Starting phenix.real_space_refine on Fri Feb 6 20:11:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ry6_19588/02_2026/8ry6_19588.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ry6_19588/02_2026/8ry6_19588.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ry6_19588/02_2026/8ry6_19588.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ry6_19588/02_2026/8ry6_19588.map" model { file = "/net/cci-nas-00/data/ceres_data/8ry6_19588/02_2026/8ry6_19588.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ry6_19588/02_2026/8ry6_19588.cif" } resolution = 3.22 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= 0.002 sd= 0.017 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: 4 Type Number sf(0) Gaussians S 112 5.16 5 C 17008 2.51 5 N 4920 2.21 5 O 5272 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27312 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3414 Classifications: {'peptide': 469} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 446} Restraints were copied for chains: B, C, D, E, F, G, H Time building chain proxies: 3.11, per 1000 atoms: 0.11 Number of scatterers: 27312 At special positions: 0 Unit cell: (129.684, 129.684, 128.374, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 112 16.00 O 5272 8.00 N 4920 7.00 C 17008 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: 2.41 Conformation dependent library (CDL) restraints added in 1.2 seconds 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6720 Finding SS restraints... Secondary structure from input PDB file: 160 helices and 40 sheets defined 42.9% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 15 through 17 No H-bonds generated for 'chain 'A' and resid 15 through 17' Processing helix chain 'A' and resid 30 through 34 Processing helix chain 'A' and resid 58 through 68 removed outlier: 3.553A pdb=" N ALA A 62 " --> pdb=" O GLY A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 92 Processing helix chain 'A' and resid 108 through 117 Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 166 through 174 Processing helix chain 'A' and resid 196 through 204 removed outlier: 3.778A pdb=" N GLY A 204 " --> pdb=" O ALA A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 239 Processing helix chain 'A' and resid 252 through 266 removed outlier: 3.687A pdb=" N LEU A 265 " --> pdb=" O ALA A 261 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASP A 266 " --> pdb=" O VAL A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 288 Processing helix chain 'A' and resid 303 through 309 Processing helix chain 'A' and resid 314 through 330 Processing helix chain 'A' and resid 341 through 352 removed outlier: 3.688A pdb=" N VAL A 345 " --> pdb=" O HIS A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 364 removed outlier: 3.832A pdb=" N GLY A 364 " --> pdb=" O TRP A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 397 Processing helix chain 'A' and resid 401 through 411 removed outlier: 4.352A pdb=" N PHE A 411 " --> pdb=" O ARG A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 448 removed outlier: 4.203A pdb=" N HIS A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 458 Processing helix chain 'A' and resid 465 through 470 removed outlier: 3.968A pdb=" N GLY A 468 " --> pdb=" O SER A 465 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA A 470 " --> pdb=" O ALA A 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 17 No H-bonds generated for 'chain 'B' and resid 15 through 17' Processing helix chain 'B' and resid 30 through 34 Processing helix chain 'B' and resid 58 through 68 removed outlier: 3.553A pdb=" N ALA B 62 " --> pdb=" O GLY B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 92 Processing helix chain 'B' and resid 108 through 117 Processing helix chain 'B' and resid 149 through 153 Processing helix chain 'B' and resid 166 through 174 Processing helix chain 'B' and resid 196 through 204 removed outlier: 3.779A pdb=" N GLY B 204 " --> pdb=" O ALA B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 239 Processing helix chain 'B' and resid 252 through 266 removed outlier: 3.687A pdb=" N LEU B 265 " --> pdb=" O ALA B 261 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP B 266 " --> pdb=" O VAL B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 288 Processing helix chain 'B' and resid 303 through 309 Processing helix chain 'B' and resid 314 through 330 Processing helix chain 'B' and resid 341 through 352 removed outlier: 3.688A pdb=" N VAL B 345 " --> pdb=" O HIS B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 364 removed outlier: 3.832A pdb=" N GLY B 364 " --> pdb=" O TRP B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 397 Processing helix chain 'B' and resid 401 through 411 removed outlier: 4.352A pdb=" N PHE B 411 " --> pdb=" O ARG B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 448 removed outlier: 4.203A pdb=" N HIS B 435 " --> pdb=" O ASP B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 458 Processing helix chain 'B' and resid 465 through 470 removed outlier: 3.968A pdb=" N GLY B 468 " --> pdb=" O SER B 465 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA B 470 " --> pdb=" O ALA B 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 17 No H-bonds generated for 'chain 'C' and resid 15 through 17' Processing helix chain 'C' and resid 30 through 34 Processing helix chain 'C' and resid 58 through 68 removed outlier: 3.554A pdb=" N ALA C 62 " --> pdb=" O GLY C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 92 Processing helix chain 'C' and resid 108 through 117 Processing helix chain 'C' and resid 149 through 153 Processing helix chain 'C' and resid 166 through 174 Processing helix chain 'C' and resid 196 through 204 removed outlier: 3.778A pdb=" N GLY C 204 " --> pdb=" O ALA C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 239 Processing helix chain 'C' and resid 252 through 266 removed outlier: 3.688A