Starting phenix.real_space_refine on Fri Jul 3 01:58:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cyf_30499/07_2026/7cyf_30499_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cyf_30499/07_2026/7cyf_30499.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7cyf_30499/07_2026/7cyf_30499_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cyf_30499/07_2026/7cyf_30499_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7cyf_30499/07_2026/7cyf_30499.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cyf_30499/07_2026/7cyf_30499.map" } resolution = 3.15 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2124 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 S 54 5.16 5 Na 3 4.78 5 C 6504 2.51 5 N 1617 2.21 5 O 1815 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9996 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2474 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 17, 'TRANS': 316} Chain breaks: 1 Chain: "B" Number of atoms: 2474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2474 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 17, 'TRANS': 316} Chain breaks: 1 Chain: "C" Number of atoms: 2474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2474 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 17, 'TRANS': 316} Chain breaks: 1 Chain: "D" Number of atoms: 834 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 109, 831 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 3, 'TRANS': 105} Conformer: "B" Number of residues, atoms: 109, 831 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 3, 'TRANS': 105} bond proxies already assigned to first conformer: 838 Chain: "E" Number of atoms: 834 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 109, 831 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 3, 'TRANS': 105} Conformer: "B" Number of residues, atoms: 109, 831 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 3, 'TRANS': 105} bond proxies already assigned to first conformer: 838 Chain: "F" Number of atoms: 834 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 109, 831 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 3, 'TRANS': 105} Conformer: "B" Number of residues, atoms: 109, 831 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 3, 'TRANS': 105} bond proxies already assigned to first conformer: 838 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' NA': 1} Chain breaks: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' NA': 1} Chain breaks: 1 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' NA': 1} Chain breaks: 1 Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'AMP%rna2p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna2p': 1} Chain: "E" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'AMP%rna2p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna2p': 1} Chain: "F" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'AMP%rna2p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna2p': 1} Time building chain proxies: 2.33, per 1000 atoms: 0.23 Number of scatterers: 9996 At special positions: 0 Unit cell: (104, 95.68, 85.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 54 16.00 P 3 15.00 Na 3 11.00 O 1815 8.00 N 1617 7.00 C 6504 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS D 105 " - pdb=" SG CYS D 110 " distance=2.02 Simple disulfide: pdb=" SG CYS E 105 " - pdb=" SG CYS E 110 " distance=2.02 Simple disulfide: pdb=" SG CYS F 105 " - pdb=" SG CYS F 110 " distance=2.02 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 Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 346.8 milliseconds 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2400 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 1 sheets defined 60.0% alpha, 2.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 4 through 17 removed outlier: 3.561A pdb=" N LEU A 8 " --> pdb=" O LEU A 4 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR A 9 " --> pdb=" O SER A 5 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N ASP A 10 " --> pdb=" O ASN A 6 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL A 12 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY A 13 " --> pdb=" O THR A 9 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER A 17 " --> pdb=" O GLY A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 32 removed outlier: 5.119A pdb=" N LEU A 23 " --> pdb=" O THR A 19 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE A 29 " --> pdb=" O GLY A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 48 removed outlier: 3.625A pdb=" N ILE A 45 " --> pdb=" O ALA A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 61 removed outlier: 4.013A pdb=" N ALA A 61 " --> pdb=" O THR A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 91 removed outlier: 3.908A pdb=" N VAL A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU A 80 " --> pdb=" O PHE A 76 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL A 85 " --> pdb=" O GLY A 81 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE A 86 " --> pdb=" O ILE A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 112 removed outlier: 3.532A pdb=" N ALA A 112 " --> pdb=" O GLY A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 126 removed outlier: 3.853A pdb=" N ALA A 121 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 140 removed outlier: 3.769A pdb=" N GLY A 137 " --> pdb=" O ALA A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 164 removed outlier: 3.549A pdb=" N ALA A 151 " --> pdb=" O ALA A 147 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VAL A 154 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LYS A 161 " --> pdb=" O ILE A 157 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG A 162 " --> pdb=" O TYR A 158 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS A 163 " --> pdb=" O LEU A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 216 removed outlier: 3.923A pdb=" N ILE A 215 " --> pdb=" O ILE A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 236 Processing helix chain 'A' and resid 239 through 244 removed outlier: 3.690A pdb=" N GLU A 244 " --> pdb=" O GLU A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 250 No H-bonds generated for 'chain 'A' and resid 248 through 250' Processing helix chain 'A' and resid 251 through 268 removed outlier: 3.606A pdb=" N SER A 256 " --> pdb=" O ARG A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 297 removed outlier: 3.723A pdb=" N VAL A 282 " --> pdb=" O GLN A 278 " (cutoff:3.500A) Proline residue: A 288 - end of helix removed outlier: 3.663A pdb=" N GLY A 292 " --> pdb=" O PRO A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 322 removed outlier: 3.645A pdb=" N VAL A 315 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA A 320 " --> pdb=" O LEU A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 349 removed outlier: 3.689A pdb=" N TYR A 344 " --> pdb=" O ASN A 340 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY A 346 " --> pdb=" O SER A 342 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER A 347 " --> pdb=" O ALA A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 359 Processing helix chain 'A' and resid 360 through 371 removed outlier: 3.554A pdb=" N LEU A 367 " --> pdb=" O LEU A 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 17 removed outlier: 3.561A pdb=" N LEU B 8 " --> pdb=" O LEU B 4 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR B 9 " --> pdb=" O SER B 5 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N ASP B 10 " --> pdb=" O ASN B 6 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL B 12 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLY B 13 " --> pdb=" O THR B 9 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER B 17 " --> pdb=" O GLY B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 32 removed outlier: 5.119A pdb=" N LEU B 23 " --> pdb=" O THR B 19 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE B 29 " --> pdb=" O GLY B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 48 removed outlier: 3.625A pdb=" N ILE B 45 " --> pdb=" O ALA B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 61 removed outlier: 4.012A pdb=" N ALA B 61 " --> pdb=" O THR B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 91 removed outlier: 3.908A pdb=" N VAL B 78 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU B 80 " --> pdb=" O PHE B 76 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL B 85 " --> pdb=" O GLY B 81 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE B 86 " --> pdb=" O ILE B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 112 Processing helix chain 'B' and resid 114 through 126 removed outlier: 3.745A pdb=" N ALA B 121 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 140 removed outlier: 3.770A pdb=" N GLY B 137 " --> pdb=" O ALA B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 164 removed outlier: 3.549A pdb=" N ALA B 151 " --> pdb=" O ALA B 147 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE B 152 " --> pdb=" O LEU B 148 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N VAL B 154 " --> pdb=" O THR B 150 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LYS B 161 " --> pdb=" O ILE B 157 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG B 162 " --> pdb=" O TYR B 158 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS B 163 " --> pdb=" O LEU B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 216 removed outlier: 3.922A pdb=" N ILE B 215 " --> pdb=" O ILE B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 236 Processing helix chain 'B' and resid 239 through 244 removed outlier: 3.690A pdb=" N GLU B 244 " --> pdb=" O GLU B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 250 No H-bonds generated for 'chain 'B' and resid 248 through 250' Processing helix chain 'B' and resid 251 through 268 removed outlier: 3.605A pdb=" N SER B 256 " --> pdb=" O ARG B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 297 removed outlier: 3.723A pdb=" N VAL B 282 " --> pdb=" O GLN B 278 " (cutoff:3.500A) Proline residue: B 288 - end of helix removed outlier: 3.663A pdb=" N GLY B 292 " --> pdb=" O PRO B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 322 removed outlier: 3.644A pdb=" N VAL B 315 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA B 320 " --> pdb=" O LEU B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 349 removed outlier: 3.689A pdb=" N TYR B 344 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY B 346 " --> pdb=" O SER B 342 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER B 347 " --> pdb=" O ALA B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 359 Processing helix chain 'B' and resid 360 through 371 removed outlier: 3.554A pdb=" N LEU B 367 " --> pdb=" O LEU B 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 17 removed outlier: 3.562A pdb=" N LEU C 8 " --> pdb=" O LEU C 4 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR C 9 " --> pdb=" O SER C 5 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N ASP C 10 " --> pdb=" O ASN C 6 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL C 12 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLY C 13 " --> pdb=" O THR C 9 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER C 17 " --> pdb=" O GLY C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 32 removed outlier: 5.120A pdb=" N LEU C 23 " --> pdb=" O THR C 19 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE C 29 " --> pdb=" O GLY C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 48 removed outlier: 3.625A pdb=" N ILE C 45 " --> pdb=" O ALA C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 61 removed outlier: 4.013A pdb=" N ALA C 61 " --> pdb=" O THR C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 91 removed outlier: 3.907A pdb=" N VAL C 78 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU C 80 " --> pdb=" O PHE C 76 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL C 85 " --> pdb=" O GLY C 81 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE C 86 " --> pdb=" O ILE C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 112 removed outlier: 3.606A pdb=" N ALA C 112 " --> pdb=" O GLY C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 126 removed outlier: 3.745A pdb=" N ALA C 121 " --> pdb=" O THR C 117 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU C 126 " --> pdb=" O LEU C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 140 removed outlier: 3.770A pdb=" N GLY C 137 " --> pdb=" O ALA C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 164 removed outlier: 3.550A pdb=" N ALA C 151 " --> pdb=" O ALA C 147 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VAL C 154 " --> pdb=" O THR C 150 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LYS C 161 " --> pdb=" O ILE C 157 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG C 162 " --> pdb=" O TYR C 158 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS C 163 " --> pdb=" O LEU C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 216 removed outlier: 3.922A pdb=" N ILE C 215 " --> pdb=" O ILE C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 236 Processing helix chain 'C' and resid 239 through 244 removed outlier: 3.690A pdb=" N GLU C 244 " --> pdb=" O GLU C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 250 No H-bonds generated for 'chain 'C' and resid 248 through 250' Processing helix chain 'C' and resid 251 through 268 removed outlier: 3.605A pdb=" N SER C 256 " --> pdb=" O ARG C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 297 removed outlier: 3.723A pdb=" N VAL C 282 " --> pdb=" O GLN C 278 " (cutoff:3.500A) Proline residue: C 288 - end of helix removed outlier: 3.664A pdb=" N GLY C 292 " --> pdb=" O PRO C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 322 removed outlier: 3.645A pdb=" N VAL C 315 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA C 320 " --> pdb=" O LEU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 349 removed outlier: 3.689A pdb=" N TYR C 344 " --> pdb=" O ASN C 340 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY C 346 " --> pdb=" O SER C 342 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER C 347 " --> pdb=" O ALA C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 359 Processing helix chain 'C' and resid 360 through 371 removed outlier: 3.555A pdb=" N LEU C 367 " --> pdb=" O LEU C 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 28 removed outlier: 3.872A pdb=" N GLY D 28 " --> pdb=" O ILE D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 81 removed outlier: 3.553A pdb=" N ALA D 72 " --> pdb=" O THR D 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 28 removed outlier: 3.871A pdb=" N GLY E 28 " --> pdb=" O ILE E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 81 removed outlier: 3.554A pdb=" N ALA E 72 " --> pdb=" O THR E 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 28 removed outlier: 3.872A pdb=" N GLY F 28 " --> pdb=" O ILE F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 81 removed outlier: 3.554A pdb=" N ALA F 72 " --> pdb=" O THR F 68 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 3 through 13 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 3 through 13 current: chain 'D' and resid 59 through 66 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 59 through 66 current: chain 'E' and resid 59 through 66 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 59 through 66 current: chain 'F' and resid 59 through 66 No H-bonds generated for sheet with id=AA1 435 hydrogen bonds defined for protein. 