Starting phenix.real_space_refine on Tue Jul 29 16:36:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cyf_30499/07_2025/7cyf_30499_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cyf_30499/07_2025/7cyf_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7cyf_30499/07_2025/7cyf_30499.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cyf_30499/07_2025/7cyf_30499.map" model { file = "/net/cci-nas-00/data/ceres_data/7cyf_30499/07_2025/7cyf_30499_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cyf_30499/07_2025/7cyf_30499_neut.cif" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.57, per 1000 atoms: 0.76 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: 2.32 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 0.98 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: 2.46 Time building geometry restraints manager: 2.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2636 1.33 - 1.45: 1741 1.45 - 1.57: 5712 1.57 - 1.69: 3 1.69 - 1.81: 96 Bond restraints: 10188 Sorted by residual: bond pdb=" N ALA B 320 " pdb=" CA ALA B 320 " ideal model delta sigma weight residual 1.458 1.506 -0.048 1.30e-02 5.92e+03 1.38e+01 bond pdb=" N VAL B 113 " pdb=" CA VAL B 113 " ideal model delta sigma weight residual 1.456 1.494 -0.039 1.11e-02 8.12e+03 1.21e+01 bond pdb=" N ILE A 326 " pdb=" CA ILE A 326 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.48e+00 bond pdb=" N TYR A 140 " pdb=" CA TYR A 140 " ideal model delta sigma weight residual 1.462 1.486 -0.024 8.50e-03 1.38e+04 7.94e+00 bond pdb=" N VAL A 113 " pdb=" CA VAL A 113 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.65e+00 ... (remaining 10183 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 12924 2.29 - 4.58: 719 4.58 - 6.87: 111 6.87 - 9.16: 79 9.16 - 11.45: 15 Bond angle restraints: 13848 Sorted by residual: angle pdb=" N LEU A 50 " pdb=" CA LEU A 50 " pdb=" C LEU A 50 " ideal model delta sigma weight residual 113.18 104.56 8.62 1.33e+00 5.65e-01 4.20e+01 angle pdb=" N LEU B 50 " pdb=" CA LEU B 50 " pdb=" C LEU B 50 " ideal model delta sigma weight residual 113.18 104.59 8.59 1.33e+00 5.65e-01 4.17e+01 angle pdb=" N ALA B 320 " pdb=" CA ALA B 320 " pdb=" C ALA B 320 " ideal model delta sigma weight residual 112.23 105.15 7.08 1.26e+00 6.30e-01 3.15e+01 angle pdb=" C ALA B 112 " pdb=" CA ALA B 112 " pdb=" CB ALA B 112 " ideal model delta sigma weight residual 110.42 121.19 -10.77 1.99e+00 2.53e-01 2.93e+01 angle pdb=" CA THR A 34 " pdb=" CB THR A 34 " pdb=" CG2 THR A 34 " ideal model delta sigma weight residual 110.50 119.21 -8.71 1.70e+00 3.46e-01 2.63e+01 ... (remaining 13843 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.87: 5629 15.87 - 31.74: 303 31.74 - 47.61: 103 47.61 - 63.48: 7 63.48 - 79.35: 6 Dihedral angle restraints: 6048 sinusoidal: 2280 harmonic: 3768 Sorted by residual: dihedral pdb=" CA PHE A 308 " pdb=" C PHE A 308 " pdb=" N SER A 309 " pdb=" CA SER A 309 " ideal model delta harmonic sigma weight residual -180.00 -154.73 -25.27 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA PHE C 308 " pdb=" C PHE C 308 " pdb=" N SER C 309 " pdb=" CA SER C 309 " ideal model delta harmonic sigma weight residual -180.00 -154.76 -25.24 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA PHE B 308 " pdb=" C PHE B 308 " pdb=" N SER B 309 " pdb=" CA SER B 309 " ideal model delta harmonic sigma weight residual -180.00 -154.80 -25.20 0 5.00e+00 4.00e-02 2.54e+01 ... (remaining 6045 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1265 0.071 - 0.143: 354 0.143 - 0.214: 37 0.214 - 0.285: 16 0.285 - 0.356: 5 Chirality restraints: 1677 Sorted by residual: chirality pdb=" CA THR C 34 " pdb=" N THR C 34 " pdb=" C THR C 34 " pdb=" CB THR C 34 " both_signs ideal model delta sigma weight residual False 2.53 2.17 0.36 2.00e-01 2.50e+01 3.17e+00 chirality pdb=" CA THR A 34 " pdb=" N THR A 34 " pdb=" C THR A 34 " pdb=" CB THR A 34 " both_signs ideal model delta sigma weight residual False 2.53 2.17 0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" CA THR B 34 " pdb=" N THR B 34 " pdb=" C THR B 34 " pdb=" CB THR B 34 " both_signs ideal model delta sigma weight residual False 2.53 2.17 0.35 2.00e-01 2.50e+01 3.12e+00 ... (remaining 1674 not shown) Planarity restraints: 1704 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 329 " -0.055 5.00e-02 4.00e+02 8.20e-02 1.08e+01 pdb=" N PRO B 330 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO B 330 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 330 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 329 " 0.055 5.00e-02 4.00e+02 8.19e-02 1.07e+01 pdb=" N PRO C 330 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO C 330 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 330 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 22 " -0.010 2.00e-02 2.50e+03 1.87e-02 6.14e+00 pdb=" CG PHE B 22 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE B 22 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 PHE B 22 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE B 22 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE B 22 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE B 22 " 0.002 2.00e-02 2.50e+03 ... (remaining 1701 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 29 2.49 - 3.09: 6538 3.09 - 3.70: 15467 3.70 - 4.30: 22668 4.30 - 4.90: 37046 Nonbonded interactions: 81748 Sorted by model distance: nonbonded pdb=" O PRO A 329 " pdb=" O THR A 331 " model vdw 1.890 3.040 nonbonded pdb=" CE MET A 118 " pdb=" CD1 ILE A 319 " model vdw 1.909 3.880 nonbonded pdb=" O PHE C 110 " pdb="NA NA C 401 " model vdw 2.010 2.470 nonbonded pdb=" O PHE B 110 " pdb="NA NA B 401 " model vdw 2.061 2.470 nonbonded pdb=" O PHE A 110 " pdb="NA NA A 401 " model vdw 2.207 2.470 ... (remaining 81743 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 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 110 or resid 201)) selection = (chain 'E' and (resid 2 through 94 or resid 96 through 110 or resid 201)) selection = (chain 'F' and (resid 2 through 94 or resid 96 through 110 or resid 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: 0.