE cc_start: 0.8914 (m-80) cc_final: 0.8325 (m-80) REVERT: A 290 GLN cc_start: 0.9585 (tt0) cc_final: 0.9256 (tm-30) REVERT: B 102 TYR cc_start: 0.6832 (OUTLIER) cc_final: 0.6375 (t80) REVERT: B 113 MET cc_start: 0.8772 (mmm) cc_final: 0.8521 (mmt) REVERT: B 187 MET cc_start: 0.8939 (mmm) cc_final: 0.8684 (mmm) REVERT: B 210 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.8493 (tp40) REVERT: B 263 TRP cc_start: 0.8101 (m-10) cc_final: 0.7497 (m-10) REVERT: B 266 PHE cc_start: 0.8761 (m-80) cc_final: 0.8204 (m-80) REVERT: B 267 TRP cc_start: 0.6696 (m100) cc_final: 0.6477 (m100) REVERT: B 322 LEU cc_start: 0.9685 (OUTLIER) cc_final: 0.9361 (mm) REVERT: C 42 MET cc_start: 0.8847 (ttp) cc_final: 0.8594 (ttt) REVERT: C 113 MET cc_start: 0.8779 (mmm) cc_final: 0.8353 (mmt) REVERT: C 187 MET cc_start: 0.8998 (mmm) cc_final: 0.8698 (mmm) REVERT: C 201 GLN cc_start: 0.7086 (OUTLIER) cc_final: 0.6628 (mp10) REVERT: C 266 PHE cc_start: 0.8678 (m-80) cc_final: 0.8137 (m-80) REVERT: C 267 TRP cc_start: 0.6563 (m100) cc_final: 0.5696 (m100) REVERT: D 102 TYR cc_start: 0.7055 (OUTLIER) cc_final: 0.6831 (t80) REVERT: D 113 MET cc_start: 0.8675 (mmm) cc_final: 0.8352 (mmt) REVERT: D 187 MET cc_start: 0.8876 (mmm) cc_final: 0.8638 (mmm) REVERT: D 263 TRP cc_start: 0.7914 (m-10) cc_final: 0.7644 (m100) REVERT: D 266 PHE cc_start: 0.9018 (m-80) cc_final: 0.8496 (m-80) REVERT: D 267 TRP cc_start: 0.6921 (m100) cc_final: 0.6352 (m100) REVERT: D 311 MET cc_start: 0.9394 (mmm) cc_final: 0.9170 (mmm) REVERT: D 314 CYS cc_start: 0.9584 (m) cc_final: 0.9101 (p) REVERT: E 102 TYR cc_start: 0.6894 (OUTLIER) cc_final: 0.6316 (t80) REVERT: E 187 MET cc_start: 0.8900 (mmm) cc_final: 0.8604 (mmm) REVERT: E 266 PHE cc_start: 0.8771 (m-80) cc_final: 0.8329 (m-80) REVERT: E 267 TRP cc_start: 0.6592 (m100) cc_final: 0.6087 (m100) outliers start: 31 outliers final: 20 residues processed: 167 average time/residue: 0.1013 time to fit residues: 27.3424 Evaluate side-chains 162 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 0.607 ------------------------------------------------------------------------------- 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 251 MET Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 300 LYS Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain C residue 201 GLN Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 244 MET 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 D residue 204 ASP Chi-restraints excluded: chain E residue 65 CYS Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 102 TYR 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: 0.0570 chunk 40 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 chunk 21 optimal weight: 7.9990 chunk 12 optimal weight: 0.7980 chunk 77 optimal weight: 5.9990 chunk 118 optimal weight: 0.0970 chunk 0 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 overall best weight: 0.5296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.059268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.046782 restraints weight = 92366.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.048087 restraints weight = 56408.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.048986 restraints weight = 40226.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.049586 restraints weight = 31645.