Starting phenix.real_space_refine on Sat Jul 4 15:05:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gu9_51605/07_2026/9gu9_51605.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gu9_51605/07_2026/9gu9_51605.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9gu9_51605/07_2026/9gu9_51605.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gu9_51605/07_2026/9gu9_51605.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9gu9_51605/07_2026/9gu9_51605.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gu9_51605/07_2026/9gu9_51605.map" } resolution = 2.74 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 21 5.49 5 S 119 5.16 5 C 13713 2.51 5 N 3696 2.21 5 O 4025 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21574 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3051 Classifications: {'peptide': 385} Link IDs: {'PTRANS': 17, 'TRANS': 367} Chain breaks: 2 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D, E, F, G Time building chain proxies: 3.43, per 1000 atoms: 0.16 Number of scatterers: 21574 At special positions: 0 Unit cell: (141.038, 136.676, 138.857, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 119 16.00 P 21 15.00 O 4025 8.00 N 3696 7.00 C 13713 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.85 Conformation dependent library (CDL) restraints added in 1.0 seconds 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4998 Finding SS restraints... Secondary structure from input PDB file: 119 helices and 28 sheets defined 50.4% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 49 through 55 removed outlier: 3.583A pdb=" N GLY A 55 " --> pdb=" O PHE A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 83 removed outlier: 3.808A pdb=" N ILE A 60 " --> pdb=" O GLY A 56 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ARG A 81 " --> pdb=" O ARG A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 106 removed outlier: 3.916A pdb=" N ALA A 97 " --> pdb=" O ASP A 93 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N TRP A 98 " --> pdb=" O LYS A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 199 Processing helix chain 'A' and resid 224 through 228 Processing helix chain 'A' and resid 233 through 248 Processing helix chain 'A' and resid 248 through 255 removed outlier: 4.127A pdb=" N TYR A 252 " --> pdb=" O ASN A 248 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER A 253 " --> pdb=" O GLY A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 285 Processing helix chain 'A' and resid 299 through 309 Processing helix chain 'A' and resid 321 through 324 removed outlier: 3.946A pdb=" N ALA A 324 " --> pdb=" O ILE A 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 321 through 324' Processing helix chain 'A' and resid 341 through 350 Processing helix chain 'A' and resid 366 through 370 Processing helix chain 'A' and resid 390 through 402 Processing helix chain 'A' and resid 405 through 420 removed outlier: 3.505A pdb=" N ASP A 420 " --> pdb=" O VAL A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 435 Processing helix chain 'A' and resid 438 through 446 Processing helix chain 'A' and resid 447 through 451 Processing helix chain 'B' and resid 49 through 55 removed outlier: 3.583A pdb=" N GLY B 55 " --> pdb=" O PHE B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 83 removed outlier: 3.809A pdb=" N ILE B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ARG B 81 " --> pdb=" O ARG B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 106 removed outlier: 3.915A pdb=" N ALA B 97 " --> pdb=" O ASP B 93 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N TRP B 98 " --> pdb=" O LYS B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 199 Processing helix chain 'B' and resid 224 through 228 Processing helix chain 'B' and resid 233 through 248 Processing helix chain 'B' and resid 248 through 255 removed outlier: 4.129A pdb=" N TYR B 252 " --> pdb=" O ASN B 248 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER B 253 " --> pdb=" O GLY B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 285 Processing helix chain 'B' and resid 299 through 309 Processing helix chain 'B' and resid 321 through 324 removed outlier: 3.947A pdb=" N ALA B 324 " --> pdb=" O ILE B 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 321 through 324' Processing helix chain 'B' and resid 341 through 350 Processing helix chain 'B' and resid 366 through 370 Processing helix chain 'B' and resid 390 through 402 Processing helix chain 'B' and resid 405 through 420 removed outlier: 3.504A pdb=" N ASP B 420 " --> pdb=" O VAL B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 435 Processing helix chain 'B' and resid 438 through 446 Processing helix chain 'B' and resid 447 through 451 Processing helix chain 'C' and resid 49 through 55 removed outlier: 3.584A pdb=" N GLY C 55 " --> pdb=" O PHE C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 83 removed outlier: 3.808A pdb=" N ILE C 60 " --> pdb=" O GLY C 56 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ARG C 81 " --> pdb=" O ARG C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 106 removed outlier: 3.915A pdb=" N ALA C 97 " --> pdb=" O ASP C 93 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N TRP C 98 " --> pdb=" O LYS C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 199 Processing helix chain 'C' and resid 224 through 228 Processing helix chain 'C' and resid 233 through 248 Processing helix chain 'C' and resid 248 through 255 removed outlier: 4.128A pdb=" N TYR C 252 " --> pdb=" O ASN C 248 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER C 253 " --> pdb=" O GLY C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 285 Processing helix chain 'C' and resid 299 through 309 Processing helix chain 'C' and resid 321 through 324 removed outlier: 3.948A pdb=" N ALA C 324 " --> pdb=" O ILE C 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 321 through 324' Processing helix chain 'C' and resid 341 through 350 Processing helix chain 'C' and resid 366 through 370 Processing helix chain 'C' and resid 390 through 402 Processing helix chain 'C' and resid 405 through 420 removed outlier: 3.505A pdb=" N ASP C 420 " --> pdb=" O VAL C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 435 Processing helix chain 'C' and resid 438 through 446 Processing helix chain 'C' and resid 447 through 451 Processing helix chain 'D' and resid 49 through 55 removed outlier: 3.583A pdb=" N GLY D 55 " --> pdb=" O PHE D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 83 removed outlier: 3.808A pdb=" N ILE D 60 " --> pdb=" O GLY D 56 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ARG D 81 " --> pdb=" O ARG D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 106 removed outlier: 3.915A pdb=" N ALA D 97 " --> pdb=" O ASP D 93 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N TRP D 98 " --> pdb=" O LYS D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 199 Processing helix chain 'D' and resid 224 through 228 Processing helix chain 'D' and resid 233 through 248 Processing helix chain 'D' and resid 248 through 255 removed outlier: 4.128A pdb=" N TYR D 252 " --> pdb=" O ASN D 248 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER D 253 " --> pdb=" O GLY D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 285 Processing helix chain 'D' and resid 299 through 309 Processing helix chain 'D' and resid 321 through 324 removed outlier: 3.947A pdb=" N ALA D 324 " --> pdb=" O ILE D 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 321 through 324' Processing helix chain 'D' and resid 341 through 350 Processing helix chain 'D' and resid 366 through 370 Processing helix chain 'D' and resid 390 through 402 Processing helix chain 'D' and resid 405 through 420 removed outlier: 3.505A pdb=" N ASP D 420 " --> pdb=" O VAL D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 435 Processing helix chain 'D' and resid 438 through 446 Processing helix chain 'D' and resid 447 through 451 Processing helix chain 'E' and resid 49 through 55 removed outlier: 3.584A pdb=" N GLY E 55 " --> pdb=" O PHE E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 83 removed outlier: 3.808A pdb=" N ILE E 60 " --> pdb=" O GLY E 56 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ARG E 81 " --> pdb=" O ARG