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 26.010 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.073 10191 Z= 0.411 Angle : 1.302 11.455 13854 Z= 0.675 Chirality : 0.067 0.356 1677 Planarity : 0.008 0.082 1704 Dihedral : 11.590 79.350 3639 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer: Outliers : 1.90 % Allowed : 6.86 % Favored : 91.24 % Cbeta Deviations : 0.42 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.012 0.003 TRP C 135 HIS 0.021 0.006 HIS B 303 PHE 0.039 0.004 PHE B 22 TYR 0.028 0.003 TYR E 87 ARG 0.018 0.002 ARG A 269 Details of bonding type rmsd hydrogen bonds : bond 0.32308 ( 435) hydrogen bonds : angle 10.17854 ( 1269) SS BOND : bond 0.01303 ( 3) SS BOND : angle 1.81482 ( 6) covalent geometry : bond 0.00943 (10188) covalent geometry : angle 1.30205 (13848) *********************** 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 : 0.970 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: 0.7707 (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: 0.7659 (mp10) cc_final: 0.7400 (mm110) REVERT: B 70 MET cc_start: 0.7609 (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: 0.7462 (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: 0.2514 time to fit residues: 101.5406 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 : 1.145 ------------------------------------------------------------------------------- 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 108 optimal weight: 0.7980 chunk 97 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 75 optimal weight: 9.9990 chunk 117 optimal weight: 5.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 ASN A 14 GLN A 291 HIS A 340 ASN B 6 ASN B 14 GLN B 291 HIS B 340 ASN C 6 ASN C 14 GLN C 340 ASN D 59 ASN E 44 ASN ** E 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 ASN F 59 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.119980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.093145 restraints weight = 30321.961| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 3.30 r_work: 0.2720 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2726 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2726 r_free = 0.2726 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2726 r_free = 0.2726 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2726 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2333 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= 0.146 Angle : 0.767 6.730 13854 Z= 0.377 Chirality : 0.046 0.224 1677 Planarity : 0.006 0.070 1704 Dihedral : 6.882 51.908 1454 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.57 % Allowed : 12.67 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.01 (0.19), residues: 1314 helix: -2.51 (0.14), residues: 792 sheet: -2.09 (0.46), residues: 105 loop : -2.69 (0.27), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 267 HIS 0.012 0.003 HIS C 303 PHE 0.014 0.002 PHE C 364 TYR 0.015 0.002 TYR A 344 ARG 0.003 0.000 ARG E 78 Details of bonding type rmsd hydrogen bonds : bond 0.04578 ( 435) hydrogen bonds : angle 4.53493 ( 1269) SS BOND : bond 0.00419 ( 3) SS BOND : angle 0.77833 ( 6) covalent geometry : bond 0.00330 (10188) covalent geometry : angle 0.76725 (13848) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 233 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ASP cc_start: 0.8347 (OUTLIER) cc_final: 0.7836 (m-30) REVERT: A 17 SER cc_start: 0.8770 (t) cc_final: 0.8228 (p) REVERT: A 35 GLN cc_start: 0.8036 (mp10) cc_final: 0.7631 (mm110) REVERT: A 40 GLU cc_start: 0.8138 (tt0) cc_final: 0.7804 (mt-10) REVERT: A 62 ILE cc_start: 0.9011 (tt) cc_final: 0.8605 (tt) REVERT: A 90 PHE cc_start: 0.8431 (m-80) cc_final: 0.8229 (m-80) REVERT: A 156 ASN cc_start: 0.8486 (t160) cc_final: 0.8155 (t0) REVERT: A 238 LYS cc_start: 0.8401 (mtmt) cc_final: 0.8035 (mttt) REVERT: A 250 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8159 (pp) REVERT: A 275 LYS cc_start: 0.8597 (ttmp) cc_final: 0.8032 (mtmt) REVERT: A 278 GLN cc_start: 0.7999 (pt0) cc_final: 0.7420 (mt0) REVERT: A 298 LEU cc_start: 0.8635 (tp) cc_final: 0.8435 (tp) REVERT: B 3 PHE cc_start: 0.7634 (t80) cc_final: 0.7312 (t80) REVERT: B 10 ASP cc_start: 0.8451 (t0) cc_final: 0.8080 (m-30) REVERT: B 35 GLN cc_start: 0.8020 (mp10) cc_final: 0.7697 (mm110) REVERT: B 40 GLU cc_start: 0.8338 (tt0) cc_final: 0.7817 (mt-10) REVERT: B 79 ILE cc_start: 0.7998 (mm) cc_final: 0.7774 (mt) REVERT: B 238 LYS cc_start: 0.8810 (mtmt) cc_final: 0.8511 (mtmt) REVERT: B 250 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8178 (pp) REVERT: B 272 GLU cc_start: 0.8351 (tt0) cc_final: 0.8059 (tt0) REVERT: B 275 LYS cc_start: 0.8470 (ttmp) cc_final: 0.8014 (mtmt) REVERT: B 278 GLN cc_start: 0.7846 (pt0) cc_final: 0.7326 (mt0) REVERT: B 298 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8496 (tp) REVERT: C 10 ASP cc_start: 0.8296 (t0) cc_final: 0.7963 (m-30) REVERT: C 40 GLU cc_start: 0.8320 (mt-10) cc_final: 0.7984 (mt-10) REVERT: C 79 ILE cc_start: 0.8047 (mm) cc_final: 0.7829 (mt) REVERT: C 132 TYR cc_start: 0.8762 (p90) cc_final: 0.8383 (p90) REVERT: C 250 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8316 (pp) REVERT: C 259 MET cc_start: 0.9194 (mmt) cc_final: 0.8913 (mmt) REVERT: C 275 LYS cc_start: 0.8572 (ttmp) cc_final: 0.8171 (mtmt) REVERT: C 278 GLN cc_start: 0.8051 (pt0) cc_final: 0.7389 (mt0) REVERT: D 57 GLU cc_start: 0.7749 (pm20) cc_final: 0.7488 (mt-10) REVERT: D 67 GLU cc_start: 0.8445 (tt0) cc_final: 0.8057 (mt-10) REVERT: F 6 ASN cc_start: 0.8798 (m-40) cc_final: 