pdb=" N LEU C 265 " --> pdb=" O ALA C 261 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASP C 266 " --> pdb=" O VAL C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 288 Processing helix chain 'C' and resid 303 through 309 Processing helix chain 'C' and resid 314 through 330 Processing helix chain 'C' and resid 341 through 352 removed outlier: 3.688A pdb=" N VAL C 345 " --> pdb=" O HIS C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 364 removed outlier: 3.831A pdb=" N GLY C 364 " --> pdb=" O TRP C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 397 Processing helix chain 'C' and resid 401 through 411 removed outlier: 4.352A pdb=" N PHE C 411 " --> pdb=" O ARG C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 448 removed outlier: 4.204A pdb=" N HIS C 435 " --> pdb=" O ASP C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 458 Processing helix chain 'C' and resid 465 through 470 removed outlier: 3.968A pdb=" N GLY C 468 " --> pdb=" O SER C 465 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA C 470 " --> pdb=" O ALA C 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 17 No H-bonds generated for 'chain 'D' and resid 15 through 17' Processing helix chain 'D' and resid 30 through 34 Processing helix chain 'D' and resid 58 through 68 removed outlier: 3.553A pdb=" N ALA D 62 " --> pdb=" O GLY D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 92 Processing helix chain 'D' and resid 108 through 117 Processing helix chain 'D' and resid 149 through 153 Processing helix chain 'D' and resid 166 through 174 Processing helix chain 'D' and resid 196 through 204 removed outlier: 3.778A pdb=" N GLY D 204 " --> pdb=" O ALA D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 239 Processing helix chain 'D' and resid 252 through 266 removed outlier: 3.688A pdb=" N LEU D 265 " --> pdb=" O ALA D 261 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP D 266 " --> pdb=" O VAL D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 288 Processing helix chain 'D' and resid 303 through 309 Processing helix chain 'D' and resid 314 through 330 Processing helix chain 'D' and resid 341 through 352 removed outlier: 3.687A pdb=" N VAL D 345 " --> pdb=" O HIS D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 364 removed outlier: 3.832A pdb=" N GLY D 364 " --> pdb=" O TRP D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 397 Processing helix chain 'D' and resid 401 through 411 removed outlier: 4.353A pdb=" N PHE D 411 " --> pdb=" O ARG D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 448 removed outlier: 4.204A pdb=" N HIS D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 458 Processing helix chain 'D' and resid 465 through 470 removed outlier: 3.968A pdb=" N GLY D 468 " --> pdb=" O SER D 465 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA D 470 " --> pdb=" O ALA D 467 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 17 No H-bonds generated for 'chain 'E' and resid 15 through 17' Processing helix chain 'E' and resid 30 through 34 Processing helix chain 'E' and resid 58 through 68 removed outlier: 3.553A pdb=" N ALA E 62 " --> pdb=" O GLY E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 92 Processing helix chain 'E' and resid 108 through 117 Processing helix chain 'E' and resid 149 through 153 Processing helix chain 'E' and resid 166 through 174 Processing helix chain 'E' and resid 196 through 204 removed outlier: 3.778A pdb=" N GLY E 204 " --> pdb=" O ALA E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 239 Processing helix chain 'E' and resid 252 through 266 removed outlier: 3.687A pdb=" N LEU E 265 " --> pdb=" O ALA E 261 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASP E 266 " --> pdb=" O VAL E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 288 Processing helix chain 'E' and resid 303 through 309 Processing helix chain 'E' and resid 314 through 330 Processing helix chain 'E' and resid 341 through 352 removed outlier: 3.688A pdb=" N VAL E 345 " --> pdb=" O HIS E 341 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 364 removed outlier: 3.831A pdb=" N GLY E 364 " --> pdb=" O TRP E 361 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 397 Processing helix chain 'E' and resid 401 through 411 removed outlier: 4.353A pdb=" N PHE E 411 " --> pdb=" O ARG E 407 " (cutoff:3.500A) Processing helix chain 'E' and resid 429 through 448 removed outlier: 4.203A pdb=" N HIS E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 451 through 458 Processing helix chain 'E' and resid 465 through 470 removed outlier: 3.968A pdb=" N GLY E 468 " --> pdb=" O SER E 465 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA E 470 " --> pdb=" O ALA E 467 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 17 No H-bonds generated for 'chain 'F' and resid 15 through 17' Processing helix chain 'F' and resid 30 through 34 Processing helix chain 'F' and resid 58 through 68 removed outlier: 3.554A pdb=" N ALA F 62 " --> pdb=" O GLY F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 92 Processing helix chain 'F' and resid 108 through 117 Processing helix chain 'F' and resid 149 through 153 Processing helix chain 'F' and resid 166 through 174 Processing helix chain 'F' and resid 196 through 204 removed outlier: 3.778A pdb=" N GLY F 204 " --> pdb=" O ALA F 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 239 Processing helix chain 'F' and resid 252 through 266 removed outlier: 3.687A pdb=" N LEU F 265 " --> pdb=" O ALA F 261 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASP F 266 " --> pdb=" O VAL F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 278 through 288 Processing helix chain 'F' and resid 303 through 309 Processing helix chain 'F' and resid 314 through 330 Processing helix chain 'F' and resid 341 through 352 removed outlier: 3.688A pdb=" N VAL F 345 " --> pdb=" O HIS F 341 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 