Starting phenix.real_space_refine on Wed Mar 4 06:26:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cyf_30499/03_2026/7cyf_30499_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cyf_30499/03_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_30499/03_2026/7cyf_30499_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cyf_30499/03_2026/7cyf_30499_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7cyf_30499/03_2026/7cyf_30499.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cyf_30499/03_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-5986/lib/python3.9/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, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 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: 2.50, per 1000 atoms: 0.25 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: 0.57 Conformation dependent library (CDL) restraints added in 515.0 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: 0.20 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: 1.43 Time building geometry restraints manager: 0.82 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 2.470 nonbonded pdb=" O PHE B 110 " pdb="NA NA B 401 " model vdw 2.061 2.470 nonbonded pdb=" O PHE A 110 " pdb="NA NA A 401 " model vdw 2.207 2.470 ... (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: 0.02 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: 0.600 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.850 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 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 covalent geometry : bond 0.00943 (10188) covalent geometry : angle 1.30205 (13848) SS BOND : bond 0.01303 ( 3) SS BOND : angle 1.81482 ( 6) hydrogen bonds : bond 0.32308 ( 435) hydrogen bonds : angle 10.17854 ( 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 : 0.296 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: 0.1138 time to fit residues: 45.8940 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 : 0.359 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3273 r_free = 0.3273 target = 0.120236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.093447 restraints weight = 25616.292| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 2.97 r_work: 0.2753 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2757 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2757 r_free = 0.2757 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 = 0.2757 r_free = 0.2757 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2757 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10191 Z= 0.145 Angle : 0.763 6.615 13854 Z= 0.374 Chirality : 0.046 0.221 1677 Planarity : 0.006 0.069 1704 Dihedral : 6.898 52.112 1454 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.48 % Allowed : 12.67 % 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 : -2.69 (0.27), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 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 A 303 Details of bonding type rmsd covalent geometry : bond 0.00324 (10188) covalent geometry : angle 0.76267 (13848) SS BOND : bond 0.00402 ( 3) SS BOND : angle 0.73541 ( 6) hydrogen bonds : bond 0.04634 ( 435) hydrogen bonds : angle 4.56286 ( 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 260 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 234 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ASP cc_start: 0.8335 (OUTLIER) cc_final: 0.7824 (m-30) REVERT: A 17 SER cc_start: 0.8761 (t) cc_final: 0.8219 (p) REVERT: A 35 GLN cc_start: 0.8029 (mp10) cc_final: 0.7634 (mm110) REVERT: A 40 GLU cc_start: 0.8047 (tt0) cc_final: 0.7715 (mt-10) REVERT: A 62 ILE cc_start: 0.9004 (tt) cc_final: 0.8604 (tt) REVERT: A 156 ASN cc_start: 0.8463 (t160) cc_final: 0.8124 (t0) REVERT: A 238 LYS cc_start: 0.8414 (mtmt) cc_final: 0.8069 (mttt) REVERT: A 250 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8155 (pp) REVERT: A 275 LYS cc_start: 0.8594 (ttmp) cc_final: 0.8029 (mtmt) REVERT: A 278 GLN cc_start: 0.7967 (pt0) cc_final: 0.7389 (mt0) REVERT: A 298 LEU cc_start: 0.8630 (tp) cc_final: 0.8417 (tp) REVERT: B 3 PHE cc_start: 0.7615 (t80) cc_final: 0.7303 (t80) REVERT: B 10 ASP cc_start: 0.8437 (t0) cc_final: 0.8067 (m-30) REVERT: B 35 GLN cc_start: 0.7989 (mp10) cc_final: 0.7674 (mm110) REVERT: B 40 GLU cc_start: 0.8297 (tt0) cc_final: 0.7775 (mt-10) REVERT: B 79 ILE cc_start: 0.7980 (mm) cc_final: 0.7760 (mt) REVERT: B 238 LYS cc_start: 0.8801 (mtmt) cc_final: 0.8502 (mtmt) REVERT: B 250 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8168 (pp) REVERT: B 272 GLU cc_start: 0.8309 (tt0) cc_final: 0.7994 (tt0) REVERT: B 275 LYS cc_start: 0.8468 (ttmp) cc_final: 0.8013 (mtmt) REVERT: B 278 GLN cc_start: 0.7805 (pt0) cc_final: 0.7288 (mt0) REVERT: B 298 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8496 (tp) REVERT: C 10 ASP cc_start: 0.8278 (t0) cc_final: 0.7923 (m-30) REVERT: C 40 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7933 (mt-10) REVERT: C 79 ILE cc_start: 0.8030 (mm) cc_final: 0.7814 (mt) REVERT: C 132 TYR cc_start: 0.8748 (p90) cc_final: 0.8378 (p90) REVERT: C 250 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8310 (pp) REVERT: C 259 MET cc_start: 0.9174 (mmt) cc_final: 0.8901 (mmt) REVERT: C 275 LYS cc_start: 0.8571 (ttmp) cc_final: 0.8174 (mtmt) REVERT: C 278 GLN cc_start: 0.8019 (pt0) cc_final: 0.7357 (mt0) REVERT: D 57 GLU cc_start: 0.7712 (pm20) cc_final: 0.7477 (mt-10) REVERT: D 67 GLU cc_start: 0.8420 (tt0) cc_final: 0.8027 (mt-10) REVERT: F 6 ASN cc_start: 0.8773 (m-40) cc_final: 0.8558 (m-40) outliers start: 26 outliers final: 16 residues processed: 250 average time/residue: 0.0915 time to fit residues: 32.6070 Evaluate side-chains 210 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 189 time to evaluate : 0.287 ------------------------------------------------------------------------------- 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: 0.9990 chunk 37 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 124 optimal weight: 8.9990 chunk 120 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3269 r_free = 0.3269 target = 0.119589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.092751 restraints weight = 28814.060| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 3.12 r_work: 0.2743 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2742 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2742 r_free = 0.2742 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2742 r_free = 0.2742 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2742 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10191 Z= 0.131 Angle : 0.714 9.612 13854 Z= 0.341 Chirality : 0.045 0.233 1677 Planarity : 0.005 0.059 1704 Dihedral : 6.251 48.655 1445 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 4.00 % Allowed : 14.00 % Favored : 82.00 % 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: -2.63 (0.21), residues: 1314 helix: -1.27 (0.17), residues: 816 sheet: -1.95 (0.45), residues: 105 loop : -2.35 (0.28), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 78 TYR 0.014 0.001 TYR A 140 PHE 0.010 0.001 PHE C 364 TRP 0.010 0.002 TRP A 135 HIS 0.012 0.003 HIS C 303 Details of bonding type rmsd covalent geometry : bond 0.00301 (10188) covalent geometry : angle 0.71356 (13848) SS BOND : bond 0.00314 ( 3) SS BOND : angle 0.59093 ( 6) hydrogen bonds : bond 0.03933 ( 435) hydrogen bonds : angle 4.01802 ( 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 229 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 187 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 10 ASP cc_start: 0.8366 (OUTLIER) cc_final: 0.7872 (m-30) REVERT: A 35 GLN cc_start: 0.7929 (mp10) cc_final: 0.7610 (mm110) REVERT: A 80 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8379 (tt) REVERT: A 238 LYS cc_start: 0.8429 (mtmt) cc_final: 0.7965 (mttt) REVERT: A 250 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8087 (pp) REVERT: A 275 LYS cc_start: 0.8545 (ttmp) cc_final: 0.8055 (mtmt) REVERT: A 278 GLN cc_start: 0.7947 (pt0) cc_final: 0.7368 (mt0) REVERT: B 3 PHE cc_start: 0.7599 (t80) cc_final: 0.7304 (t80) REVERT: B 10 ASP cc_start: 0.8409 (t0) cc_final: 0.8079 (m-30) REVERT: B 35 GLN cc_start: 0.7919 (mp10) cc_final: 0.7694 (mm110) REVERT: B 79 ILE cc_start: 0.8039 (mm) cc_final: 0.7800 (mt) REVERT: B 161 LYS cc_start: 0.8040 (ptpt) cc_final: 0.7815 (ptpp) REVERT: B 238 LYS cc_start: 0.8838 (mtmt) cc_final: 0.8485 (mtmt) REVERT: B 243 TYR cc_start: 0.9103 (t80) cc_final: 0.8879 (t80) REVERT: B 250 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8106 (pp) REVERT: B 272 GLU cc_start: 0.8359 (tt0) cc_final: 0.8063 (tt0) REVERT: B 275 LYS cc_start: 0.8449 (ttmp) cc_final: 0.8117 (mtmt) REVERT: B 278 GLN cc_start: 0.7831 (pt0) cc_final: 0.7288 (mt0) REVERT: B 298 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8577 (tp) REVERT: C 10 ASP cc_start: 0.8285 (t0) cc_final: 0.7941 (m-30) REVERT: C 15 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8828 (mp) REVERT: C 79 ILE cc_start: 0.8051 (mm) cc_final: 0.7812 (mt) REVERT: C 89 ARG cc_start: 0.8185 (tmt-80) cc_final: 0.7807 (ttt-90) REVERT: C 132 TYR cc_start: 0.8782 (p90) cc_final: 0.8339 (p90) REVERT: C 250 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8298 (pp) REVERT: C 275 LYS cc_start: 0.8514 (ttmp) cc_final: 0.8146 (mtmt) REVERT: D 57 GLU cc_start: 0.7692 (pm20) cc_final: 0.7443 (mt-10) REVERT: D 67 GLU cc_start: 0.8439 (tt0) cc_final: 0.7950 (mt-10) REVERT: F 6 ASN cc_start: 0.8789 (m-40) cc_final: 0.8577 (m-40) REVERT: F 100 TYR cc_start: 0.8605 (m-80) cc_final: 0.8357 (m-80) outliers start: 42 outliers final: 24 residues processed: 215 average time/residue: 0.0988 time to fit residues: 29.9770 Evaluate side-chains 210 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 179 time to evaluate : 0.356 ------------------------------------------------------------------------------- 