Starting phenix.real_space_refine on Fri Sep 11 20:36:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cyf_30499/09_2026/7cyf_30499_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cyf_30499/09_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_30499/09_2026/7cyf_30499_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cyf_30499/09_2026/7cyf_30499_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7cyf_30499/09_2026/7cyf_30499.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cyf_30499/09_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-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9996 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2474 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 17, 'TRANS': 316} Chain breaks: 1 Chain: "B" Number of atoms: 2474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2474 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 17, 'TRANS': 316} Chain breaks: 1 Chain: "C" Number of atoms: 2474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2474 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 17, 'TRANS': 316} Chain breaks: 1 Chain: "D" Number of atoms: 834 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 109, 831 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 3, 'TRANS': 105} Conformer: "B" Number of residues, atoms: 109, 831 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 3, 'TRANS': 105} bond proxies already assigned to first conformer: 838 Chain: "E" Number of atoms: 834 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 109, 831 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 3, 'TRANS': 105} Conformer: "B" Number of residues, atoms: 109, 831 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 3, 'TRANS': 105} bond proxies already assigned to first conformer: 838 Chain: "F" Number of atoms: 834 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 109, 831 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 3, 'TRANS': 105} Conformer: "B" Number of residues, atoms: 109, 831 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 3, 'TRANS': 105} bond proxies already assigned to first conformer: 838 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 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: 2.75, per 1000 atoms: 0.28 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: 0.78 Conformation dependent library (CDL) restraints added in 509.7 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: 0.25 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: 1.29 Time building geometry restraints manager: 1.08 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: 12948 2.29 - 4.58: 703 4.58 - 6.87: 109 6.87 - 9.16: 73 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: 5632 15.87 - 31.74: 300 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: 1268 0.071 - 0.143: 354 0.143 - 0.214: 37 0.214 - 0.285: 13 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: 0.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.430 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.073 10191 Z= 0.408 Angle : 1.285 11.455 13854 Z= 0.672 Chirality : 0.066 0.356 1677 Planarity : 0.008 0.082 1704 Dihedral : 11.567 79.350 3639 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer: Outliers : 1.90 % Allowed : 6.86 % Favored : 91.24 % Cbeta Deviations : 0.42 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.27 (0.15), residues: 1314 helix: -4.50 (0.08), residues: 813 sheet: -2.16 (0.48), residues: 102 loop : -3.29 (0.24), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.002 ARG A 269 TYR 0.028 0.003 TYR E 87 PHE 0.039 0.004 PHE B 22 TRP 0.012 0.003 TRP C 135 HIS 0.021 0.006 HIS B 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00938 / 0.41 (10188) covalent geometry : angle 1.28422 / 0.67 (13848) SS BOND : bond 0.01303 / 0.65 ( 3) SS BOND : angle 1.81482 / 0.83 ( 6) hydrogen bonds : bond 0.32308 / 20.69 ( 435) hydrogen bonds : angle 10.17854 / 6.97 ( 1269) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 286 time to evaluate : 0.360 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: 0.1038 time to fit residues: 42.7147 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 : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 319 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 6.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 6 ASN A 14 GLN A 291 HIS A 340 ASN B 6 ASN B 14 GLN B 291 HIS B 340 ASN C 6 ASN C 14 GLN C 340 ASN D 59 ASN E 44 ASN ** E 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 ASN F 59 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.120457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.093939 restraints weight = 25624.287| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 2.93 r_work: 0.2757 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2770 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2770 r_free = 0.2770 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2769 r_free = 0.2769 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.2769 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10191 Z= 0.147 Angle : 0.754 6.715 13854 Z= 0.373 Chirality : 0.046 0.226 1677 Planarity : 0.006 0.069 1704 Dihedral : 7.123 50.850 1454 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % 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: -4.04 (0.19), residues: 1314 helix: -2.54 (0.14), residues: 792 sheet: -2.05 (0.46), residues: 105 loop : -2.70 (0.27), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 99 TYR 0.014 0.002 TYR A 344 PHE 0.014 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/Z covalent geometry : bond 0.00320 / 0.15 (10188) covalent geometry : angle 0.75356 / 0.37 (13848) SS BOND : bond 0.00369 / 0.18 ( 3) SS BOND : angle 0.78342 / 0.37 ( 6) hydrogen bonds : bond 0.04712 / 3.08 ( 435) hydrogen bonds : angle 4.58030 / 3.08 ( 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 256 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 230 time to evaluate : 0.286 Fit side-chains revert: symmetry clash REVERT: A 10 ASP cc_start: 0.8339 (OUTLIER) cc_final: 0.7834 (m-30) REVERT: A 17 SER cc_start: 0.8776 (t) cc_final: 0.8238 (p) REVERT: A 35 GLN cc_start: 0.8026 (mp10) cc_final: 0.7637 (mm110) REVERT: A 40 GLU cc_start: 0.8036 (tt0) cc_final: 0.7698 (mt-10) REVERT: A 62 ILE cc_start: 0.9006 (tt) cc_final: 0.8608 (tt) REVERT: A 238 LYS cc_start: 0.8420 (mtmt) cc_final: 0.8065 (mttt) REVERT: A 250 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8152 (pp) REVERT: A 275 LYS cc_start: 0.8595 (ttmp) cc_final: 0.8032 (mtmt) REVERT: A 278 GLN cc_start: 0.7941 (pt0) cc_final: 0.7375 (mt0) REVERT: A 298 LEU cc_start: 0.8631 (tp) cc_final: 0.8415 (tp) REVERT: A 359 VAL cc_start: 0.8748 (p) cc_final: 0.8504 (t) REVERT: B 3 PHE cc_start: 0.7597 (t80) cc_final: 0.7304 (t80) REVERT: B 10 ASP cc_start: 0.8434 (t0) cc_final: 0.8068 (m-30) REVERT: B 35 GLN cc_start: 0.7985 (mp10) cc_final: 0.7674 (mm110) REVERT: B 79 ILE cc_start: 0.7987 (mm) cc_final: 0.7767 (mt) REVERT: B 238 LYS cc_start: 0.8796 (mtmt) cc_final: 0.8496 (mtmt) REVERT: B 250 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8174 (pp) REVERT: B 272 GLU cc_start: 0.8305 (tt0) cc_final: 0.7990 (tt0) REVERT: B 275 LYS cc_start: 0.8467 (ttmp) cc_final: 0.8012 (mtmt) REVERT: B 278 GLN cc_start: 0.7798 (pt0) cc_final: 0.7285 (mt0) REVERT: B 298 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8496 (tp) REVERT: C 10 ASP cc_start: 0.8272 (t0) cc_final: 0.7922 (m-30) REVERT: C 40 GLU cc_start: 0.8274 (mt-10) cc_final: 0.7916 (mt-10) REVERT: C 79 ILE cc_start: 0.8038 (mm) cc_final: 0.7820 (mt) REVERT: C 132 TYR cc_start: 0.8751 (p90) cc_final: 0.8367 (p90) REVERT: C 250 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8316 (pp) REVERT: C 259 MET cc_start: 0.9169 (mmt) cc_final: 0.8860 (mmt) REVERT: C 275 LYS cc_start: 0.8572 (ttmp) cc_final: 0.8172 (mtmt) REVERT: C 278 GLN cc_start: 0.8012 (pt0) cc_final: 0.7355 (mt0) REVERT: D 57 GLU cc_start: 0.7711 (pm20) cc_final: 0.7491 (mt-10) REVERT: D 67 GLU cc_start: 0.8406 (tt0) cc_final: 0.8078 (tt0) REVERT: F 6 ASN cc_start: 0.8763 (m-40) cc_final: 0.8547 (m-40) outliers start: 26 outliers final: 16 residues processed: 246 average time/residue: 0.0894 time to fit residues: 31.6632 Evaluate side-chains 207 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 186 time to evaluate : 0.266 ------------------------------------------------------------------------------- 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: 0.9990 chunk 31 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 124 optimal weight: 8.9990 chunk 120 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 ASN D 44 ASN E 50 GLN F 44 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.119402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.092471 restraints weight = 28888.027| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 3.16 r_work: 0.2740 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2749 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2749 r_free = 0.2749 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 = 0.2749 r_free = 0.2749 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2749 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10191 Z= 0.128 Angle : 0.703 9.544 13854 Z= 0.338 Chirality : 0.044 0.208 1677 Planarity : 0.005 0.058 1704 Dihedral : 6.505 50.480 1445 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 4.00 % Allowed : 14.10 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.63 (0.21), residues: 1314 helix: -1.29 (0.17), residues: 816 sheet: -1.87 (0.45), residues: 105 loop : -2.33 (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 0.011 0.001 PHE B 364 TRP 0.010 0.002 TRP A 135 HIS 0.012 0.003 HIS C 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (10188) covalent geometry : angle 0.70323 / 0.34 (13848) SS BOND : bond 0.00326 / 0.16 ( 3) SS BOND : angle 0.59696 / 0.28 ( 6) hydrogen bonds : bond 0.03918 / 2.59 ( 435) hydrogen bonds : angle 4.02672 / 2.70 ( 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 230 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 188 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ASP cc_start: 0.8358 (OUTLIER) cc_final: 0.7859 (m-30) REVERT: A 35 GLN cc_start: 0.7917 (mp10) cc_final: 0.7585 (mm110) REVERT: A 80 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8345 (tt) REVERT: A 238 LYS cc_start: 0.8425 (mtmt) cc_final: 0.7958 (mttt) REVERT: A 250 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8096 (pp) REVERT: A 275 LYS cc_start: 0.8543 (ttmp) cc_final: 0.8055 (mtmt) REVERT: A 278 GLN cc_start: 0.7934 (pt0) cc_final: 0.7343 (mt0) REVERT: B 3 PHE cc_start: 0.7611 (t80) cc_final: 0.7302 (t80) REVERT: B 10 ASP cc_start: 0.8412 (t0) cc_final: 0.8076 (m-30) REVERT: B 35 GLN cc_start: 0.7898 (mp10) cc_final: 0.7664 (mm110) REVERT: B 79 ILE cc_start: 0.7993 (mm) cc_final: 0.7758 (mt) REVERT: B 161 LYS cc_start: 0.8002 (ptpt) cc_final: 0.7780 (ptpp) REVERT: B 238 LYS cc_start: 0.8829 (mtmt) cc_final: 0.8470 (mtmt) REVERT: B 250 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8106 (pp) REVERT: B 272 GLU cc_start: 0.8392 (tt0) cc_final: 0.8086 (tt0) REVERT: B 275 LYS cc_start: 0.8441 (ttmp) cc_final: 0.8110 (mtmt) REVERT: B 278 GLN cc_start: 0.7823 (pt0) cc_final: 0.7266 (mt0) REVERT: B 298 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8553 (tp) REVERT: C 10 ASP cc_start: 0.8288 (t0) cc_final: 0.7950 (m-30) REVERT: C 79 ILE cc_start: 0.8007 (mm) cc_final: 0.7777 (mt) REVERT: C 89 ARG cc_start: 0.8185 (tmt-80) cc_final: 0.7838 (ttt-90) REVERT: C 132 TYR cc_start: 0.8775 (p90) cc_final: 0.8324 (p90) REVERT: C 250 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8290 (pp) REVERT: C 275 LYS cc_start: 0.8503 (ttmp) cc_final: 0.8127 (mtmt) REVERT: D 57 GLU cc_start: 0.7652 (pm20) cc_final: 0.7400 (mt-10) REVERT: D 67 GLU cc_start: 0.8452 (tt0) cc_final: 0.7959 (mt-10) REVERT: F 6 ASN cc_start: 0.8786 (m-40) cc_final: 0.8582 (m-40) outliers start: 42 outliers final: 23 residues processed: 216 average time/residue: 0.0965 time to fit residues: 29.5144 Evaluate side-chains 206 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 177 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 215 ILE 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: 0.9990 chunk 85 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 86 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 119 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 291 HIS E 50 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.118294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.093768 restraints weight = 17815.087| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 2.30 r_work: 0.2809 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2782 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2782 r_free = 0.2782 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2782 r_free = 0.2782 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2782 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10191 Z= 0.139 Angle : 0.689 8.151 13854 Z= 0.333 Chirality : 0.045 0.248 1677 Planarity : 0.004 0.053 1704 Dihedral : 6.352 50.403 1444 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 4.67 % Allowed : 13.62 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.22), residues: 1314 helix: -0.60 (0.18), residues: 813 sheet: -1.57 (0.48), residues: 99 loop : -2.33 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 78 TYR 0.012 0.001 TYR A 344 PHE 0.012 0.001 PHE C 110 TRP 0.010 0.002 TRP B 267 HIS 0.012 0.003 HIS B 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (10188) covalent geometry : angle 0.68947 / 0.33 (13848) SS BOND : bond 0.00386 / 0.19 ( 3) SS BOND : angle 0.56311 / 0.26 ( 6) hydrogen bonds : bond 0.03704 / 2.45 ( 435) hydrogen bonds : angle 3.85502 / 2.58 ( 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 233 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 184 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ASP cc_start: 0.8370 (OUTLIER) cc_final: 0.7916 (m-30) REVERT: A 16 GLN cc_start: 0.8303 (mm-40) cc_final: 0.7886 (mt0) REVERT: A 35 GLN cc_start: 0.7908 (mp10) cc_final: 0.7630 (mm110) REVERT: A 80 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8341 (tt) REVERT: A 158 TYR cc_start: 0.8605 (t80) cc_final: 0.8293 (t80) REVERT: A 238 LYS cc_start: 0.8414 (mtmt) cc_final: 0.7958 (mttt) REVERT: A 250 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8092 (pp) REVERT: A 275 LYS cc_start: 0.8535 (ttmp) cc_final: 0.8038 (mtmt) REVERT: A 278 GLN cc_start: 0.7914 (pt0) cc_final: 0.7358 (mt0) REVERT: B 3 PHE cc_start: 0.7722 (t80) cc_final: 0.7454 (t80) REVERT: B 10 ASP cc_start: 0.8385 (t0) cc_final: 0.8135 (m-30) REVERT: B 79 ILE cc_start: 0.8144 (mm) cc_final: 0.7886 (mt) REVERT: B 132 TYR cc_start: 0.8649 (p90) cc_final: 0.8304 (p90) REVERT: B 238 LYS cc_start: 0.8804 (mtmt) cc_final: 0.8405 (mtmt) REVERT: B 250 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8107 (pp) REVERT: B 272 GLU cc_start: 0.8259 (tt0) cc_final: 0.7993 (tt0) REVERT: B 275 LYS cc_start: 0.8429 (ttmp) cc_final: 0.8111 (mtmt) REVERT: B 278 GLN cc_start: 0.7789 (pt0) cc_final: 0.7269 (mt0) REVERT: B 298 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8685 (tp) REVERT: B 359 VAL cc_start: 0.8829 (p) cc_final: 0.8480 (t) REVERT: C 10 ASP cc_start: 0.8265 (t0) cc_final: 0.7969 (m-30) REVERT: C 40 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7577 (mm-30) REVERT: C 79 ILE cc_start: 0.8179 (mm) cc_final: 0.7936 (mt) REVERT: C 89 ARG cc_start: 0.8192 (tmt-80) cc_final: 0.7840 (ttt-90) REVERT: C 132 TYR cc_start: 0.8827 (p90) cc_final: 0.8258 (p90) REVERT: C 250 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8249 (pp) REVERT: C 259 MET cc_start: 0.9178 (mmt) cc_final: 0.8945 (mmp) REVERT: C 275 LYS cc_start: 0.8508 (ttmp) cc_final: 0.8136 (mtmt) REVERT: D 67 GLU cc_start: 0.8272 (tt0) cc_final: 0.7981 (tt0) REVERT: E 26 GLU cc_start: 0.8795 (mt-10) cc_final: 0.8529 (mt-10) REVERT: F 100 