Starting phenix.real_space_refine on Fri Sep 19 00:43:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gu9_51605/09_2025/9gu9_51605.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gu9_51605/09_2025/9gu9_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9gu9_51605/09_2025/9gu9_51605.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gu9_51605/09_2025/9gu9_51605.map" model { file = "/net/cci-nas-00/data/ceres_data/9gu9_51605/09_2025/9gu9_51605.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gu9_51605/09_2025/9gu9_51605.cif" } 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-2.0-5805/lib/python3.9/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: 3.24, per 1000 atoms: 0.15 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: 1.91 Conformation dependent library (CDL) restraints added in 901.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.89 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: 4.25 Time building geometry restraints manager: 2.55 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=" CB GLN B 82 " pdb=" CG GLN B 82 " ideal model delta sigma weight residual 1.520 1.585 -0.065 3.00e-02 1.11e+03 4.65e+00 bond pdb=" CB GLN G 82 " pdb=" CG GLN G 82 " ideal model delta sigma weight residual 1.520 1.585 -0.065 3.00e-02 1.11e+03 4.63e+00 bond pdb=" CB GLN A 82 " pdb=" CG GLN A 82 " ideal model delta sigma weight residual 1.520 1.584 -0.064 3.00e-02 1.11e+03 4.60e+00 bond pdb=" CB GLN E 82 " pdb=" CG GLN E 82 " ideal model delta sigma weight residual 1.520 1.584 -0.064 3.00e-02 1.11e+03 4.59e+00 bond pdb=" CB GLN F 82 " pdb=" CG GLN F 82 " ideal model delta sigma weight residual 1.520 1.584 -0.064 3.00e-02 1.11e+03 4.59e+00 ... (remaining 22038 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 29203 2.25 - 4.51: 513 4.51 - 6.76: 62 6.76 - 9.02: 35 9.02 - 11.27: 7 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 - 20.44: 11822 20.44 - 40.89: 1079 40.89 - 61.33: 322 61.33 - 81.77: 49 81.77 - 102.21: 7 Dihedral angle restraints: 13279 sinusoidal: 5495 harmonic: 7784 Sorted by residual: dihedral pdb=" CA MET A 83 " pdb=" C MET A 83 " pdb=" N ILE A 84 " pdb=" CA ILE A 84 " ideal model delta harmonic sigma weight residual -180.00 -160.25 -19.75 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA MET C 83 " pdb=" C MET C 83 " pdb=" N ILE C 84 " pdb=" CA ILE C 84 " ideal model delta harmonic sigma weight residual 180.00 -160.25 -19.75 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA MET G 83 " pdb=" C MET G 83 " pdb=" N ILE G 84 " pdb=" CA ILE G 84 " ideal model delta harmonic sigma weight residual -180.00 -160.26 -19.74 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 13276 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 2192 0.029 - 0.059: 643 0.059 - 0.088: 250 0.088 - 0.117: 175 0.117 - 0.146: 44 Chirality restraints: 3304 Sorted by residual: chirality pdb=" CA ILE A 89 " pdb=" N ILE A 89 " pdb=" C ILE A 89 " pdb=" CB ILE A 89 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.36e-01 chirality pdb=" CA ILE F 89 " pdb=" N ILE F 89 " pdb=" C ILE F 89 " pdb=" CB ILE F 89 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.34e-01 chirality pdb=" CA ILE B 89 " pdb=" N ILE B 89 " pdb=" C ILE B 89 " pdb=" CB ILE B 89 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.25e-01 ... (remaining 3301 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: 0.07 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: 3.140 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: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 19.270 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 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 : 0.004 0.065 22043 Z= 0.178 Angle : 0.770 11.273 29820 Z= 0.384 Chirality : 0.040 0.146 3304 Planarity : 0.004 0.039 3752 Dihedral : 17.281 102.212 8281 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 aren 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 covalent geometry : bond 0.00428 (22043) covalent geometry : angle 0.76980 (29820) hydrogen bonds : bond 0.18848 ( 1160) hydrogen bonds : angle 6.64840 ( 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 : 0.930 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: 0.7962 time to fit residues: 199.4179 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 : 0.907 ------------------------------------------------------------------------------- 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: 4.9990 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: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 ASN A 429 GLN ** A 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 ASN B 429 GLN C 106 HIS ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 ASN C 429 GLN D 106 HIS ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 189 ASN D 429 GLN E 106 HIS ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 189 ASN E 429 GLN ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 189 ASN F 429 GLN G 106 HIS G 108 GLN ** G 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 189 ASN G 429 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.068578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.044241 