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 15 LEU Chi-restraints excluded: chain C residue 72 LEU 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 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: 2.9990 chunk 85 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 chunk 86 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 119 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 291 HIS E 50 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.118672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.093814 restraints weight = 17783.294| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 2.31 r_work: 0.2771 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2774 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2774 r_free = 0.2774 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2774 r_free = 0.2774 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2774 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10191 Z= 0.137 Angle : 0.692 7.922 13854 Z= 0.332 Chirality : 0.045 0.210 1677 Planarity : 0.004 0.053 1704 Dihedral : 6.095 49.314 1444 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 4.57 % Allowed : 13.81 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.22), residues: 1314 helix: -0.60 (0.18), residues: 813 sheet: -1.76 (0.46), residues: 105 loop : -2.27 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 78 TYR 0.013 0.001 TYR A 344 PHE 0.011 0.001 PHE C 110 TRP 0.010 0.002 TRP C 135 HIS 0.011 0.003 HIS B 303 Details of bonding type rmsd covalent geometry : bond 0.00321 (10188) covalent geometry : angle 0.69181 (13848) SS BOND : bond 0.00373 ( 3) SS BOND : angle 0.56979 ( 6) hydrogen bonds : bond 0.03672 ( 435) hydrogen bonds : angle 3.84558 ( 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 232 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 184 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ASP cc_start: 0.8380 (OUTLIER) cc_final: 0.7927 (m-30) REVERT: A 16 GLN cc_start: 0.8299 (mm-40) cc_final: 0.7873 (mt0) REVERT: A 35 GLN cc_start: 0.7911 (mp10) cc_final: 0.7623 (mm110) REVERT: A 80 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8321 (tt) REVERT: A 158 TYR cc_start: 0.8589 (t80) cc_final: 0.8273 (t80) REVERT: A 238 LYS cc_start: 0.8404 (mtmt) cc_final: 0.7955 (mttt) REVERT: A 244 GLU cc_start: 0.8545 (pt0) cc_final: 0.8222 (pt0) REVERT: A 250 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8057 (pp) REVERT: A 275 LYS cc_start: 0.8525 (ttmp) cc_final: 0.8036 (mtmt) REVERT: A 278 GLN cc_start: 0.7914 (pt0) cc_final: 0.7342 (mt0) REVERT: A 359 VAL cc_start: 0.8796 (m) cc_final: 0.8533 (p) REVERT: B 3 PHE cc_start: 0.7704 (t80) cc_final: 0.7437 (t80) REVERT: B 10 ASP cc_start: 0.8382 (t0) cc_final: 0.8128 (m-30) REVERT: B 35 GLN cc_start: 0.7788 (mp10) cc_final: 0.7588 (mm110) REVERT: B 79 ILE cc_start: 0.8107 (mm) cc_final: 0.7854 (mt) REVERT: B 132 TYR cc_start: 0.8644 (p90) cc_final: 0.8288 (p90) REVERT: B 238 LYS cc_start: 0.8805 (mtmt) cc_final: 0.8396 (mtmt) REVERT: B 250 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8096 (pp) REVERT: B 272 GLU cc_start: 0.8270 (tt0) cc_final: 0.8007 (tt0) REVERT: B 275 LYS cc_start: 0.8416 (ttmp) cc_final: 0.8097 (mtmt) REVERT: B 278 GLN cc_start: 0.7798 (pt0) cc_final: 0.7270 (mt0) REVERT: B 298 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8687 (tp) REVERT: B 359 VAL cc_start: 0.8816 (p) cc_final: 0.8464 (t) REVERT: C 10 ASP cc_start: 0.8267 (t0) cc_final: 0.7961 (m-30) REVERT: C 15 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8791 (mp) REVERT: C 40 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7557 (mm-30) REVERT: C 79 ILE cc_start: 0.8149 (mm) cc_final: 0.7913 (mt) REVERT: C 132 TYR cc_start: 0.8826 (p90) cc_final: 0.8264 (p90) REVERT: C 250 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8241 (pp) REVERT: C 259 MET cc_start: 0.9186 (mmt) cc_final: 0.8943 (mmp) REVERT: C 275 LYS cc_start: 0.8505 (ttmp) cc_final: 0.8137 (mtmt) REVERT: D 50 GLN cc_start: 0.7022 (mp10) cc_final: 0.6767 (mm-40) REVERT: D 67 GLU cc_start: 0.8273 (tt0) cc_final: 0.7977 (tt0) REVERT: E 26 GLU cc_start: 0.8779 (mt-10) cc_final: 0.8512 (mt-10) outliers start: 48 outliers final: 33 residues processed: 218 average time/residue: 0.0932 time to fit residues: 28.8351 Evaluate side-chains 218 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 177 time to evaluate : 0.361 ------------------------------------------------------------------------------- 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 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 331 THR Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 74 VAL 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 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 15 LEU 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 106 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 88 optimal weight: 0.3980 chunk 51 