0.8581 (m-40) outliers start: 27 outliers final: 16 residues processed: 250 average time/residue: 0.2909 time to fit residues: 104.8031 Evaluate side-chains 210 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 189 time to evaluate : 1.242 ------------------------------------------------------------------------------- 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 18 optimal weight: 0.8980 chunk 26 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 78 optimal weight: 2.9990 chunk 72 optimal weight: 0.0050 chunk 83 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3263 r_free = 0.3263 target = 0.119163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.092166 restraints weight = 29375.054| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 3.14 r_work: 0.2737 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2739 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2739 r_free = 0.2739 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2739 r_free = 0.2739 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2739 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2815 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= 0.132 Angle : 0.714 9.657 13854 Z= 0.341 Chirality : 0.045 0.233 1677 Planarity : 0.005 0.059 1704 Dihedral : 6.257 49.138 1445 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 4.19 % Allowed : 13.81 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.21), residues: 1314 helix: -1.26 (0.17), residues: 816 sheet: -1.97 (0.45), residues: 105 loop : -2.36 (0.28), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 135 HIS 0.012 0.003 HIS C 303 PHE 0.010 0.001 PHE A 22 TYR 0.014 0.001 TYR A 140 ARG 0.005 0.000 ARG D 78 Details of bonding type rmsd hydrogen bonds : bond 0.03942 ( 435) hydrogen bonds : angle 4.02066 ( 1269) SS BOND : bond 0.00358 ( 3) SS BOND : angle 0.59703 ( 6) covalent geometry : bond 0.00302 (10188) covalent geometry : angle 0.71441 (13848) *********************** 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 232 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 188 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ASP cc_start: 0.8366 (OUTLIER) cc_final: 0.7871 (m-30) REVERT: A 35 GLN cc_start: 0.7936 (mp10) cc_final: 0.7609 (mm110) REVERT: A 80 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8366 (tt) REVERT: A 238 LYS cc_start: 0.8437 (mtmt) cc_final: 0.7972 (mttt) REVERT: A 250 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8080 (pp) REVERT: A 275 LYS cc_start: 0.8557 (ttmp) cc_final: 0.8056 (mtmt) REVERT: A 278 GLN cc_start: 0.7943 (pt0) cc_final: 0.7362 (mt0) REVERT: B 3 PHE cc_start: 0.7588 (t80) cc_final: 0.7307 (t80) REVERT: B 10 ASP cc_start: 0.8411 (t0) cc_final: 0.8078 (m-30) REVERT: B 35 GLN cc_start: 0.7804 (mp10) cc_final: 0.7595 (mm110) REVERT: B 79 ILE cc_start: 0.8030 (mm) cc_final: 0.7792 (mt) REVERT: B 161 LYS cc_start: 0.8039 (ptpt) cc_final: 0.7816 (ptpp) REVERT: B 238 LYS cc_start: 0.8834 (mtmt) cc_final: 0.8484 (mtmt) REVERT: B 243 TYR cc_start: 0.9107 (t80) cc_final: 0.8865 (t80) REVERT: B 250 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8101 (pp) REVERT: B 272 GLU cc_start: 0.8383 (tt0) cc_final: 0.8076 (tt0) REVERT: B 275 LYS cc_start: 0.8449 (ttmp) cc_final: 0.8113 (mtmt) REVERT: B 278 GLN cc_start: 0.7830 (pt0) cc_final: 0.7279 (mt0) REVERT: B 298 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8571 (tp) REVERT: C 10 ASP cc_start: 0.8295 (t0) cc_final: 0.7954 (m-30) REVERT: C 79 ILE cc_start: 0.8051 (mm) cc_final: 0.7815 (mt) REVERT: C 89 ARG cc_start: 0.8222 (tmt-80) cc_final: 0.7857 (ttt-90) REVERT: C 132 TYR cc_start: 0.8782 (p90) cc_final: 0.8332 (p90) REVERT: C 250 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8297 (pp) REVERT: C 275 LYS cc_start: 0.8518 (ttmp) cc_final: 0.8136 (mtmt) REVERT: D 57 GLU cc_start: 0.7703 (pm20) cc_final: 0.7445 (mt-10) REVERT: D 67 GLU cc_start: 0.8443 (tt0) cc_final: 0.7952 (mt-10) REVERT: F 6 ASN cc_start: 0.8787 (m-40) cc_final: 0.8582 (m-40) outliers start: 44 outliers final: 24 residues processed: 218 average time/residue: 0.2178 time to fit residues: 66.5021 Evaluate side-chains 209 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 179 time to evaluate : 0.954 ------------------------------------------------------------------------------- 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 68 THR Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain F residue 86 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 54 optimal weight: 0.6980 chunk 67 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 23 optimal weight: 0.0470 chunk 113 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.9082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3288 r_free = 0.3288 target = 0.120835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.094401 restraints weight = 23975.243| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 2.80 r_work: 0.2791 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2772 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2772 r_free = 0.2772 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2772 r_free = 0.2772 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2772 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10191 Z= 0.124 Angle : 0.677 7.901 13854 Z= 0.324 Chirality : 0.044 0.207 1677 Planarity : 0.004 0.054 1704 Dihedral : 6.026 48.418 1444 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.22), residues: 1314 helix: -0.56 (0.18), residues: 813 sheet: -1.69 (0.47), residues: 99 loop : -2.29 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 267 HIS 0.012 0.003 HIS C 303 PHE 0.010 0.001 PHE B 364 TYR 0.013 0.001 TYR A 344 ARG 0.005 0.000 ARG F 78 Details of bonding type rmsd hydrogen bonds : bond 0.03474 ( 435) hydrogen bonds : angle 3.79199 ( 1269) SS