restraints weight = 82862.836| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 3.86 r_work: 0.2637 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 22043 Z= 0.207 Angle : 0.638 6.607 29820 Z= 0.323 Chirality : 0.044 0.169 3304 Planarity : 0.006 0.076 3752 Dihedral : 10.649 123.274 3078 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.23 % Allowed : 20.72 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.17), residues: 2653 helix: 2.35 (0.16), residues: 1120 sheet: -0.78 (0.20), residues: 560 loop : -0.23 (0.21), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 255 TYR 0.010 0.001 TYR D 96 PHE 0.031 0.002 PHE D 99 TRP 0.017 0.002 TRP E 251 HIS 0.009 0.001 HIS A 106 Details of bonding type rmsd covalent geometry : bond 0.00470 (22043) covalent geometry : angle 0.63782 (29820) hydrogen bonds : bond 0.04305 ( 1160) hydrogen bonds : angle 4.99330 ( 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 239 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 187 time to evaluate : 0.876 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: A 178 TYR cc_start: 0.6902 (t80) cc_final: 0.6401 (t80) REVERT: A 182 HIS cc_start: 0.8430 (p-80) cc_final: 0.8218 (p-80) REVERT: A 209 PHE cc_start: 0.9125 (t80) cc_final: 0.8884 (t80) REVERT: A 214 ARG cc_start: 0.9455 (OUTLIER) cc_final: 0.9173 (ptt90) REVERT: B 178 TYR cc_start: 0.6857 (t80) cc_final: 0.6273 (t80) REVERT: B 182 HIS cc_start: 0.8317 (p90) cc_final: 0.8020 (p-80) REVERT: C 178 TYR cc_start: 0.6891 (t80) cc_final: 0.6444 (t80) REVERT: D 178 TYR cc_start: 0.6858 (t80) cc_final: 0.6311 (t80) REVERT: D 182 HIS cc_start: 0.8439 (p-80) cc_final: 0.8232 (p-80) REVERT: E 87 LEU cc_start: 0.8553 (pp) cc_final: 0.8323 (pp) REVERT: E 178 TYR cc_start: 0.6697 (t80) cc_final: 0.6285 (t80) REVERT: E 182 HIS cc_start: 0.8541 (p-80) cc_final: 0.8336 (p-80) REVERT: F 178 TYR cc_start: 0.6922 (t80) cc_final: 0.6581 (t80) REVERT: G 174 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.8757 (mm) REVERT: G 178 TYR cc_start: 0.6883 (t80) cc_final: 0.6384 (t80) REVERT: G 445 MET cc_start: 0.9441 (mmp) cc_final: 0.9101 (mtm) outliers start: 52 outliers final: 16 residues processed: 216 average time/residue: 0.6829 time to fit residues: 166.6984 Evaluate side-chains 202 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 184 time to evaluate : 0.871 ------------------------------------------------------------------------------- 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 59 MET Chi-restraints excluded: chain B residue 184 PHE Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 424 SER Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 184 PHE Chi-restraints excluded: chain E residue 424 SER Chi-restraints excluded: chain F residue 160 MET Chi-restraints excluded: chain G residue 160 MET Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain G residue 184 PHE 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: 8.9990 chunk 245 optimal weight: 0.9980 chunk 261 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 chunk 14 optimal weight: 8.9990 chunk 219 optimal weight: 0.9980 chunk 76 optimal weight: 110.0000 chunk 93 optimal weight: 0.9980 chunk 125 optimal weight: 9.9990 chunk 200 optimal weight: 6.9990 chunk 228 optimal weight: 40.0000 overall best weight: 2.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 122 GLN ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 122 GLN G 122 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.068566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.044151 restraints weight = 82116.655| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 3.84 r_work: 0.2634 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.1844 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= 0.165 Angle : 0.581 8.847 29820 Z= 0.290 Chirality : 0.042 0.149 3304 Planarity : 0.005 0.058 3752 Dihedral : 10.387 119.244 3066 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.40 % Allowed : 22.01 % Favored : 75.59 % 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 aren not related in a simple way. whole: 1.23 (0.17), residues: 2653 helix: 2.48 (0.16), residues: 1120 sheet: -0.80 (0.19), residues: 588 loop : -0.05 (0.21), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 255 TYR 0.018 0.001 TYR G 80 PHE 0.009 0.001 PHE F 209 TRP 0.015 0.002 TRP G 251 HIS 0.008 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00374 (22043) covalent geometry : angle 0.58108 (29820) hydrogen bonds : bond 0.03676 ( 1160) hydrogen bonds : angle 4.62359 ( 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 252 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 196 time to evaluate : 0.610 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 80 TYR cc_start: 0.7119 (p90) cc_final: 0.6895 (p90) REVERT: A 178 TYR cc_start: 0.6866 (t80) cc_final: 0.6318 (t80) REVERT: A 182 HIS cc_start: 0.8355 (OUTLIER) cc_final: 0.8152 (p-80) REVERT: B 103 MET cc_start: 0.9345 (ppp) cc_final: 0.9081 (ppp) REVERT: B 178 TYR cc_start: 0.6886 (t80) cc_final: 0.6530 (t80) REVERT: B 182 HIS cc_start: 