364 removed outlier: 3.832A pdb=" N GLY F 364 " --> pdb=" O TRP F 361 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 397 Processing helix chain 'F' and resid 401 through 411 removed outlier: 4.352A pdb=" N PHE F 411 " --> pdb=" O ARG F 407 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 448 removed outlier: 4.204A pdb=" N HIS F 435 " --> pdb=" O ASP F 431 " (cutoff:3.500A) Processing helix chain 'F' and resid 451 through 458 Processing helix chain 'F' and resid 465 through 470 removed outlier: 3.968A pdb=" N GLY F 468 " --> pdb=" O SER F 465 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA F 470 " --> pdb=" O ALA F 467 " (cutoff:3.500A) Processing helix chain 'G' and resid 15 through 17 No H-bonds generated for 'chain 'G' and resid 15 through 17' Processing helix chain 'G' and resid 30 through 34 Processing helix chain 'G' and resid 58 through 68 removed outlier: 3.553A pdb=" N ALA G 62 " --> pdb=" O GLY G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 92 Processing helix chain 'G' and resid 108 through 117 Processing helix chain 'G' and resid 149 through 153 Processing helix chain 'G' and resid 166 through 174 Processing helix chain 'G' and resid 196 through 204 removed outlier: 3.779A pdb=" N GLY G 204 " --> pdb=" O ALA G 200 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 239 Processing helix chain 'G' and resid 252 through 266 removed outlier: 3.687A pdb=" N LEU G 265 " --> pdb=" O ALA G 261 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASP G 266 " --> pdb=" O VAL G 262 " (cutoff:3.500A) Processing helix chain 'G' and resid 278 through 288 Processing helix chain 'G' and resid 303 through 309 Processing helix chain 'G' and resid 314 through 330 Processing helix chain 'G' and resid 341 through 352 removed outlier: 3.688A pdb=" N VAL G 345 " --> pdb=" O HIS G 341 " (cutoff:3.500A) Processing helix chain 'G' and resid 359 through 364 removed outlier: 3.832A pdb=" N GLY G 364 " --> pdb=" O TRP G 361 " (cutoff:3.500A) Processing helix chain 'G' and resid 389 through 397 Processing helix chain 'G' and resid 401 through 411 removed outlier: 4.353A pdb=" N PHE G 411 " --> pdb=" O ARG G 407 " (cutoff:3.500A) Processing helix chain 'G' and resid 429 through 448 removed outlier: 4.203A pdb=" N HIS G 435 " --> pdb=" O ASP G 431 " (cutoff:3.500A) Processing helix chain 'G' and resid 451 through 458 Processing helix chain 'G' and resid 465 through 470 removed outlier: 3.968A pdb=" N GLY G 468 " --> pdb=" O SER G 465 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA G 470 " --> pdb=" O ALA G 467 " (cutoff:3.500A) Processing helix chain 'H' and resid 15 through 17 No H-bonds generated for 'chain 'H' and resid 15 through 17' Processing helix chain 'H' and resid 30 through 34 Processing helix chain 'H' and resid 58 through 68 removed outlier: 3.553A pdb=" N ALA H 62 " --> pdb=" O GLY H 58 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 92 Processing helix chain 'H' and resid 108 through 117 Processing helix chain 'H' and resid 149 through 153 Processing helix chain 'H' and resid 166 through 174 Processing helix chain 'H' and resid 196 through 204 removed outlier: 3.779A pdb=" N GLY H 204 " --> pdb=" O ALA H 200 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 239 Processing helix chain 'H' and resid 252 through 266 removed outlier: 3.686A pdb=" N LEU H 265 " --> pdb=" O ALA H 261 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASP H 266 " --> pdb=" O VAL H 262 " (cutoff:3.500A) Processing helix chain 'H' and resid 278 through 288 Processing helix chain 'H' and resid 303 through 309 Processing helix chain 'H' and resid 314 through 330 Processing helix chain 'H' and resid 341 through 352 removed outlier: 3.688A pdb=" N VAL H 345 " --> pdb=" O HIS H 341 " (cutoff:3.500A) Processing helix chain 'H' and resid 359 through 364 removed outlier: 3.832A pdb=" N GLY H 364 " --> pdb=" O TRP H 361 " (cutoff:3.500A) Processing helix chain 'H' and resid 389 through 397 Processing helix chain 'H' and resid 401 through 411 removed outlier: 4.352A pdb=" N PHE H 411 " --> pdb=" O ARG H 407 " (cutoff:3.500A) Processing helix chain 'H' and resid 429 through 448 removed outlier: 4.204A pdb=" N HIS H 435 " --> pdb=" O ASP H 431 " (cutoff:3.500A) Processing helix chain 'H' and resid 451 through 458 Processing helix chain 'H' and resid 465 through 470 removed outlier: 3.968A pdb=" N GLY H 468 " --> pdb=" O SER H 465 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA H 470 " --> pdb=" O ALA H 467 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 4 removed outlier: 6.515A pdb=" N ARG A 3 " --> pdb=" O LEU A 461 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N VAL A 463 " --> pdb=" O ARG A 3 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 50 removed outlier: 6.054A pdb=" N VAL A 72 " --> pdb=" O ALA A 219 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N ALA A 221 " --> pdb=" O VAL A 72 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LEU A 74 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP A 246 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LEU A 271 " --> pdb=" O ILE A 292 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N LYS A 294 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA A 273 " --> pdb=" O LYS A 294 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL A 293 " --> pdb=" O TRP A 334 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL A 333 " --> pdb=" O ASN A 355 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N MET A 357 " --> pdb=" O VAL A 333 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ALA A 335 " --> pdb=" O MET A 357 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL A 49 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 102 through 103 removed outlier: 4.348A pdb=" N GLY A 134 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N PHE A 128 " --> pdb=" O