E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 106 removed outlier: 3.915A pdb=" N ALA E 97 " --> pdb=" O ASP E 93 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N TRP E 98 " --> pdb=" O LYS E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 199 Processing helix chain 'E' and resid 224 through 228 Processing helix chain 'E' and resid 233 through 248 Processing helix chain 'E' and resid 248 through 255 removed outlier: 4.128A pdb=" N TYR E 252 " --> pdb=" O ASN E 248 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER E 253 " --> pdb=" O GLY E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 285 Processing helix chain 'E' and resid 299 through 309 Processing helix chain 'E' and resid 321 through 324 removed outlier: 3.948A pdb=" N ALA E 324 " --> pdb=" O ILE E 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 321 through 324' Processing helix chain 'E' and resid 341 through 350 Processing helix chain 'E' and resid 366 through 370 Processing helix chain 'E' and resid 390 through 402 Processing helix chain 'E' and resid 405 through 420 removed outlier: 3.505A pdb=" N ASP E 420 " --> pdb=" O VAL E 416 " (cutoff:3.500A) Processing helix chain 'E' and resid 424 through 435 Processing helix chain 'E' and resid 438 through 446 Processing helix chain 'E' and resid 447 through 451 Processing helix chain 'F' and resid 49 through 55 removed outlier: 3.583A pdb=" N GLY F 55 " --> pdb=" O PHE F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 83 removed outlier: 3.808A pdb=" N ILE F 60 " --> pdb=" O GLY F 56 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ARG F 81 " --> pdb=" O ARG F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 106 removed outlier: 3.915A pdb=" N ALA F 97 " --> pdb=" O ASP F 93 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N TRP F 98 " --> pdb=" O LYS F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 199 Processing helix chain 'F' and resid 224 through 228 Processing helix chain 'F' and resid 233 through 248 Processing helix chain 'F' and resid 248 through 255 removed outlier: 4.128A pdb=" N TYR F 252 " --> pdb=" O ASN F 248 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER F 253 " --> pdb=" O GLY F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 285 Processing helix chain 'F' and resid 299 through 309 Processing helix chain 'F' and resid 321 through 324 removed outlier: 3.947A pdb=" N ALA F 324 " --> pdb=" O ILE F 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 321 through 324' Processing helix chain 'F' and resid 341 through 350 Processing helix chain 'F' and resid 366 through 370 Processing helix chain 'F' and resid 390 through 402 Processing helix chain 'F' and resid 405 through 420 removed outlier: 3.505A pdb=" N ASP F 420 " --> pdb=" O VAL F 416 " (cutoff:3.500A) Processing helix chain 'F' and resid 424 through 435 Processing helix chain 'F' and resid 438 through 446 Processing helix chain 'F' and resid 447 through 451 Processing helix chain 'G' and resid 49 through 55 removed outlier: 3.583A pdb=" N GLY G 55 " --> pdb=" O PHE G 52 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 83 removed outlier: 3.808A pdb=" N ILE G 60 " --> pdb=" O GLY G 56 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ARG G 81 " --> pdb=" O ARG G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 106 removed outlier: 3.915A pdb=" N ALA G 97 " --> pdb=" O ASP G 93 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N TRP G 98 " --> pdb=" O LYS G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 183 through 199 Processing helix chain 'G' and resid 224 through 228 Processing helix chain 'G' and resid 233 through 248 Processing helix chain 'G' and resid 248 through 255 removed outlier: 4.128A pdb=" N TYR G 252 " --> pdb=" O ASN G 248 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER G 253 " --> pdb=" O GLY G 249 " (cutoff:3.500A) Processing helix chain 'G' and resid 272 through 285 Processing helix chain 'G' and resid 299 through 309 Processing helix chain 'G' and resid 321 through 324 removed outlier: 3.947A pdb=" N ALA G 324 " --> pdb=" O ILE G 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 321 through 324' Processing helix chain 'G' and resid 341 through 350 Processing helix chain 'G' and resid 366 through 370 Processing helix chain 'G' and resid 390 through 402 Processing helix chain 'G' and resid 405 through 420 removed outlier: 3.505A pdb=" N ASP G 420 " --> pdb=" O VAL G 416 " (cutoff:3.500A) Processing helix chain 'G' and resid 424 through 435 Processing helix chain 'G' and resid 438 through 446 Processing helix chain 'G' and resid 447 through 451 Processing sheet with id=AA1, first strand: chain 'A' and resid 139 through 144 removed outlier: 3.645A pdb=" N ARG A 154 " --> pdb=" O GLY A 139 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU A 151 " --> pdb=" O LEU A 177 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 113 through 114 removed outlier: 6.559A pdb=" N LEU A 114 " --> pdb=" O ILE G 89 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N SER G 91 " --> pdb=" O LEU A 114 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU G 151 " --> pdb=" O LEU G 177 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG G 154 " --> pdb=" O GLY G 139 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 117 through 123 removed outlier: 3.657A pdb=" N SER A 127 " --> pdb=" O HIS A 123 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 202 through 203 removed outlier: 3.826A pdb=" N LYS A 220 " --> pdb=" O THR A 203 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 212 through 215 removed outlier: 3.710A pdb=" N GLU A 212 " --> pdb=" O PHE A 209 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N SER A 208 " --> pdb=" O ILE A 290 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ILE A 359 " --> pdb=" O SER A 314 " (cutoff:3.500A) removed outlier: 8.904A pdb=" N TYR A 382 " --> pdb=" O ARG A 260 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLY A 262 " --> pdb=" O TYR A 382 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N VAL A 384 " --> pdb=" O GLY A 262 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU A 264 " --> pdb=" O VAL A 384 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 139 through 144 removed outlier: 3.645A pdb=" N ARG B 154 " --> pdb=" O GLY B 139 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU B 151 " --> pdb=" O LEU B 177 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 117 through 123 removed outlier: 3.657A pdb=" N SER B 127 " --> pdb=" O HIS B 123 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 202 through 203 removed outlier: 3.826A pdb=" N LYS B 220 " --> pdb=" O THR B 203 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 212 through 215 removed outlier: 3.710A pdb=" N GLU B 212 " --> pdb=" O PHE B 209 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N SER B 208 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ILE B 359 " --> pdb=" O SER B 314 " (cutoff:3.500A) removed outlier: 8.904A pdb=" N TYR B 382 " --> pdb=" O ARG B 260 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLY B 262 " --> pdb=" O TYR B 382 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N VAL B 384 " --> pdb=" O GLY B 262 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU B 264 " --> pdb=" O VAL B 384 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 139 through 144 removed outlier: 3.645A pdb=" N ARG C 154 " --> pdb=" O GLY C 139 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU C 151 " --> pdb=" O LEU C 177 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 117 through 123 removed outlier: 3.658A pdb=" N SER C 127 " --> pdb=" O HIS C 123 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 202 through 203 removed outlier: 3.825A pdb=" N LYS C 220 " --> pdb=" O THR C 203 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 212 through 215 removed outlier: 3.709A pdb=" N GLU C 212 " --> pdb=" O PHE C 209 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N SER C 208 " --> pdb=" O ILE C 290 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ILE C 359 " --> pdb=" O SER C 314 " (cutoff:3.500A) removed outlier: 8.904A pdb=" N TYR C 382 " --> pdb=" O ARG C 260 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N GLY C 262 " --> pdb=" O TYR C 382 