TYR cc_start: 0.8652 (m-80) cc_final: 0.8317 (m-80) outliers start: 49 outliers final: 35 residues processed: 218 average time/residue: 0.0873 time to fit residues: 27.2813 Evaluate side-chains 219 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 177 time to evaluate : 0.380 ------------------------------------------------------------------------------- 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 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 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 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 324 SER 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: 2.9990 chunk 71 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 67 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 88 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 89 optimal weight: 0.2980 chunk 98 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 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 = 0.3270 r_free = 0.3270 target = 0.119551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.092576 restraints weight = 28122.577| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 3.09 r_work: 0.2737 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2734 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2734 r_free = 0.2734 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2734 r_free = 0.2734 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2734 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10191 Z= 0.124 Angle : 0.664 6.986 13854 Z= 0.321 Chirality : 0.044 0.209 1677 Planarity : 0.004 0.052 1704 Dihedral : 6.198 49.954 1444 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 5.14 % Allowed : 14.76 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.23), residues: 1314 helix: -0.08 (0.19), residues: 792 sheet: -1.44 (0.48), residues: 99 loop : -2.42 (0.27), residues: 423 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 0.011 0.001 PHE C 364 TRP 0.010 0.002 TRP B 267 HIS 0.012 0.003 HIS B 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 (10188) covalent geometry : angle 0.66441 / 0.32 (13848) SS BOND : bond 0.00319 / 0.16 ( 3) SS BOND : angle 0.43012 / 0.20 ( 6) hydrogen bonds : bond 0.03405 / 2.24 ( 435) hydrogen bonds : angle 3.74000 / 2.50 ( 1269) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 185 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: A 10 ASP cc_start: 0.8359 (OUTLIER) cc_final: 0.7975 (m-30) REVERT: A 16 GLN cc_start: 0.8327 (mm-40) cc_final: 0.8007 (mt0) REVERT: A 80 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8335 (tt) REVERT: A 158 TYR cc_start: 0.8634 (t80) cc_final: 0.8297 (t80) REVERT: A 238 LYS cc_start: 0.8399 (mtmt) cc_final: 0.7947 (mttt) REVERT: A 250 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8047 (pp) REVERT: A 275 LYS cc_start: 0.8496 (ttmp) cc_final: 0.8011 (mtmt) REVERT: A 278 GLN cc_start: 0.7992 (pt0) cc_final: 0.7396 (mt0) REVERT: A 359 VAL cc_start: 0.8772 (m) cc_final: 0.8492 (p) REVERT: B 3 PHE cc_start: 0.7671 (t80) cc_final: 0.7340 (t80) REVERT: B 10 ASP cc_start: 0.8411 (t0) cc_final: 0.8156 (m-30) REVERT: B 79 ILE cc_start: 0.8141 (mm) cc_final: 0.7878 (mt) REVERT: B 132 TYR cc_start: 0.8681 (p90) cc_final: 0.8329 (p90) REVERT: B 161 LYS cc_start: 0.7967 (ptpt) cc_final: 0.7761 (ptpp) REVERT: B 238 LYS cc_start: 0.8786 (mtmt) cc_final: 0.8536 (mtmt) REVERT: B 250 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8074 (pp) REVERT: B 264 MET cc_start: 0.8741 (mtp) cc_final: 0.8495 (mtm) REVERT: B 272 GLU cc_start: 0.8352 (tt0) cc_final: 0.8069 (tt0) REVERT: B 275 LYS cc_start: 0.8397 (ttmp) cc_final: 0.8111 (mtmt) REVERT: B 278 GLN cc_start: 0.7866 (pt0) cc_final: 0.7322 (mt0) REVERT: B 359 VAL cc_start: 0.8892 (p) cc_final: 0.8582 (t) REVERT: C 10 ASP cc_start: 0.8263 (t0) cc_final: 0.7981 (m-30) REVERT: C 79 ILE cc_start: 0.8097 (mm) cc_final: 0.7851 (mt) REVERT: C 132 TYR cc_start: 0.8871 (p90) cc_final: 0.8328 (p90) REVERT: C 250 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8278 (pp) REVERT: C 259 MET cc_start: 0.9177 (mmt) cc_final: 0.8950 (mmp) REVERT: C 275 LYS cc_start: 0.8495 (ttmp) cc_final: 0.8185 (mtmt) REVERT: D 67 GLU cc_start: 0.8408 (tt0) cc_final: 0.8093 (tt0) REVERT: D 78 ARG cc_start: 0.8664 (mtp85) cc_final: 0.8430 (mtp180) REVERT: F 100 TYR cc_start: 0.8681 (m-80) cc_final: 0.8329 (m-80) outliers start: 54 outliers final: 36 residues processed: 220 average time/residue: 0.0999 time to fit residues: 31.4474 Evaluate side-chains 219 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 178 time to evaluate : 0.370 ------------------------------------------------------------------------------- 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 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 227 MET Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 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 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: 1.9990 chunk 14 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 121 optimal weight: 0.9980 chunk 42 optimal weight: 10.0000 chunk 108 optimal weight: 0.0270 chunk 8 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 89 optimal weight: 8.9990 chunk 118 optimal weight: 0.9980 overall best weight: 1.4042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 35 GLN ** B 291 HIS ** 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 = 0.3237 r_free = 0.3237 target = 0.117197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.091348 restraints weight = 22003.914| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 2.61 r_work: 0.2759 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2740 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2740 r_free = 0.2740 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2740 r_free = 0.2740 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2740 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10191 Z= 0.140 Angle : 0.675 6.786 13854 Z= 0.326 Chirality : 0.044 0.209 1677 Planarity : 0.004 0.049 1704 Dihedral : 6.220 50.239 1444 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 5.62 % Allowed : 14.67 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.23), residues: 1314 helix: 0.03 (0.19), residues: 810 sheet: -1.39 (0.47), residues: 105 loop : -2.14 (0.28), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 78 TYR 0.012 0.001 TYR E 100 PHE 0.014 0.001 PHE A 3 TRP 0.010 0.002 TRP B 135 HIS 0.011 0.003 HIS B 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 (10188) covalent geometry : angle 0.67513 / 0.33 (13848) SS BOND : bond 0.00352 / 0.18 ( 3) SS BOND : angle 0.48702 / 0.22 ( 6) hydrogen bonds : bond 0.03525 / 2.32 ( 435) hydrogen bonds : angle 3.73608 / 2.50 ( 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 244 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 185 time to evaluate : 0.454 Fit side-chains REVERT: A 10 ASP cc_start: 0.8402 (OUTLIER) cc_final: 0.8081 (m-30) REVERT: A 16 GLN cc_start: 0.8337 (mm-40) cc_final: 0.8032 (mt0) REVERT: A 80 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8233 (tt) REVERT: A 158 TYR cc_start: 0.8633 (t80) cc_final: 0.8272 (t80) REVERT: A 238 LYS cc_start: 0.8411 (mtmt) cc_final: 0.7958 (mttt) REVERT: A 250 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8098 (pp) REVERT: A 275 LYS cc_start: 0.8540 (ttmp) cc_final: 0.8057 (mtmt) REVERT: A 278 GLN cc_start: 0.7936 (pt0) cc_final: 0.7366 (mt0) REVERT: A 359 VAL cc_start: 0.8829 (m) cc_final: 0.8546 (p) REVERT: B 3 PHE cc_start: 0.7816 (t80) cc_final: 0.7408 (t80) REVERT: B 10 ASP cc_start: 0.8385 (t0) cc_final: 0.8166 (m-30) REVERT: B 70 MET cc_start: 0.7958 (mtm) cc_final: 0.7581 (mtt) REVERT: B 79 ILE cc_start: 0.8139 (mm) cc_final: 0.7866 (mt) REVERT: B 132 TYR cc_start: 0.8695 (p90) cc_final: 0.8373 (p90) REVERT: B 238 LYS cc_start: 0.8787 (mtmt) cc_final: 0.8547 (mtmt) REVERT: B 250 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8080 (pp) REVERT: B 272 GLU cc_start: 0.8282 (tt0) cc_final: 0.7998 (tt0) REVERT: B 275 LYS cc_start: 0.8455 (ttmp) cc_final: 0.8125 (mtmt) REVERT: B 278 GLN cc_start: 0.7853 (pt0) cc_final: 0.7314 (mt0) REVERT: B 359 VAL cc_start: 0.8893 (p) cc_final: 0.8652 (t) REVERT: C 10 ASP cc_start: 0.8274 (t0) cc_final: 0.8050 (m-30) REVERT: C 49 MET cc_start: 0.8270 (OUTLIER) cc_final: 0.7635 (ptm) REVERT: C 79 ILE cc_start: 0.8114 (mm) cc_final: 0.7883 (mt) REVERT: C 89 ARG cc_start: 0.8168 (tmt-80) cc_final: 0.7834 (ttt-90) REVERT: C 132 TYR cc_start: 0.8877 (p90) cc_final: 0.8409 (p90) REVERT: C 250 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8358 (pp) REVERT: C 259 MET cc_start: 0.9164 (mmt) cc_final: 0.8913 (mmp) REVERT: C 275 LYS cc_start: 0.8514 (ttmp) cc_final: 0.8190 (mtmt) REVERT: D 67 GLU cc_start: 0.8285 (tt0) cc_final: 0.7829 (mt-10) outliers start: 59 outliers final: 44 residues processed: 226 average time/residue: 0.1002 time to fit residues: 32.3736 Evaluate side-chains 223 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 173 time to evaluate : 0.371 ------------------------------------------------------------------------------- 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 40 GLU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 303 HIS Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 227 MET 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 36 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 106 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 118 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 104 optimal weight: 0.1980 chunk 21 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3266 r_free = 0.3266 target = 0.119491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.091865 restraints weight = 30484.401| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 3.22 r_work: 0.2719 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2714 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2714 r_free = 0.2714 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2714 r_free = 0.2714 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2714 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10191 Z= 0.122 Angle : 0.654 6.949 13854 Z= 0.315 Chirality : 0.044 0.206 1677 Planarity : 0.004 0.048 1704 Dihedral : 6.127 49.768 1444 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 5.81 % Allowed : 15.24 % Favored : 78.95 % 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: -0.94 (0.23), residues: 1314 helix: 0.24 (0.19), residues: 807 sheet: -1.22 (0.48), residues: 99 loop : -2.10 (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 0.026 0.001 PHE A 3 TRP 0.011 0.002 TRP B 135 HIS 0.011 0.003 HIS C 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 (10188) covalent geometry : angle 0.65375 / 0.32 (13848) SS BOND : bond 0.00284 / 0.14 ( 3) SS BOND : angle 0.44374 / 0.20 ( 6) hydrogen bonds : bond 0.03274 / 2.15 ( 435) hydrogen bonds : angle 3.68580 / 2.48 ( 1269) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 176 time to evaluate : 0.395 Fit side-chains REVERT: A 10 ASP cc_start: 0.8408 (OUTLIER) cc_final: 0.8107 (m-30) REVERT: A 16 GLN cc_start: 0.8346 (mm-40) cc_final: 0.8101 (mt0) REVERT: A 80 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8325 (tt) REVERT: A 238 LYS cc_start: 0.8436 (mtmt) cc_final: 0.7993 (mttt) REVERT: A 250 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8064 (pp) REVERT: A 275 LYS cc_start: 0.8512 (ttmp) cc_final: 0.8060 (mtmt) REVERT: A 278 GLN cc_start: 0.8045 (pt0) cc_final: 0.7449 (mt0) REVERT: A 359 VAL cc_start: 0.8831 (m) cc_final: 0.8572 (p) REVERT: B 79 ILE cc_start: 0.8134 (mm) cc_final: 0.7862 (mt) REVERT: B 132 TYR cc_start: 0.8735 (p90) cc_final: 0.8420 (p90) REVERT: B 238 LYS cc_start: 0.8764 (mtmt) cc_final: 0.8426 (mtmt) REVERT: B 250 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8019 (pp) REVERT: B 275 LYS cc_start: 0.8419 (ttmp) cc_final: 0.8120 (mtmt) REVERT: B 300 MET cc_start: 0.8313 (mmt) cc_final: 0.7685 (mmt) REVERT: B 359 VAL cc_start: 0.8905 (p) cc_final: 0.8693 (t) REVERT: C 10 ASP cc_start: 0.8279 (t0) cc_final: 0.8064 (m-30) REVERT: C 36 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7844 (tt) REVERT: C 79 ILE cc_start: 0.8079 (mm) cc_final: 0.7835 (mt) REVERT: C 89 ARG cc_start: 0.8172 (tmt-80) cc_final: 0.7847 (ttt-90) REVERT: C 132 TYR cc_start: 0.8877 (p90) cc_final: 0.8398 (p90) REVERT: C 250 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8287 (pp) REVERT: C 259 MET cc_start: 0.9176 (mmt) cc_final: 0.8951 (mmp) REVERT: C 275 LYS cc_start: 0.8504 (ttmp) cc_final: 0.8190 (mtmt) REVERT: D 67 GLU cc_start: 0.8390 (tt0) cc_final: 0.8082 (tt0) REVERT: F 100 TYR cc_start: 0.8767 (m-80) cc_final: 0.8421 (m-80) outliers start: 61 outliers final: 46 residues processed: 218 average time/residue: 0.1028 time to fit residues: 32.2503 Evaluate side-chains 226 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 174 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 303 HIS Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 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 227 MET 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 36 LEU Chi-restraints excluded: chain C residue 72 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 324 SER 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 55 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: 2.9990 chunk 6 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 chunk 112 optimal weight: 3.9990 chunk 59 optimal weight: 8.9990 chunk 76 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 113 optimal weight: 7.9990 chunk 105 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.115382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.087714 restraints weight = 30377.465| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 3.09 r_work: 0.2703 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2672 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2672 r_free = 0.2672 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2672 r_free = 0.2672 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2672 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10191 Z= 0.165 Angle : 0.710 8.876 13854 Z= 0.341 Chirality : 0.045 0.217 1677 Planarity : 0.004 0.049 1704 Dihedral : 6.325 50.996 1444 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 5.71 % Allowed : 14.76 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.23), residues: 1314 helix: 0.06 (0.19), residues: 828 sheet: -1.13 (0.47), residues: 105 loop : -2.01 (0.29), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 78 TYR 0.012 0.001 TYR D 87 PHE 0.013 0.002 PHE C 110 TRP 0.010 0.002 TRP C 135 HIS 0.010 0.003 HIS C 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.16 (10188) covalent geometry : angle 0.71022 / 0.34 (13848) SS BOND : bond 0.00440 / 0.22 ( 3) SS BOND : angle 0.55938 / 0.25 ( 6) hydrogen bonds : bond 0.03736 / 2.46 ( 435) hydrogen bonds : angle 3.73357 / 2.51 ( 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 235 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 175 time to evaluate : 0.418 Fit side-chains revert: symmetry clash REVERT: A 10 ASP cc_start: 0.8424 (OUTLIER) cc_final: 0.8147 (m-30) REVERT: A 16 GLN cc_start: 0.8364 (mm-40) cc_final: 0.8074 (mt0) REVERT: A 80 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8265 (tt) REVERT: A 238 LYS cc_start: 0.8424 (mtmt) cc_final: 0.7934 (mttt) REVERT: A 250 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8139 (pp) REVERT: A 275 LYS cc_start: 0.8561 (ttmp) cc_final: 0.8075 (mtmt) REVERT: A 278 GLN cc_start: 0.8046 (pt0) cc_final: 0.7484 (mt0) REVERT: B 10 ASP cc_start: 0.8279 (m-30) cc_final: 0.8025 (m-30) REVERT: B 70 MET cc_start: 0.7959 (mtm) cc_final: 0.7605 (mtt) REVERT: B 79 ILE cc_start: 0.8187 (mm) cc_final: 0.7935 (mt) REVERT: B 127 GLU cc_start: 0.7905 (tp30) cc_final: 0.7636 (tp30) REVERT: B 132 TYR cc_start: 0.8745 (p90) cc_final: 0.8407 (p90) REVERT: B 238 LYS cc_start: 0.8773 (mtmt) cc_final: 0.8412 (mtmt) REVERT: B 250 