1269 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: 1.15 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2636 1.33 - 1.45: 1741 1.45 - 1.57: 5712 1.57 - 1.69: 3 1.69 - 1.81: 96 Bond restraints: 10188 Sorted by residual: bond pdb=" N ALA B 320 " pdb=" CA ALA B 320 " ideal model delta sigma weight residual 1.458 1.506 -0.048 1.30e-02 5.92e+03 1.38e+01 bond pdb=" N VAL B 113 " pdb=" CA VAL B 113 " ideal model delta sigma weight residual 1.456 1.494 -0.039 1.11e-02 8.12e+03 1.21e+01 bond pdb=" N ILE A 326 " pdb=" CA ILE A 326 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.48e+00 bond pdb=" N TYR A 140 " pdb=" CA TYR A 140 " ideal model delta sigma weight residual 1.462 1.486 -0.024 8.50e-03 1.38e+04 7.94e+00 bond pdb=" N VAL A 113 " pdb=" CA VAL A 113 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.65e+00 ... (remaining 10183 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 12924 2.29 - 4.58: 719 4.58 - 6.87: 111 6.87 - 9.16: 79 9.16 - 11.45: 15 Bond angle restraints: 13848 Sorted by residual: angle pdb=" N LEU A 50 " pdb=" CA LEU A 50 " pdb=" C LEU A 50 " ideal model delta sigma weight residual 113.18 104.56 8.62 1.33e+00 5.65e-01 4.20e+01 angle pdb=" N LEU B 50 " pdb=" CA LEU B 50 " pdb=" C LEU B 50 " ideal model delta sigma weight residual 113.18 104.59 8.59 1.33e+00 5.65e-01 4.17e+01 angle pdb=" N ALA B 320 " pdb=" CA ALA B 320 " pdb=" C ALA B 320 " ideal model delta sigma weight residual 112.23 105.15 7.08 1.26e+00 6.30e-01 3.15e+01 angle pdb=" C ALA B 112 " pdb=" CA ALA B 112 " pdb=" CB ALA B 112 " ideal model delta sigma weight residual 110.42 121.19 -10.77 1.99e+00 2.53e-01 2.93e+01 angle pdb=" CA THR A 34 " pdb=" CB THR A 34 " pdb=" CG2 THR A 34 " ideal model delta sigma weight residual 110.50 119.21 -8.71 1.70e+00 3.46e-01 2.63e+01 ... (remaining 13843 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.87: 5629 15.87 - 31.74: 303 31.74 - 47.61: 103 47.61 - 63.48: 7 63.48 - 79.35: 6 Dihedral angle restraints: 6048 sinusoidal: 2280 harmonic: 3768 Sorted by residual: dihedral pdb=" CA PHE A 308 " pdb=" C PHE A 308 " pdb=" N SER A 309 " pdb=" CA SER A 309 " ideal model delta harmonic sigma weight residual -180.00 -154.73 -25.27 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA PHE C 308 " pdb=" C PHE C 308 " pdb=" N SER C 309 " pdb=" CA SER C 309 " ideal model delta harmonic sigma weight residual -180.00 -154.76 -25.24 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA PHE B 308 " pdb=" C PHE B 308 " pdb=" N SER B 309 " pdb=" CA SER B 309 " ideal model delta harmonic sigma weight residual -180.00 -154.80 -25.20 0 5.00e+00 4.00e-02 2.54e+01 ... (remaining 6045 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1265 0.071 - 0.143: 354 0.143 - 0.214: 37 0.214 - 0.285: 16 0.285 - 0.356: 5 Chirality restraints: 1677 Sorted by residual: chirality pdb=" CA THR C 34 " pdb=" N THR C 34 " pdb=" C THR C 34 " pdb=" CB THR C 34 " both_signs ideal model delta sigma weight residual False 2.53 2.17 0.36 2.00e-01 2.50e+01 3.17e+00 chirality pdb=" CA THR A 34 " pdb=" N THR A 34 " pdb=" C THR A 34 " pdb=" CB THR A 34 " both_signs ideal model delta sigma weight residual False 2.53 2.17 0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" CA THR B 34 " pdb=" N THR B 34 " pdb=" C THR B 34 " pdb=" CB THR B 34 " both_signs ideal model delta sigma weight residual False 2.53 2.17 0.35 2.00e-01 2.50e+01 3.12e+00 ... (remaining 1674 not shown) Planarity restraints: 1704 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 329 " -0.055 5.00e-02 4.00e+02 8.20e-02 1.08e+01 pdb=" N PRO B 330 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO B 330 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 330 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 329 " 0.055 5.00e-02 4.00e+02 8.19e-02 1.07e+01 pdb=" N PRO C 330 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO C 330 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 330 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 22 " -0.010 2.00e-02 2.50e+03 1.87e-02 6.14e+00 pdb=" CG PHE B 22 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE B 22 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 PHE B 22 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE B 22 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE B 22 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE B 22 " 0.002 2.00e-02 2.50e+03 ... (remaining 1701 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 29 2.49 - 3.09: 6538 3.09 - 3.70: 15467 3.70 - 4.30: 22668 4.30 - 4.90: 37046 Nonbonded interactions: 81748 Sorted by model distance: nonbonded pdb=" O PRO A 329 " pdb=" O THR A 331 " model vdw 1.890 3.040 nonbonded pdb=" CE MET A 118 " pdb=" CD1 ILE A 319 " model vdw 1.909 3.880 nonbonded pdb=" O PHE C 110 " pdb="NA NA C 401 " model vdw 2.010 3.210 nonbonded pdb=" O PHE B 110 " pdb="NA NA B 401 " model vdw 2.061 3.210 nonbonded pdb=" O PHE A 110 " pdb="NA NA A 401 " model vdw 2.207 3.210 ... (remaining 81743 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' selection = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and (resid 2 through 94 or resid 96 through 201)) selection = (chain 'E' and (resid 2 through 94 or resid 96 through 201)) selection = (chain 'F' and (resid 2 through 94 or resid 96 through 201)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.390 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 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 : 0.009 0.073 10191 Z= 0.411 Angle : 1.302 11.455 13854 Z= 0.675 Chirality : 0.067 0.356 1677 Planarity : 0.008 0.082 1704 Dihedral : 11.590 79.350 3639 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer: Outliers : 1.90 % Allowed : 6.86 % Favored : 91.24 % Cbeta Deviations : 0.42 % 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: -6.27 (0.15), residues: 1314 helix: -4.50 (0.08), residues: 813 sheet: -2.16 (0.48), residues: 102 loop : -3.29 (0.24), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.002 ARG A 269 TYR 0.028 0.003 TYR E 87 PHE 0.039 0.004 PHE B 22 TRP 0.012 0.003 TRP C 135 HIS 0.021 0.006 HIS B 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00943 / 0.41 (10188) covalent geometry : angle 1.30205 / 0.68 (13848) SS BOND : bond 0.01303 / 0.65 ( 3) SS BOND : angle 1.81482 / 0.83 ( 6) hydrogen bonds : bond 0.32308 / 20.69 ( 435) hydrogen bonds : angle 10.17854 / 6.97 ( 1269) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 286 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 PHE cc_start: 0.8296 (t80) cc_final: 0.7964 (t80) REVERT: A 17 SER cc_start: 0.9023 (t) cc_final: 0.8491 (p) REVERT: A 35 GLN cc_start: 0.7669 (mp10) cc_final: 0.7278 (mm110) REVERT: A 129 LYS cc_start: 0.7685 (mmtt) cc_final: 0.7461 (mttp) REVERT: A 238 LYS cc_start: 0.8660 (mtmt) cc_final: 0.8164 (mttt) REVERT: A 250 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8519 (pp) REVERT: A 252 ARG cc_start: 0.8341 (ttm110) cc_final: 0.7411 (mtt180) REVERT: A 275 LYS cc_start: 0.8583 (ttmp) cc_final: 0.8003 (mtmt) REVERT: A 278 GLN cc_start: 0.7508 (pt0) cc_final: 0.7242 (mt0) REVERT: A 319 ILE cc_start: 0.8152 (OUTLIER) cc_final: 0.7934 (mt) REVERT: B 3 PHE cc_start: 0.7914 (t80) cc_final: 0.7706 (t80) REVERT: B 16 GLN cc_start: 0.8446 (mm-40) cc_final: 0.8223 (mm-40) REVERT: B 17 SER cc_start: 0.9006 (t) cc_final: 0.8380 (p) REVERT: B 35 GLN cc_start: 0.7658 (mp10) cc_final: 0.7400 (mm110) REVERT: B 70 MET cc_start: 0.7608 (mtp) cc_final: 0.7393 (mtm) REVERT: B 79 ILE cc_start: 0.7905 (mm) cc_final: 0.7677 (mt) REVERT: B 238 LYS cc_start: 0.8686 (mtmt) cc_final: 0.8344 (mtmt) REVERT: B 250 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8290 (pp) REVERT: B 252 ARG cc_start: 0.8077 (ttm110) cc_final: 0.7085 (mtt180) REVERT: B 259 MET cc_start: 0.8700 (mmm) cc_final: 0.8453 (mmt) REVERT: B 275 LYS cc_start: 0.8412 (ttmp) cc_final: 0.7909 (mtmt) REVERT: B 278 GLN cc_start: 0.7306 (pt0) cc_final: 0.7012 (mt0) REVERT: B 298 LEU cc_start: 0.8956 (tm) cc_final: 0.8738 (tp) REVERT: B 300 MET cc_start: 0.8412 (mmm) cc_final: 0.7881 (mmt) REVERT: C 3 PHE cc_start: 0.7845 (t80) cc_final: 0.7577 (t80) REVERT: C 17 SER cc_start: 0.9120 (t) cc_final: 0.8532 (p) REVERT: C 79 ILE cc_start: 0.7954 (mm) cc_final: 0.7750 (mt) REVERT: C 129 LYS cc_start: 0.7794 (mmtt) cc_final: 0.7461 (mttp) REVERT: C 132 TYR cc_start: 0.8616 (p90) cc_final: 0.8253 (p90) REVERT: C 238 LYS cc_start: 0.8574 (mtmt) cc_final: 0.8231 (mttt) REVERT: C 250 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8561 (pp) REVERT: C 252 ARG cc_start: 0.8121 (ttm110) cc_final: 0.7674 (ttm170) REVERT: C 275 LYS cc_start: 0.8552 (ttmp) cc_final: 0.7994 (mtmt) REVERT: C 278 GLN cc_start: 0.7541 (pt0) cc_final: 0.7140 (mt0) REVERT: C 300 MET cc_start: 0.8483 (mmm) cc_final: 0.7977 (mmt) REVERT: D 57 GLU cc_start: 0.7177 (pm20) cc_final: 0.6898 (mp0) REVERT: D 67 GLU cc_start: 0.7815 (tt0) cc_final: 0.7567 (mt-10) REVERT: E 53 THR cc_start: 0.8830 (p) cc_final: 0.8622 (m) REVERT: E 57 GLU cc_start: 0.7081 (pm20) cc_final: 0.6859 (pm20) REVERT: F 69 ARG cc_start: 0.8473 (tpt-90) cc_final: 0.8128 (tpt-90) outliers start: 20 outliers final: 7 residues processed: 301 average time/residue: 0.0927 time to fit residues: 38.0187 Evaluate side-chains 224 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 213 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 319 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 6.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 6 ASN A 14 GLN A 291 HIS A 340 ASN B 6 ASN B 14 GLN B 291 HIS B 340 ASN C 6 ASN C 14 GLN C 340 ASN D 59 ASN E 44 ASN ** E 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 ASN F 59 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.120336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.093646 restraints weight = 25616.144| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 2.96 r_work: 0.2751 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2758 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2758 r_free = 0.2758 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2758 r_free = 0.2758 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.2758 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10191 Z= 0.144 Angle : 0.764 6.696 13854 Z= 0.375 Chirality : 0.046 0.224 1677 Planarity : 0.006 0.069 1704 Dihedral : 6.873 51.898 1454 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.57 % Allowed : 12.57 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.03 (0.19), residues: 1314 helix: -2.53 (0.14), residues: 792 sheet: -2.09 (0.46), residues: 105 loop : -2.68 (0.27), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 78 TYR 0.015 0.002 TYR A 344 PHE 0.013 0.002 PHE C 364 TRP 0.009 0.002 TRP B 267 HIS 0.012 0.003 HIS C 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (10188) covalent geometry : angle 0.76424 / 0.38 (13848) SS BOND : bond 0.00425 / 0.21 ( 3) SS BOND : angle 0.75797 / 0.36 ( 6) hydrogen bonds : bond 0.04630 / 3.03 ( 435) hydrogen bonds : angle 4.54935 / 3.06 ( 1269) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 231 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: A 10 ASP cc_start: 0.8331 (OUTLIER) cc_final: 0.7821 (m-30) REVERT: A 17 SER cc_start: 0.8749 (t) cc_final: 0.8202 (p) REVERT: A 35 GLN cc_start: 0.8028 (mp10) cc_final: 0.7635 (mm110) REVERT: A 40 GLU cc_start: 0.8085 (tt0) cc_final: 0.7755 (mt-10) REVERT: A 62 ILE cc_start: 0.9005 (tt) cc_final: 0.8603 (tt) REVERT: A 238 LYS cc_start: 0.8416 (mtmt) cc_final: 0.8032 (mttt) REVERT: A 250 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8171 (pp) REVERT: A 275 LYS cc_start: 0.8592 (ttmp) cc_final: 0.8028 (mtmt) REVERT: A 278 GLN cc_start: 0.7961 (pt0) cc_final: 0.7386 (mt0) REVERT: A 298 LEU cc_start: 0.8627 (tp) cc_final: 0.8415 (tp) REVERT: B 3 PHE cc_start: 0.7627 (t80) cc_final: 0.7299 (t80) REVERT: B 10 ASP cc_start: 0.8436 (t0) cc_final: 0.8070 (m-30) REVERT: B 35 GLN cc_start: 0.7986 (mp10) cc_final: 0.7674 (mm110) REVERT: B 40 GLU cc_start: 0.8286 (tt0) cc_final: 0.7765 (mt-10) REVERT: B 79 ILE cc_start: 0.7982 (mm) cc_final: 0.7760 (mt) REVERT: B 238 LYS cc_start: 0.8803 (mtmt) cc_final: 0.8501 (mtmt) REVERT: B 250 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8159 (pp) REVERT: B 272 GLU cc_start: 0.8315 (tt0) cc_final: 0.8001 (tt0) REVERT: B 275 LYS cc_start: 0.8462 (ttmp) cc_final: 0.8025 (mtmt) REVERT: B 278 GLN cc_start: 0.7817 (pt0) cc_final: 0.7296 (mt0) REVERT: B 298 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8491 (tp) REVERT: C 10 ASP cc_start: 0.8277 (t0) cc_final: 0.7929 (m-30) REVERT: C 40 GLU cc_start: 0.8284 (mt-10) cc_final: 0.7934 (mt-10) REVERT: C 79 ILE cc_start: 0.8031 (mm) cc_final: 0.7817 (mt) REVERT: C 89 ARG cc_start: 0.8298 (tmt-80) cc_final: 0.7991 (tpt-90) REVERT: C 132 TYR cc_start: 0.8755 (p90) cc_final: 0.8392 (p90) REVERT: C 250 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8321 (pp) REVERT: C 259 MET cc_start: 0.9175 (mmt) cc_final: 0.8883 (mmt) REVERT: C 275 LYS cc_start: 0.8563 (ttmp) cc_final: 0.8169 (mtmt) REVERT: C 278 GLN cc_start: 0.8015 (pt0) cc_final: 0.7357 (mt0) REVERT: D 57 GLU cc_start: 0.7714 (pm20) cc_final: 0.7482 (mt-10) REVERT: D 67 GLU cc_start: 0.8414 (tt0) cc_final: 0.8027 (mt-10) REVERT: F 6 ASN cc_start: 0.8770 (m-40) cc_final: 0.8552 (m-40) outliers start: 27 outliers final: 16 residues processed: 249 average time/residue: 0.0761 time to fit residues: 27.4974 Evaluate side-chains 209 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 188 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain E residue 68 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 93 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 124 optimal weight: 10.0000 chunk 120 optimal weight: 0.8980 chunk 82 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 ASN D 44 ASN E 50 GLN F 44 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.118607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.091505 restraints weight = 28892.637| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 3.18 r_work: 0.2729 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2724 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2724 r_free = 0.2724 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2724 r_free = 0.2724 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2724 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10191 Z= 0.138 Angle : 0.721 9.772 13854 Z= 0.345 Chirality : 0.045 0.226 1677 Planarity : 0.005 0.059 1704 Dihedral : 6.280 50.224 1445 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 4.29 % Allowed : 13.62 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.64 (0.21), residues: 1314 helix: -1.25 (0.17), residues: 810 sheet: -1.93 (0.45), residues: 105 loop : -2.44 (0.28), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 78 TYR 0.015 0.002 TYR A 140 PHE 0.011 0.001 PHE C 110 TRP 0.011 0.002 TRP A 135 HIS 0.012 0.003 HIS C 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (10188) covalent geometry : angle 0.72129 / 0.35 (13848) SS BOND : bond 0.00354 / 0.18 ( 3) SS BOND : angle 0.62446 / 0.29 ( 6) hydrogen bonds : bond 0.04003 / 2.65 ( 435) hydrogen bonds : angle 4.03701 / 2.71 ( 1269) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 189 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: A 10 ASP cc_start: 0.8358 (OUTLIER) cc_final: 0.7885 (m-30) REVERT: A 35 GLN cc_start: 0.7915 (mp10) cc_final: 0.7586 (mm110) REVERT: A 80 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8354 (tt) REVERT: A 238 LYS cc_start: 0.8433 (mtmt) cc_final: 0.7967 (mttt) REVERT: A 250 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8084 (pp) REVERT: A 275 LYS cc_start: 0.8553 (ttmp) cc_final: 0.8034 (mtmt) REVERT: A 278 GLN cc_start: 0.7965 (pt0) cc_final: 0.7375 (mt0) REVERT: B 3 PHE cc_start: 0.7584 (t80) cc_final: 0.7301 (t80) REVERT: B 10 ASP cc_start: 0.8431 (t0) cc_final: 0.8092 (m-30) REVERT: B 35 GLN cc_start: 0.7822 (mp10) cc_final: 0.7597 (mm110) REVERT: B 79 ILE cc_start: 0.8006 (mm) cc_final: 0.7760 (mt) REVERT: B 161 LYS cc_start: 0.8008 (ptpt) cc_final: 0.7787 (ptpp) REVERT: B 238 LYS cc_start: 0.8830 (mtmt) cc_final: 0.8473 (mtmt) REVERT: B 243 TYR cc_start: 0.9105 (t80) cc_final: 0.8864 (t80) REVERT: B 250 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8111 (pp) REVERT: B 272 GLU cc_start: 0.8409 (tt0) cc_final: 0.8128 (tt0) REVERT: B 275 LYS cc_start: 0.8465 (ttmp) cc_final: 0.8111 (mtmt) REVERT: B 278 GLN cc_start: 0.7829 (pt0) cc_final: 0.7274 (mt0) REVERT: B 298 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8622 (tp) REVERT: C 10 ASP cc_start: 0.8300 (t0) cc_final: 0.7948 (m-30) REVERT: C 79 ILE cc_start: 0.8020 (mm) cc_final: 0.7793 (mt) REVERT: C 89 ARG cc_start: 0.8213 (tmt-80) cc_final: 0.7840 (ttt-90) REVERT: C 132 TYR cc_start: 0.8776 (p90) cc_final: 0.8313 (p90) REVERT: C 250 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8282 (pp) REVERT: C 275 LYS cc_start: 0.8524 (ttmp) cc_final: 0.8126 (mtmt) REVERT: D 57 GLU cc_start: 0.7646 (pm20) cc_final: 0.7414 (mt-10) REVERT: D 67 GLU cc_start: 0.8450 (tt0) cc_final: 0.7958 (mt-10) REVERT: F 6 ASN cc_start: 0.8791 (m-40) cc_final: 0.8579 (m-40) outliers start: 45 outliers final: 26 residues processed: 220 average time/residue: 0.0832 time to fit residues: 26.0694 Evaluate side-chains 209 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 177 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 50 GLN Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain F residue 86 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 15 optimal weight: 0.9990 chunk 85 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 119 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 128 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 chunk 87 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 291 HIS E 50 GLN E 52 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.118428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.093520 restraints weight = 17846.309| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 2.31 r_work: 0.2775 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2773 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2773 r_free = 0.2773 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2773 r_free = 0.2773 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2773 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10191 Z= 0.138 Angle : 0.694 8.026 13854 Z= 0.333 Chirality : 0.045 0.211 1677 Planarity : 0.004 0.054 1704 Dihedral : 6.102 48.673 1444 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 4.57 % Allowed : 13.52 % Favored : 81.90 % 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: -1.90 (0.22), residues: 1314 helix: -0.61 (0.18), residues: 813 sheet: -1.73 (0.46), residues: 105 loop : -2.28 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 78 TYR 0.014 0.001 TYR A 140 PHE 0.012 0.001 PHE C 110 TRP 0.011 0.002 TRP B 267 HIS 0.012 0.003 HIS B 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (10188) covalent geometry : angle 0.69375 / 0.33 (13848) SS BOND : bond 0.00384 / 0.19 ( 3) SS BOND : angle 0.55808 / 0.26 ( 6) hydrogen bonds : bond 0.03663 / 2.42 ( 435) hydrogen bonds : angle 3.83665 / 2.57 ( 1269) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 180 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ASP cc_start: 0.8371 (OUTLIER) cc_final: 0.7950 (m-30) REVERT: A 16 GLN cc_start: 0.8316 (mm-40) cc_final: 0.7888 (mt0) REVERT: A 35 GLN cc_start: 0.7929 (mp10) cc_final: 0.7641 (mm110) REVERT: A 80 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8349 (tt) REVERT: A 158 TYR cc_start: 0.8632 (t80) cc_final: 0.8324 (t80) REVERT: A 238 LYS cc_start: 0.8408 (mtmt) cc_final: 0.8020 (mttt) REVERT: A 244 GLU cc_start: 0.8522 (pt0) cc_final: 0.8203 (pt0) REVERT: A 250 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8082 (pp) REVERT: A 275 LYS cc_start: 0.8528 (ttmp) cc_final: 0.8024 (mtmt) REVERT: A 278 GLN cc_start: 0.7910 (pt0) cc_final: 0.7354 (mt0) REVERT: A 359 VAL cc_start: 0.8804 (m) cc_final: 0.8541 (p) REVERT: B 3 PHE cc_start: 0.7720 (t80) cc_final: 0.7435 (t80) REVERT: B 10 ASP cc_start: 0.8384 (t0) cc_final: 0.8122 (m-30) REVERT: B 79 ILE cc_start: 0.8162 (mm) cc_final: 0.7878 (mt) REVERT: B 132 TYR cc_start: 0.8650 (p90) cc_final: 0.8297 (p90) REVERT: B 238 LYS cc_start: 0.8803 (mtmt) cc_final: 0.8400 (mtmt) REVERT: B 250 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8098 (pp) REVERT: B 272 GLU cc_start: 0.8266 (tt0) cc_final: 0.8006 (tt0) REVERT: B 275 LYS cc_start: 0.8419 (ttmp) cc_final: 0.8089 (mtmt) REVERT: B 278 GLN cc_start: 0.7783 (pt0) cc_final: 0.7256 (mt0) REVERT: B 359 VAL cc_start: 0.8810 (p) cc_final: 0.8454 (t) REVERT: C 10 ASP cc_start: 0.8262 (t0) cc_final: 0.7956 (m-30) REVERT: C 40 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7564 (mm-30) REVERT: C 79 ILE cc_start: 0.8169 (mm) cc_final: 0.7928 (mt) REVERT: C 132 TYR cc_start: 0.8831 (p90) cc_final: 0.8259 (p90) REVERT: C 250 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8249 (pp) REVERT: C 259 MET cc_start: 0.9188 (mmt) cc_final: 0.8945 (mmp) REVERT: C 275 LYS cc_start: 0.8515 (ttmp) cc_final: 0.8132 (mtmt) REVERT: D 67 GLU cc_start: 0.8253 (tt0) cc_final: 0.7964 (tt0) REVERT: E 26 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8512 (mt-10) REVERT: F 100 TYR cc_start: 0.8613 (m-80) cc_final: 0.8292 (m-80) outliers start: 48 outliers final: 34 residues processed: 215 average time/residue: 0.0760 time to fit residues: 23.4493 Evaluate side-chains 213 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 173 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 50 GLN Chi-restraints excluded: chain E residue 52 ASN Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain F residue 86 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 106 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 46 optimal weight: 8.9990 chunk 67 optimal weight: 0.9990 chunk 39 optimal weight: 0.0980 chunk 108 optimal weight: 4.9990 chunk 88 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 291 HIS ** E 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.120428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.093308 restraints weight = 28072.433| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 3.03 r_work: 0.2756 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2746 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2746 r_free = 0.2746 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2746 r_free = 0.2746 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2746 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10191 Z= 0.118 Angle : 0.665 6.937 13854 Z= 0.318 Chirality : 0.044 0.207 1677 Planarity : 0.004 0.052 1704 Dihedral : 5.941 47.150 1444 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 4.38 % Allowed : 15.14 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.23), residues: 1314 helix: -0.09 (0.19), residues: 792 sheet: -1.54 (0.47), residues: 99 loop : -2.40 (0.27), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 78 TYR 0.013 0.001 TYR A 344 PHE 0.011 0.001 PHE C 364 TRP 0.013 0.002 TRP B 267 HIS 0.012 0.003 HIS B 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (10188) covalent geometry : angle 0.66463 / 0.32 (13848) SS BOND : bond 0.00290 / 0.15 ( 3) SS BOND : angle 0.40561 / 0.19 ( 6) hydrogen bonds : bond 0.03293 / 2.17 ( 435) hydrogen bonds : angle 3.72303 / 2.49 ( 1269) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 193 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: A 10 ASP cc_start: 0.8367 (OUTLIER) cc_final: 0.7972 (m-30) REVERT: A 16 GLN cc_start: 0.8313 (mm-40) cc_final: 0.7996 (mt0) REVERT: A 80 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8351 (tt) REVERT: A 158 TYR cc_start: 0.8636 (t80) cc_final: 0.8308 (t80) REVERT: A 238 LYS cc_start: 0.8400 (mtmt) cc_final: 0.7964 (mttt) REVERT: A 250 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8019 (pp) REVERT: A 275 LYS cc_start: 0.8485 (ttmp) cc_final: 0.8022 (mtmt) REVERT: A 278 GLN cc_start: 0.7983 (pt0) cc_final: 0.7390 (mt0) REVERT: A 359 VAL cc_start: 0.8798 (m) cc_final: 0.8552 (p) REVERT: B 3 PHE cc_start: 0.7664 (t80) cc_final: 0.7362 (t80) REVERT: B 10 ASP cc_start: 0.8382 (t0) cc_final: 0.8144 (m-30) REVERT: B 79 ILE cc_start: 0.8136 (mm) cc_final: 0.7859 (mt) REVERT: B 132 TYR cc_start: 0.8662 (p90) cc_final: 0.8289 (p90) REVERT: B 238 LYS cc_start: 0.8784 (mtmt) cc_final: 0.8539 (mtmt) REVERT: B 250 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8047 (pp) REVERT: B 272 GLU cc_start: 0.8333 (tt0) cc_final: 0.8094 (tt0) REVERT: B 275 LYS cc_start: 0.8366 (ttmp) cc_final: 0.8104 (mtmt) REVERT: B 278 GLN cc_start: 0.7842 (pt0) cc_final: 0.7308 (mt0) REVERT: B 359 VAL cc_start: 0.8877 (p) cc_final: 0.8546 (t) REVERT: C 10 ASP cc_start: 0.8266 (t0) cc_final: 0.7995 (m-30) REVERT: C 79 ILE cc_start: 0.8103 (mm) cc_final: 0.7857 (mt) REVERT: C 132 TYR cc_start: 0.8870 (p90) cc_final: 0.8347 (p90) REVERT: C 250 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8272 (pp) REVERT: C 259 MET cc_start: 0.9186 (mmt) cc_final: 0.8945 (mmp) REVERT: C 275 LYS cc_start: 0.8486 (ttmp) cc_final: 0.8162 (mtmt) REVERT: D 57 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7185 (mp0) REVERT: D 67 GLU cc_start: 0.8358 (tt0) cc_final: 0.8038 (tt0) REVERT: D 78 ARG cc_start: 0.8662 (mtp85) cc_final: 0.8437 (mtp180) REVERT: F 100 TYR cc_start: 0.8669 (m-80) cc_final: 0.8400 (m-80) outliers start: 46 outliers final: 32 residues processed: 223 average time/residue: 0.0798 time to fit residues: 25.5271 Evaluate side-chains 218 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 180 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 303 HIS Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 303 HIS Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 52 ASN Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain F residue 86 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 2 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 116 optimal weight: 0.9990 chunk 121 optimal weight: 0.9980 chunk 42 optimal weight: 7.9990 chunk 108 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 89 optimal weight: 8.9990 chunk 118 optimal weight: 1.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 35 GLN E 52 ASN F 52 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.118663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.092853 restraints weight = 21973.216| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 2.62 r_work: 0.2785 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2767 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2767 r_free = 0.2767 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2767 r_free = 0.2767 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2767 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10191 Z= 0.124 Angle : 0.666 7.292 13854 Z= 0.319 Chirality : 0.044 0.208 1677 Planarity : 0.004 0.050 1704 Dihedral : 5.896 46.783 1444 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 5.62 % Allowed : 14.67 % Favored : 79.71 % 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: -1.16 (0.23), residues: 1314 helix: 0.06 (0.19), residues: 810 sheet: -1.43 (0.48), residues: 99 loop : -2.14 (0.28), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 78 TYR 0.014 0.001 TYR E 100 PHE 0.013 0.001 PHE A 3 TRP 0.012 0.002 TRP B 267 HIS 0.011 0.003 HIS B 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 (10188) covalent geometry : angle 0.66605 / 0.32 (13848) SS BOND : bond 0.00294 / 0.15 ( 3) SS BOND : angle 0.41841 / 0.19 ( 6) hydrogen bonds : bond 0.03328 / 2.19 ( 435) hydrogen bonds : angle 3.67647 / 2.47 ( 1269) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 192 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: A 10 ASP cc_start: 0.8389 (OUTLIER) cc_final: 0.8059 (m-30) REVERT: A 16 GLN cc_start: 0.8303 (mm-40) cc_final: 0.8001 (mt0) REVERT: A 80 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8299 (tt) REVERT: A 158 TYR cc_start: 0.8611 (t80) cc_final: 0.8255 (t80) REVERT: A 238 LYS cc_start: 0.8397 (mtmt) cc_final: 0.7938 (mttt) REVERT: A 250 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.7993 (pp) REVERT: A 275 LYS cc_start: 0.8513 (ttmp) cc_final: 0.8033 (mtmt) REVERT: A 278 GLN cc_start: 0.7942 (pt0) cc_final: 0.7346 (mt0) REVERT: A 359 VAL cc_start: 0.8756 (m) cc_final: 0.8504 (p) REVERT: B 70 MET cc_start: 0.7944 (mtm) cc_final: 0.7579 (mtt) REVERT: B 79 ILE cc_start: 0.8092 (mm) cc_final: 0.7813 (mt) REVERT: B 132 TYR cc_start: 0.8657 (p90) cc_final: 0.8295 (p90) REVERT: B 238 LYS cc_start: 0.8773 (mtmt) cc_final: 0.8543 (mtmt) REVERT: B 250 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8045 (pp) REVERT: B 275 LYS cc_start: 0.8389 (ttmp) cc_final: 0.8108 (mtmt) REVERT: B 278 GLN cc_start: 0.7822 (pt0) cc_final: 0.7292 (mt0) REVERT: B 359 VAL cc_start: 0.8878 (p) cc_final: 0.8609 (t) REVERT: C 10 ASP cc_start: 0.8218 (t0) cc_final: 0.7997 (m-30) REVERT: C 79 ILE cc_start: 0.8058 (mm) cc_final: 0.7821 (mt) REVERT: C 89 ARG cc_start: 0.8153 (tmt-80) cc_final: 0.7831 (ttt-90) REVERT: C 132 TYR cc_start: 0.8861 (p90) cc_final: 0.8367 (p90) REVERT: C 250 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8292 (pp) REVERT: C 259 MET cc_start: 0.9167 (mmt) cc_final: 0.8921 (mmp) REVERT: C 275 LYS cc_start: 0.8469 (ttmp) cc_final: 0.8188 (mtmt) REVERT: D 57 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.7130 (mp0) REVERT: D 67 GLU cc_start: 0.8241 (tt0) cc_final: 0.7795 (mt-10) REVERT: F 100 TYR cc_start: 0.8623 (m-80) cc_final: 0.8332 (m-80) outliers start: 59 outliers final: 40 residues processed: 229 average time/residue: 0.0799 time to fit residues: 26.2069 Evaluate side-chains 229 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 183 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 303 HIS Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 303 HIS Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 303 HIS Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 52 ASN Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain F residue 86 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 106 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 chunk 37 optimal weight: 0.8980 chunk 56 optimal weight: 6.9990 chunk 118 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 104 optimal weight: 0.3980 chunk 21 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 52 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.117138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.089524 restraints weight = 30674.239| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 3.24 r_work: 0.2695 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2690 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2690 r_free = 0.2690 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2690 r_free = 0.2690 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2690 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10191 Z= 0.141 Angle : 0.679 6.215 13854 Z= 0.326 Chirality : 0.045 0.209 1677 Planarity : 0.004 0.049 1704 Dihedral : 5.920 46.726 1444 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 5.52 % Allowed : 14.95 % Favored : 79.52 % 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: -1.05 (0.23), residues: 1314 helix: 0.15 (0.19), residues: 810 sheet: -1.37 (0.48), residues: 99 loop : -2.14 (0.28), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 78 TYR 0.012 0.001 TYR A 344 PHE 0.012 0.001 PHE C 110 