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N VAL C 384 " --> pdb=" O GLY C 262 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU C 264 " --> pdb=" O VAL C 384 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 139 through 144 removed outlier: 3.645A pdb=" N ARG D 154 " --> pdb=" O GLY D 139 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU D 151 " --> pdb=" O LEU D 177 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 117 through 123 removed outlier: 3.658A pdb=" N SER D 127 " --> pdb=" O HIS D 123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 202 through 203 removed outlier: 3.826A pdb=" N LYS D 220 " --> pdb=" O THR D 203 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 212 through 215 removed outlier: 3.709A pdb=" N GLU D 212 " --> pdb=" O PHE D 209 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N SER D 208 " --> pdb=" O ILE D 290 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ILE D 359 " --> pdb=" O SER D 314 " (cutoff:3.500A) removed outlier: 8.904A pdb=" N TYR D 382 " --> pdb=" O ARG D 260 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLY D 262 " --> pdb=" O TYR D 382 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N VAL D 384 " --> pdb=" O GLY D 262 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU D 264 " --> pdb=" O VAL D 384 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 139 through 144 removed outlier: 3.644A pdb=" N ARG E 154 " --> pdb=" O GLY E 139 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU E 151 " --> pdb=" O LEU E 177 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 117 through 123 removed outlier: 3.658A pdb=" N SER E 127 " --> pdb=" O HIS E 123 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 202 through 203 removed outlier: 3.825A pdb=" N LYS E 220 " --> pdb=" O THR E 203 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 212 through 215 removed outlier: 3.709A pdb=" N GLU E 212 " --> pdb=" O PHE E 209 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N SER E 208 " --> pdb=" O ILE E 290 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ILE E 359 " --> pdb=" O SER E 314 " (cutoff:3.500A) removed outlier: 8.904A pdb=" N TYR E 382 " --> pdb=" O ARG E 260 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLY E 262 " --> pdb=" O TYR E 382 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N VAL E 384 " --> pdb=" O GLY E 262 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU E 264 " --> pdb=" O VAL E 384 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 139 through 144 removed outlier: 3.644A pdb=" N ARG F 154 " --> pdb=" O GLY F 139 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU F 151 " --> pdb=" O LEU F 177 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 117 through 123 removed outlier: 3.658A pdb=" N SER F 127 " --> pdb=" O HIS F 123 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 202 through 203 removed outlier: 3.826A pdb=" N LYS F 220 " --> pdb=" O THR F 203 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 212 through 215 removed outlier: 3.710A pdb=" N GLU F 212 " --> pdb=" O PHE F 209 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N SER F 208 " --> pdb=" O ILE F 290 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ILE F 359 " --> pdb=" O SER F 314 " (cutoff:3.500A) removed outlier: 8.904A pdb=" N TYR F 382 " --> pdb=" O ARG F 260 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLY F 262 " --> pdb=" O TYR F 382 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N VAL F 384 " --> pdb=" O GLY F 262 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU F 264 " --> pdb=" O VAL F 384 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 117 through 123 removed outlier: 3.658A pdb=" N SER G 127 " --> pdb=" O HIS G 123 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 202 through 203 removed outlier: 3.825A pdb=" N LYS G 220 " --> pdb=" O THR G 203 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 212 through 215 removed outlier: 3.709A pdb=" N GLU G 212 " --> pdb=" O PHE G 209 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N SER G 208 " --> pdb=" O ILE G 290 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ILE G 359 " --> pdb=" O SER G 314 " (cutoff:3.500A) removed outlier: 8.904A pdb=" N TYR G 382 " --> pdb=" O ARG G 260 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLY G 262 " --> pdb=" O TYR G 382 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N VAL G 384 " --> pdb=" O GLY G 262 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU G 264 " --> pdb=" O VAL G 384 " (cutoff:3.500A) 1160 hydrogen bonds defined for protein. 3228 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: 4.12 Time building geometry restraints manager: 2.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 7010 1.36 - 1.51: 6366 1.51 - 1.66: 8450 1.66 - 1.80: 140 1.80 - 1.95: 77 Bond restraints: 22043 Sorted by residual: bond pdb=" O3B AGS D 501 " pdb=" PB AGS D 501 " ideal model delta sigma weight residual 1.673 1.577 0.096 2.00e-02 2.50e+03 2.31e+01 bond pdb=" O3B AGS G 501 " pdb=" PB AGS G 501 " ideal model delta sigma weight residual 1.673 1.578 0.095 2.00e-02 2.50e+03 2.28e+01 bond pdb=" O3B AGS A 501 " pdb=" PB AGS A 501 " ideal model delta sigma weight residual 1.673 1.578 0.095 2.00e-02 2.50e+03 2.26e+01 bond pdb=" O3B AGS F 501 " pdb=" PB AGS F 501 " ideal model delta sigma weight residual 1.673 1.578 0.095 2.00e-02 2.50e+03 2.26e+01 bond pdb=" O3B AGS C 501 " pdb=" PB AGS C 501 " ideal model delta sigma weight residual 1.673 1.578 0.095 2.00e-02 2.50e+03 2.25e+01 ... (remaining 22038 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 29049 2.25 - 4.51: 604 4.51 - 6.76: 76 6.76 - 9.02: 77 9.02 - 11.27: 14 Bond angle restraints: 29820 Sorted by residual: angle pdb=" CB GLN F 82 " pdb=" CG GLN F 82 " pdb=" CD GLN F 82 " ideal model delta sigma weight residual 112.60 119.62 -7.02 1.70e+00 3.46e-01 1.71e+01 angle pdb=" CB GLN D 82 " pdb=" CG GLN D 82 " pdb=" CD GLN D 82 " ideal model delta sigma weight residual 112.60 119.62 -7.02 1.70e+00 3.46e-01 1.70e+01 angle pdb=" CB GLN E 82 " pdb=" CG GLN E 82 " pdb=" CD GLN E 82 " ideal model delta sigma weight residual 112.60 119.61 -7.01 1.70e+00 3.46e-01 1.70e+01 angle pdb=" CB GLN C 82 " pdb=" CG GLN C 82 " pdb=" CD GLN C 82 " ideal model delta sigma weight residual 112.60 119.60 -7.00 1.70e+00 3.46e-01 1.70e+01 angle pdb=" CB GLN B 82 " pdb=" CG GLN B 82 " pdb=" CD GLN B 82 " ideal model delta sigma weight residual 112.60 119.59 -6.99 1.70e+00 3.46e-01 1.69e+01 ... (remaining 29815 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.18: 12760 31.18 - 62.35: 561 62.35 - 93.53: 56 93.53 - 124.71: 21 124.71 - 155.88: 7 Dihedral angle restraints: 13405 sinusoidal: 5621 harmonic: 7784 Sorted by residual: dihedral pdb=" O3A AGS A 501 " pdb=" O3B AGS A 501 " pdb=" PB AGS A 501 " pdb=" PG AGS A 501 " ideal model delta sinusoidal sigma weight residual -107.39 48.49 -155.88 1 3.00e+01 1.11e-03 2.04e+01 dihedral pdb=" O3A AGS F 501 " pdb=" O3B AGS F 501 " pdb=" PB AGS F 501 " pdb=" PG AGS F 501 " ideal model delta sinusoidal sigma weight residual -107.39 48.47 -155.86 1 3.00e+01 1.11e-03 2.04e+01 dihedral pdb=" O3A AGS B 501 " pdb=" O3B AGS B 501 " pdb=" PB AGS B 501 " pdb=" PG AGS B 501 " ideal model delta sinusoidal sigma weight residual -107.39 48.47 -155.86 1 3.00e+01 1.11e-03 2.04e+01 ... (remaining 13402 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2734 0.051 - 0.103: 445 0.103 - 0.154: 104 0.154 - 0.205: 0 0.205 - 0.256: 7 Chirality restraints: 3290 Sorted by residual: chirality pdb=" C3' AGS B 501 " pdb=" C2' AGS B 501 " pdb=" C4' AGS B 501 " pdb=" O3' AGS B 501 " both_signs ideal model delta sigma weight residual False -2.37 -2.63 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" C3' AGS D 501 " pdb=" C2' AGS D 501 " pdb=" C4' AGS D 501 " pdb=" O3' AGS D 501 " both_signs ideal model delta sigma weight residual False -2.37 -2.63 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" C3' AGS C 501 " pdb=" C2' AGS C 501 " pdb=" C4' AGS C 501 " pdb=" O3' AGS C 501 " both_signs ideal model delta sigma weight residual False -2.37 -2.63 0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 3287 not shown) Planarity restraints: 3752 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 99 " -0.011 