PRO A 132 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 161 through 162 removed outlier: 6.392A pdb=" N ALA A 161 " --> pdb=" O THR A 185 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 373 through 374 Processing sheet with id=AA6, first strand: chain 'B' and resid 3 through 4 removed outlier: 6.516A pdb=" N ARG B 3 " --> pdb=" O LEU B 461 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N VAL B 463 " --> pdb=" O ARG B 3 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 49 through 50 removed outlier: 6.054A pdb=" N VAL B 72 " --> pdb=" O ALA B 219 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ALA B 221 " --> pdb=" O VAL B 72 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LEU B 74 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP B 246 " --> pdb=" O VAL B 222 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LEU B 271 " --> pdb=" O ILE B 292 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N LYS B 294 " --> pdb=" O LEU B 271 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA B 273 " --> pdb=" O LYS B 294 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL B 293 " --> pdb=" O TRP B 334 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL B 333 " --> pdb=" O ASN B 355 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N MET B 357 " --> pdb=" O VAL B 333 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ALA B 335 " --> pdb=" O MET B 357 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL B 49 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 102 through 103 removed outlier: 4.348A pdb=" N GLY B 134 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N PHE B 128 " --> pdb=" O PRO B 132 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 161 through 162 removed outlier: 6.392A pdb=" N ALA B 161 " --> pdb=" O THR B 185 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 373 through 374 Processing sheet with id=AB2, first strand: chain 'C' and resid 3 through 4 removed outlier: 6.515A pdb=" N ARG C 3 " --> pdb=" O LEU C 461 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N VAL C 463 " --> pdb=" O ARG C 3 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 49 through 50 removed outlier: 6.053A pdb=" N VAL C 72 " --> pdb=" O ALA C 219 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N ALA C 221 " --> pdb=" O VAL C 72 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LEU C 74 " --> pdb=" O ALA C 221 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP C 246 " --> pdb=" O VAL C 222 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LEU C 271 " --> pdb=" O ILE C 292 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N LYS C 294 " --> pdb=" O LEU C 271 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA C 273 " --> pdb=" O LYS C 294 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL C 293 " --> pdb=" O TRP C 334 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL C 333 " --> pdb=" O ASN C 355 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N MET C 357 " --> pdb=" O VAL C 333 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ALA C 335 " --> pdb=" O MET C 357 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL C 49 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 102 through 103 removed outlier: 4.348A pdb=" N GLY C 134 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N PHE C 128 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 161 through 162 removed outlier: 6.393A pdb=" N ALA C 161 " --> pdb=" O THR C 185 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 373 through 374 Processing sheet with id=AB7, first strand: chain 'D' and resid 3 through 4 removed outlier: 6.515A pdb=" N ARG D 3 " --> pdb=" O LEU D 461 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N VAL D 463 " --> pdb=" O ARG D 3 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 49 through 50 removed outlier: 6.053A pdb=" N VAL D 72 " --> pdb=" O ALA D 219 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N ALA D 221 " --> pdb=" O VAL D 72 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LEU D 74 " --> pdb=" O ALA D 221 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP D 246 " --> pdb=" O VAL D 222 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LEU D 271 " --> pdb=" O ILE D 292 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N LYS D 294 " --> pdb=" O LEU D 271 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA D 273 " --> pdb=" O LYS D 294 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL D 293 " --> pdb=" O TRP D 334 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL D 333 " --> pdb=" O ASN D 355 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N MET D 357 " --> pdb=" O VAL D 333 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ALA D 335 " --> pdb=" O MET D 357 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N VAL D 49 " --> pdb=" O ILE D 358 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 102 through 103 removed outlier: 4.349A pdb=" N GLY D 134 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N PHE D 128 " --> pdb=" O PRO D 132 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 161 through 162 removed outlier: 6.392A pdb=" N ALA D 161 " --> pdb=" O THR D 185 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 373 through 374 Processing sheet with id=AC3, first strand: chain 'E' and resid 3 through 4 removed outlier: 6.515A pdb=" N ARG E 3 " --> pdb=" O LEU E 461 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N VAL E 463 " --> pdb=" O ARG E 3 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 49 through 50 removed outlier: 6.054A pdb=" N VAL E 72 " --> pdb=" O ALA E 219 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N ALA E 221 " --> pdb=" O VAL E 72 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LEU E 74 " --> pdb=" O ALA E 221 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP E 246 " --> pdb=" O VAL E 222 