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.115758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.088686 restraints weight = 28260.285| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 2.96 r_work: 0.2680 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2680 ------------------------------------------------------------------------------- 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 = 0.22 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 = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2680 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10191 Z= 0.172 Angle : 0.720 7.221 13854 Z= 0.347 Chirality : 0.046 0.222 1677 Planarity : 0.004 0.052 1704 Dihedral : 6.122 48.498 1444 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 5.33 % Allowed : 14.19 % 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: -1.63 (0.23), residues: 1314 helix: -0.30 (0.19), residues: 804 sheet: -1.64 (0.46), residues: 105 loop : -2.34 (0.28), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 78 TYR 0.013 0.002 TYR A 344 PHE 0.016 0.002 PHE C 110 TRP 0.010 0.002 TRP B 135 HIS 0.011 0.003 HIS B 303 Details of bonding type rmsd covalent geometry : bond 0.00422 (10188) covalent geometry : angle 0.71958 (13848) SS BOND : bond 0.00475 ( 3) SS BOND : angle 0.61104 ( 6) hydrogen bonds : bond 0.03908 ( 435) hydrogen bonds : angle 3.84050 ( 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 230 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 174 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ASP cc_start: 0.8443 (OUTLIER) cc_final: 0.8084 (m-30) REVERT: A 16 GLN cc_start: 0.8360 (mm-40) cc_final: 0.7956 (mt0) REVERT: A 80 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8270 (tt) REVERT: A 158 TYR cc_start: 0.8608 (t80) cc_final: 0.8244 (t80) REVERT: A 238 LYS cc_start: 0.8411 (mtmt) cc_final: 0.7970 (mttt) REVERT: A 250 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8124 (pp) REVERT: A 275 LYS cc_start: 0.8584 (ttmp) cc_final: 0.8032 (mtmt) REVERT: A 278 GLN cc_start: 0.7987 (pt0) cc_final: 0.7402 (mt0) REVERT: B 3 PHE cc_start: 0.7758 (t80) cc_final: 0.7363 (t80) REVERT: B 10 ASP cc_start: 0.8402 (t0) cc_final: 0.8131 (m-30) REVERT: B 35 GLN cc_start: 0.7980 (mp10) cc_final: 0.7647 (mm110) REVERT: B 79 ILE cc_start: 0.8117 (mm) cc_final: 0.7869 (mt) REVERT: B 132 TYR cc_start: 0.8681 (p90) cc_final: 0.8353 (p90) REVERT: B 238 LYS cc_start: 0.8800 (mtmt) cc_final: 0.8459 (mtmt) REVERT: B 250 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8104 (pp) REVERT: B 275 LYS cc_start: 0.8468 (ttmp) cc_final: 0.8095 (mtmt) REVERT: B 278 GLN cc_start: 0.7888 (pt0) cc_final: 0.7347 (mt0) REVERT: B 359 VAL cc_start: 0.8920 (p) cc_final: 0.8621 (t) REVERT: C 10 ASP cc_start: 0.8331 (t0) cc_final: 0.7987 (m-30) REVERT: C 15 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8736 (mp) REVERT: C 79 ILE cc_start: 0.8142 (mm) cc_final: 0.7915 (mt) REVERT: C 132 TYR cc_start: 0.8870 (p90) cc_final: 0.8331 (p90) REVERT: C 250 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8287 (pp) REVERT: C 259 MET cc_start: 0.9207 (mmt) cc_final: 0.8942 (mmp) REVERT: C 275 LYS cc_start: 0.8602 (ttmp) cc_final: 0.8146 (mtmt) REVERT: D 67 GLU cc_start: 0.8386 (tt0) cc_final: 0.8076 (tt0) REVERT: D 78 ARG cc_start: 0.8650 (mtp85) cc_final: 0.8417 (mtp180) outliers start: 56 outliers final: 42 residues processed: 219 average time/residue: 0.0889 time to fit residues: 27.8628 Evaluate side-chains 218 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 170 time to evaluate : 0.362 ------------------------------------------------------------------------------- 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 326 ILE 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 309 SER Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain C residue 15 LEU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 2 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 116 optimal weight: 0.9990 chunk 121 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 89 optimal weight: 8.9990 chunk 118 optimal weight: 1.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 291 HIS ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.117379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.091649 restraints weight = 21889.185| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 2.58 r_work: 0.2737 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2752 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2752 r_free = 0.2752 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2752 r_free = 0.2752 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2752 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3309 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= 0.132 Angle : 0.677 6.568 13854 Z= 0.325 Chirality : 0.044 0.213 1677 Planarity : 0.004 0.052 1704 Dihedral : 5.987 46.904 1444 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 5.33 % Allowed : 14.86 % Favored : 79.81 % 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: -1.23 (0.23), residues: 1314 helix: -0.01 (0.19), residues: 810 sheet: -1.46 (0.47), residues: 99 loop : -2.16 (0.28), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 78 TYR 0.013 0.001 TYR A 344 PHE 0.012 0.001 PHE A 3 TRP 0.011 0.002 TRP B 267 HIS 0.013 0.003 HIS B 303 Details of bonding type rmsd covalent geometry : bond 0.00311 (10188) covalent geometry : angle 0.67661 (13848) SS BOND : bond 0.00371 ( 3) SS BOND : angle 0.49286 ( 6) hydrogen bonds : bond 0.03440 ( 435) hydrogen bonds : angle 3.73406 ( 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 236 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 180 time to evaluate : 0.294 Fit side-chains revert: symmetry clash REVERT: A 10 ASP cc_start: 0.8400 (OUTLIER) cc_final: 0.8085 (m-30) REVERT: A 16 GLN cc_start: 0.8349 (mm-40) cc_final: 0.8050 (mt0) REVERT: A 80 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8202 (tt) REVERT: A 238 LYS cc_start: 0.8386 (mtmt) cc_final: 0.7912 (mttt) REVERT: A 250 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8096 (pp) REVERT: A 275 LYS cc_start: 0.8636 (ttmp) cc_final: 0.8078 (mtmt) REVERT: A 278 GLN cc_start: 0.7893 (pt0) cc_final: 0.7328 (mt0) REVERT: A 359 VAL cc_start: 0.8819 (m) cc_final: 0.8545 (p) REVERT: B 3 PHE cc_start: 0.7756 (t80) cc_final: 0.7308 (t80) REVERT: B 10 ASP cc_start: 0.8375 (t0) cc_final: 0.8171 (m-30) REVERT: B 35 GLN cc_start: 0.7933 (mp10) cc_final: 0.7656 (mm110) REVERT: B 79 ILE cc_start: 0.8081 (mm) cc_final: 0.7817 (mt) REVERT: B 132 TYR cc_start: 0.8685 (p90) cc_final: 0.8381 (p90) REVERT: B 238 LYS cc_start: 0.8756 (mtmt) cc_final: 0.8519 (mtmt) REVERT: B 240 GLU cc_start: 0.8065 (mp0) cc_final: 0.7842 (mp0) REVERT: B 250 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8085 (pp) REVERT: B 275 LYS cc_start: 0.8470 (ttmp) cc_final: 0.8112 (mtmt) REVERT: B 278 GLN cc_start: 0.7818 (pt0) cc_final: 0.7280 (mt0) REVERT: B 359 VAL cc_start: 0.8892 (p) cc_final: 0.8659 (t) REVERT: C 10 ASP cc_start: 0.8301 (t0) cc_final: 0.8041 (m-30) REVERT: C 79 ILE cc_start: 0.8105 (mm) cc_final: 0.7880 (mt) REVERT: C 132 TYR cc_start: 0.8868 (p90) cc_final: 0.8366 (p90) REVERT: C 250 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8247 (pp) REVERT: C 259 MET cc_start: 0.9161 (mmt) cc_final: 0.8910 (mmp) REVERT: C 275 LYS cc_start: 0.8583 (ttmp) cc_final: 0.8154 (mtmt) REVERT: D 67 GLU cc_start: 0.8304 (tt0) cc_final: 0.7998 (tt0) REVERT: E 78 ARG cc_start: 0.8608 (mtp85) cc_final: 0.8361 (mtp180) outliers start: 56 outliers final: 40 residues processed: 224 average time/residue: 0.0927 time to fit residues: 29.9109 Evaluate side-chains 213 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 168 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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 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 323 SER 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 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 331 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 106 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 37 optimal weight: 0.0070 chunk 56 optimal weight: 6.9990 chunk 118 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.124095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.097066 restraints weight = 29953.685| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 3.19 r_work: 0.2733 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2729 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2729 r_free = 0.2729 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2729 r_free = 0.2729 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2729 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3470 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= 0.117 Angle : 0.652 6.441 13854 Z= 0.312 Chirality : 0.044 0.205 1677 Planarity : 0.004 0.050 1704 Dihedral : 5.842 45.880 1444 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 5.14 % Allowed : 15.14 % 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: -0.93 (0.23), residues: 1314 helix: 0.28 (0.19), residues: 807 sheet: -1.34 (0.48), residues: 99 loop : -2.14 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 78 TYR 0.013 0.001 TYR A 344 PHE 0.028 0.001 PHE A 3 TRP 0.012 0.002 TRP B 267 HIS 0.013 0.003 HIS B 303 Details of bonding type rmsd covalent geometry : bond 0.00267 (10188) covalent geometry : angle 0.65219 (13848) SS BOND : bond 0.00277 ( 3) SS BOND : angle 0.42684 ( 6) hydrogen bonds : bond 0.03144 ( 435) hydrogen bonds : angle 3.66505 ( 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 234 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 180 time to evaluate : 0.289 Fit side-chains revert: symmetry clash REVERT: A 10 ASP cc_start: 0.8390 (OUTLIER) cc_final: 0.8089 (m-30) REVERT: A 16 GLN cc_start: 0.8342 (mm-40) cc_final: 0.8091 (mt0) REVERT: A 80 