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8127 (pp) REVERT: B 275 LYS cc_start: 0.8549 (ttmp) cc_final: 0.8146 (mtmt) REVERT: B 278 GLN cc_start: 0.7937 (pt0) cc_final: 0.7406 (mt0) REVERT: C 10 ASP cc_start: 0.8274 (t0) cc_final: 0.8040 (m-30) REVERT: C 17 SER cc_start: 0.8731 (t) cc_final: 0.8140 (p) REVERT: C 79 ILE cc_start: 0.8135 (mm) cc_final: 0.7900 (mt) REVERT: C 132 TYR cc_start: 0.8892 (p90) cc_final: 0.8476 (p90) REVERT: C 250 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8211 (pp) REVERT: C 259 MET cc_start: 0.9174 (mmt) cc_final: 0.8924 (mmt) REVERT: C 275 LYS cc_start: 0.8596 (ttmp) cc_final: 0.8169 (mtmt) REVERT: D 67 GLU cc_start: 0.8376 (tt0) cc_final: 0.8075 (tt0) outliers start: 60 outliers final: 45 residues processed: 221 average time/residue: 0.1033 time to fit residues: 32.7686 Evaluate side-chains 221 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 171 time to evaluate : 0.398 ------------------------------------------------------------------------------- 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 40 GLU 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 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 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 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 55 ASP Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 55 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: 3.9990 chunk 17 optimal weight: 0.0050 chunk 102 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 67 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 ASN E 50 GLN F 52 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.119061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.092097 restraints weight = 26232.600| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 2.88 r_work: 0.2744 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2743 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2743 r_free = 0.2743 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 = 0.2743 r_free = 0.2743 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2743 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.3565 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= 0.119 Angle : 0.662 7.704 13854 Z= 0.316 Chirality : 0.044 0.206 1677 Planarity : 0.004 0.048 1704 Dihedral : 6.116 49.509 1444 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 4.86 % Allowed : 15.52 % 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: -0.80 (0.24), residues: 1314 helix: 0.38 (0.19), residues: 807 sheet: -0.94 (0.49), residues: 99 loop : -2.20 (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 B 344 PHE 0.009 0.001 PHE C 364 TRP 0.013 0.002 TRP B 267 HIS 0.011 0.003 HIS C 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (10188) covalent geometry : angle 0.66255 / 0.32 (13848) SS BOND : bond 0.00272 / 0.14 ( 3) SS BOND : angle 0.48118 / 0.22 ( 6) hydrogen bonds : bond 0.03213 / 2.10 ( 435) hydrogen bonds : angle 3.65820 / 2.47 ( 1269) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 181 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: A 10 ASP cc_start: 0.8370 (OUTLIER) cc_final: 0.8120 (m-30) REVERT: A 16 GLN cc_start: 0.8331 (mm-40) cc_final: 0.8109 (mt0) REVERT: A 80 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8276 (tt) REVERT: A 238 LYS cc_start: 0.8391 (mtmt) cc_final: 0.7990 (mttt) REVERT: A 250 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8089 (pp) REVERT: A 275 LYS cc_start: 0.8409 (ttmp) cc_final: 0.8073 (mtmt) REVERT: A 359 VAL cc_start: 0.8842 (m) cc_final: 0.8601 (p) REVERT: B 10 ASP cc_start: 0.8293 (m-30) cc_final: 0.8038 (m-30) REVERT: B 40 GLU cc_start: 0.7701 (tt0) cc_final: 0.7298 (tt0) REVERT: B 70 MET cc_start: 0.7936 (mtm) cc_final: 0.7600 (mtt) REVERT: B 79 ILE cc_start: 0.8106 (mm) cc_final: 0.7834 (mt) REVERT: B 132 TYR cc_start: 0.8774 (p90) cc_final: 0.8423 (p90) REVERT: B 238 LYS cc_start: 0.8745 (mtmt) cc_final: 0.8479 (mtmt) REVERT: B 250 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.7956 (pp) REVERT: B 275 LYS cc_start: 0.8480 (ttmp) cc_final: 0.8120 (mtmt) REVERT: B 300 MET cc_start: 0.8177 (mmt) cc_final: 0.7784 (mmt) REVERT: C 79 ILE cc_start: 0.8011 (mm) cc_final: 0.7781 (mt) REVERT: C 132 TYR cc_start: 0.8903 (p90) cc_final: 0.8486 (p90) REVERT: C 250 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8180 (pp) REVERT: C 259 MET cc_start: 0.9138 (mmt) cc_final: 0.8914 (mmp) REVERT: C 275 LYS cc_start: 0.8537 (ttmp) cc_final: 0.8161 (mtmt) REVERT: D 67 GLU cc_start: 0.8276 (tt0) cc_final: 0.7963 (tt0) REVERT: F 100 TYR cc_start: 0.8696 (m-80) cc_final: 0.8461 (m-80) outliers start: 51 outliers final: 44 residues processed: 219 average time/residue: 0.1006 time to fit residues: 31.6743 Evaluate side-chains 222 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 173 time to evaluate : 0.386 ------------------------------------------------------------------------------- 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 40 GLU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 303 HIS Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 303 HIS Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 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 55 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: 0.9990 chunk 11 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 60 