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LEU E 271 " --> pdb=" O ILE E 292 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N LYS E 294 " --> pdb=" O LEU E 271 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA E 273 " --> pdb=" O LYS E 294 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL E 293 " --> pdb=" O TRP E 334 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL E 333 " --> pdb=" O ASN E 355 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N MET E 357 " --> pdb=" O VAL E 333 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ALA E 335 " --> pdb=" O MET E 357 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL E 49 " --> pdb=" O ILE E 358 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 102 through 103 removed outlier: 4.348A pdb=" N GLY E 134 " --> pdb=" O VAL E 126 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N PHE E 128 " --> pdb=" O PRO E 132 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 161 through 162 removed outlier: 6.393A pdb=" N ALA E 161 " --> pdb=" O THR E 185 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'E' and resid 373 through 374 Processing sheet with id=AC8, first strand: chain 'F' and resid 3 through 4 removed outlier: 6.514A pdb=" N ARG F 3 " --> pdb=" O LEU F 461 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N VAL F 463 " --> pdb=" O ARG F 3 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 49 through 50 removed outlier: 6.053A pdb=" N VAL F 72 " --> pdb=" O ALA F 219 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ALA F 221 " --> pdb=" O VAL F 72 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LEU F 74 " --> pdb=" O ALA F 221 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP F 246 " --> pdb=" O VAL F 222 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N LEU F 271 " --> pdb=" O ILE F 292 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N LYS F 294 " --> pdb=" O LEU F 271 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ALA F 273 " --> pdb=" O LYS F 294 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL F 293 " --> pdb=" O TRP F 334 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL F 333 " --> pdb=" O ASN F 355 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N MET F 357 " --> pdb=" O VAL F 333 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ALA F 335 " --> pdb=" O MET F 357 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL F 49 " --> pdb=" O ILE F 358 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 102 through 103 removed outlier: 4.348A pdb=" N GLY F 134 " --> pdb=" O VAL F 126 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N PHE F 128 " --> pdb=" O PRO F 132 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 161 through 162 removed outlier: 6.392A pdb=" N ALA F 161 " --> pdb=" O THR F 185 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'F' and resid 373 through 374 Processing sheet with id=AD4, first strand: chain 'G' and resid 3 through 4 removed outlier: 6.514A pdb=" N ARG G 3 " --> pdb=" O LEU G 461 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N VAL G 463 " --> pdb=" O ARG G 3 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 49 through 50 removed outlier: 6.054A pdb=" N VAL G 72 " --> pdb=" O ALA G 219 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N ALA G 221 " --> pdb=" O VAL G 72 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LEU G 74 " --> pdb=" O ALA G 221 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP G 246 " --> pdb=" O VAL G 222 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LEU G 271 " --> pdb=" O ILE G 292 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N LYS G 294 " --> pdb=" O LEU G 271 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ALA G 273 " --> pdb=" O LYS G 294 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL G 293 " --> pdb=" O TRP G 334 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL G 333 " --> pdb=" O ASN G 355 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N MET G 357 " --> pdb=" O VAL G 333 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ALA G 335 " --> pdb=" O MET G 357 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N VAL G 49 " --> pdb=" O ILE G 358 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 102 through 103 removed outlier: 4.348A pdb=" N GLY G 134 " --> pdb=" O VAL G 126 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N PHE G 128 " --> pdb=" O PRO G 132 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 161 through 162 removed outlier: 6.392A pdb=" N ALA G 161 " --> pdb=" O THR G 185 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'G' and resid 373 through 374 Processing sheet with id=AD9, first strand: chain 'H' and resid 3 through 4 removed outlier: 6.514A pdb=" N ARG H 3 " --> pdb=" O LEU H 461 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N VAL H 463 " --> pdb=" O ARG H 3 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 49 through 50 removed outlier: 6.054A pdb=" N VAL H 72 " --> pdb=" O ALA H 219 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N ALA H 221 " --> pdb=" O VAL H 72 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LEU H 74 " --> pdb=" O ALA H 221 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP H 246 " --> pdb=" O VAL H 222 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LEU H 271 " --> pdb=" O ILE H 292 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N LYS H 294 " --> pdb=" O LEU H 271 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ALA H 273 " --> pdb=" O LYS H 294 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL H 293 " --> pdb=" O TRP H 334 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL H 333 " --> pdb=" O ASN H 355 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N MET H 357 " --> pdb=" O VAL H 333 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ALA H 335 " --> pdb=" O MET H 357 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL H 49 " --> pdb=" O ILE H 358 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 102 through 103 removed outlier: 4.348A pdb=" N GLY H 134 " --> pdb=" O VAL H 126 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N PHE H 128 " --> pdb=" O PRO H 132 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 161 through 162 removed outlier: 6.393A pdb=" N ALA H 161 " --> pdb=" O THR H 185 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'H' and resid 373 through 374 1096 hydrogen bonds defined for protein. 