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8284 (tt) REVERT: A 238 LYS cc_start: 0.8429 (mtmt) cc_final: 0.7982 (mttt) REVERT: A 250 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8026 (pp) REVERT: A 275 LYS cc_start: 0.8591 (ttmp) cc_final: 0.8097 (mtmt) REVERT: A 359 VAL cc_start: 0.8761 (m) cc_final: 0.8513 (p) REVERT: B 70 MET cc_start: 0.7965 (mtm) cc_final: 0.7610 (mtt) REVERT: B 79 ILE cc_start: 0.8102 (mm) cc_final: 0.7831 (mt) REVERT: B 132 TYR cc_start: 0.8719 (p90) cc_final: 0.8415 (p90) REVERT: B 238 LYS cc_start: 0.8762 (mtmt) cc_final: 0.8469 (mtmt) REVERT: B 250 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8028 (pp) REVERT: B 275 LYS cc_start: 0.8454 (ttmp) cc_final: 0.8136 (mtmt) REVERT: B 359 VAL cc_start: 0.8919 (p) cc_final: 0.8700 (t) REVERT: C 79 ILE cc_start: 0.8089 (mm) cc_final: 0.7841 (mt) REVERT: C 132 TYR cc_start: 0.8867 (p90) cc_final: 0.8447 (p90) REVERT: C 250 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8291 (pp) REVERT: C 259 MET cc_start: 0.9178 (mmt) cc_final: 0.8934 (mmp) REVERT: C 275 LYS cc_start: 0.8492 (ttmp) cc_final: 0.8157 (mtmt) REVERT: D 67 GLU cc_start: 0.8339 (tt0) cc_final: 0.8018 (tt0) outliers start: 54 outliers final: 41 residues processed: 218 average time/residue: 0.0903 time to fit residues: 28.1424 Evaluate side-chains 219 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 173 time to evaluate : 0.376 ------------------------------------------------------------------------------- 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 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 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 15 LEU 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 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 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: 5.9990 chunk 6 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 112 optimal weight: 3.9990 chunk 59 optimal weight: 0.1980 chunk 76 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.113548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.085875 restraints weight = 30493.906| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 3.10 r_work: 0.2643 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2637 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2637 r_free = 0.2637 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2637 r_free = 0.2637 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2637 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10191 Z= 0.189 Angle : 0.745 9.385 13854 Z= 0.356 Chirality : 0.047 0.226 1677 Planarity : 0.005 0.051 1704 Dihedral : 6.177 48.144 1444 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 5.14 % Allowed : 15.05 % Favored : 79.81 % 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: -1.11 (0.23), residues: 1314 helix: 0.01 (0.19), residues: 825 sheet: -1.33 (0.47), residues: 105 loop : -2.03 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 269 TYR 0.014 0.002 TYR D 87 PHE 0.015 0.002 PHE C 110 TRP 0.011 0.002 TRP B 135 HIS 0.011 0.003 HIS B 303 Details of bonding type rmsd covalent geometry : bond 0.00469 (10188) covalent geometry : angle 0.74469 (13848) SS BOND : bond 0.00487 ( 3) SS BOND : angle 0.62004 ( 6) hydrogen bonds : bond 0.03986 ( 435) hydrogen bonds : angle 3.79058 ( 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 228 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 174 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ASP cc_start: 0.8417 (OUTLIER) cc_final: 0.8128 (m-30) REVERT: A 16 GLN cc_start: 0.8388 (mm-40) cc_final: 0.8105 (mt0) REVERT: A 80 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8245 (tt) REVERT: A 238 LYS cc_start: 0.8429 (mtmt) cc_final: 0.7968 (mttt) REVERT: A 250 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8126 (pp) REVERT: A 275 LYS cc_start: 0.8576 (ttmp) cc_final: 0.8042 (mtmt) REVERT: A 278 GLN cc_start: 0.8024 (pt0) cc_final: 0.7468 (mt0) REVERT: B 10 ASP cc_start: 0.8270 (m-30) cc_final: 0.8018 (m-30) REVERT: B 70 MET cc_start: 0.7995 (mtm) cc_final: 0.7595 (mtt) REVERT: B 127 GLU cc_start: 0.7957 (tp30) cc_final: 0.7660 (tp30) REVERT: B 132 TYR cc_start: 0.8716 (p90) cc_final: 0.8376 (p90) REVERT: B 238 LYS cc_start: 0.8770 (mtmt) cc_final: 0.8439 (mtmt) REVERT: B 250 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8174 (pp) REVERT: B 275 LYS cc_start: 0.8549 (ttmp) cc_final: 0.8109 (mtmt) REVERT: B 278 GLN cc_start: 0.7940 (pt0) cc_final: 0.7400 (mt0) REVERT: C 10 ASP cc_start: 0.8305 (m-30) cc_final: 0.8060 (m-30) REVERT: C 17 SER cc_start: 0.8718 (t) cc_final: 0.8122 (p) REVERT: C 79 ILE cc_start: 0.8126 (mm) cc_final: 0.7907 (mt) REVERT: C 132 TYR cc_start: 0.8866 (p90) cc_final: 0.8433 (p90) REVERT: C 250 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8306 (pp) REVERT: C 275 LYS cc_start: 0.8629 (ttmp) cc_final: 0.8156 (mtmt) REVERT: D 67 GLU cc_start: 0.8418 (tt0) cc_final: 0.8102 (tt0) outliers start: 54 