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 113 optimal weight: 0.7980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.119044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.092137 restraints weight = 25379.020| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 2.83 r_work: 0.2752 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2741 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2741 r_free = 0.2741 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 = 0.2741 r_free = 0.2741 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2741 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10191 Z= 0.123 Angle : 0.669 8.733 13854 Z= 0.320 Chirality : 0.044 0.205 1677 Planarity : 0.004 0.048 1704 Dihedral : 6.108 49.798 1444 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 4.76 % Allowed : 15.52 % 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: -0.70 (0.24), residues: 1314 helix: 0.44 (0.19), residues: 807 sheet: -0.86 (0.49), residues: 99 loop : -2.14 (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 0.009 0.001 PHE C 364 TRP 0.012 0.002 TRP B 267 HIS 0.011 0.003 HIS C 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 (10188) covalent geometry : angle 0.66954 / 0.32 (13848) SS BOND : bond 0.00284 / 0.14 ( 3) SS BOND : angle 0.43880 / 0.20 ( 6) hydrogen bonds : bond 0.03250 / 2.14 ( 435) hydrogen bonds : angle 3.66470 / 2.48 ( 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: 50 poor density : 173 time to evaluate : 0.387 Fit side-chains REVERT: A 10 ASP cc_start: 0.8352 (OUTLIER) cc_final: 0.8106 (m-30) REVERT: A 80 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8293 (tt) REVERT: A 238 LYS cc_start: 0.8355 (mtmt) cc_final: 0.7989 (mtpt) REVERT: A 250 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8059 (pp) REVERT: A 275 LYS cc_start: 0.8545 (ttmp) cc_final: 0.8110 (mtmt) REVERT: B 10 ASP cc_start: 0.8340 (m-30) cc_final: 0.8084 (m-30) REVERT: B 40 GLU cc_start: 0.7719 (tt0) cc_final: 0.7304 (tt0) REVERT: B 70 MET cc_start: 0.7956 (mtm) cc_final: 0.7618 (mtt) REVERT: B 79 ILE cc_start: 0.8110 (mm) cc_final: 0.7840 (mt) REVERT: B 118 MET cc_start: 0.8599 (ttt) cc_final: 0.8367 (ttp) REVERT: B 132 TYR cc_start: 0.8769 (p90) cc_final: 0.8457 (p90) REVERT: B 238 LYS cc_start: 0.8761 (mtmt) cc_final: 0.8492 (mtmt) REVERT: B 250 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.7950 (pp) REVERT: B 275 LYS cc_start: 0.8461 (ttmp) cc_final: 0.8107 (mtmt) REVERT: B 300 MET cc_start: 0.8286 (mmt) cc_final: 0.7701 (mmt) REVERT: C 79 ILE cc_start: 0.8028 (mm) cc_final: 0.7788 (mt) REVERT: C 89 ARG cc_start: 0.8088 (tmt-80) cc_final: 0.7760 (ttt-90) REVERT: C 132 TYR cc_start: 0.8906 (p90) cc_final: 0.8542 (p90) REVERT: C 240 GLU cc_start: 0.8546 (mp0) cc_final: 0.7745 (mp0) REVERT: C 250 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8177 (pp) REVERT: C 259 MET cc_start: 0.9122 (mmt) cc_final: 0.8893 (mmp) REVERT: C 275 LYS cc_start: 0.8519 (ttmp) cc_final: 0.8168 (mtmt) REVERT: D 57 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7206 (mp0) REVERT: D 67 GLU cc_start: 0.8237 (tt0) cc_final: 0.7783 (mt-10) outliers start: 50 outliers final: 41 residues processed: 210 average time/residue: 0.0999 time to fit residues: 30.5034 Evaluate side-chains 218 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 171 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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 250 LEU Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 303 HIS Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 303 HIS Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 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 55 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 99 optimal weight: 5.9990 chunk 35 optimal weight: 0.4980 chunk 114 optimal weight: 7.9990 chunk 53 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.121323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.093487 restraints weight = 30053.556| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 3.27 r_work: 0.2781 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2745 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2745 r_free = 0.2745 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2745 r_free = 0.2745 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2745 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.3713 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= 0.115 Angle : 0.652 8.411 13854 Z= 0.312 Chirality : 0.044 0.201 1677 Planarity : 0.004 0.048 1704 Dihedral : 6.032 49.175 1444 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 4.48 % Allowed : 15.71 % 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: -0.58 (0.24), residues: 1314 helix: 0.55 (0.19), residues: 807 sheet: -0.84 (0.49), residues: 99 loop : -2.09 (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 0.009 0.001 PHE A 364 TRP 0.013 0.002 TRP B 267 HIS 0.011 0.003 HIS C 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (10188) covalent geometry : angle 0.65209 / 0.31 (13848) SS BOND : bond 0.00229 / 0.12 ( 3) SS BOND : angle 0.42829 / 0.20 ( 6) hydrogen bonds : bond 0.03056 / 2.00 ( 435) hydrogen bonds : angle 3.62640 / 2.46 ( 1269) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2356.45 seconds wall clock time: 41 minutes 8.67 seconds (2468.67 seconds total)