3072 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: 6.07 Time building geometry restraints manager: 3.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9554 1.34 - 1.46: 4201 1.46 - 1.57: 13805 1.57 - 1.69: 0 1.69 - 1.81: 192 Bond restraints: 27752 Sorted by residual: bond pdb=" N ASP G 18 " pdb=" CA ASP G 18 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.26e-02 6.30e+03 7.41e+00 bond pdb=" N ASP C 18 " pdb=" CA ASP C 18 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.26e-02 6.30e+03 7.39e+00 bond pdb=" N ASP B 18 " pdb=" CA ASP B 18 " ideal model delta sigma weight residual 1.456 1.489 -0.034 1.26e-02 6.30e+03 7.22e+00 bond pdb=" N ASP D 18 " pdb=" CA ASP D 18 " ideal model delta sigma weight residual 1.456 1.489 -0.034 1.26e-02 6.30e+03 7.21e+00 bond pdb=" N ASP E 18 " pdb=" CA ASP E 18 " ideal model delta sigma weight residual 1.456 1.489 -0.034 1.26e-02 6.30e+03 7.18e+00 ... (remaining 27747 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 37149 1.64 - 3.28: 515 3.28 - 4.93: 104 4.93 - 6.57: 0 6.57 - 8.21: 8 Bond angle restraints: 37776 Sorted by residual: angle pdb=" CA ASP F 378 " pdb=" CB ASP F 378 " pdb=" CG ASP F 378 " ideal model delta sigma weight residual 112.60 115.73 -3.13 1.00e+00 1.00e+00 9.81e+00 angle pdb=" CA ASP H 378 " pdb=" CB ASP H 378 " pdb=" CG ASP H 378 " ideal model delta sigma weight residual 112.60 115.73 -3.13 1.00e+00 1.00e+00 9.81e+00 angle pdb=" CA ASP C 378 " pdb=" CB ASP C 378 " pdb=" CG ASP C 378 " ideal model delta sigma weight residual 112.60 115.73 -3.13 1.00e+00 1.00e+00 9.81e+00 angle pdb=" CA ASP B 378 " pdb=" CB ASP B 378 " pdb=" CG ASP B 378 " ideal model delta sigma weight residual 112.60 115.72 -3.12 1.00e+00 1.00e+00 9.70e+00 angle pdb=" CA ASP A 378 " pdb=" CB ASP A 378 " pdb=" CG ASP A 378 " ideal model delta sigma weight residual 112.60 115.70 -3.10 1.00e+00 1.00e+00 9.62e+00 ... (remaining 37771 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.76: 15009 15.76 - 31.53: 1143 31.53 - 47.29: 368 47.29 - 63.05: 64 63.05 - 78.81: 8 Dihedral angle restraints: 16592 sinusoidal: 6072 harmonic: 10520 Sorted by residual: dihedral pdb=" CB ARG G 146 " pdb=" CG ARG G 146 " pdb=" CD ARG G 146 " pdb=" NE ARG G 146 " ideal model delta sinusoidal sigma weight residual 60.00 113.47 -53.47 3 1.50e+01 4.44e-03 9.21e+00 dihedral pdb=" CB ARG B 146 " pdb=" CG ARG B 146 " pdb=" CD ARG B 146 " pdb=" NE ARG B 146 " ideal model delta sinusoidal sigma weight residual 60.00 113.46 -53.46 3 1.50e+01 4.44e-03 9.21e+00 dihedral pdb=" CB ARG E 146 " pdb=" CG ARG E 146 " pdb=" CD ARG E 146 " pdb=" NE ARG E 146 " ideal model delta sinusoidal sigma weight residual 60.00 113.43 -53.43 3 1.50e+01 4.44e-03 9.20e+00 ... (remaining 16589 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 2560 0.026 - 0.052: 1075 0.052 - 0.078: 439 0.078 - 0.104: 268 0.104 - 0.130: 154 Chirality restraints: 4496 Sorted by residual: chirality pdb=" CA VAL H 297 " pdb=" N VAL H 297 " pdb=" C VAL H 297 " pdb=" CB VAL H 297 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.21e-01 chirality pdb=" CA VAL B 297 " pdb=" N VAL B 297 " pdb=" C VAL B 297 " pdb=" CB VAL B 297 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.20e-01 chirality pdb=" CA VAL E 297 " pdb=" N VAL E 297 " pdb=" C VAL E 297 " pdb=" CB VAL E 297 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.19e-01 ... (remaining 4493 not shown) Planarity restraints: 5000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 378 " 0.012 2.00e-02 2.50e+03 2.41e-02 5.79e+00 pdb=" C ASP C 378 " -0.042 2.00e-02 2.50e+03 pdb=" O ASP C 378 " 0.015 2.00e-02 2.50e+03 pdb=" N ARG C 379 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP G 378 " -0.012 2.00e-02 2.50e+03 2.40e-02 5.77e+00 pdb=" C ASP G 378 " 0.042 2.00e-02 2.50e+03 pdb=" O ASP G 378 " -0.015 2.00e-02 2.50e+03 pdb=" N ARG G 379 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 378 " -0.012 2.00e-02 2.50e+03 2.40e-02 5.75e+00 pdb=" C ASP A 378 " 0.041 2.00e-02 2.50e+03 pdb=" O ASP A 378 " -0.015 2.00e-02 2.50e+03 pdb=" N ARG A 379 " -0.014 2.00e-02 2.50e+03 ... (remaining 4997 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 6748 2.79 - 3.32: 25730 3.32 - 3.85: 44289 3.85 - 4.37: 53068 4.37 - 4.90: 90610 Nonbonded interactions: 220445 Sorted by model distance: nonbonded pdb=" O ALA F 394 " pdb=" OG1 THR F 397 " model vdw 2.263 3.040 nonbonded pdb=" O ALA C 394 " pdb=" OG1 THR C 397 " model vdw 2.264 3.040 nonbonded pdb=" O ALA A 394 " pdb=" OG1 THR A 397 " model vdw 2.264 3.040 nonbonded pdb=" O ALA B 394 " pdb=" OG1 THR B 397 " model vdw 2.264 3.040 nonbonded pdb=" O ALA D 394 " pdb=" OG1 THR D 397 " model vdw 2.264 3.040 ... (remaining 220440 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: 0.10 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' selection = chain 'H' } 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: 1.870 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: 0.030 Extract box with map and model: 0.450 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 23.180 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 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 : 0.003 0.039 27752 Z= 0.145 Angle : 0.504 8.211 37776 Z= 0.273 Chirality : 0.042 0.130 4496 Planarity : 0.004 0.027 5000 Dihedral : 12.684 78.815 9872 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.53 % Allowed : 14.00 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.14), residues: 3736 helix: 1.84 (0.14), residues: 1392 sheet: -0.23 (0.21), residues: 576 loop : 1.00 (0.15), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 426 TYR 0.006 0.001 TYR H 385 PHE 0.022 0.001 PHE E 89 TRP 0.002 0.000 TRP B 334 HIS 0.004 0.001 HIS C 435 Details of bonding type rmsd covalent geometry : bond 0.00285 (27752) covalent geometry : angle 0.50410 (37776) hydrogen bonds : bond 0.17634 ( 1096) hydrogen bonds : angle 5.27902 ( 3072) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 248 time to evaluate : 1.021 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: B 61 MET cc_start: 0.8447 (tpp) cc_final: 0.8239 (tpp) REVERT: B 396 ARG cc_start: 0.8313 (ttp-110) cc_final: 0.7387 (tpt170) REVERT: D 378 ASP cc_start: 0.8173 (t0) cc_final: 0.7922 (t0) REVERT: E 255 MET cc_start: 0.8494 (tpp) cc_final: 0.8264 (tpp) REVERT: F 390 LYS cc_start: 0.8097 (mmtt) cc_final: 0.7746 (mmtm) REVERT: G 146 ARG cc_start: 0.8272 (mtp-110) cc_final: 0.7730 (mtm180) REVERT: G 328 GLN cc_start: 0.8730 (tp40) cc_final: 0.8425 (tm-30) REVERT: G 396 ARG cc_start: 0.8078 (ttp-110) cc_final: 0.7736 (tpt-90) outliers start: 15 outliers final: 10 residues processed: 262 average time/residue: 0.2152 time to fit residues: 85.1136 Evaluate side-chains 181 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 171 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 418 SER Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain H residue 183 VAL Chi-restraints excluded: chain H residue 418 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.0970 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 0.0970 chunk 298 optimal weight: 10.0000 overall best weight: 1.1580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 HIS A 233 GLN C 233 GLN ** E 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 8 HIS H 176 HIS H 233 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.070847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.050935 restraints weight = 87033.868| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 3.62 r_work: 0.2758 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 27752 Z= 0.122 Angle : 0.480 6.548 37776 Z= 0.250 Chirality : 0.042 0.157 4496 Planarity : 0.004 0.041 5000 Dihedral : 3.710 29.712 4074 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.28 % Allowed : 14.67 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.14), residues: 3736 helix: 1.60 (0.14), residues: 1416 sheet: 0.02 (0.21), residues: 616 loop : 0.93 (0.16), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 379 TYR 0.014 0.001 TYR B 385 PHE 0.018 0.001 PHE D 128 TRP 0.004 0.001 TRP B 361 HIS 0.004 0.001 HIS G 435 Details of bonding type rmsd covalent geometry : bond 0.00269 (27752) covalent geometry : angle 0.48032 (37776) hydrogen bonds : bond 0.03477 ( 1096) hydrogen bonds : angle 4.04351 ( 3072) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 180 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.9172 (mtp) cc_final: 0.8940 (mtt) REVERT: A 61 MET cc_start: 0.8915 (tpp) cc_final: 0.7468 (tpp) REVERT: A 308 MET cc_start: 0.8979 (mmm) cc_final: 0.8662 (mmm) REVERT: B 376 ARG cc_start: 0.9233 (ttm170) cc_final: 0.8815 (ttp80) REVERT: B 396 ARG cc_start: 0.8700 (ttp-110) cc_final: 0.7611 (tpt170) REVERT: C 61 MET cc_start: 0.8725 (tpp) cc_final: 0.7550 (tpp) REVERT: C 184 MET cc_start: 0.8048 (OUTLIER) cc_final: 0.7616 (mmm) REVERT: C 308 MET cc_start: 0.8786 (mmm) cc_final: 0.8585 (mmm) REVERT: C 328 GLN cc_start: 0.8603 (tm-30) cc_final: 0.8402 (tm-30) REVERT: D 376 ARG cc_start: 0.9230 (ttm170) cc_final: 0.8950 (ttp-170) REVERT: E 61 MET cc_start: 0.8921 (tpp) cc_final: 0.7906 (tpp) REVERT: E 255 MET cc_start: 0.8820 (tpp) cc_final: 0.8346 (tpp) REVERT: E 376 ARG cc_start: 0.8525 (mmp-170) cc_final: 0.8316 (mmp-170) REVERT: E 377 ASP cc_start: 0.9047 (t0) cc_final: 0.8699 (t0) REVERT: F 61 MET cc_start: 0.8329 (tpp) cc_final: 0.7901 (tpp) REVERT: F 390 LYS cc_start: 0.8525 (mmtt) cc_final: 0.8204 (mmtm) REVERT: G 61 MET cc_start: 0.8568 (tpp) cc_final: 0.8218 (tpp) REVERT: G 328 GLN cc_start: 0.8947 (tp40) cc_final: 0.8469 (tm-30) REVERT: G 376 ARG cc_start: 0.8539 (mmp-170) cc_final: 0.8301 (mmp-170) REVERT: G 377 ASP cc_start: 0.9114 (t0) cc_final: 0.8646 (p0) REVERT: G 379 ARG cc_start: 0.9303 (ttm-80) cc_final: 0.8965 (mtp-110) REVERT: H 61 MET cc_start: 0.8249 (tpp) cc_final: 0.7928 (tpp) REVERT: H 118 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.7441 (ptpp) REVERT: H 373 LEU cc_start: 0.9292 (mt) cc_final: 0.9070 (mp) outliers start: 36 outliers final: 18 residues processed: 210 average time/residue: 0.2034 time to fit residues: 64.8612 Evaluate side-chains 181 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 161 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain C residue 302 MET Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 416 SER Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain H residue 118 LYS Chi-restraints excluded: chain H residue 141 CYS Chi-restraints excluded: chain H residue 183 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 252 optimal weight: 6.9990 chunk 320 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 240 optimal weight: 7.9990 chunk 343 optimal weight: 0.5980 chunk 105 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 chunk 199 optimal weight: 10.0000 chunk 358 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 217 optimal weight: 1.