0.8221 (p90) cc_final: 0.7901 (p-80) REVERT: B 427 GLN cc_start: 0.9570 (mt0) cc_final: 0.9279 (mt0) REVERT: C 103 MET cc_start: 0.9380 (ppp) cc_final: 0.9085 (ppp) REVERT: C 178 TYR cc_start: 0.6836 (t80) cc_final: 0.6318 (t80) REVERT: D 178 TYR cc_start: 0.6757 (t80) cc_final: 0.6445 (t80) REVERT: D 427 GLN cc_start: 0.9582 (mt0) cc_final: 0.9285 (mt0) REVERT: E 103 MET cc_start: 0.9393 (ppp) cc_final: 0.9076 (ppp) REVERT: E 108 GLN cc_start: 0.9133 (mp10) cc_final: 0.8888 (mp10) REVERT: E 178 TYR cc_start: 0.6715 (t80) cc_final: 0.6265 (t80) REVERT: E 399 MET cc_start: 0.9468 (mmm) cc_final: 0.9222 (mmm) REVERT: F 178 TYR cc_start: 0.6892 (t80) cc_final: 0.6562 (t80) REVERT: F 427 GLN cc_start: 0.9572 (mt0) cc_final: 0.9298 (mt0) REVERT: F 445 MET cc_start: 0.9413 (mtm) cc_final: 0.9149 (mtp) REVERT: G 178 TYR cc_start: 0.6786 (t80) cc_final: 0.6452 (t80) REVERT: G 182 HIS cc_start: 0.8403 (p-80) cc_final: 0.8143 (p-80) REVERT: G 445 MET cc_start: 0.9440 (mmp) cc_final: 0.9081 (mtm) outliers start: 56 outliers final: 19 residues processed: 232 average time/residue: 0.6229 time to fit residues: 165.0276 Evaluate side-chains 209 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 189 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 HIS Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain B residue 424 SER Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain D residue 160 MET Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 310 MET Chi-restraints excluded: chain E residue 424 SER Chi-restraints excluded: chain F residue 160 MET Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain G residue 160 MET Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 184 PHE Chi-restraints excluded: chain G residue 299 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: 5.9990 chunk 28 optimal weight: 9.9990 chunk 242 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 3 optimal weight: 20.0000 chunk 175 optimal weight: 2.9990 chunk 240 optimal weight: 6.9990 chunk 209 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 GLN B 393 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.068774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.044135 restraints weight = 82174.107| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 3.85 r_work: 0.2641 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22043 Z= 0.148 Angle : 0.573 11.130 29820 Z= 0.283 Chirality : 0.042 0.163 3304 Planarity : 0.004 0.056 3752 Dihedral : 10.387 118.551 3066 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.70 % Allowed : 21.84 % Favored : 75.46 % 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 aren not related in a simple way. whole: 1.40 (0.17), residues: 2653 helix: 2.52 (0.16), residues: 1127 sheet: -0.60 (0.20), residues: 588 loop : 0.10 (0.21), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 255 TYR 0.019 0.001 TYR E 80 PHE 0.030 0.001 PHE D 99 TRP 0.014 0.001 TRP E 251 HIS 0.008 0.001 HIS D 113 Details of bonding type rmsd covalent geometry : bond 0.00339 (22043) covalent geometry : angle 0.57314 (29820) hydrogen bonds : bond 0.03302 ( 1160) hydrogen bonds : angle 4.38569 ( 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 264 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 201 time to evaluate : 0.919 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 80 TYR cc_start: 0.7062 (OUTLIER) cc_final: 0.6841 (p90) REVERT: A 178 TYR cc_start: 0.6777 (t80) cc_final: 0.6467 (t80) REVERT: A 214 ARG cc_start: 0.9488 (ptm-80) cc_final: 0.9153 (ptt180) REVERT: A 445 MET cc_start: 0.9424 (mtm) cc_final: 0.9144 (mtm) REVERT: B 178 TYR cc_start: 0.6812 (t80) cc_final: 0.6473 (t80) REVERT: C 178 TYR cc_start: 0.6803 (t80) cc_final: 0.6445 (t80) REVERT: D 178 TYR cc_start: 0.6761 (t80) cc_final: 0.6451 (t80) REVERT: E 178 TYR cc_start: 0.6654 (t80) cc_final: 0.6132 (t80) REVERT: E 399 MET cc_start: 0.9516 (mmm) cc_final: 0.9286 (mmm) REVERT: F 83 MET cc_start: 0.6597 (ttt) cc_final: 0.6331 (mtp) REVERT: F 103 MET cc_start: 0.9206 (ppp) cc_final: 0.8984 (ppp) REVERT: F 178 TYR cc_start: 0.6948 (t80) cc_final: 0.6627 (t80) REVERT: F 427 GLN cc_start: 0.9590 (mt0) cc_final: 0.9275 (mt0) REVERT: F 445 MET cc_start: 0.9416 (mtm) cc_final: 0.9162 (mtp) REVERT: G 178 TYR cc_start: 0.6728 (t80) cc_final: 0.6381 (t80) REVERT: G 445 MET cc_start: 0.9427 (mmp) cc_final: 0.9076 (mtm) outliers start: 63 outliers final: 28 residues processed: 249 average time/residue: 0.5870 time to fit residues: 168.7280 Evaluate side-chains 221 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 192 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 TYR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 424 SER 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 B residue 424 SER Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 397 MET Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 299 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 111 SER Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 424 SER Chi-restraints excluded: chain F residue 203 THR Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain G residue 160 