BOND : bond 0.00286 ( 3) SS BOND : angle 0.50195 ( 6) covalent geometry : bond 0.00283 (10188) covalent geometry : angle 0.67691 (13848) *********************** 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 229 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 187 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ASP cc_start: 0.8354 (OUTLIER) cc_final: 0.7933 (m-30) REVERT: A 16 GLN cc_start: 0.8254 (mm-40) cc_final: 0.7861 (mt0) REVERT: A 35 GLN cc_start: 0.7913 (mp10) cc_final: 0.7618 (mm110) REVERT: A 80 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8317 (tt) REVERT: A 158 TYR cc_start: 0.8669 (t80) cc_final: 0.8400 (t80) REVERT: A 238 LYS cc_start: 0.8398 (mtmt) cc_final: 0.8013 (mttt) REVERT: A 250 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8053 (pp) REVERT: A 275 LYS cc_start: 0.8529 (ttmp) cc_final: 0.8061 (mtmt) REVERT: A 278 GLN cc_start: 0.7924 (pt0) cc_final: 0.7331 (mt0) REVERT: A 359 VAL cc_start: 0.8806 (m) cc_final: 0.8551 (p) REVERT: B 3 PHE cc_start: 0.7670 (t80) cc_final: 0.7343 (t80) REVERT: B 10 ASP cc_start: 0.8391 (t0) cc_final: 0.8129 (m-30) REVERT: B 79 ILE cc_start: 0.8099 (mm) cc_final: 0.7840 (mt) REVERT: B 132 TYR cc_start: 0.8641 (p90) cc_final: 0.8262 (p90) REVERT: B 161 LYS cc_start: 0.8004 (ptpt) cc_final: 0.7790 (ptpp) REVERT: B 238 LYS cc_start: 0.8820 (mtmt) cc_final: 0.8447 (mtmt) REVERT: B 243 TYR cc_start: 0.9127 (t80) cc_final: 0.8858 (t80) REVERT: B 250 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8069 (pp) REVERT: B 272 GLU cc_start: 0.8312 (tt0) cc_final: 0.8024 (tt0) REVERT: B 275 LYS cc_start: 0.8389 (ttmp) cc_final: 0.8092 (mtmt) REVERT: B 278 GLN cc_start: 0.7782 (pt0) cc_final: 0.7245 (mt0) REVERT: B 359 VAL cc_start: 0.8803 (p) cc_final: 0.8465 (t) REVERT: C 10 ASP cc_start: 0.8272 (t0) cc_final: 0.7972 (m-30) REVERT: C 40 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7632 (mm-30) REVERT: C 79 ILE cc_start: 0.8067 (mm) cc_final: 0.7822 (mt) REVERT: C 132 TYR cc_start: 0.8792 (p90) cc_final: 0.8238 (p90) REVERT: C 250 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8241 (pp) REVERT: C 259 MET cc_start: 0.9194 (mmt) cc_final: 0.8977 (mmp) REVERT: C 275 LYS cc_start: 0.8473 (ttmp) cc_final: 0.8166 (mtmt) REVERT: D 67 GLU cc_start: 0.8335 (tt0) cc_final: 0.7870 (mt-10) REVERT: F 100 TYR cc_start: 0.8566 (m-80) cc_final: 0.8310 (m-80) outliers start: 42 outliers final: 28 residues processed: 214 average time/residue: 0.2128 time to fit residues: 64.1997 Evaluate side-chains 213 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 179 time to evaluate : 1.009 ------------------------------------------------------------------------------- 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 125 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain D residue 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 5 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 111 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 2.9990 chunk 62 optimal weight: 8.9990 chunk 79 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.112801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.085915 restraints weight = 25557.914| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 2.82 r_work: 0.2648 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2649 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2649 r_free = 0.2649 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2649 r_free = 0.2649 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2649 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 10191 Z= 0.213 Angle : 0.777 7.409 13854 Z= 0.377 Chirality : 0.048 0.232 1677 Planarity : 0.005 0.059 1704 Dihedral : 6.315 50.486 1444 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 5.62 % Allowed : 14.10 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.22), residues: 1314 helix: -0.53 (0.18), residues: 828 sheet: -1.65 (0.47), residues: 105 loop : -2.24 (0.28), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 135 HIS 0.011 0.003 HIS B 303 PHE 0.023 0.002 PHE C 110 TYR 0.017 0.002 TYR D 87 ARG 0.006 0.001 ARG B 269 Details of bonding type rmsd hydrogen bonds : bond 0.04411 ( 435) hydrogen bonds : angle 3.91781 ( 1269) SS BOND : bond 0.00579 ( 3) SS BOND : angle 0.68828 ( 6) covalent geometry : bond 0.00527 (10188) covalent geometry : angle 0.77671 (13848) *********************** 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 238 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 179 time to evaluate : 1.138 Fit side-chains revert: symmetry clash REVERT: A 10 ASP cc_start: 0.8448 (OUTLIER) cc_final: 0.8110 (m-30) REVERT: A 80 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8235 (tt) REVERT: A 156 ASN cc_start: 0.8637 (t160) cc_final: 0.8233 (t0) REVERT: A 158 TYR cc_start: 0.8611 (t80) cc_final: 0.8234 (t80) REVERT: A 238 LYS cc_start: 0.8405 (mtmt) cc_final: 0.7958 (mttt) REVERT: A 250 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8176 (pp) REVERT: A 275 LYS cc_start: 0.8682 (ttmp) cc_final: 0.8187 (mtmt) REVERT: A 278 GLN cc_start: 0.7996 (pt0) cc_final: 0.7420 (mt0) REVERT: B 3 PHE cc_start: 0.7784 (t80) cc_final: 0.7344 (t80) REVERT: B 10 ASP cc_start: 0.8451 (t0) cc_final: 0.8133 (m-30) REVERT: B 238 LYS cc_start: 0.8831 (mtmt) cc_final: 0.8447 (mtmt) REVERT: B 240 GLU cc_start: 0.8326 (mp0) cc_final: 0.8119 (mp0) REVERT: B 250 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8196 (pp) REVERT: B 275 LYS cc_start: 0.8564 (ttmp) cc_final: 0.8130 (mtmt) REVERT: B 278 GLN cc_start: 0.7915 (pt0) cc_final: 0.7380 (mt0) REVERT: B 359 VAL cc_start: 0.8946 (p) cc_final: 0.8704 (t) REVERT: C 10 ASP cc_start: 0.8436 (t0) cc_final: 0.8071 (m-30) REVERT: C 17 SER cc_start: 0.8729 (t) cc_final: 0.8142 (p) REVERT: C 79 ILE cc_start: 0.8145 (mm) cc_final: 0.7925 (mt) REVERT: C 