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.050021 restraints weight = 26720.958| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.4726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14985 Z= 0.120 Angle : 0.725 13.565 20310 Z= 0.340 Chirality : 0.044 0.191 2285 Planarity : 0.003 0.034 2535 Dihedral : 3.787 16.110 2055 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.74 % Allowed : 20.25 % Favored : 78.01 % 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: 0.73 (0.19), residues: 1765 helix: 2.15 (0.18), residues: 695 sheet: 1.09 (0.26), residues: 415 loop : -1.88 (0.19), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 409 TYR 0.017 0.001 TYR B 325 PHE 0.035 0.001 PHE E 422 TRP 0.093 0.003 TRP A 267 HIS 0.002 0.000 HIS E 133 Details of bonding type rmsd covalent geometry : bond 0.00261 (14975) covalent geometry : angle 0.72504 (20285) SS BOND : bond 0.00199 ( 5) SS BOND : angle 0.17658 ( 10) hydrogen bonds : bond 0.04020 ( 755) hydrogen bonds : angle 3.85776 ( 2640) link_NAG-ASN : bond 0.00188 ( 5) link_NAG-ASN : angle 0.76436 ( 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 173 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 145 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 MET cc_start: 0.8597 (ptm) cc_final: 0.8236 (ttp) REVERT: A 113 MET cc_start: 0.8913 (mmm) cc_final: 0.8418 (mmt) REVERT: A 187 MET cc_start: 0.8965 (mmm) cc_final: 0.8689 (mmm) REVERT: A 266 PHE cc_start: 0.8764 (m-80) cc_final: 0.8290 (m-80) REVERT: A 287 MET cc_start: 0.9409 (ttt) cc_final: 0.9185 (ppp) REVERT: A 290 GLN cc_start: 0.9606 (tt0) cc_final: 0.9309 (tm-30) REVERT: A 300 LYS cc_start: 0.9460 (OUTLIER) cc_final: 0.9002 (mtmm) REVERT: B 102 TYR cc_start: 0.6810 (OUTLIER) cc_final: 0.6374 (t80) REVERT: B 113 MET cc_start: 0.8742 (mmm) cc_final: 0.8516 (mmt) REVERT: B 187 MET cc_start: 0.8970 (mmm) cc_final: 0.8727 (mmm) REVERT: B 210 GLN cc_start: 0.8819 (OUTLIER) cc_final: 0.8364 (tp40) REVERT: B 263 TRP cc_start: 0.8001 (m-10) cc_final: 0.7555 (m-10) REVERT: B 266 PHE cc_start: 0.8760 (m-80) cc_final: 0.8247 (m-80) REVERT: B 322 LEU cc_start: 0.9686 (OUTLIER) cc_final: 0.9356 (mm) REVERT: C 80 MET cc_start: 0.8182 (tpt) cc_final: 0.7758 (mmm) REVERT: C 113 MET cc_start: 0.8722 (mmm) cc_final: 0.8486 (mmt) REVERT: C 187 MET cc_start: 0.9068 (mmm) cc_final: 0.8837 (mmm) REVERT: C 201 GLN cc_start: 0.7128 (OUTLIER) cc_final: 0.6646 (mp10) REVERT: C 266 PHE cc_start: 0.8690 (m-80) cc_final: 0.8204 (m-80) REVERT: D 113 MET cc_start: 0.8641 (mmm) cc_final: 0.8381 (mmt) REVERT: D 187 MET cc_start: 0.8958 (mmm) cc_final: 0.8696 (mmm) REVERT: D 266 PHE cc_start: 0.9024 (m-80) cc_final: 0.8377 (m-80) REVERT: D 267 TRP cc_start: 0.6735 (m100) cc_final: 0.6172 (m100) REVERT: D 314 CYS cc_start: 0.9614 (m) cc_final: 0.9038 (p) REVERT: E 102 TYR cc_start: 0.6795 (OUTLIER) cc_final: 0.6292 (t80) REVERT: E 187 MET cc_start: 0.8897 (mmm) cc_final: 0.8635 (mmm) REVERT: E 266 PHE cc_start: 0.8761 (m-80) cc_final: 0.8330 (m-80) outliers start: 28 outliers final: 14 residues processed: 170 average time/residue: 0.0980 time to fit residues: 27.1602 Evaluate side-chains 159 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 300 LYS Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain C residue 201 GLN Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain E residue 65 CYS Chi-restraints excluded: chain E residue 102 TYR Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 421 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 18 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 122 optimal weight: 7.9990 chunk 170 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 78 optimal weight: 0.0170 chunk 126 optimal weight: 1.9990 chunk 118 optimal weight: 0.0970 overall best weight: 0.6016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.059424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.047031 restraints weight = 91147.