MET 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: 8.9990 chunk 37 optimal weight: 0.4980 chunk 19 optimal weight: 0.8980 chunk 1 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 84 optimal weight: 9.9990 chunk 187 optimal weight: 0.0670 chunk 92 optimal weight: 8.9990 chunk 180 optimal weight: 0.5980 chunk 145 optimal weight: 1.9990 chunk 200 optimal weight: 4.9990 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 HIS B 119 ASN ** B 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 427 GLN C 414 ASN D 414 ASN E 427 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.069751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.045146 restraints weight = 81712.225| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 3.89 r_work: 0.2670 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 22043 Z= 0.108 Angle : 0.583 11.277 29820 Z= 0.282 Chirality : 0.041 0.166 3304 Planarity : 0.004 0.051 3752 Dihedral : 10.316 116.497 3066 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.23 % Allowed : 22.01 % 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 aren not related in a simple way. whole: 1.60 (0.17), residues: 2653 helix: 2.53 (0.16), residues: 1127 sheet: -0.35 (0.20), residues: 623 loop : 0.33 (0.22), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 255 TYR 0.015 0.001 TYR G 80 PHE 0.020 0.001 PHE F 99 TRP 0.014 0.001 TRP E 251 HIS 0.005 0.001 HIS C 106 Details of bonding type rmsd covalent geometry : bond 0.00247 (22043) covalent geometry : angle 0.58343 (29820) hydrogen bonds : bond 0.03023 ( 1160) hydrogen bonds : angle 4.23654 ( 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 251 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 199 time to evaluate : 0.833 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 80 TYR cc_start: 0.7024 (OUTLIER) cc_final: 0.6817 (p90) REVERT: A 178 TYR cc_start: 0.6783 (t80) cc_final: 0.6475 (t80) REVERT: A 214 ARG cc_start: 0.9488 (ptm-80) cc_final: 0.9192 (ptt90) REVERT: A 427 GLN cc_start: 0.9544 (mt0) cc_final: 0.9318 (mt0) REVERT: A 445 MET cc_start: 0.9396 (mtm) cc_final: 0.9138 (mtm) REVERT: B 178 TYR cc_start: 0.6797 (t80) cc_final: 0.6492 (t80) REVERT: B 182 HIS cc_start: 0.8286 (p-80) cc_final: 0.7994 (p-80) REVERT: C 178 TYR cc_start: 0.6754 (t80) cc_final: 0.6399 (t80) REVERT: C 427 GLN cc_start: 0.9591 (mt0) cc_final: 0.9263 (mt0) REVERT: C 445 MET cc_start: 0.9409 (mmp) cc_final: 0.9093 (mtm) REVERT: D 178 TYR cc_start: 0.6734 (t80) cc_final: 0.6424 (t80) REVERT: D 399 MET cc_start: 0.9512 (mmm) cc_final: 0.9301 (mmm) REVERT: D 427 GLN cc_start: 0.9567 (mt0) cc_final: 0.9230 (mt0) REVERT: E 178 TYR cc_start: 0.6685 (t80) cc_final: 0.6236 (t80) REVERT: E 399 MET cc_start: 0.9515 (mmm) cc_final: 0.9262 (mmm) REVERT: F 83 MET cc_start: 0.6605 (ttt) cc_final: 0.6386 (mtp) REVERT: F 103 MET cc_start: 0.9210 (ppp) cc_final: 0.8981 (ppp) REVERT: F 178 TYR cc_start: 0.6937 (t80) cc_final: 0.6638 (t80) REVERT: F 427 GLN cc_start: 0.9569 (mt0) cc_final: 0.9274 (mt0) REVERT: F 445 MET cc_start: 0.9384 (mtm) cc_final: 0.9000 (mtm) REVERT: G 103 MET cc_start: 0.9396 (tmm) cc_final: 0.9171 (ppp) REVERT: G 178 TYR cc_start: 0.6724 (t80) cc_final: 0.6418 (t80) REVERT: G 182 HIS cc_start: 0.8377 (p-80) cc_final: 0.8149 (p-80) outliers start: 52 outliers final: 23 residues processed: 239 average time/residue: 0.6221 time to fit residues: 170.4924 Evaluate side-chains 215 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 191 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 TYR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 397 MET 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 E residue 87 LEU Chi-restraints excluded: chain E residue 110 VAL 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 F residue 110 VAL Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 360 THR Chi-restraints excluded: chain G residue 176 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: 0.9990 chunk 243 optimal weight: 1.9990 chunk 213 optimal weight: 1.9990 chunk 92 optimal weight: 10.0000 chunk 143 optimal weight: 0.8980 chunk 175 optimal weight: 5.9990 chunk 125 optimal weight: 40.0000 chunk 33 optimal weight: 5.9990 chunk 176 optimal weight: 0.6980 chunk 85 optimal weight: 6.9990 chunk 95 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 GLN ** B 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 GLN B 414 ASN ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 ASN ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 278 GLN D 393 GLN ** E 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 278 GLN ** F 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 278 GLN F 393 GLN F 414 ASN ** G 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 414 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.069304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.044924 restraints weight = 82563.235| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 3.86 r_work: 0.2667 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22043 Z= 0.111 Angle : 0.579 10.247 29820 Z= 0.278 Chirality : 0.041 0.157 3304 Planarity : 0.004 0.049 3752 