2.00e-02 2.50e+03 1.39e-02 3.40e+00 pdb=" CG PHE B 99 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE B 99 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE B 99 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE B 99 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 99 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 99 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 99 " 0.011 2.00e-02 2.50e+03 1.39e-02 3.40e+00 pdb=" CG PHE C 99 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE C 99 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE C 99 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE C 99 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE C 99 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE C 99 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 99 " -0.011 2.00e-02 2.50e+03 1.39e-02 3.38e+00 pdb=" CG PHE F 99 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE F 99 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE F 99 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE F 99 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE F 99 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE F 99 " -0.002 2.00e-02 2.50e+03 ... (remaining 3749 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 371 2.64 - 3.21: 21491 3.21 - 3.77: 35456 3.77 - 4.34: 46687 4.34 - 4.90: 75693 Nonbonded interactions: 179698 Sorted by model distance: nonbonded pdb=" O LEU E 298 " pdb=" OG SER E 339 " model vdw 2.076 3.040 nonbonded pdb=" O LEU D 298 " pdb=" OG SER D 339 " model vdw 2.077 3.040 nonbonded pdb=" O LEU A 298 " pdb=" OG SER A 339 " model vdw 2.077 3.040 nonbonded pdb=" O LEU F 298 " pdb=" OG SER F 339 " model vdw 2.077 3.040 nonbonded pdb=" O LEU G 298 " pdb=" OG SER G 339 " model vdw 2.077 3.040 ... (remaining 179693 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.530 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 18.830 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 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 : 0.005 0.096 22043 Z= 0.236 Angle : 0.868 11.273 29820 Z= 0.406 Chirality : 0.042 0.256 3290 Planarity : 0.004 0.039 3752 Dihedral : 18.152 155.882 8407 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.90 % Allowed : 22.52 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.17), residues: 2653 helix: 2.37 (0.16), residues: 1120 sheet: -0.76 (0.20), residues: 560 loop : -0.18 (0.22), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 109 TYR 0.008 0.001 TYR B 382 PHE 0.032 0.002 PHE B 99 TRP 0.008 0.001 TRP A 251 HIS 0.006 0.001 HIS C 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.24 (22043) covalent geometry : angle 0.86765 / 0.41 (29820) hydrogen bonds : bond 0.18848 / 12.68 ( 1160) hydrogen bonds : angle 6.64840 / 4.74 ( 3228) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 203 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8594 (mm) REVERT: A 178 TYR cc_start: 0.6905 (t80) cc_final: 0.6476 (t80) REVERT: B 174 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8646 (mm) REVERT: B 178 TYR cc_start: 0.6823 (t80) cc_final: 0.6293 (t80) REVERT: C 174 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8643 (mm) REVERT: C 178 TYR cc_start: 0.6883 (t80) cc_final: 0.6378 (t80) REVERT: C 445 MET cc_start: 0.9329 (mmp) cc_final: 0.9103 (mtm) REVERT: D 174 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8663 (mm) REVERT: D 178 TYR cc_start: 0.6933 (t80) cc_final: 0.6530 (t80) REVERT: E 174 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8636 (mm) REVERT: E 178 TYR cc_start: 0.6857 (t80) cc_final: 0.6566 (t80) REVERT: F 149 PHE cc_start: 0.8950 (m-10) cc_final: 0.8464 (m-10) REVERT: F 174 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8593 (mm) REVERT: F 178 TYR cc_start: 0.6901 (t80) cc_final: 0.6340 (t80) REVERT: F 209 PHE cc_start: 0.8785 (t80) cc_final: 0.8388 (t80) REVERT: G 178 TYR cc_start: 0.6957 (t80) cc_final: 0.6417 (t80) outliers start: 21 outliers final: 0 residues processed: 224 average time/residue: 0.7345 time to fit residues: 184.6419 Evaluate side-chains 178 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 172 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain F residue 174 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 7.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 429 GLN ** A 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 GLN ** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 429 GLN ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 429 GLN E 189 ASN E 429 GLN ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 429 GLN ** F 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 122 GLN G 429 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.068727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.044347 restraints weight = 82684.626| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 3.90 r_work: 0.2639 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 22043 Z= 0.167 Angle : 0.603 6.908 29820 Z= 0.303 Chirality : 0.043 0.150 3290 Planarity : 0.005 0.056 3752 Dihedral : 11.876 152.293 3204 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.27 % Allowed : 21.02 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.17), residues: 2653 helix: 2.56 (0.16), residues: 1120 sheet: -0.92 (0.19), residues: 588 loop : 0.03 (0.22), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 255 TYR 0.008 0.001 TYR G 80 PHE 0.029 0.001 PHE D 99 TRP 0.015 0.002 TRP C 251 HIS 0.007 0.002 HIS F 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 (22043) covalent geometry : angle 0.60295 / 0.30 (29820) hydrogen bonds : bond 0.03504 / 2.33 ( 1160) hydrogen bonds : angle 4.69287 / 3.32 ( 3228) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 200 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 TYR cc_start: 0.6888 (t80) cc_final: 0.6349 (t80) REVERT: A 182 HIS cc_start: 0.8320 (p-80) cc_final: 0.8092 (p-80) REVERT: A 214 ARG cc_start: 0.9477 (OUTLIER) cc_final: 0.9212 (ptt90) REVERT: A 427 GLN cc_start: 0.9565 (mt0) cc_final: 0.9250 (mt0) REVERT: B 87 LEU cc_start: 0.8514 (pp) cc_final: 0.8261 (pp) REVERT: B 178 TYR cc_start: 0.6915 (t80) cc_final: 0.6320 (t80) REVERT: B 182 HIS cc_start: 0.8224 (p90) cc_final: 0.7877 (p-80) REVERT: B 427 GLN cc_start: 0.9597 (mt0) cc_final: 0.9350 (mt0) REVERT: C 87 LEU cc_start: 0.8494 (pp) cc_final: 0.8292 (pp) REVERT: C 178 TYR cc_start: 0.6877 (t80) cc_final: 0.6379 (t80) REVERT: D 178 TYR cc_start: 0.6816 (t80) cc_final: 0.6286 (t80) REVERT: D 427 GLN cc_start: 0.9611 (mt0) cc_final: 0.9311 (mt0) REVERT: E 87 LEU cc_start: 0.8516 (pp) cc_final: 0.8218 (pp) REVERT: E 178 TYR cc_start: 0.6771 (t80) cc_final: 0.6304 (t80) REVERT: E 399 MET cc_start: 0.9515 (mmm) cc_final: 0.9309 (mmm) REVERT: F 178 TYR cc_start: 0.6966 (t80) cc_final: 0.6610 (t80) REVERT: F 209 PHE cc_start: 0.9117 (t80) cc_final: 0.8814 (t80) REVERT: F 427 GLN cc_start: 0.9603 (mt0) cc_final: 0.9327 (mt0) REVERT: F 445 MET cc_start: 0.9414 (mtm) cc_final: 0.9136 (mtm) REVERT: G 178 TYR cc_start: 0.6808 (t80) cc_final: 0.6447 (t80) outliers start: 53 outliers final: 16 residues processed: 231 average time/residue: 0.6469 time to fit residues: 169.6986 Evaluate side-chains 211 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 194 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain B residue 424 SER Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain D residue 160 MET Chi-restraints excluded: chain D residue 214 ARG Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain E residue 59 MET Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 424 SER Chi-restraints excluded: chain F residue 160 MET Chi-restraints excluded: chain F residue 214 ARG Chi-restraints excluded: chain G residue 160 MET Chi-restraints excluded: chain G residue 214 ARG Chi-restraints excluded: chain G residue 424 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 252 optimal weight: 3.9990 chunk 245 optimal weight: 1.9990 chunk 261 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 14 optimal weight: 9.9990 chunk 219 optimal weight: 0.8980 chunk 76 optimal weight: 120.0000 chunk 93 optimal weight: 0.9990 chunk 125 optimal weight: 0.8980 chunk 200 optimal weight: 5.9990 chunk 228 optimal weight: 40.