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.048318 restraints weight = 55658.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.049210 restraints weight = 39849.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.049823 restraints weight = 31363.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.050218 restraints weight = 26428.909| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.4844 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 : 0.744 13.724 20310 Z= 0.346 Chirality : 0.045 0.370 2285 Planarity : 0.003 0.044 2535 Dihedral : 3.759 14.887 2055 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.18 % Allowed : 21.24 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.19), residues: 1765 helix: 1.98 (0.18), residues: 700 sheet: 1.28 (0.27), residues: 390 loop : -1.89 (0.19), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 333 TYR 0.016 0.001 TYR B 325 PHE 0.027 0.001 PHE A 422 TRP 0.070 0.003 TRP C 263 HIS 0.002 0.000 HIS E 133 Details of bonding type rmsd covalent geometry : bond 0.00263 (14975) covalent geometry : angle 0.74406 (20285) SS BOND : bond 0.00184 ( 5) SS BOND : angle 0.21363 ( 10) hydrogen bonds : bond 0.03964 ( 755) hydrogen bonds : angle 3.83129 ( 2640) link_NAG-ASN : bond 0.00150 ( 5) link_NAG-ASN : angle 0.79792 ( 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 163 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 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: symmetry clash revert: symmetry clash REVERT: A 42 MET cc_start: 0.8571 (ptm) cc_final: 0.8212 (ttp) REVERT: A 113 MET cc_start: 0.8907 (mmm) cc_final: 0.8375 (mmt) REVERT: A 187 MET cc_start: 0.9032 (mmm) cc_final: 0.8771 (mmm) REVERT: A 266 PHE cc_start: 0.8695 (m-80) cc_final: 0.8243 (m-80) REVERT: A 287 MET cc_start: 0.9418 (ttt) cc_final: 0.9208 (ppp) REVERT: A 290 GLN cc_start: 0.9585 (tt0) cc_final: 0.9326 (tm-30) REVERT: B 102 TYR cc_start: 0.6936 (OUTLIER) cc_final: 0.6470 (t80) REVERT: B 187 MET cc_start: 0.8956 (mmm) cc_final: 0.8707 (mmm) REVERT: B 210 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.8387 (tp40) REVERT: B 263 TRP cc_start: 0.7909 (m-10) cc_final: 0.7453 (m-10) REVERT: B 266 PHE cc_start: 0.8703 (m-80) cc_final: 0.8194 (m-80) REVERT: B 322 LEU cc_start: 0.9687 (OUTLIER) cc_final: 0.9368 (mm) REVERT: C 113 MET cc_start: 0.8716 (mmm) cc_final: 0.8427 (mmt) REVERT: C 187 MET cc_start: 0.9123 (mmm) cc_final: 0.8896 (mmm) REVERT: C 201 GLN cc_start: 0.7006 (OUTLIER) cc_final: 0.6481 (mp10) REVERT: C 266 PHE cc_start: 0.8658 (m-80) cc_final: 0.8160 (m-80) REVERT: D 113 MET cc_start: 0.8655 (mmm) cc_final: 0.8391 (mmt) REVERT: D 266 PHE cc_start: 0.8913 (m-80) cc_final: 0.8358 (m-80) REVERT: D 267 TRP cc_start: 0.6733 (m100) cc_final: 0.6088 (m100) REVERT: D 314 CYS cc_start: 0.9594 (m) cc_final: 0.9011 (p) REVERT: E 102 TYR cc_start: 0.6827 (OUTLIER) cc_final: 0.6337 (t80) REVERT: E 187 MET cc_start: 0.8900 (mmm) cc_final: 0.8650 (mmm) REVERT: E 263 TRP cc_start: 0.8103 (m100) cc_final: 0.7765 (m100) REVERT: E 266 PHE cc_start: 0.8719 (m-80) cc_final: 0.8300 (m-80) REVERT: E 267 TRP cc_start: 0.6489 (m100) cc_final: 0.6084 (m100) outliers start: 19 outliers final: 12 residues processed: 162 average