Dihedral : 10.231 115.973 3066 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.32 % Allowed : 22.39 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.70 (0.17), residues: 2653 helix: 2.61 (0.16), residues: 1127 sheet: -0.24 (0.20), residues: 623 loop : 0.35 (0.22), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 112 TYR 0.014 0.001 TYR B 80 PHE 0.033 0.001 PHE D 99 TRP 0.013 0.001 TRP G 251 HIS 0.007 0.001 HIS C 106 Details of bonding type rmsd covalent geometry : bond 0.00257 (22043) covalent geometry : angle 0.57867 (29820) hydrogen bonds : bond 0.02875 ( 1160) hydrogen bonds : angle 4.12110 ( 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 249 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 195 time to evaluate : 0.887 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 178 TYR cc_start: 0.6807 (t80) cc_final: 0.6560 (t80) REVERT: A 182 HIS cc_start: 0.8391 (p-80) cc_final: 0.8157 (p-80) REVERT: A 427 GLN cc_start: 0.9552 (mt0) cc_final: 0.9331 (mt0) REVERT: A 445 MET cc_start: 0.9340 (mtm) cc_final: 0.9078 (mtm) REVERT: B 103 MET cc_start: 0.9223 (ppp) cc_final: 0.8965 (ppp) REVERT: B 178 TYR cc_start: 0.6796 (t80) cc_final: 0.6486 (t80) REVERT: B 182 HIS cc_start: 0.8241 (p-80) cc_final: 0.7987 (p-80) REVERT: C 178 TYR cc_start: 0.6821 (t80) cc_final: 0.6433 (t80) REVERT: C 427 GLN cc_start: 0.9595 (mt0) cc_final: 0.9289 (mt0) REVERT: C 445 MET cc_start: 0.9384 (mmp) cc_final: 0.9101 (mtm) REVERT: D 178 TYR cc_start: 0.6781 (t80) cc_final: 0.6500 (t80) REVERT: D 427 GLN cc_start: 0.9589 (mt0) cc_final: 0.9270 (mt0) REVERT: E 103 MET cc_start: 0.9242 (ppp) cc_final: 0.8950 (ppp) REVERT: E 178 TYR cc_start: 0.6714 (t80) cc_final: 0.6217 (t80) REVERT: F 90 GLN cc_start: 0.8728 (pm20) cc_final: 0.8497 (tm130) REVERT: F 178 TYR cc_start: 0.6911 (t80) cc_final: 0.6658 (t80) REVERT: F 427 GLN cc_start: 0.9591 (mt0) cc_final: 0.9313 (mt0) REVERT: F 445 MET cc_start: 0.9366 (mtm) cc_final: 0.9093 (mtp) REVERT: G 103 MET cc_start: 0.9353 (tmm) cc_final: 0.9096 (ppp) REVERT: G 178 TYR cc_start: 0.6764 (t80) cc_final: 0.6457 (t80) REVERT: G 182 HIS cc_start: 0.8387 (p-80) cc_final: 0.8146 (p-80) REVERT: G 399 MET cc_start: 0.9540 (mmm) cc_final: 0.9335 (mmm) REVERT: G 445 MET cc_start: 0.9429 (mmp) cc_final: 0.9086 (mtm) outliers start: 54 outliers final: 27 residues processed: 235 average time/residue: 0.6311 time to fit residues: 170.3277 Evaluate side-chains 215 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 188 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 384 VAL Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 397 MET Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 397 MET 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 87 LEU Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 321 ILE Chi-restraints excluded: chain F residue 360 THR Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 384 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 53 optimal weight: 0.9980 chunk 230 optimal weight: 40.0000 chunk 43 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 150 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 chunk 198 optimal weight: 5.9990 chunk 241 optimal weight: 5.9990 chunk 127 optimal weight: 6.9990 chunk 157 optimal weight: 6.9990 chunk 83 optimal weight: 30.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 GLN A 393 GLN ** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 GLN C 278 GLN C 393 GLN ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 278 GLN ** E 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 278 GLN E 393 GLN E 414 ASN E 427 GLN ** F 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 278 GLN G 278 GLN G 393 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.067206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.042817 restraints weight = 83713.039| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 3.82 r_work: 0.2594 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 22043 Z= 0.252 Angle : 0.638 11.750 29820 Z= 0.310 Chirality : 0.042 0.155 3304 Planarity : 0.004 0.052 3752 Dihedral : 10.336 118.367 3066 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.53 % Allowed : 22.48 % Favored : 74.99 % 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 aren not related in a simple way. whole: 1.66 (0.17), residues: 2653 helix: 2.66 (0.16), residues: 1127 sheet: -0.40 (0.20), residues: 623 loop : 0.31 (0.22), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 112 TYR 0.018 0.001 TYR A 80 PHE 0.022 0.002 PHE A 99 TRP 0.012 0.001 TRP D 251 HIS 0.005 0.001 HIS C 182 Details of bonding type rmsd covalent geometry : bond 0.00577 (22043) covalent geometry : angle 0.63768 (29820) hydrogen bonds : bond 0.03266 ( 1160) hydrogen bonds : angle 4.25015 ( 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 253 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 194 time to evaluate : 0.756 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: 0.6557 (t80) REVERT: A 214 ARG cc_start: 0.9485 (ptm-80) cc_final: 0.9186 (ptt90) REVERT: A 445 MET cc_start: 0.9380 (mtm) cc_final: 0.9108 (mtm) REVERT: B 103 MET