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 427 GLN ** F 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.069357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.044770 restraints weight = 81854.243| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 3.88 r_work: 0.2653 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22043 Z= 0.127 Angle : 0.553 10.744 29820 Z= 0.272 Chirality : 0.041 0.165 3290 Planarity : 0.004 0.040 3752 Dihedral : 11.204 150.838 3192 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.62 % Allowed : 21.32 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.17), residues: 2653 helix: 2.74 (0.16), residues: 1127 sheet: -0.63 (0.19), residues: 588 loop : 0.18 (0.22), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 77 TYR 0.013 0.001 TYR G 80 PHE 0.007 0.001 PHE D 184 TRP 0.014 0.001 TRP E 251 HIS 0.004 0.001 HIS B 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (22043) covalent geometry : angle 0.55343 / 0.27 (29820) hydrogen bonds : bond 0.03138 / 2.08 ( 1160) hydrogen bonds : angle 4.31570 / 3.06 ( 3228) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 205 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 TYR cc_start: 0.6832 (t80) cc_final: 0.6545 (t80) REVERT: A 427 GLN cc_start: 0.9557 (mt0) cc_final: 0.9202 (mt0) REVERT: B 178 TYR cc_start: 0.6773 (t80) cc_final: 0.6493 (t80) REVERT: B 427 GLN cc_start: 0.9585 (mt0) cc_final: 0.9312 (mt0) REVERT: C 178 TYR cc_start: 0.6848 (t80) cc_final: 0.6484 (t80) REVERT: C 445 MET cc_start: 0.9428 (mmp) cc_final: 0.9126 (mtm) REVERT: D 178 TYR cc_start: 0.6822 (t80) cc_final: 0.6498 (t80) REVERT: D 427 GLN cc_start: 0.9586 (mt0) cc_final: 0.9285 (mt0) REVERT: E 80 TYR cc_start: 0.7366 (OUTLIER) cc_final: 0.7146 (p90) REVERT: E 178 TYR cc_start: 0.6659 (t80) cc_final: 0.6136 (t80) REVERT: E 399 MET cc_start: 0.9517 (mmm) cc_final: 0.9311 (mmm) REVERT: F 177 LEU cc_start: 0.9272 (mm) cc_final: 0.9060 (mm) REVERT: F 178 TYR cc_start: 0.6932 (t80) cc_final: 0.6599 (t80) REVERT: F 209 PHE cc_start: 0.9164 (t80) cc_final: 0.8849 (t80) REVERT: F 427 GLN cc_start: 0.9590 (mt0) cc_final: 0.9307 (mt0) REVERT: F 445 MET cc_start: 0.9427 (mtm) cc_final: 0.9108 (mtm) REVERT: G 178 TYR cc_start: 0.6693 (t80) cc_final: 0.6425 (t80) REVERT: G 445 MET cc_start: 0.9424 (mmp) cc_final: 0.9075 (mtm) outliers start: 61 outliers final: 14 residues processed: 245 average time/residue: 0.6045 time to fit residues: 169.7252 Evaluate side-chains 212 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 197 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain D residue 214 ARG Chi-restraints excluded: chain D residue 321 ILE Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain E residue 80 TYR Chi-restraints excluded: chain E residue 424 SER Chi-restraints excluded: chain F residue 203 THR Chi-restraints excluded: chain F residue 214 ARG Chi-restraints excluded: chain G residue 203 THR Chi-restraints excluded: chain G residue 424 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 257 optimal weight: 5.9990 chunk 142 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 242 optimal weight: 8.9990 chunk 56 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 3 optimal weight: 10.0000 chunk 175 optimal weight: 0.9980 chunk 240 optimal weight: 1.9990 chunk 209 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 106 HIS A 122 GLN A 393 GLN B 106 HIS B 393 GLN C 106 HIS D 106 HIS D 122 GLN D 393 GLN E 106 HIS E 393 GLN F 106 HIS F 122 GLN F 393 GLN G 106 HIS G 393 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.068878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.044541 restraints weight = 82538.396| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 3.86 r_work: 0.2648 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22043 Z= 0.121 Angle : 0.564 11.091 29820 Z= 0.271 Chirality : 0.041 0.142 3290 Planarity : 0.004 0.040 3752 Dihedral : 10.890 144.503 3192 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.40 % Allowed : 21.84 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.17), residues: 2653 helix: 2.74 (0.16), residues: 1127 sheet: -0.33 (0.20), residues: 623 loop : 0.33 (0.22), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 109 TYR 0.013 0.001 TYR B 80 PHE 0.028 0.001 PHE D 99 TRP 0.013 0.001 TRP D 251 HIS 0.003 0.001 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (22043) covalent geometry : angle 0.56414 / 0.27 (29820) hydrogen bonds : bond 0.02929 / 1.94 ( 1160) hydrogen bonds : angle 4.12789 / 2.93 ( 3228) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 200 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 TYR cc_start: 0.6852 (t80) cc_final: 0.6553 (t80) REVERT: A 427 GLN cc_start: 0.9567 (mt0) cc_final: 0.9311 (mt0) REVERT: A 445 MET cc_start: 0.9370 (mtm) cc_final: 0.9079 (mtm) REVERT: B 178 TYR cc_start: 0.6765 (t80) cc_final: 0.6454 (t80) REVERT: B 182 HIS cc_start: 0.8208 (p-80) cc_final: 0.7901 (p-80) REVERT: B 427 GLN cc_start: 0.9601 (mt0) cc_final: 0.9323 (mt0) REVERT: C 59 MET cc_start: 0.9634 (mpt) cc_final: 0.9208 (tmm) REVERT: C 80 TYR cc_start: 0.7080 (OUTLIER) cc_final: 0.6838 (p90) REVERT: C 178 TYR cc_start: 0.6772 (t80) cc_final: 0.6416 (t80) REVERT: C 445 MET cc_start: 0.9412 (mmp) cc_final: 0.9136 (mtm) REVERT: D 178 TYR cc_start: 0.6692 (t80) cc_final: 0.6400 (t80) REVERT: D 427 GLN cc_start: 0.9606 (mt0) cc_final: 0.9295 (mt0) REVERT: E 80 TYR cc_start: 0.7352 (OUTLIER) cc_final: 0.7091 (p90) REVERT: E 103 MET cc_start: 0.9288 (ppp) cc_final: 0.9071 (ppp) REVERT: E 178 TYR cc_start: 0.6644 (t80) cc_final: 0.6085 (t80) REVERT: F 103 MET cc_start: 0.9212 (ppp) cc_final: 0.8934 (ppp) REVERT: F 178 TYR cc_start: 0.6765 (t80) cc_final: 0.6452 (t80) REVERT: F 209 PHE cc_start: 0.9204 (t80) cc_final: 0.8891 (t80) REVERT: F 427 GLN cc_start: 0.9604 (mt0) cc_final: 0.9319 (mt0) REVERT: F 445 MET cc_start: 0.9392 (mtm) cc_final: 0.9002 (mtm) REVERT: G 178 TYR cc_start: 0.6650 (t80) cc_final: 0.6378 (t80) REVERT: G 445 MET cc_start: 0.9437 (mmp) cc_final: 0.9097 (mtm) outliers start: 56 outliers final: 28 residues processed: 239 average time/residue: 0.5966 time to fit residues: 163.7250 Evaluate side-chains 222 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 192 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain B residue 160 MET Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 397 MET Chi-restraints excluded: chain C residue 80 TYR Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 214 ARG Chi-restraints excluded: chain D residue 321 ILE Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain E residue 80 TYR Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 424 SER Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 203 THR Chi-restraints excluded: chain F residue 214 ARG Chi-restraints excluded: chain G residue 80 TYR Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 203 THR Chi-restraints excluded: chain G residue 424 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 122 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 24 optimal weight: 0.7980 chunk 84 optimal weight: 8.9990 chunk 187 optimal weight: 0.9980 chunk 92 optimal weight: 5.9990 chunk 180 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 200 optimal weight: 0.0980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 393 GLN C 414 ASN D 414 ASN ** E 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 414 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.069129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.044886 restraints weight = 82659.605| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 3.87 r_work: 0.2662 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 22043 Z= 0.107 Angle : 0.564 11.244 29820 Z= 0.271 Chirality : 0.041 0.190 3290 Planarity : 0.004 0.038 3752 Dihedral : 10.590 137.105 3192 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.83 % Allowed : 22.14 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.17), residues: 2653 helix: 2.78 (0.16), residues: 1127 sheet: -0.13 (0.21), residues: 623 loop : 0.41 (0.22), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 77 TYR 0.013 0.001 TYR G 80 PHE 0.020 0.001 PHE A 99 TRP 0.013 0.001 TRP D 251 HIS 0.003 0.001 HIS F 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (22043) covalent geometry : angle 0.56373 / 