outliers final: 45 residues processed: 217 average time/residue: 0.0942 time to fit residues: 28.8401 Evaluate side-chains 218 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 168 time to evaluate : 0.362 ------------------------------------------------------------------------------- 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 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 242 VAL Chi-restraints excluded: chain A residue 250 LEU 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 323 SER 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 242 VAL 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 15 LEU 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 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 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: 10.0000 chunk 17 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 67 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 ASN ** E 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.118325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.091305 restraints weight = 26204.452| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 2.87 r_work: 0.2739 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2720 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2720 r_free = 0.2720 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2720 r_free = 0.2720 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2720 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10191 Z= 0.123 Angle : 0.680 9.237 13854 Z= 0.322 Chirality : 0.045 0.210 1677 Planarity : 0.004 0.050 1704 Dihedral : 5.966 46.175 1444 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 4.67 % Allowed : 15.81 % 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: -0.88 (0.23), residues: 1314 helix: 0.34 (0.19), residues: 810 sheet: -1.15 (0.48), residues: 99 loop : -2.23 (0.28), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 78 TYR 0.013 0.001 TYR B 344 PHE 0.013 0.001 PHE B 3 TRP 0.013 0.002 TRP B 267 HIS 0.012 0.003 HIS B 303 Details of bonding type rmsd covalent geometry : bond 0.00285 (10188) covalent geometry : angle 0.67976 (13848) SS BOND : bond 0.00298 ( 3) SS BOND : angle 0.49167 ( 6) hydrogen bonds : bond 0.03246 ( 435) hydrogen bonds : angle 3.67995 ( 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 223 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 174 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ASP cc_start: 0.8379 (OUTLIER) cc_final: 0.8116 (m-30) REVERT: A 16 GLN cc_start: 0.8377 (mm-40) cc_final: 0.8155 (mt0) REVERT: A 80 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8273 (tt) REVERT: A 238 LYS cc_start: 0.8393 (mtmt) cc_final: 0.7970 (mttt) REVERT: A 250 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8093 (pp) REVERT: A 275 LYS cc_start: 0.8651 (ttmp) cc_final: 0.8113 (mtmt) REVERT: B 10 ASP cc_start: 0.8311 (m-30) cc_final: 0.8074 (m-30) REVERT: B 127 GLU cc_start: 0.7900 (tp30) cc_final: 0.7608 (tp30) REVERT: B 132 TYR cc_start: 0.8739 (p90) cc_final: 0.8387 (p90) REVERT: B 238 LYS cc_start: 0.8754 (mtmt) cc_final: 0.8467 (mtmt) REVERT: B 250 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8032 (pp) REVERT: B 275 LYS cc_start: 0.8527 (ttmp) cc_final: 0.8120 (mtmt) REVERT: B 300 MET cc_start: 0.8363 (mmm) cc_final: 0.8095 (mmt) REVERT: C 10 ASP cc_start: 0.8296 (m-30) cc_final: 0.8009 (m-30) REVERT: C 49 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.7322 (ptm) REVERT: C 79 ILE cc_start: 0.8114 (mm) cc_final: 0.7880 (mt) REVERT: C 132 TYR cc_start: 0.8870 (p90) cc_final: 0.8437 (p90) REVERT: C 250 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8229 (pp) REVERT: C 259 MET cc_start: 0.9239 (mmp) cc_final: 0.9022 (mmp) REVERT: C 275 LYS cc_start: 0.8570 (ttmp) cc_final: 0.8157 (mtmt) REVERT: D 67 GLU cc_start: 0.8299 (tt0) cc_final: 0.7980 (tt0) outliers start: 49 outliers final: 40 residues processed: 211 average time/residue: 0.0888 time to fit residues: 26.6331 Evaluate side-chains 212 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 166 time to evaluate : 0.351 ------------------------------------------------------------------------------- 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 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 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 15 LEU Chi-restraints excluded: chain C residue 49 MET 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 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 68 THR 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: 0.7980 chunk 11 optimal weight: 0.9980 chunk 102 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 63 optimal weight: 0.6980 chunk 25 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 113 optimal weight: 6.