cc_start: 0.9268 (ppp) cc_final: 0.9047 (ppp) REVERT: B 178 TYR cc_start: 0.6741 (t80) cc_final: 0.6413 (t80) REVERT: B 182 HIS cc_start: 0.8257 (p-80) cc_final: 0.7975 (p-80) REVERT: C 178 TYR cc_start: 0.6821 (t80) cc_final: 0.6453 (t80) REVERT: C 182 HIS cc_start: 0.8439 (p-80) cc_final: 0.8178 (p-80) REVERT: D 178 TYR cc_start: 0.6747 (t80) cc_final: 0.6484 (t80) REVERT: E 178 TYR cc_start: 0.6740 (t80) cc_final: 0.6259 (t80) REVERT: E 182 HIS cc_start: 0.8559 (p-80) cc_final: 0.8268 (p-80) REVERT: F 103 MET cc_start: 0.9241 (ppp) cc_final: 0.9019 (ppp) REVERT: F 178 TYR cc_start: 0.6911 (t80) cc_final: 0.6628 (t80) REVERT: F 445 MET cc_start: 0.9420 (mtm) cc_final: 0.9146 (mtp) REVERT: G 103 MET cc_start: 0.9375 (tmm) cc_final: 0.9143 (ppp) REVERT: G 178 TYR cc_start: 0.6776 (t80) cc_final: 0.6475 (t80) outliers start: 59 outliers final: 32 residues processed: 235 average time/residue: 0.5882 time to fit residues: 159.6737 Evaluate side-chains 222 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 190 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 360 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 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 B residue 397 MET Chi-restraints excluded: chain B residue 424 SER 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 D residue 176 THR Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 424 SER Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 360 THR Chi-restraints excluded: chain F residue 384 VAL 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 384 VAL 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: 5.9990 chunk 16 optimal weight: 7.9990 chunk 139 optimal weight: 0.8980 chunk 38 optimal weight: 100.0000 chunk 166 optimal weight: 0.0970 chunk 17 optimal weight: 0.8980 chunk 165 optimal weight: 5.9990 chunk 197 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 chunk 101 optimal weight: 0.0980 chunk 224 optimal weight: 1.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 ASN C 278 GLN E 427 GLN G 278 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.069307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.045098 restraints weight = 82791.968| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 3.88 r_work: 0.2671 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 22043 Z= 0.107 Angle : 0.619 11.391 29820 Z= 0.293 Chirality : 0.041 0.195 3304 Planarity : 0.004 0.051 3752 Dihedral : 10.231 114.500 3066 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.23 % Allowed : 22.65 % Favored : 75.12 % 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 aren not related in a simple way. whole: 1.79 (0.17), residues: 2653 helix: 2.64 (0.16), residues: 1127 sheet: -0.12 (0.21), residues: 623 loop : 0.39 (0.22), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 112 TYR 0.014 0.001 TYR A 80 PHE 0.032 0.001 PHE D 99 TRP 0.014 0.001 TRP B 251 HIS 0.006 0.001 HIS F 182 Details of bonding type rmsd covalent geometry : bond 0.00242 (22043) covalent geometry : angle 0.61933 (29820) hydrogen bonds : bond 0.02839 ( 1160) hydrogen bonds : angle 4.05727 ( 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 250 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 198 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 MET cc_start: 0.9206 (ppp) cc_final: 0.8964 (ppp) REVERT: A 178 TYR cc_start: 0.6778 (t80) cc_final: 0.6497 (t80) REVERT: A 214 ARG cc_start: 0.9490 (ptm-80) cc_final: 0.9240 (ptt90) REVERT: A 427 GLN cc_start: 0.9540 (mt0) cc_final: 0.9292 (mt0) REVERT: A 445 MET cc_start: 0.9345 (mtm) cc_final: 0.9056 (mtm) REVERT: B 103 MET cc_start: 0.9235 (ppp) cc_final: 0.8961 (ppp) REVERT: B 178 TYR cc_start: 0.6619 (t80) cc_final: 0.6315 (t80) REVERT: B 182 HIS cc_start: 0.8176 (p-80) cc_final: 0.7940 (p-80) REVERT: C 103 MET cc_start: 0.9232 (ppp) cc_final: 0.8986 (ppp) REVERT: C 178 TYR cc_start: 0.6742 (t80) cc_final: 0.6417 (t80) REVERT: C 427 GLN cc_start: 0.9587 (mt0) cc_final: 0.9364 (mt0) REVERT: C 445 MET cc_start: 0.9403 (mmp) cc_final: 0.9131 (mtm) REVERT: D 178 TYR cc_start: 0.6687 (t80) cc_final: 0.6424 (t80) REVERT: D 427 GLN cc_start: 0.9591 (mt0) cc_final: 0.9263 (mt0) REVERT: E 103 MET cc_start: 0.9230 (ppp) cc_final: 0.8951 (ppp) REVERT: E 108 GLN cc_start: 0.9097 (mp10) cc_final: 0.8820 (mp10) REVERT: E 178 TYR cc_start: 0.6729 (t80) cc_final: 0.6206 (t80) REVERT: E 182 HIS cc_start: 0.8480 (p-80) cc_final: 0.8252 (p-80) REVERT: F 178 TYR cc_start: 0.6794 (t80) cc_final: 0.6533 (t80) REVERT: F 183 LEU cc_start: 0.9354 (mm) cc_final: 0.9054 (mm) REVERT: F 427 GLN cc_start: 0.9589 (mt0) cc_final: 0.9296 (mt0) REVERT: F 445 MET cc_start: 0.9350 (mtm) cc_final: 0.9093 (mtp) REVERT: G 103 MET cc_start: 0.9360 (tmm) cc_final: 0.9119 (ppp) REVERT: G 178 TYR cc_start: 0.6564 (t80) cc_final: 0.6291 (t80) REVERT: G 445 MET cc_start: 0.9411 (mmp) cc_final: 0.9070 (mtm) outliers start: 52 outliers final: 33 residues processed: 236 average time/residue: 0.6436 time to fit residues: 173.6629 Evaluate side-chains 226 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 193 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 