132 TYR cc_start: 0.8873 (p90) cc_final: 0.8422 (p90) REVERT: C 250 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8345 (pp) REVERT: C 275 LYS cc_start: 0.8634 (ttmp) cc_final: 0.8244 (mtmt) REVERT: C 278 GLN cc_start: 0.8068 (pt0) cc_final: 0.7394 (mt0) REVERT: D 67 GLU cc_start: 0.8375 (tt0) cc_final: 0.8063 (tt0) REVERT: D 78 ARG cc_start: 0.8651 (mtp85) cc_final: 0.8437 (mtp180) REVERT: E 26 GLU cc_start: 0.8731 (mt-10) cc_final: 0.8524 (mt-10) outliers start: 59 outliers final: 41 residues processed: 223 average time/residue: 0.2050 time to fit residues: 64.7895 Evaluate side-chains 216 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 170 time to evaluate : 1.036 ------------------------------------------------------------------------------- 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 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 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 326 ILE Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 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 72 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 303 HIS Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 348 SER Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 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 35 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 116 optimal weight: 0.9990 chunk 93 optimal weight: 0.5980 chunk 80 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.116182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.089276 restraints weight = 25401.263| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 2.81 r_work: 0.2698 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2698 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2698 r_free = 0.2698 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2698 r_free = 0.2698 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2698 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10191 Z= 0.145 Angle : 0.694 6.939 13854 Z= 0.334 Chirality : 0.045 0.216 1677 Planarity : 0.004 0.052 1704 Dihedral : 6.111 47.831 1444 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 4.95 % Allowed : 15.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.23), residues: 1314 helix: -0.03 (0.19), residues: 804 sheet: -1.64 (0.46), residues: 105 loop : -2.28 (0.28), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 267 HIS 0.011 0.003 HIS B 303 PHE 0.011 0.001 PHE C 110 TYR 0.013 0.001 TYR A 344 ARG 0.006 0.000 ARG E 78 Details of bonding type rmsd hydrogen bonds : bond 0.03618 ( 435) hydrogen bonds : angle 3.75071 ( 1269) SS BOND : bond 0.00386 ( 3) SS BOND : angle 0.54887 ( 6) covalent geometry : bond 0.00347 (10188) covalent geometry : angle 0.69369 (13848) *********************** 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 225 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 173 time to evaluate : 0.974 Fit side-chains revert: symmetry clash REVERT: A 10 ASP cc_start: 0.8413 (OUTLIER) cc_final: 0.8088 (m-30) REVERT: A 16 GLN cc_start: 0.8359 (mm-40) cc_final: 0.8012 (mt0) REVERT: A 80 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8211 (tt) REVERT: A 238 LYS cc_start: 0.8386 (mtmt) cc_final: 0.7933 (mttt) REVERT: A 250 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8147 (pp) REVERT: A 275 LYS cc_start: 0.8696 (ttmp) cc_final: 0.8105 (mtmt) REVERT: A 278 GLN cc_start: 0.7914 (pt0) cc_final: 0.7341 (mt0) REVERT: A 359 VAL cc_start: 0.8853 (m) cc_final: 0.8562 (p) REVERT: B 3 PHE cc_start: 0.7760 (t80) cc_final: 0.7244 (t80) REVERT: B 10 ASP cc_start: 0.8372 (t0) cc_final: 0.8171 (m-30) REVERT: B 238 LYS cc_start: 0.8787 (mtmt) cc_final: 0.8462 (mtmt) REVERT: B 250 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8121 (pp) REVERT: B 275 LYS cc_start: 0.8533 (ttmp) cc_final: 0.8122 (mtmt) REVERT: B 278 GLN cc_start: 0.7847 (pt0) cc_final: 0.7314 (mt0) REVERT: B 359 VAL cc_start: 0.8913 (p) cc_final: 0.8692 (t) REVERT: C 10 ASP cc_start: 0.8301 (t0) cc_final: 0.8007 (m-30) REVERT: C 79 ILE cc_start: 0.8126 (mm) cc_final: 0.7903 (mt) REVERT: C 132 TYR cc_start: 0.8872 (p90) cc_final: 0.8423 (p90) REVERT: C 250 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8250 (pp) REVERT: C 259 MET cc_start: 0.9163 (mmt) cc_final: 0.8915 (mmt) REVERT: C 275 LYS cc_start: 0.8638 (ttmp) cc_final: 0.8284 (mtmt) REVERT: D 67 GLU cc_start: 0.8375 (tt0) cc_final: 0.7894 (mt-10) REVERT: E 78 ARG cc_start: 0.8610 (mtp85) cc_final: 0.8371 (mtp180) outliers start: 52 outliers final: 42 residues processed: 214 average time/residue: 0.2046 time to fit residues: 61.8712 Evaluate side-chains 217 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 170 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 303 HIS Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 303 HIS Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 348 SER Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain F residue 86 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 23 optimal weight: 7.9990 chunk 128 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 12 optimal weight: 7.9990 chunk 67 optimal weight: 0.7980 chunk 124 optimal weight: 10.