time/residue: 0.0989 time to fit residues: 25.8809 Evaluate side-chains 152 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 0.602 ------------------------------------------------------------------------------- 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 137 THR Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 300 LYS Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain C residue 201 GLN Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain E residue 102 TYR Chi-restraints excluded: chain E residue 421 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 76 optimal weight: 10.0000 chunk 125 optimal weight: 5.9990 chunk 142 optimal weight: 0.2980 chunk 24 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 92 optimal weight: 0.0370 chunk 57 optimal weight: 0.0870 chunk 45 optimal weight: 6.9990 chunk 171 optimal weight: 9.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 201 GLN ** B 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 GLN ** D 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 201 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.059932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.047599 restraints weight = 90735.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.048891 restraints weight = 55649.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.049787 restraints weight = 39803.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.050406 restraints weight = 31360.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.050848 restraints weight = 26387.513| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.4976 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= 0.123 Angle : 0.770 13.875 20310 Z= 0.357 Chirality : 0.045 0.251 2285 Planarity : 0.003 0.063 2535 Dihedral : 3.758 18.084 2055 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.37 % Allowed : 21.80 % Favored : 76.83 % 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: 0.58 (0.19), residues: 1765 helix: 1.90 (0.18), residues: 700 sheet: 1.23 (0.26), residues: 390 loop : -1.88 (0.19), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 333 TYR 0.015 0.001 TYR B 325 PHE 0.039 0.001 PHE E 422 TRP 0.073 0.002 TRP C 263 HIS 0.002 0.000 HIS D 225 Details of bonding type rmsd covalent geometry : bond 0.00266 (14975) covalent geometry : angle 0.76976 (20285) SS BOND : bond 0.00194 ( 5) SS BOND : angle 0.18429 ( 10) hydrogen bonds : bond 0.03933 ( 755) hydrogen bonds : angle 3.79803 ( 2640) link_NAG-ASN : bond 0.00187 ( 5) link_NAG-ASN : angle 0.74009 ( 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 163 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 MET cc_start: 0.8606 (ptm) cc_final: 0.8220 (ttp) REVERT: A 113 MET cc_start: 0.8712 (mmm) cc_final: 0.8501 (mmm) REVERT: A 187 MET cc_start: 0.9073 (mmm) cc_final: 0.8804 (mmm) REVERT: A 266 PHE cc_start: 0.8740 (m-80) cc_final: 0.8293 (m-80) REVERT: A 290 GLN cc_start: 0.9614 (tt0) cc_final: 0.9370 (tm-30) REVERT: A 300 LYS cc_start: 0.9444 (OUTLIER) cc_final: 0.8995 (mtmm) REVERT: B 102 TYR cc_start: 0.6840 (OUTLIER) cc_final: 0.6553 (t80) REVERT: B 187 MET cc_start: 0.8959 (mmm) cc_final: 0.8621 (mmm) REVERT: B 201 GLN cc_start: 0.6806 (OUTLIER) cc_final: 0.6382 (mp10) REVERT: B 210 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8373 (tp40) REVERT: B 263 TRP cc_start: 0.7817 (m-10) cc_final: 0.7387 (m-10) REVERT: B 266 PHE cc_start: 0.8734 (m-80) cc_final: 0.8253 (m-80) REVERT: B 322 LEU cc_start: 0.9691 (OUTLIER) cc_final: 