TYR 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 360 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain B residue 80 TYR 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 384 VAL Chi-restraints excluded: chain B residue 397 MET Chi-restraints excluded: chain C residue 80 TYR Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 108 GLN Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain D residue 80 TYR 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 299 THR Chi-restraints excluded: chain F residue 80 TYR 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 321 ILE Chi-restraints excluded: chain F residue 360 THR Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 384 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 206 optimal weight: 0.7980 chunk 220 optimal weight: 0.9980 chunk 214 optimal weight: 0.8980 chunk 0 optimal weight: 90.0000 chunk 216 optimal weight: 7.9990 chunk 174 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 134 optimal weight: 0.0070 chunk 93 optimal weight: 0.9980 chunk 75 optimal weight: 0.3980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 278 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.069483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.045256 restraints weight = 82896.637| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 3.87 r_work: 0.2678 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 22043 Z= 0.106 Angle : 0.631 12.137 29820 Z= 0.295 Chirality : 0.041 0.185 3304 Planarity : 0.004 0.047 3752 Dihedral : 10.121 113.479 3066 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.67 % Allowed : 23.21 % Favored : 75.12 % 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 aren not related in a simple way. whole: 1.93 (0.17), residues: 2653 helix: 2.75 (0.16), residues: 1127 sheet: -0.01 (0.21), residues: 623 loop : 0.44 (0.23), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 214 TYR 0.013 0.001 TYR A 80 PHE 0.026 0.001 PHE A 99 TRP 0.013 0.001 TRP B 251 HIS 0.005 0.000 HIS F 106 Details of bonding type rmsd covalent geometry : bond 0.00248 (22043) covalent geometry : angle 0.63090 (29820) hydrogen bonds : bond 0.02753 ( 1160) hydrogen bonds : angle 4.01091 ( 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 236 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 197 time to evaluate : 0.886 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 178 TYR cc_start: 0.6708 (t80) cc_final: 0.6482 (t80) REVERT: A 183 LEU cc_start: 0.9388 (mm) cc_final: 0.8978 (mm) REVERT: A 427 GLN cc_start: 0.9551 (mt0) cc_final: 0.9213 (mt0) REVERT: A 445 MET cc_start: 0.9320 (mtm) cc_final: 0.9052 (mtm) REVERT: B 103 MET cc_start: 0.9239 (ppp) cc_final: 0.9025 (ppp) REVERT: B 178 TYR cc_start: 0.6589 (t80) cc_final: 0.6311 (t80) REVERT: C 59 MET cc_start: 0.9639 (mpt) cc_final: 0.9187 (tpp) REVERT: C 178 TYR cc_start: 0.6681 (t80) cc_final: 0.6392 (t80) REVERT: C 427 GLN cc_start: 0.9595 (mt0) cc_final: 0.9379 (mt0) REVERT: C 445 MET cc_start: 0.9403 (mmp) cc_final: 0.9167 (mtm) REVERT: D 178 TYR cc_start: 0.6657 (t80) cc_final: 0.6425 (t80) REVERT: D 427 GLN cc_start: 0.9595 (mt0) cc_final: 0.9282 (mt0) REVERT: E 108 GLN cc_start: 0.9080 (mp10) cc_final: 0.8790 (mp10) REVERT: E 178 TYR cc_start: 0.6692 (t80) cc_final: 0.6128 (t80) REVERT: E 182 HIS cc_start: 0.8413 (p-80) cc_final: 0.8193 (p-80) REVERT: F 178 TYR cc_start: 0.6803 (t80) cc_final: 0.6544 (t80) REVERT: F 427 GLN cc_start: 0.9590 (mt0) cc_final: 0.9310 (mt0) REVERT: F 445 MET cc_start: 0.9355 (mtm) cc_final: 0.9085 (mtp) REVERT: G 178 TYR cc_start: 0.6569 (t80) cc_final: 0.6324 (t80) REVERT: G 182 HIS cc_start: 0.8435 (p-80) cc_final: 0.8163 (p-80) REVERT: G 445 MET cc_start: 0.9395 (mmp) cc_final: 0.9073 (mtm) outliers start: 39 outliers final: 31 residues processed: 226 average time/residue: 0.6359 time to fit residues: 164.7573 Evaluate side-chains 223 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 192 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 TYR 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 384 VAL Chi-restraints excluded: chain B residue 80 TYR 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 384 VAL Chi-restraints excluded: chain B residue 397 MET Chi-restraints excluded: chain C residue 80 TYR Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 110 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 87 LEU Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 424 SER Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 321 ILE Chi-restraints excluded: chain F residue 360 THR Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 384 VAL 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: 5.9990 chunk 11 optimal weight: 20.0000 chunk 252 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 48 optimal weight: 20.0000 chunk 139 optimal weight: 1.9990 chunk 134 optimal weight: 6.