TRP 0.010 0.002 TRP B 135 HIS 0.011 0.003 HIS B 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 (10188) covalent geometry : angle 0.67898 / 0.33 (13848) SS BOND : bond 0.00363 / 0.18 ( 3) SS BOND : angle 0.48786 / 0.23 ( 6) hydrogen bonds : bond 0.03510 / 2.31 ( 435) hydrogen bonds : angle 3.70501 / 2.49 ( 1269) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 179 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: A 10 ASP cc_start: 0.8396 (OUTLIER) cc_final: 0.8063 (m-30) REVERT: A 16 GLN cc_start: 0.8353 (mm-40) cc_final: 0.8075 (mt0) REVERT: A 80 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8282 (tt) REVERT: A 238 LYS cc_start: 0.8436 (mtmt) cc_final: 0.7960 (mttt) REVERT: A 250 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8069 (pp) REVERT: A 275 LYS cc_start: 0.8523 (ttmp) cc_final: 0.8059 (mtmt) REVERT: A 278 GLN cc_start: 0.8044 (pt0) cc_final: 0.7451 (mt0) REVERT: A 359 VAL cc_start: 0.8854 (m) cc_final: 0.8589 (p) REVERT: A 367 LEU cc_start: 0.8421 (tp) cc_final: 0.8165 (mp) REVERT: B 10 ASP cc_start: 0.8241 (m-30) cc_final: 0.7923 (m-30) REVERT: B 79 ILE cc_start: 0.8073 (mm) cc_final: 0.7802 (mt) REVERT: B 132 TYR cc_start: 0.8699 (p90) cc_final: 0.8383 (p90) REVERT: B 238 LYS cc_start: 0.8770 (mtmt) cc_final: 0.8539 (mtmt) REVERT: B 250 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8062 (pp) REVERT: B 275 LYS cc_start: 0.8398 (ttmp) cc_final: 0.8115 (mtmt) REVERT: B 278 GLN cc_start: 0.7893 (pt0) cc_final: 0.7336 (mt0) REVERT: B 300 MET cc_start: 0.8344 (mmm) cc_final: 0.7974 (mmt) REVERT: B 359 VAL cc_start: 0.8912 (p) cc_final: 0.8685 (t) REVERT: C 10 ASP cc_start: 0.8291 (t0) cc_final: 0.8028 (m-30) REVERT: C 79 ILE cc_start: 0.8100 (mm) cc_final: 0.7871 (mt) REVERT: C 89 ARG cc_start: 0.8170 (tmt-80) cc_final: 0.7833 (ttt-90) REVERT: C 132 TYR cc_start: 0.8864 (p90) cc_final: 0.8405 (p90) REVERT: C 250 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8265 (pp) REVERT: C 259 MET cc_start: 0.9179 (mmt) cc_final: 0.8929 (mmp) REVERT: C 275 LYS cc_start: 0.8532 (ttmp) cc_final: 0.8177 (mtmt) REVERT: D 67 GLU cc_start: 0.8361 (tt0) cc_final: 0.8051 (tt0) outliers start: 58 outliers final: 45 residues processed: 220 average time/residue: 0.0820 time to fit residues: 25.9413 Evaluate side-chains 228 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 178 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 303 HIS Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 303 HIS Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 303 HIS Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 348 SER Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 52 ASN Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain F residue 86 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 2 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 112 optimal weight: 7.9990 chunk 59 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 113 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 52 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.115574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.088032 restraints weight = 30426.731| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 3.21 r_work: 0.2676 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2673 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2673 r_free = 0.2673 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2673 r_free = 0.2673 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2673 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10191 Z= 0.154 Angle : 0.697 8.641 13854 Z= 0.334 Chirality : 0.046 0.213 1677 Planarity : 0.004 0.049 1704 Dihedral : 5.971 46.862 1444 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 5.52 % Allowed : 15.24 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.23), residues: 1314 helix: 0.20 (0.19), residues: 810 sheet: -1.35 (0.46), residues: 105 loop : -2.12 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 78 TYR 0.012 0.001 TYR A 344 PHE 0.027 0.002 PHE A 3 TRP 0.010 0.002 TRP B 135 HIS 0.011 0.003 HIS B 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.15 (10188) covalent geometry : angle 0.69731 / 0.33 (13848) SS BOND : bond 0.00411 / 0.21 ( 3) SS BOND : angle 0.52690 / 0.24 ( 6) hydrogen bonds : bond 0.03594 / 2.37 ( 435) hydrogen bonds : angle 3.72689 / 2.50 ( 1269) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 175 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: A 10 ASP cc_start: 0.8420 (OUTLIER) cc_final: 0.8106 (m-30) REVERT: A 16 GLN cc_start: 0.8333 (mm-40) cc_final: 0.8039 (mt0) REVERT: A 80 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8296 (tt) REVERT: A 238 LYS cc_start: 0.8432 (mtmt) cc_final: 0.7950 (mttt) REVERT: A 250 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8081 (pp) REVERT: A 275 LYS cc_start: 0.8615 (ttmp) cc_final: 0.8112 (mtmt) REVERT: A 278 GLN cc_start: 0.8014 (pt0) cc_final: 0.7442 (mt0) REVERT: A 359 VAL cc_start: 0.8874 (m) cc_final: 0.8604 (p) REVERT: B 10 ASP cc_start: 0.8262 (m-30) cc_final: 0.8001 (m-30) REVERT: B 70 MET cc_start: 0.7960 (mtm) cc_final: 0.7648 (mtt) REVERT: B 79 ILE cc_start: 0.8134 (mm) cc_final: 0.7877 (mt) REVERT: B 132 TYR cc_start: 0.8722 (p90) cc_final: 0.8441 (p90) REVERT: B 238 LYS cc_start: 0.8777 (mtmt) cc_final: 0.8543 (mtmt) REVERT: B 250 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8046 (pp) REVERT: B 275 LYS cc_start: 0.8453 (ttmp) cc_final: 0.8112 (mtmt) REVERT: B 278 GLN cc_start: 0.7891 (pt0) cc_final: 0.7341 (mt0) REVERT: C 10 ASP cc_start: 0.8294 (t0) cc_final: 0.8026 (m-30) REVERT: C 79 ILE cc_start: 0.8111 (mm) cc_final: 0.7872 (mt) REVERT: C 132 TYR cc_start: 0.8877 (p90) cc_final: 0.8450 (p90) REVERT: C 250 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8236 (pp) REVERT: C 259 MET cc_start: 0.9178 (mmt) cc_final: 0.8923 (mmt) REVERT: C 275 LYS cc_start: 0.8561 (ttmp) cc_final: 0.8156 (mtmt) REVERT: D 67 GLU cc_start: 0.8383 (tt0) cc_final: 0.8066 (tt0) outliers start: 58 outliers final: 46 residues processed: 222 average time/residue: 0.0789 time to fit residues: 25.3383 Evaluate side-chains 222 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 171 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 303 HIS Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 303 HIS Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 303 HIS Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 348 SER Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain F residue 86 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 46 optimal weight: 9.9990 chunk 17 optimal weight: 0.0870 chunk 102 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 67 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 35 optimal weight: 0.0970 chunk 29 optimal weight: 0.4980 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.121477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.094467 restraints weight = 26137.009| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 2.96 r_work: 0.2765 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2769 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2769 r_free = 0.2769 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2769 r_free = 0.2769 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2769 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 10191 Z= 0.112 Angle : 0.664 9.866 13854 Z= 0.313 Chirality : 0.044 0.202 1677 Planarity : 0.004 0.048 1704 Dihedral : 5.787 43.113 1444 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 4.29 % Allowed : 16.57 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.76 (0.24), residues: 1314 helix: 0.56 (0.20), residues: 789 sheet: -1.19 (0.48), residues: 99 loop : -2.34 (0.27), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 78 TYR 0.013 0.001 TYR B 344 PHE 0.010 0.001 PHE B 364 TRP 0.015 0.002 TRP B 267 HIS 