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.117148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.090005 restraints weight = 26640.386| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 2.89 r_work: 0.2711 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2708 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2708 r_free = 0.2708 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2708 r_free = 0.2708 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2708 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.3390 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= 0.135 Angle : 0.673 6.188 13854 Z= 0.323 Chirality : 0.044 0.214 1677 Planarity : 0.004 0.051 1704 Dihedral : 5.999 46.978 1444 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 5.71 % Allowed : 15.14 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.23), residues: 1314 helix: 0.17 (0.19), residues: 810 sheet: -1.48 (0.47), residues: 105 loop : -2.17 (0.28), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 267 HIS 0.013 0.003 HIS B 303 PHE 0.009 0.001 PHE C 110 TYR 0.012 0.001 TYR A 344 ARG 0.005 0.000 ARG E 78 Details of bonding type rmsd hydrogen bonds : bond 0.03459 ( 435) hydrogen bonds : angle 3.68583 ( 1269) SS BOND : bond 0.00336 ( 3) SS BOND : angle 0.50164 ( 6) covalent geometry : bond 0.00322 (10188) covalent geometry : angle 0.67283 (13848) *********************** 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: 60 poor density : 177 time to evaluate : 1.003 Fit side-chains revert: symmetry clash REVERT: A 3 PHE cc_start: 0.8165 (t80) cc_final: 0.7959 (t80) REVERT: A 10 ASP cc_start: 0.8414 (OUTLIER) cc_final: 0.8108 (m-30) REVERT: A 16 GLN cc_start: 0.8343 (mm-40) cc_final: 0.8012 (mt0) REVERT: A 40 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7927 (tt0) REVERT: A 80 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8250 (tt) REVERT: A 238 LYS cc_start: 0.8424 (mtmt) cc_final: 0.7960 (mttt) REVERT: A 250 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8127 (pp) REVERT: A 275 LYS cc_start: 0.8675 (ttmp) cc_final: 0.8134 (mtmt) REVERT: A 278 GLN cc_start: 0.7940 (pt0) cc_final: 0.7367 (mt0) REVERT: B 3 PHE cc_start: 0.7712 (t80) cc_final: 0.7162 (t80) REVERT: B 70 MET cc_start: 0.7924 (mtm) cc_final: 0.7579 (mtt) REVERT: B 238 LYS cc_start: 0.8782 (mtmt) cc_final: 0.8444 (mtmt) REVERT: B 250 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8063 (pp) REVERT: B 275 LYS cc_start: 0.8496 (ttmp) cc_final: 0.8121 (mtmt) REVERT: C 10 ASP cc_start: 0.8274 (t0) cc_final: 0.8027 (m-30) REVERT: C 49 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.7752 (ptm) REVERT: C 79 ILE cc_start: 0.8123 (mm) cc_final: 0.7901 (mt) REVERT: C 132 TYR cc_start: 0.8879 (p90) cc_final: 0.8480 (p90) REVERT: C 220 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7688 (pt0) REVERT: C 250 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8347 (pp) REVERT: C 259 MET cc_start: 0.9138 (mmt) cc_final: 0.8887 (mmt) REVERT: C 275 LYS cc_start: 0.8598 (ttmp) cc_final: 0.8147 (mtmt) REVERT: C 360 CYS cc_start: 0.8074 (t) cc_final: 0.7826 (m) REVERT: D 67 GLU cc_start: 0.8361 (tt0) cc_final: 0.8043 (tt0) outliers start: 60 outliers final: 44 residues processed: 221 average time/residue: 0.2200 time to fit residues: 68.2248 Evaluate side-chains 222 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 170 time to evaluate : 1.095 ------------------------------------------------------------------------------- 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 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 323 SER Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 303 HIS Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain C residue 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 220 GLN Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 303 HIS Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 348 SER Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 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 0 optimal weight: 10.0000 chunk 71 optimal weight: 0.9980 chunk 42 optimal weight: 9.9990 chunk 65 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 119 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.115962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.089285 restraints weight = 24176.067| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 2.74 r_work: 0.2706 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2704 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2704 r_free = 0.2704 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2704 r_free = 0.2704 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2704 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10191 Z= 0.146 Angle : 0.703 9.508 13854 Z= 0.334 Chirality : 0.045 0.215 1677 Planarity : 0.004 0.050 1704 Dihedral : 6.012 46.596 1444 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 5.90 % Allowed : 15.05 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.23), residues: 1314 helix: 0.12 (0.19), residues: 831 sheet: -1.43 (0.47), residues: 105 loop : -2.04 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 135 HIS 0.013 0.003 HIS B 303 PHE 0.011 0.001 PHE C 364 TYR 0.012 0.001 TYR B 344 ARG 0.005 0.000 ARG D 78 Details of bonding type rmsd hydrogen bonds : bond 0.03548 ( 435) hydrogen bonds : angle 3.71250 ( 1269) SS BOND : bond 0.00385 ( 3) SS BOND : angle 0.52265 ( 6) covalent geometry : bond 0.00353 (10188) covalent geometry : angle 0.70336 (13848) *********************** 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 230 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 168 time to evaluate : 1.048 Fit side-chains REVERT: A 3 PHE cc_start: 0.8153 (t80) cc_final: 0.7904 (t80) REVERT: A 10 ASP cc_start: 0.8406 (OUTLIER) cc_final: 0.8113 (m-30) REVERT: A 16 GLN cc_start: 0.8338 (mm-40) cc_final: 0.8061 (mt0) REVERT: A 40 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7866 (tt0) REVERT: A 80 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8246 (tt) REVERT: A 238 LYS cc_start: 0.8418 (mtmt) cc_final: 0.7944 (mttt) REVERT: A 244 GLU cc_start: 0.8543 (pt0) cc_final: 0.8274 (pt0) REVERT: A 250 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8120 (pp) REVERT: A 275 LYS cc_start: 0.8701 (ttmp) cc_final: 0.8147 (mtmt) REVERT: A 278 GLN cc_start: 0.7963 (pt0) cc_final: 0.7408 (mt0) REVERT: B 3 PHE cc_start: 0.7730 (t80) cc_final: 0.7420 (t80) REVERT: B 40 GLU cc_start: 0.7756 (tt0) cc_final: 0.7291 (tt0) REVERT: B 238 LYS cc_start: 0.8775 (mtmt) cc_final: 0.8436 (mtmt) REVERT: B 250 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8084 (pp) REVERT: B 275 LYS cc_start: 0.8506 (ttmp) cc_final: 0.8120 (mtmt) REVERT: C 10 ASP cc_start: 0.8260 (t0) cc_final: 0.8007 (m-30) REVERT: C 79 ILE cc_start: 0.8133 (mm) cc_final: 0.7902 (mt) REVERT: C 132 TYR cc_start: 0.8881 (p90) cc_final: 0.8445 (p90) REVERT: C 220 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7703 (pt0) REVERT: C 250 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8296 (pp) REVERT: C 259 MET cc_start: 0.9129 (mmt) cc_final: 0.8852 (mmt) REVERT: C 275 LYS cc_start: 0.8609 (ttmp) cc_final: 0.8170 (mtmt) REVERT: D 67 GLU cc_start: 0.8326 (tt0) cc_final: 0.8017 (tt0) REVERT: E 50 GLN cc_start: 0.7075 (pt0) cc_final: 0.6822 (pt0) outliers start: 62 outliers final: 50 residues processed: 219 average time/residue: 0.2228 time to fit residues: 69.3145 Evaluate side-chains 222 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 165 time to evaluate : 1.087 ------------------------------------------------------------------------------- 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 241 SER Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 303 HIS Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 303 HIS Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 220 GLN Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 303 HIS Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 348 SER Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain F residue 86 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 70 optimal weight: 3.9990 chunk 75 optimal weight: 0.0980 chunk 47 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 93 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.121029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.093765 restraints weight = 26631.483| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 2.98 r_work: 0.2765 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2746 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2746 r_free = 0.2746 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2746 r_free = 0.2746 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2746 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10191 Z= 0.114 Angle : 0.661 8.146 13854 Z= 0.313 Chirality : 0.044 0.203 1677 Planarity : 0.004 0.049 1704 Dihedral : 5.821 44.502 1444 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 5.43 % Allowed : 15.71 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.24), residues: 1314 helix: 0.57 (0.20), residues: 795 sheet: -1.26 (0.48), residues: 99 loop : -2.37 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 267 HIS 0.014 0.003 HIS B 303 PHE 0.009 0.001 PHE C 364 TYR 0.013 0.001 TYR A 344 ARG 0.006 0.000 ARG D 78 Details of bonding type rmsd hydrogen bonds : bond 0.03045 ( 435) hydrogen bonds : angle 3.62637 ( 1269) SS BOND : bond 0.00217 ( 3) SS BOND : angle 0.42258 ( 6) covalent geometry : bond 0.00258 (10188) covalent geometry : angle 0.66068 (13848) *********************** 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 234 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 177 time to evaluate : 1.170 Fit side-chains REVERT: A 3 PHE cc_start: 0.8092 (t80) cc_final: 0.7839 (t80) REVERT: A 10 ASP cc_start: 0.8346 (OUTLIER) cc_final: 0.8079 (m-30) REVERT: A 16 GLN cc_start: 0.8262 (mm-40) cc_final: 0.8047 (mt0) REVERT: A 40 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7252 (tt0) REVERT: A 80 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8275 (tt) REVERT: A 238 LYS cc_start: 0.8317 (mtmt) cc_final: 0.7878 (mttt) REVERT: A 250 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8019 (pp) REVERT: A 275 LYS cc_start: 0.8671 (ttmp) cc_final: 0.8184 (mtmt) REVERT: A 359 VAL cc_start: 0.8803 (m) cc_final: 0.8493 (t) REVERT: B 3 PHE cc_start: 0.7763 (t80) cc_final: 0.7416 (t80) REVERT: B 40 GLU cc_start: 0.7711 (tt0) cc_final: 0.7278 (tt0) REVERT: B 70 MET cc_start: 0.7855 (mtm) cc_final: 0.7580 (mtt) REVERT: B 161 LYS cc_start: 0.7817 (ptpt) cc_final: 0.7604 (ptpp) REVERT: B 238 LYS cc_start: 0.8765 (mtmt) cc_final: 0.8482 (mtmt) REVERT: B 250 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.7977 (pp) REVERT: B 275 LYS cc_start: 0.8565 (ttmp) cc_final: 0.8147 (mtmt) REVERT: C 49 MET cc_start: 0.8240 (OUTLIER) cc_final: 0.7669 (ptm) REVERT: C 79 ILE cc_start: 0.8081 (mm) cc_final: 0.7844 (mt) REVERT: C 132 TYR cc_start: 0.8849 (p90) cc_final: 0.8424 (p90) REVERT: C 250 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8181 (pp) REVERT: C 259 MET cc_start: 0.9104 (mmt) cc_final: 0.8866 (mmt) REVERT: C 275 LYS cc_start: 0.8514 (ttmp) cc_final: 0.8158 (mtmt) REVERT: D 50 GLN cc_start: 0.6934 (mm-40) cc_final: 0.6548 (pt0) REVERT: D 57 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7216 (mp0) REVERT: D 67 GLU cc_start: 0.8258 (tt0) cc_final: 0.7805 (mt-10) outliers start: 57 outliers final: 43 residues processed: 218 average time/residue: 0.2091 time to fit residues: 64.8027 Evaluate side-chains 219 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 168 time to evaluate : 1.136 ------------------------------------------------------------------------------- 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 49 MET Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 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 113 VAL Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 303 HIS Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 67 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 242 VAL Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 303 HIS Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 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 88 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 chunk 9 