0.27 (29820) hydrogen bonds : bond 0.02738 / 1.81 ( 1160) hydrogen bonds : angle 4.01730 / 2.85 ( 3228) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 203 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 TYR cc_start: 0.6846 (t80) cc_final: 0.6588 (t80) REVERT: A 399 MET cc_start: 0.9514 (mmm) cc_final: 0.9312 (mmm) REVERT: A 427 GLN cc_start: 0.9568 (mt0) cc_final: 0.9358 (mt0) REVERT: A 445 MET cc_start: 0.9371 (mtm) cc_final: 0.9085 (mtm) REVERT: B 178 TYR cc_start: 0.6644 (t80) cc_final: 0.6358 (t80) REVERT: B 427 GLN cc_start: 0.9602 (mt0) cc_final: 0.9326 (mt0) REVERT: C 59 MET cc_start: 0.9634 (mpt) cc_final: 0.9244 (tmm) REVERT: C 178 TYR cc_start: 0.6768 (t80) cc_final: 0.6416 (t80) REVERT: C 445 MET cc_start: 0.9409 (mmp) cc_final: 0.9172 (mtm) REVERT: D 178 TYR cc_start: 0.6620 (t80) cc_final: 0.6339 (t80) REVERT: D 214 ARG cc_start: 0.9513 (OUTLIER) cc_final: 0.9018 (pmm-80) REVERT: D 427 GLN cc_start: 0.9608 (mt0) cc_final: 0.9292 (mt0) REVERT: E 80 TYR cc_start: 0.7301 (OUTLIER) cc_final: 0.7039 (p90) REVERT: E 103 MET cc_start: 0.9288 (ppp) cc_final: 0.9021 (ppp) REVERT: E 178 TYR cc_start: 0.6690 (t80) cc_final: 0.6324 (t80) REVERT: F 103 MET cc_start: 0.9225 (ppp) cc_final: 0.8947 (ppp) REVERT: F 153 LYS cc_start: 0.9048 (tppp) cc_final: 0.8743 (tppt) REVERT: F 178 TYR cc_start: 0.6760 (t80) cc_final: 0.6458 (t80) REVERT: F 209 PHE cc_start: 0.9208 (t80) cc_final: 0.8909 (t80) REVERT: F 427 GLN cc_start: 0.9600 (mt0) cc_final: 0.9315 (mt0) REVERT: F 445 MET cc_start: 0.9391 (mtm) cc_final: 0.9140 (mtp) REVERT: G 103 MET cc_start: 0.9238 (ppp) cc_final: 0.9015 (ppp) REVERT: G 153 LYS cc_start: 0.9017 (tppp) cc_final: 0.8748 (tppt) REVERT: G 178 TYR cc_start: 0.6614 (t80) cc_final: 0.6342 (t80) REVERT: G 182 HIS cc_start: 0.8495 (p-80) cc_final: 0.8285 (p-80) REVERT: G 445 MET cc_start: 0.9419 (mmp) cc_final: 0.9095 (mtm) outliers start: 66 outliers final: 38 residues processed: 253 average time/residue: 0.5604 time to fit residues: 163.8032 Evaluate side-chains 239 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 199 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 TYR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 160 MET Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 397 MET Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 214 ARG Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain E residue 80 TYR Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 424 SER Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 203 THR Chi-restraints excluded: chain F residue 214 ARG Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain G residue 80 TYR Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 203 THR Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 424 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 215 optimal weight: 0.8980 chunk 243 optimal weight: 0.9980 chunk 213 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 143 optimal weight: 0.9990 chunk 175 optimal weight: 0.9980 chunk 125 optimal weight: 30.0000 chunk 33 optimal weight: 3.9990 chunk 176 optimal weight: 8.9990 chunk 85 optimal weight: 5.9990 chunk 95 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 414 ASN F 106 HIS F 414 ASN G 119 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.069610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.045352 restraints weight = 82351.049| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 3.91 r_work: 0.2679 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 22043 Z= 0.102 Angle : 0.561 9.569 29820 Z= 0.269 Chirality : 0.040 0.160 3290 Planarity : 0.004 0.040 3752 Dihedral : 10.331 123.251 3192 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.79 % Allowed : 22.44 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.18), residues: 2653 helix: 2.85 (0.16), residues: 1127 sheet: -0.01 (0.21), residues: 623 loop : 0.49 (0.23), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 112 TYR 0.012 0.001 TYR G 80 PHE 0.027 0.001 PHE D 99 TRP 0.012 0.001 TRP D 251 HIS 0.004 0.001 HIS E 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.10 (22043) covalent geometry : angle 0.56101 / 0.27 (29820) hydrogen bonds : bond 0.02602 / 1.73 ( 1160) hydrogen bonds : angle 3.93245 / 2.79 ( 3228) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 211 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 LYS cc_start: 0.9083 (tppp) cc_final: 0.8807 (tppp) REVERT: A 178 TYR cc_start: 0.6699 (t80) cc_final: 0.6426 (t80) REVERT: A 399 MET cc_start: 0.9531 (mmm) cc_final: 0.9316 (mmm) REVERT: A 427 GLN cc_start: 0.9573 (mt0) cc_final: 0.9315 (mt0) REVERT: A 445 MET cc_start: 0.9339 (mtm) cc_final: 0.9037 (mtm) REVERT: B 178 TYR cc_start: 0.6745 (t80) cc_final: 0.6452 (t80) REVERT: B 427 GLN cc_start: 0.9590 (mt0) cc_final: 0.9317 (mt0) REVERT: C 59 MET cc_start: 0.9642 (mpt) cc_final: 0.9238 (tmm) REVERT: C 153 LYS cc_start: 0.9015 (tppp) cc_final: 0.8785 (tppt) REVERT: C 178 TYR cc_start: 0.6730 (t80) cc_final: 0.6412 (t80) REVERT: C 182 HIS cc_start: 0.8380 (p-80) cc_final: 0.8147 (p-80) REVERT: C 445 MET cc_start: 0.9389 (mmp) cc_final: 0.9179 (mtm) REVERT: D 90 GLN cc_start: 0.8540 (pp30) cc_final: 0.8288 (pm20) REVERT: D 178 TYR cc_start: 0.6597 (t80) cc_final: 0.6348 (t80) REVERT: D 427 GLN cc_start: 0.9599 (mt0) cc_final: 0.9274 (mt0) REVERT: E 80 TYR cc_start: 0.7202 (OUTLIER) cc_final: 0.6977 (p90) REVERT: E 103 MET cc_start: 0.9280 (ppp) cc_final: 0.8967 (ppp) REVERT: E 178 TYR cc_start: 0.6617 (t80) cc_final: 0.6312 (t80) REVERT: F 153 LYS cc_start: 0.9026 (tppp) cc_final: 0.8721 (tppt) REVERT: F 178 TYR cc_start: 0.6737 (t80) cc_final: 0.6478 (t80) REVERT: F 209 PHE cc_start: 0.9207 (t80) cc_final: 0.8748 (t80) REVERT: F 214 ARG cc_start: 0.9555 (OUTLIER) cc_final: 0.9228 (ptt180) REVERT: F 427 GLN cc_start: 0.9593 (mt0) cc_final: 0.9319 (mt0) REVERT: F 445 MET cc_start: 0.9393 (mtm) cc_final: 0.9018 (mtm) REVERT: G 103 MET cc_start: 0.9263 (ppp) cc_final: 0.8994 (ppp) REVERT: G 153 LYS cc_start: 0.9032 (tppp) cc_final: 0.8760 (tppp) REVERT: G 178 TYR cc_start: 0.6674 (t80) cc_final: 0.6403 (t80) REVERT: G 183 LEU cc_start: 0.9286 (mm) cc_final: 0.8864 (mm) outliers start: 65 outliers final: 35 residues processed: 255 average time/residue: 0.5994 time to fit residues: 175.4844 Evaluate side-chains 239 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 202 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 TYR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 160 MET Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain E residue 80 TYR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 203 THR Chi-restraints excluded: chain F residue 214 ARG Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 203 THR Chi-restraints excluded: chain G residue 424 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 53 optimal weight: 0.0060 chunk 230 optimal weight: 7.9990 chunk 43 optimal weight: 10.0000 chunk 67 optimal weight: 3.9990 chunk 150 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 198 optimal weight: 6.9990 chunk 241 optimal weight: 5.9990 chunk 127 optimal weight: 5.9990 chunk 157 optimal weight: 5.9990 chunk 83 optimal weight: 30.0000 overall best weight: 3.