0.011 0.003 HIS B 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (10188) covalent geometry : angle 0.66379 / 0.31 (13848) SS BOND : bond 0.00200 / 0.10 ( 3) SS BOND : angle 0.40145 / 0.19 ( 6) hydrogen bonds : bond 0.03025 / 1.97 ( 435) hydrogen bonds : angle 3.65907 / 2.47 ( 1269) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 183 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: A 10 ASP cc_start: 0.8372 (OUTLIER) cc_final: 0.8103 (m-30) REVERT: A 16 GLN cc_start: 0.8332 (mm-40) cc_final: 0.8103 (mt0) REVERT: A 80 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8316 (tt) REVERT: A 238 LYS cc_start: 0.8333 (mtmt) cc_final: 0.7961 (mtpt) REVERT: A 250 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.7990 (pp) REVERT: A 275 LYS cc_start: 0.8540 (ttmp) cc_final: 0.8124 (mtmt) REVERT: A 359 VAL cc_start: 0.8830 (m) cc_final: 0.8588 (p) REVERT: B 10 ASP cc_start: 0.8288 (m-30) cc_final: 0.8012 (m-30) REVERT: B 40 GLU cc_start: 0.7720 (tt0) cc_final: 0.7270 (tt0) REVERT: B 70 MET cc_start: 0.7918 (mtm) cc_final: 0.7618 (mtt) REVERT: B 79 ILE cc_start: 0.8092 (mm) cc_final: 0.7813 (mt) REVERT: B 132 TYR cc_start: 0.8731 (p90) cc_final: 0.8442 (p90) REVERT: B 238 LYS cc_start: 0.8761 (mtmt) cc_final: 0.8458 (mtmt) REVERT: B 250 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.7923 (pp) REVERT: B 275 LYS cc_start: 0.8414 (ttmp) cc_final: 0.8106 (mtmt) REVERT: C 79 ILE cc_start: 0.8020 (mm) cc_final: 0.7772 (mt) REVERT: C 89 ARG cc_start: 0.8104 (tmt-80) cc_final: 0.7783 (ttt-90) REVERT: C 132 TYR cc_start: 0.8890 (p90) cc_final: 0.8511 (p90) REVERT: C 250 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8159 (pp) REVERT: C 259 MET cc_start: 0.9149 (mmt) cc_final: 0.8926 (mmp) REVERT: C 262 MET cc_start: 0.8929 (OUTLIER) cc_final: 0.8545 (mmt) REVERT: C 275 LYS cc_start: 0.8475 (ttmp) cc_final: 0.8166 (mtmt) REVERT: D 57 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7237 (mp0) REVERT: D 67 GLU cc_start: 0.8287 (tt0) cc_final: 0.7984 (tt0) REVERT: F 100 TYR cc_start: 0.8709 (m-80) cc_final: 0.8392 (m-80) outliers start: 45 outliers final: 34 residues processed: 215 average time/residue: 0.0851 time to fit residues: 26.1280 Evaluate side-chains 212 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 171 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 303 HIS Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 303 HIS Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 303 HIS Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain F residue 86 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 121 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.115075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.088242 restraints weight = 25650.333| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 2.82 r_work: 0.2684 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2680 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2680 r_free = 0.2680 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2680 r_free = 0.2680 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2680 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10191 Z= 0.167 Angle : 0.735 10.822 13854 Z= 0.348 Chirality : 0.047 0.212 1677 Planarity : 0.004 0.050 1704 Dihedral : 6.037 48.612 1444 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 4.86 % Allowed : 15.71 % Favored : 79.43 % 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: -0.89 (0.23), residues: 1314 helix: 0.19 (0.19), residues: 825 sheet: -1.13 (0.47), residues: 105 loop : -1.98 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 78 TYR 0.012 0.002 TYR D 87 PHE 0.019 0.002 PHE A 296 TRP 0.009 0.002 TRP B 135 HIS 0.010 0.003 HIS C 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 (10188) covalent geometry : angle 0.73470 / 0.35 (13848) SS BOND : bond 0.00422 / 0.21 ( 3) SS BOND : angle 0.56764 / 0.26 ( 6) hydrogen bonds : bond 0.03788 / 2.49 ( 435) hydrogen bonds : angle 3.76631 / 2.53 ( 1269) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 175 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: A 10 ASP cc_start: 0.8391 (OUTLIER) cc_final: 0.8121 (m-30) REVERT: A 16 GLN cc_start: 0.8325 (mm-40) cc_final: 0.8031 (mt0) REVERT: A 80 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8274 (tt) REVERT: A 156 ASN cc_start: 0.8683 (t160) cc_final: 0.8320 (t0) REVERT: A 238 LYS cc_start: 0.8453 (mtmt) cc_final: 0.8004 (mtpt) REVERT: A 250 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8028 (pp) REVERT: A 275 LYS cc_start: 0.8552 (ttmp) cc_final: 0.8114 (mtmt) REVERT: A 278 GLN cc_start: 0.8012 (pt0) cc_final: 0.7453 (mt0) REVERT: B 10 ASP cc_start: 0.8381 (m-30) cc_final: 0.8161 (m-30) REVERT: B 40 GLU cc_start: 0.7765 (tt0) cc_final: 0.7301 (tt0) REVERT: B 70 MET cc_start: 0.7948 (mtm) cc_final: 0.7585 (mtt) REVERT: B 79 ILE cc_start: 0.8125 (mm) cc_final: 0.7866 (mt) REVERT: B 132 TYR cc_start: 0.8736 (p90) cc_final: 0.8393 (p90) REVERT: B 238 LYS cc_start: 0.8764 (mtmt) cc_final: 0.8486 (mtmt) REVERT: B 250 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8082 (pp) REVERT: B 275 LYS cc_start: 0.8513 (ttmp) cc_final: 0.8136 (mtmt) REVERT: B 278 GLN cc_start: 0.7892 (pt0) cc_final: 0.7340 (mt0) REVERT: C 79 ILE cc_start: 0.8089 (mm) cc_final: 0.7853 (mt) REVERT: C 132 TYR cc_start: 0.8892 (p90) cc_final: 0.8547 (p90) REVERT: C 240 GLU cc_start: 0.8662 (mp0) cc_final: 0.7811 (mp0) REVERT: C 250 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8257 (pp) REVERT: C 259 MET cc_start: 0.9133 (mmt) cc_final: 0.8863 (mmt) REVERT: C 275 LYS cc_start: 0.8577 (ttmp) cc_final: 0.8160 (mtmt) REVERT: D 67 GLU cc_start: 0.8337 (tt0) cc_final: 0.8035 (tt0) REVERT: E 50 GLN cc_start: 0.7051 (pt0) cc_final: 0.6778 (pt0) outliers start: 51 outliers final: 39 residues processed: 214 average time/residue: 0.0885 time to fit residues: 27.1403 Evaluate side-chains 215 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 171 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 303 HIS Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 303 HIS Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 348 SER Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain F residue 86 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 99 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 28 optimal weight: 0.4980 chunk 90 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.117615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.090000 restraints weight = 30354.345| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 3.10 r_work: 0.2705 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2705 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2705 r_free = 0.2705 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2705 r_free = 0.2705 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2705 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10191 Z= 0.128 Angle : 0.690 9.428 13854 Z= 0.326 Chirality : 0.045 0.210 1677 Planarity : 0.004 0.049 1704 Dihedral : 5.918 46.379 1444 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 4.48 % Allowed : 16.10 % Favored : 79.43 % 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: -0.76 (0.23), residues: 1314 helix: 0.41 (0.19), residues: 807 sheet: -0.95 (0.49), residues: 99 loop : -2.18 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 78 TYR 0.012 0.001 TYR B 344 PHE 0.012 0.001 PHE A 364 TRP 0.012 0.002 TRP B 267 HIS 0.017 0.003 HIS B 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (10188) covalent geometry : angle 0.68986 / 0.33 (13848) SS BOND : bond 0.00298 / 0.15 ( 3) SS BOND : angle 0.52554 / 0.25 ( 6) hydrogen bonds : bond 0.03321 / 2.18 ( 435) hydrogen bonds : angle 3.72371 / 2.52 ( 1269) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1980.53 seconds wall clock time: 34 minutes 36.49 seconds (2076.49 seconds total)