optimal weight: 0.0570 chunk 16 optimal weight: 0.0070 chunk 83 optimal weight: 0.0670 chunk 58 optimal weight: 9.9990 chunk 85 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 91 optimal weight: 8.9990 chunk 95 optimal weight: 0.6980 chunk 111 optimal weight: 0.8980 overall best weight: 0.2854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.123917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.098078 restraints weight = 22603.782| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.68 r_work: 0.2851 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2822 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2822 r_free = 0.2822 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2822 r_free = 0.2822 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2822 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 10191 Z= 0.108 Angle : 0.645 8.041 13854 Z= 0.304 Chirality : 0.044 0.197 1677 Planarity : 0.004 0.047 1704 Dihedral : 5.653 44.530 1444 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 4.38 % Allowed : 16.57 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.24), residues: 1314 helix: 0.74 (0.20), residues: 792 sheet: -1.17 (0.48), residues: 99 loop : -2.29 (0.27), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 267 HIS 0.013 0.003 HIS B 303 PHE 0.009 0.001 PHE C 364 TYR 0.013 0.001 TYR A 344 ARG 0.006 0.000 ARG D 78 Details of bonding type rmsd hydrogen bonds : bond 0.02838 ( 435) hydrogen bonds : angle 3.58889 ( 1269) SS BOND : bond 0.00155 ( 3) SS BOND : angle 0.35440 ( 6) covalent geometry : bond 0.00237 (10188) covalent geometry : angle 0.64462 (13848) ********************** 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 230 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 184 time to evaluate : 1.027 Fit side-chains REVERT: A 3 PHE cc_start: 0.8145 (t80) cc_final: 0.7885 (t80) REVERT: A 10 ASP cc_start: 0.8316 (t0) cc_final: 0.8055 (m-30) REVERT: A 80 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8249 (tt) REVERT: A 238 LYS cc_start: 0.8322 (mtmt) cc_final: 0.7925 (mtpt) REVERT: A 250 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8139 (pp) REVERT: A 275 LYS cc_start: 0.8514 (ttmp) cc_final: 0.8154 (mtmt) REVERT: A 359 VAL cc_start: 0.8735 (m) cc_final: 0.8484 (t) REVERT: B 3 PHE cc_start: 0.7786 (t80) cc_final: 0.7459 (t80) REVERT: B 36 LEU cc_start: 0.7841 (tt) cc_final: 0.6918 (tt) REVERT: B 40 GLU cc_start: 0.7690 (tt0) cc_final: 0.7188 (tt0) REVERT: B 118 MET cc_start: 0.8505 (ttt) cc_final: 0.8296 (ttp) REVERT: B 238 LYS cc_start: 0.8706 (mtmt) cc_final: 0.8453 (mtmt) REVERT: B 250 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.7837 (pp) REVERT: B 275 LYS cc_start: 0.8490 (ttmp) cc_final: 0.8162 (mtmt) REVERT: C 79 ILE cc_start: 0.7983 (mm) cc_final: 0.7745 (mt) REVERT: C 89 ARG cc_start: 0.8119 (tmt-80) cc_final: 0.7824 (ttt-90) REVERT: C 132 TYR cc_start: 0.8848 (p90) cc_final: 0.8531 (p90) REVERT: C 250 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8070 (pp) REVERT: C 259 MET cc_start: 0.9066 (mmt) cc_final: 0.8833 (mmt) REVERT: C 275 LYS cc_start: 0.8446 (ttmp) cc_final: 0.8214 (mtmt) REVERT: D 57 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7258 (mp0) REVERT: D 67 GLU cc_start: 0.8209 (tt0) cc_final: 0.7800 (mt-10) REVERT: E 50 GLN cc_start: 0.6721 (pt0) cc_final: 0.6358 (pt0) REVERT: F 100 TYR cc_start: 0.8588 (m-80) cc_final: 0.8339 (m-80) outliers start: 46 outliers final: 33 residues processed: 217 average time/residue: 0.2103 time to fit residues: 64.8810 Evaluate side-chains 208 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 170 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 303 HIS Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain C residue 67 LEU 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 242 VAL Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 303 HIS Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain F residue 86 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 77 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 4 optimal weight: 0.0050 chunk 97 optimal weight: 0.8980 chunk 127 optimal weight: 5.9990 chunk 62 optimal weight: 0.0980 chunk 112 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 109 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 overall best weight: 0.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.121570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.095611 restraints weight = 22757.440| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 2.64 r_work: 0.2789 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2804 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2804 r_free = 0.2804 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2803 r_free = 0.2803 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2803 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.3797 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= 0.116 Angle : 0.658 7.959 13854 Z= 0.310 Chirality : 0.044 0.195 1677 Planarity : 0.004 0.047 1704 Dihedral : 5.707 45.118 1443 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 4.38 % Allowed : 16.76 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.24), residues: 1314 helix: 0.78 (0.19), residues: 792 sheet: -1.07 (0.48), residues: 99 loop : -2.26 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 267 HIS 0.016 0.003 HIS B 303 PHE 0.009 0.001 PHE C 364 TYR 0.012 0.001 TYR A 344 ARG 0.006 0.000 ARG D 78 Details of bonding type rmsd hydrogen bonds : bond 0.03007 ( 435) hydrogen bonds : angle 3.58225 ( 1269) SS BOND : bond 0.00231 ( 3) SS BOND : angle 0.35387 ( 6) covalent geometry : bond 0.00268 (10188) covalent geometry : angle 0.65778 (13848) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5076.69 seconds wall clock time: 88 minutes 34.13 seconds (5314.13 seconds total)