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3257 r_free = 0.3257 target = 0.118762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.091903 restraints weight = 25385.695| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 2.82 r_work: 0.2763 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2739 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2739 r_free = 0.2739 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2739 r_free = 0.2739 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2739 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10191 Z= 0.120 Angle : 0.673 8.500 13854 Z= 0.318 Chirality : 0.044 0.205 1677 Planarity : 0.004 0.049 1704 Dihedral : 5.863 45.895 1444 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 4.48 % Allowed : 15.90 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.23), residues: 1314 helix: 0.46 (0.19), residues: 807 sheet: -1.03 (0.49), residues: 99 loop : -2.18 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 78 TYR 0.012 0.001 TYR A 344 PHE 0.014 0.001 PHE B 3 TRP 0.012 0.002 TRP B 267 HIS 0.013 0.003 HIS B 303 Details of bonding type rmsd covalent geometry : bond 0.00280 (10188) covalent geometry : angle 0.67320 (13848) SS BOND : bond 0.00277 ( 3) SS BOND : angle 0.45092 ( 6) hydrogen bonds : bond 0.03181 ( 435) hydrogen bonds : angle 3.65517 ( 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 223 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 176 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ASP cc_start: 0.8335 (OUTLIER) cc_final: 0.8097 (m-30) REVERT: A 16 GLN cc_start: 0.8341 (mm-40) cc_final: 0.8140 (mt0) REVERT: A 80 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8306 (tt) REVERT: A 238 LYS cc_start: 0.8321 (mtmt) cc_final: 0.7952 (mtpt) REVERT: A 250 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8051 (pp) REVERT: A 275 LYS cc_start: 0.8630 (ttmp) cc_final: 0.8147 (mtmt) REVERT: B 10 ASP cc_start: 0.8374 (m-30) cc_final: 0.8152 (m-30) REVERT: B 70 MET cc_start: 0.7898 (mtm) cc_final: 0.7618 (mtt) REVERT: B 132 TYR cc_start: 0.8722 (p90) cc_final: 0.8381 (p90) REVERT: B 238 LYS cc_start: 0.8752 (mtmt) cc_final: 0.8451 (mtmt) REVERT: B 250 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8000 (pp) REVERT: B 275 LYS cc_start: 0.8490 (ttmp) cc_final: 0.8140 (mtmt) REVERT: C 10 ASP cc_start: 0.8316 (m-30) cc_final: 0.8039 (m-30) REVERT: C 79 ILE cc_start: 0.8045 (mm) cc_final: 0.7795 (mt) REVERT: C 132 TYR cc_start: 0.8797 (p90) cc_final: 0.8415 (p90) REVERT: C 240 GLU cc_start: 0.8590 (mp0) cc_final: 0.7831 (mp0) REVERT: C 250 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8156 (pp) REVERT: C 259 MET cc_start: 0.9232 (mmp) cc_final: 0.9028 (mmp) REVERT: C 275 LYS cc_start: 0.8522 (ttmp) cc_final: 0.8152 (mtmt) REVERT: D 67 GLU cc_start: 0.8247 (tt0) cc_final: 0.7803 (mt-10) outliers start: 47 outliers final: 41 residues processed: 210 average time/residue: 0.0929 time to fit residues: 27.8313 Evaluate side-chains 221 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 175 time to evaluate : 0.334 ------------------------------------------------------------------------------- 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 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 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 125 LEU Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 242 VAL 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 99 optimal weight: 5.9990 chunk 35 optimal weight: 0.2980 chunk 114 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 92 optimal weight: 0.0270 chunk 8 optimal weight: 0.8980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.118344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.090547 restraints weight = 30227.383| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 3.24 r_work: 0.2711 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2711 ------------------------------------------------------------------------------- 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 = 0.17 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 = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2705 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.456 10191 Z= 0.430 Angle : 0.970 65.877 13854 Z= 0.570 Chirality : 0.046 0.433 1677 Planarity : 0.009 0.328 1704 Dihedral : 5.862 45.897 1444 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 4.48 % Allowed : 16.00 % Favored : 79.52 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.23), residues: 1314 helix: 0.46 (0.19), residues: 807 sheet: -1.03 (0.49), residues: 99 loop : -2.19 (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 A 344 PHE 0.012 0.001 PHE B 3 TRP 0.012 0.002 TRP B 267 HIS 0.012 0.003 HIS B 303 Details of bonding type rmsd covalent geometry : bond 0.00817 (10188) covalent geometry : angle 0.97007 (13848) SS BOND : bond 0.00251 ( 3) SS BOND : angle 0.44118 ( 6) hydrogen bonds : bond 0.03178 ( 435) hydrogen bonds : angle 3.65570 ( 1269) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2203.87 seconds wall clock time: 38 minutes 29.73 seconds (2309.73 seconds total)