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 427 GLN ** 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 = 0.3536 r_free = 0.3536 target = 0.068726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.044277 restraints weight = 82998.064| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 3.90 r_work: 0.2647 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22043 Z= 0.141 Angle : 0.643 12.339 29820 Z= 0.299 Chirality : 0.041 0.167 3304 Planarity : 0.004 0.055 3752 Dihedral : 10.174 114.793 3066 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.46 % Allowed : 23.51 % 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 aren not related in a simple way. whole: 1.96 (0.18), residues: 2653 helix: 2.81 (0.16), residues: 1127 sheet: -0.05 (0.21), residues: 623 loop : 0.44 (0.23), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 214 TYR 0.012 0.001 TYR A 80 PHE 0.038 0.001 PHE D 99 TRP 0.014 0.001 TRP G 213 HIS 0.004 0.001 HIS C 182 Details of bonding type rmsd covalent geometry : bond 0.00333 (22043) covalent geometry : angle 0.64280 (29820) hydrogen bonds : bond 0.02831 ( 1160) hydrogen bonds : angle 4.01127 ( 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 233 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 199 time to evaluate : 1.015 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 103 MET cc_start: 0.9195 (ppp) cc_final: 0.8981 (ppp) REVERT: A 178 TYR cc_start: 0.6698 (t80) cc_final: 0.6498 (t80) REVERT: A 183 LEU cc_start: 0.9408 (mm) cc_final: 0.9006 (mm) REVERT: A 427 GLN cc_start: 0.9554 (mt0) cc_final: 0.9207 (mt0) REVERT: A 445 MET cc_start: 0.9323 (mtm) cc_final: 0.9057 (mtm) REVERT: B 103 MET cc_start: 0.9250 (ppp) cc_final: 0.8983 (ppp) REVERT: B 178 TYR cc_start: 0.6696 (t80) cc_final: 0.6410 (t80) REVERT: B 182 HIS cc_start: 0.8294 (p-80) cc_final: 0.8020 (p-80) REVERT: C 59 MET cc_start: 0.9610 (mpt) cc_final: 0.9168 (tmm) REVERT: C 178 TYR cc_start: 0.6696 (t80) cc_final: 0.6417 (t80) REVERT: C 427 GLN cc_start: 0.9591 (mt0) cc_final: 0.9260 (mt0) REVERT: C 445 MET cc_start: 0.9404 (mmp) cc_final: 0.9181 (mtm) REVERT: D 178 TYR cc_start: 0.6658 (t80) cc_final: 0.6418 (t80) REVERT: D 427 GLN cc_start: 0.9596 (mt0) cc_final: 0.9269 (mt0) REVERT: E 103 MET cc_start: 0.9207 (ppp) cc_final: 0.8986 (ppp) REVERT: E 178 TYR cc_start: 0.6663 (t80) cc_final: 0.6312 (t80) REVERT: F 178 TYR cc_start: 0.6833 (t80) cc_final: 0.6578 (t80) REVERT: F 427 GLN cc_start: 0.9593 (mt0) cc_final: 0.9290 (mt0) REVERT: F 445 MET cc_start: 0.9389 (mtm) cc_final: 0.9113 (mtp) REVERT: G 178 TYR cc_start: 0.6696 (t80) cc_final: 0.6406 (t80) REVERT: G 182 HIS cc_start: 0.8430 (p-80) cc_final: 0.8225 (p-80) REVERT: G 445 MET cc_start: 0.9429 (mmp) cc_final: 0.9129 (mtm) outliers start: 34 outliers final: 30 residues processed: 220 average time/residue: 0.6498 time to fit residues: 163.5955 Evaluate side-chains 226 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 196 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 TYR 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 384 VAL Chi-restraints excluded: chain B residue 80 TYR 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 384 VAL Chi-restraints excluded: chain B residue 397 MET Chi-restraints excluded: chain C residue 80 TYR Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 110 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 87 LEU Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 424 SER Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 321 ILE Chi-restraints excluded: chain F residue 360 THR Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 384 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 169 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 19 optimal weight: 0.0470 chunk 90 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 chunk 246 optimal weight: 2.9990 chunk 228 optimal weight: 0.9990 chunk 235 optimal weight: 30.0000 chunk 30 optimal weight: 0.6980 chunk 154 optimal weight: 9.9990 chunk 175 optimal weight: 1.9990 overall best weight: 0.9484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 427 GLN ** 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 = 0.3548 r_free = 0.3548 target = 0.069261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.044922 restraints weight = 82639.148| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 3.94 r_work: 0.2670 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22043 Z= 0.110 Angle : 0.644 11.971 29820 Z= 0.298 Chirality : 0.041 0.182 3304 Planarity : 0.004 0.053 3752 Dihedral : 10.140 113.553 3066 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.59 % Allowed : 23.42 % Favored : 74.99 % 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 aren not related in a simple way. whole: 1.98 (0.18), residues: 2653 helix: 2.77 (0.16), residues: 1127 sheet: 0.06 (0.21), residues: 623 loop : 0.45 (0.23), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 112 TYR 0.012 0.001 TYR A 80 PHE 0.028 0.001 PHE A 99 TRP 0.013 0.001 TRP B 251 HIS 0.004 0.001 HIS C 106 Details of bonding type rmsd covalent geometry : bond 0.00258 (22043) covalent geometry : angle 0.64357 (29820) hydrogen bonds : bond 0.02719 ( 1160) hydrogen bonds : angle 3.95322 ( 3228) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8836.50 seconds wall clock time: 151 minutes 30.98 seconds (9090.98 seconds total)