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 119 ASN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 119 ASN ** E 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.067526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.043190 restraints weight = 83236.870| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 3.86 r_work: 0.2609 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 22043 Z= 0.192 Angle : 0.605 10.039 29820 Z= 0.293 Chirality : 0.041 0.161 3290 Planarity : 0.004 0.050 3752 Dihedral : 10.013 116.928 3192 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.66 % Allowed : 22.91 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.18), residues: 2653 helix: 2.85 (0.16), residues: 1127 sheet: -0.09 (0.21), residues: 623 loop : 0.42 (0.23), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 112 TYR 0.013 0.001 TYR G 80 PHE 0.022 0.001 PHE A 99 TRP 0.011 0.001 TRP C 251 HIS 0.005 0.001 HIS E 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.19 (22043) covalent geometry : angle 0.60529 / 0.29 (29820) hydrogen bonds : bond 0.02975 / 1.97 ( 1160) hydrogen bonds : angle 4.09612 / 2.91 ( 3228) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 201 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 LYS cc_start: 0.9088 (tppp) cc_final: 0.8803 (tppp) REVERT: A 178 TYR cc_start: 0.6711 (t80) cc_final: 0.6431 (t80) REVERT: A 445 MET cc_start: 0.9365 (mtm) cc_final: 0.9098 (mtm) REVERT: B 103 MET cc_start: 0.9206 (pp-130) cc_final: 0.8880 (ppp) REVERT: B 178 TYR cc_start: 0.6785 (t80) cc_final: 0.6475 (t80) REVERT: B 182 HIS cc_start: 0.8471 (p-80) cc_final: 0.8078 (p-80) REVERT: B 427 GLN cc_start: 0.9582 (mt0) cc_final: 0.9325 (mt0) REVERT: C 59 MET cc_start: 0.9644 (mpt) cc_final: 0.9236 (tmm) REVERT: C 153 LYS cc_start: 0.9038 (tppp) cc_final: 0.8718 (tppp) REVERT: C 178 TYR cc_start: 0.6644 (t80) cc_final: 0.6357 (t80) REVERT: C 445 MET cc_start: 0.9435 (mmp) cc_final: 0.9200 (mtm) REVERT: D 59 MET cc_start: 0.9604 (mpt) cc_final: 0.9151 (tmm) REVERT: D 90 GLN cc_start: 0.8793 (pp30) cc_final: 0.8426 (pm20) REVERT: D 178 TYR cc_start: 0.6633 (t80) cc_final: 0.6403 (t80) REVERT: E 59 MET cc_start: 0.9628 (mpt) cc_final: 0.9170 (tmm) REVERT: E 80 TYR cc_start: 0.7183 (OUTLIER) cc_final: 0.6942 (p90) REVERT: E 103 MET cc_start: 0.9313 (ppp) cc_final: 0.9003 (ppp) REVERT: E 178 TYR cc_start: 0.6622 (t80) cc_final: 0.6325 (t80) REVERT: E 182 HIS cc_start: 0.8682 (p-80) cc_final: 0.8282 (p-80) REVERT: F 153 LYS cc_start: 0.9059 (tppp) cc_final: 0.8753 (tppt) REVERT: F 178 TYR cc_start: 0.6677 (t80) cc_final: 0.6441 (t80) REVERT: F 209 PHE cc_start: 0.9253 (t80) cc_final: 0.8953 (t80) REVERT: F 427 GLN cc_start: 0.9582 (mt0) cc_final: 0.9312 (mt0) REVERT: F 445 MET cc_start: 0.9416 (mtm) cc_final: 0.9150 (mtp) REVERT: G 103 MET cc_start: 0.9299 (ppp) cc_final: 0.8983 (ppp) REVERT: G 153 LYS cc_start: 0.9033 (tppp) cc_final: 0.8750 (tppp) REVERT: G 178 TYR cc_start: 0.6671 (t80) cc_final: 0.6373 (t80) REVERT: G 182 HIS cc_start: 0.8531 (p-80) cc_final: 0.8277 (p-80) REVERT: G 445 MET cc_start: 0.9440 (mmp) cc_final: 0.9140 (mtm) outliers start: 62 outliers final: 41 residues processed: 248 average time/residue: 0.5656 time to fit residues: 161.9402 Evaluate side-chains 242 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 200 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 TYR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 160 MET Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 108 GLN Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 321 ILE Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain E residue 80 TYR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 203 THR Chi-restraints excluded: chain F residue 214 ARG Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 203 THR Chi-restraints excluded: chain G residue 424 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 241 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 139 optimal weight: 2.9990 chunk 38 optimal weight: 90.0000 chunk 166 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 165 optimal weight: 5.9990 chunk 197 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 224 optimal weight: 1.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 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 = 0.3516 r_free = 0.3516 target = 0.067926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.043344 restraints weight = 83716.859| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 3.87 r_work: 0.2619 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 22043 Z= 0.152 Angle : 0.591 10.770 29820 Z= 0.283 Chirality : 0.041 0.162 3290 Planarity : 0.004 0.048 3752 Dihedral : 10.054 117.007 3192 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.53 % Allowed : 23.08 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.18), residues: 2653 helix: 2.87 (0.16), residues: 1127 sheet: -0.10 (0.21), residues: 623 loop : 0.42 (0.23), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 112 TYR 0.013 0.001 TYR G 80 PHE 0.033 0.001 PHE D 99 TRP 0.011 0.001 TRP C 251 HIS 0.002 0.001 HIS F 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (22043) covalent geometry : angle 0.59058 / 0.28 (29820) hydrogen bonds : bond 0.02820 / 1.87 ( 1160) hydrogen bonds : angle 3.99739 / 2.84 ( 3228) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 199 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 LYS cc_start: 0.9064 (tppp) cc_final: 0.8849 (tppt) REVERT: A 178 TYR cc_start: 0.6737 (t80) cc_final: 0.6467 (t80) REVERT: A 445 MET cc_start: 0.9349 (mtm) cc_final: 0.9081 (mtm) REVERT: B 178 TYR cc_start: 0.6785 (t80) cc_final: 0.6454 (t80) REVERT: B 182 HIS cc_start: 0.8429 (p-80) cc_final: 0.8227 (p-80) REVERT: B 427 GLN cc_start: 0.9589 (mt0) cc_final: 0.9300 (mt0) REVERT: C 59 MET cc_start: 0.9644 (mpt) cc_final: 0.9239 (tmm) REVERT: C 178 TYR cc_start: 0.6645 (t80) cc_final: 0.6354 (t80) REVERT: C 445 MET cc_start: 0.9432 (mmp) cc_final: 0.9197 (mtm) REVERT: D 59 MET cc_start: 0.9611 (mpt) cc_final: 0.9164 (tmm) REVERT: D 178 TYR cc_start: 0.6593 (t80) cc_final: 0.6354 (t80) REVERT: D 427 GLN cc_start: 0.9606 (mt0) cc_final: 0.9288 (mt0) REVERT: E 59 MET cc_start: 0.9632 (mpt) cc_final: 0.9199 (tmm) REVERT: E 80 TYR cc_start: 0.7104 (OUTLIER) cc_final: 0.6891 (p90) REVERT: E 103 MET cc_start: 0.9325 (ppp) cc_final: 0.9003 (ppp) REVERT: E 178 TYR cc_start: 0.6577 (t80) cc_final: 0.6318 (t80) REVERT: E 182 HIS cc_start: 0.8603 (p-80) cc_final: 0.8351 (p-80) REVERT: F 153 LYS cc_start: 0.9086 (tppp) cc_final: 0.8790 (tppt) REVERT: F 178 TYR cc_start: 0.6597 (t80) cc_final: 0.6389 (t80) REVERT: F 209 PHE cc_start: 0.9245 (t80) cc_final: 0.8917 (t80) REVERT: F 427 GLN cc_start: 0.9591 (mt0) cc_final: 0.9280 (mt0) REVERT: F 445 MET cc_start: 0.9420 (mtm) cc_final: 0.9153 (mtp) REVERT: G 103 MET cc_start: 0.9302 (ppp) cc_final: 0.8965 (ppp) REVERT: G 153 LYS cc_start: 0.9031 (tppp) cc_final: 0.8750 (tppt) REVERT: G 178 TYR cc_start: 0.6574 (t80) cc_final: 0.6319 (t80) REVERT: G 445 MET cc_start: 0.9428 (mmp) cc_final: 0.9116 (mtm) outliers start: 59 outliers final: 45 residues processed: 242 average time/residue: 0.5873 time to fit residues: 163.7152 Evaluate side-chains 242 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 196 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 TYR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 160 MET Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain C residue 80 TYR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 108 GLN Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 397 MET Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain E residue 80 TYR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain F residue 203 THR Chi-restraints excluded: chain F residue 214 ARG Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 321 ILE Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 203 THR Chi-restraints excluded: chain G residue 424 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 206 optimal weight: 0.9980 chunk 220 optimal weight: 4.9990 chunk 214 optimal weight: 0.1980 chunk 0 optimal weight: 90.0000 chunk 216 optimal weight: 0.8980 chunk 174 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 99 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 106 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 = 0.3546 r_free = 0.3546 target = 0.069293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.044939 restraints weight = 82668.563| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 3.89 r_work: 0.2670 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 22043 Z= 0.106 Angle : 0.605 11.390 29820 Z= 0.284 Chirality : 0.041 0.168 3290 Planarity : 0.004 0.041 3752 Dihedral : 10.261 124.632 3192 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.06 % Allowed : 23.42 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.18), residues: 2653 helix: 2.90 (0.16), residues: 1134 sheet: 0.00 (0.21), residues: 623 loop : 0.58 (0.23), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 112 TYR 0.012 0.001 TYR B 80 PHE 0.021 0.001 PHE A 99 TRP 0.012 0.001 TRP B 251 HIS 0.003 0.000 HIS D 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (22043) covalent geometry : angle 0.60538 / 0.28 (29820) hydrogen bonds : bond 0.02608 / 1.74 ( 1160) hydrogen bonds : angle 3.89225 / 2.77 ( 3228) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 