0.9370 (mm) REVERT: C 187 MET cc_start: 0.9112 (mmm) cc_final: 0.8881 (mmm) REVERT: C 201 GLN cc_start: 0.6885 (OUTLIER) cc_final: 0.6155 (mp10) REVERT: C 266 PHE cc_start: 0.8644 (m-80) cc_final: 0.8115 (m-80) REVERT: C 267 TRP cc_start: 0.6516 (m100) cc_final: 0.4210 (m100) REVERT: D 113 MET cc_start: 0.8674 (mmm) cc_final: 0.8401 (mmt) REVERT: D 187 MET cc_start: 0.8588 (mmm) cc_final: 0.8306 (mmm) REVERT: D 263 TRP cc_start: 0.7940 (m100) cc_final: 0.7663 (m100) REVERT: D 266 PHE cc_start: 0.8974 (m-80) cc_final: 0.8337 (m-80) REVERT: D 267 TRP cc_start: 0.6811 (m100) cc_final: 0.6263 (m100) REVERT: D 287 MET cc_start: 0.9320 (ttm) cc_final: 0.9041 (ttm) REVERT: E 42 MET cc_start: 0.8764 (ptm) cc_final: 0.8123 (ttt) REVERT: E 102 TYR cc_start: 0.6810 (OUTLIER) cc_final: 0.6495 (t80) REVERT: E 187 MET cc_start: 0.8894 (mmm) cc_final: 0.8640 (mmm) REVERT: E 263 TRP cc_start: 0.8056 (m100) cc_final: 0.7788 (m100) REVERT: E 266 PHE cc_start: 0.8730 (m-80) cc_final: 0.8336 (m-80) REVERT: E 267 TRP cc_start: 0.6381 (m100) cc_final: 0.5966 (m100) outliers start: 22 outliers final: 12 residues processed: 162 average time/residue: 0.1007 time to fit residues: 26.2988 Evaluate side-chains 154 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 201 GLN Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 300 LYS Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain C residue 201 GLN Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain E residue 102 TYR Chi-restraints excluded: chain E residue 421 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 173 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 98 optimal weight: 0.4980 chunk 21 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 20 optimal weight: 8.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 ASN ** D 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 ASN ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.059293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.046977 restraints weight = 91601.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.048259 restraints weight = 55736.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.049149 restraints weight = 39870.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.049767 restraints weight = 31358.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.050202 restraints weight = 26418.385| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.5042 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= 0.137 Angle : 0.782 13.718 20310 Z= 0.367 Chirality : 0.045 0.263 2285 Planarity : 0.003 0.049 2535 Dihedral : 3.798 20.550 2055 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.30 % Allowed : 22.42 % Favored : 76.27 % 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: 0.59 (0.19), residues: 1765 helix: 1.94 (0.19), residues: 700 sheet: 1.17 (0.26), residues: 390 loop : -1.89 (0.19), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 276 TYR 0.015 0.001 TYR B 325 PHE 0.041 0.001 PHE C 422 TRP 0.064 0.002 TRP D 263 HIS 0.002 0.001 HIS E 133 Details of bonding type rmsd covalent geometry : bond 0.00307 (14975) covalent geometry : angle 0.78235 (20285) SS BOND : bond 0.00123 ( 5) SS BOND : angle 0.44337 ( 10) hydrogen bonds : bond 0.03961 ( 755) hydrogen bonds : angle 3.85359 ( 2640) link_NAG-ASN : bond 0.00019 ( 5) link_NAG-ASN : angle 0.95686 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2416.76 seconds wall clock time: 42 minutes 41.27 seconds (2561.27 seconds total)