207 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 LYS cc_start: 0.9068 (tppp) cc_final: 0.8850 (tppt) REVERT: A 178 TYR cc_start: 0.6842 (t80) cc_final: 0.6545 (t80) REVERT: A 427 GLN cc_start: 0.9571 (mt0) cc_final: 0.9187 (mt0) REVERT: A 445 MET cc_start: 0.9312 (mtm) cc_final: 0.9069 (mtm) REVERT: B 103 MET cc_start: 0.9194 (pp-130) cc_final: 0.8862 (ppp) REVERT: B 178 TYR cc_start: 0.6691 (t80) cc_final: 0.6397 (t80) REVERT: B 427 GLN cc_start: 0.9587 (mt0) cc_final: 0.9278 (mt0) REVERT: C 59 MET cc_start: 0.9646 (mpt) cc_final: 0.9263 (tmm) REVERT: C 153 LYS cc_start: 0.9003 (tppp) cc_final: 0.8695 (tppp) REVERT: C 445 MET cc_start: 0.9386 (mmp) cc_final: 0.9181 (mtm) REVERT: D 59 MET cc_start: 0.9607 (mpt) cc_final: 0.9171 (tmm) REVERT: D 178 TYR cc_start: 0.6585 (t80) cc_final: 0.6361 (t80) REVERT: D 427 GLN cc_start: 0.9597 (mt0) cc_final: 0.9288 (mt0) REVERT: E 59 MET cc_start: 0.9642 (mpt) cc_final: 0.9210 (tmm) REVERT: E 103 MET cc_start: 0.9308 (ppp) cc_final: 0.8967 (ppp) REVERT: E 178 TYR cc_start: 0.6564 (t80) cc_final: 0.6293 (t80) REVERT: E 182 HIS cc_start: 0.8559 (p-80) cc_final: 0.8338 (p-80) REVERT: F 153 LYS cc_start: 0.9056 (tppp) cc_final: 0.8755 (tppt) REVERT: F 183 LEU cc_start: 0.9482 (mm) cc_final: 0.9092 (mm) REVERT: F 209 PHE cc_start: 0.9217 (t80) cc_final: 0.8907 (t80) REVERT: F 427 GLN cc_start: 0.9584 (mt0) cc_final: 0.9301 (mt0) REVERT: F 445 MET cc_start: 0.9405 (mtm) cc_final: 0.9169 (mtp) REVERT: G 103 MET cc_start: 0.9267 (ppp) cc_final: 0.8919 (ppp) REVERT: G 153 LYS cc_start: 0.9018 (tppp) cc_final: 0.8722 (tppt) REVERT: G 178 TYR cc_start: 0.6547 (t80) cc_final: 0.6302 (t80) REVERT: G 445 MET cc_start: 0.9415 (mmp) cc_final: 0.9165 (mtm) outliers start: 48 outliers final: 41 residues processed: 240 average time/residue: 0.5930 time to fit residues: 162.8771 Evaluate side-chains 239 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 198 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 TYR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain C residue 80 TYR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 108 GLN Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 397 MET Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain E residue 80 TYR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 203 THR Chi-restraints excluded: chain F residue 214 ARG Chi-restraints excluded: chain F residue 321 ILE Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 203 THR Chi-restraints excluded: chain G residue 307 MET Chi-restraints excluded: chain G residue 424 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 6 optimal weight: 20.0000 chunk 136 optimal weight: 2.9990 chunk 11 optimal weight: 20.0000 chunk 252 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 37 optimal weight: 0.4980 chunk 1 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 139 optimal weight: 0.8980 chunk 134 optimal weight: 6.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 278 GLN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.068562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.044117 restraints weight = 83038.330| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 3.91 r_work: 0.2644 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8915 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22043 Z= 0.137 Angle : 0.623 11.981 29820 Z= 0.295 Chirality : 0.041 0.175 3290 Planarity : 0.004 0.044 3752 Dihedral : 10.113 125.812 3192 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.93 % Allowed : 23.85 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.10 (0.18), residues: 2653 helix: 2.87 (0.16), residues: 1134 sheet: 0.01 (0.21), residues: 623 loop : 0.61 (0.23), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 214 TYR 0.023 0.001 TYR F 178 PHE 0.036 0.001 PHE D 99 TRP 0.011 0.001 TRP C 251 HIS 0.002 0.001 HIS F 440 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (22043) covalent geometry : angle 0.62287 / 0.30 (29820) hydrogen bonds : bond 0.02788 / 1.85 ( 1160) hydrogen bonds : angle 3.97398 / 2.83 ( 3228) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 198 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 LYS cc_start: 0.9054 (tppp) cc_final: 0.8830 (tppt) REVERT: A 178 TYR cc_start: 0.6811 (t80) cc_final: 0.6520 (t80) REVERT: A 427 GLN cc_start: 0.9566 (mt0) cc_final: 0.9208 (mt0) REVERT: A 445 MET cc_start: 0.9303 (mtm) cc_final: 0.8890 (mtm) REVERT: B 103 MET cc_start: 0.9206 (pp-130) cc_final: 0.8843 (ppp) REVERT: B 177 LEU cc_start: 0.9334 (mm) cc_final: 0.8835 (pp) REVERT: B 178 TYR cc_start: 0.6663 (t80) cc_final: 0.6458 (t80) REVERT: B 427 GLN cc_start: 0.9589 (mt0) cc_final: 0.9302 (mt0) REVERT: C 59 MET cc_start: 0.9648 (mpt) cc_final: 0.9264 (tmm) REVERT: C 178 TYR cc_start: 0.7229 (t80) cc_final: 0.6296 (t80) REVERT: D 59 MET cc_start: 0.9593 (mpt) cc_final: 0.9158 (tmm) REVERT: D 178 TYR cc_start: 0.6568 (t80) cc_final: 0.6319 (t80) REVERT: D 427 GLN cc_start: 0.9596 (mt0) cc_final: 0.9268 (mt0) REVERT: E 59 MET cc_start: 0.9636 (mpt) cc_final: 0.9204 (tmm) REVERT: E 103 MET cc_start: 0.9316 (ppp) cc_final: 0.8975 (ppp) REVERT: E 178 TYR cc_start: 0.6561 (t80) cc_final: 0.6307 (t80) REVERT: F 153 LYS cc_start: 0.9052 (tppp) cc_final: 0.8702 (OUTLIER) REVERT: F 182 HIS cc_start: 0.8584 (p-80) cc_final: 0.8381 (p-80) REVERT: F 209 PHE cc_start: 0.9251 (t80) cc_final: 0.8938 (t80) REVERT: F 427 GLN cc_start: 0.9588 (mt0) cc_final: 0.9287 (mt0) REVERT: F 445 MET cc_start: 0.9374 (mtm) cc_final: 0.9037 (mtp) REVERT: G 103 MET cc_start: 0.9297 (ppp) cc_final: 0.8924 (ppp) REVERT: G 153 LYS cc_start: 0.9027 (tppp) cc_final: 0.8743 (tppt) REVERT: G 178 TYR cc_start: 0.6530 (t80) cc_final: 0.6242 (t80) REVERT: G 445 MET cc_start: 0.9439 (mmp) cc_final: 0.9179 (mtm) outliers start: 45 outliers final: 41 residues processed: 230 average time/residue: 0.5811 time to fit residues: 153.6783 Evaluate side-chains 235 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 195 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 TYR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 397 MET Chi-restraints excluded: chain C residue 80 TYR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 108 GLN Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 397 MET Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain E residue 80 TYR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain F residue 203 THR Chi-restraints excluded: chain F residue 214 ARG Chi-restraints excluded: chain F residue 321 ILE Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 203 THR Chi-restraints excluded: chain G residue 424 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 169 optimal weight: 0.6980 chunk 4 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 chunk 88 optimal weight: 0.0010 chunk 246 optimal weight: 4.9990 chunk 228 optimal weight: 0.0040 chunk 235 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 154 optimal weight: 30.0000 chunk 175 optimal weight: 0.6980 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 278 GLN ** A 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 ASN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.070140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.045884 restraints weight = 82380.678| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 3.91 r_work: 0.2702 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 22043 Z= 0.100 Angle : 0.625 12.909 29820 Z= 0.291 Chirality : 0.041 0.175 3290 Planarity : 0.004 0.037 3752 Dihedral : 10.373 128.401 3192 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.80 % Allowed : 23.94 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.12 (0.18), residues: 2653 helix: 2.85 (0.16), residues: 1134 sheet: 0.07 (0.21), residues: 658 loop : 0.64 (0.24), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 214 TYR 0.021 0.001 TYR F 178 PHE 0.024 0.001 PHE A 99 TRP 0.012 0.001 TRP B 251 HIS 0.004 0.000 HIS A 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 (22043) covalent geometry : angle 0.62482 / 0.29 (29820) hydrogen bonds : bond 0.02559 / 1.70 ( 1160) hydrogen bonds : angle 3.85269 / 2.74 ( 3228) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8208.66 seconds wall clock time: 141 minutes 7.20 seconds (8467.20 seconds total)