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 GLN C 233 GLN ** E 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 233 GLN H 332 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.066359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.046283 restraints weight = 88805.217| |-----------------------------------------------------------------------------| r_work (start): 0.2774 rms_B_bonded: 3.55 r_work: 0.2631 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 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 : 0.006 0.037 27752 Z= 0.255 Angle : 0.552 4.748 37776 Z= 0.291 Chirality : 0.044 0.145 4496 Planarity : 0.004 0.045 5000 Dihedral : 4.245 35.566 4072 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.56 % Allowed : 14.00 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.14), residues: 3736 helix: 1.11 (0.13), residues: 1456 sheet: -0.27 (0.21), residues: 584 loop : 0.65 (0.15), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 146 TYR 0.011 0.002 TYR B 385 PHE 0.014 0.001 PHE A 316 TRP 0.004 0.001 TRP A 361 HIS 0.004 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00581 (27752) covalent geometry : angle 0.55240 (37776) hydrogen bonds : bond 0.04287 ( 1096) hydrogen bonds : angle 4.39259 ( 3072) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 158 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.9051 (tpp) cc_final: 0.7670 (tpp) REVERT: A 255 MET cc_start: 0.9183 (tpp) cc_final: 0.8938 (tpp) REVERT: A 328 GLN cc_start: 0.8914 (tm-30) cc_final: 0.8684 (tm-30) REVERT: A 357 MET cc_start: 0.9411 (ttt) cc_final: 0.9187 (ttt) REVERT: A 391 ARG cc_start: 0.8809 (OUTLIER) cc_final: 0.8341 (ttp80) REVERT: B 61 MET cc_start: 0.8608 (tpp) cc_final: 0.8389 (tpp) REVERT: B 184 MET cc_start: 0.8627 (mtt) cc_final: 0.8248 (mmm) REVERT: B 396 ARG cc_start: 0.8536 (ttp-110) cc_final: 0.7340 (tpt170) REVERT: C 61 MET cc_start: 0.8843 (tpp) cc_final: 0.7668 (tpp) REVERT: C 184 MET cc_start: 0.8342 (OUTLIER) cc_final: 0.7827 (tpp) REVERT: C 255 MET cc_start: 0.9118 (tpp) cc_final: 0.8901 (tpp) REVERT: C 328 GLN cc_start: 0.8842 (tm-30) cc_final: 0.8435 (tm-30) REVERT: D 233 GLN cc_start: 0.9104 (tp40) cc_final: 0.8799 (mm110) REVERT: D 379 ARG cc_start: 0.9041 (mtm-85) cc_final: 0.8699 (mtm-85) REVERT: E 61 MET cc_start: 0.9001 (tpp) cc_final: 0.7882 (tpp) REVERT: E 118 LYS cc_start: 0.9064 (OUTLIER) cc_final: 0.8662 (mtmm) REVERT: E 377 ASP cc_start: 0.9086 (t0) cc_final: 0.8651 (t0) REVERT: F 61 MET cc_start: 0.8394 (tpp) cc_final: 0.7804 (tpp) REVERT: F 390 LYS cc_start: 0.8681 (mmtt) cc_final: 0.8287 (mmtt) REVERT: G 328 GLN cc_start: 0.8987 (tp40) cc_final: 0.8540 (tm-30) REVERT: G 376 ARG cc_start: 0.8525 (mmp-170) cc_final: 0.8318 (mmp-170) REVERT: G 377 ASP cc_start: 0.9151 (t0) cc_final: 0.8645 (p0) REVERT: G 379 ARG cc_start: 0.9334 (ttm-80) cc_final: 0.8657 (mtm110) REVERT: H 61 MET cc_start: 0.8320 (tpp) cc_final: 0.7916 (tpp) REVERT: H 176 HIS cc_start: 0.9085 (m-70) cc_final: 0.8665 (t-90) REVERT: H 328 GLN cc_start: 0.8539 (tm-30) cc_final: 0.8325 (tm-30) REVERT: H 373 LEU cc_start: 0.9263 (mt) cc_final: 0.9010 (mp) outliers start: 72 outliers final: 41 residues processed: 225 average time/residue: 0.2151 time to fit residues: 72.9914 Evaluate side-chains 189 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 145 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 391 ARG Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 117 HIS Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 141 CYS Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 302 MET Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 391 ARG Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain E residue 118 LYS Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 416 SER Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 144 VAL Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 291 SER Chi-restraints excluded: chain F residue 438 SER Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain H residue 118 LYS Chi-restraints excluded: chain H residue 183 VAL Chi-restraints excluded: chain H residue 291 SER Chi-restraints excluded: chain H residue 329 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 4 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 309 optimal weight: 1.9990 chunk 271 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 320 optimal weight: 4.9990 chunk 311 optimal weight: 0.6980 chunk 228 optimal weight: 3.9990 chunk 188 optimal weight: 4.9990 chunk 351 optimal weight: 0.1980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 176 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.067765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.047786 restraints weight = 87735.645| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 3.56 r_work: 0.2675 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 27752 Z= 0.127 Angle : 0.462 6.638 37776 Z= 0.240 Chirality : 0.042 0.145 4496 Planarity : 0.004 0.045 5000 Dihedral : 3.874 32.084 4070 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.92 % Allowed : 15.24 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.14), residues: 3736 helix: 1.52 (0.14), residues: 1408 sheet: -0.15 (0.21), residues: 616 loop : 0.72 (0.15), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 391 TYR 0.013 0.001 TYR E 385 PHE 0.018 0.001 PHE E 128 TRP 0.003 0.001 TRP G 361 HIS 0.004 0.001 HIS A 435 Details of bonding type rmsd covalent geometry : bond 0.00288 (27752) covalent geometry : angle 0.46218 (37776) hydrogen bonds : bond 0.03282 ( 1096) hydrogen bonds : angle 3.96256 ( 3072) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 154 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.8978 (tpp) cc_final: 0.7595 (tpp) REVERT: A 255 MET cc_start: 0.9118 (tpp) cc_final: 0.8905 (tpp) REVERT: A 328 GLN cc_start: 0.8941 (tm-30) cc_final: 0.8563 (tm-30) REVERT: A 391 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.8351 (ttp80) REVERT: B 131 ARG cc_start: 0.8578 (mtp85) cc_final: 0.8277 (mtp85) REVERT: B 147 PHE cc_start: 0.9215 (m-80) cc_final: 0.8973 (m-80) REVERT: B 357 MET cc_start: 0.9326 (ttm) cc_final: 0.9105 (ttp) REVERT: B 396 ARG cc_start: 0.8550 (ttp-110) cc_final: 0.7338 (tpt170) REVERT: C 61 MET cc_start: 0.8779 (tpp) cc_final: 0.7651 (tpp) REVERT: C 184 MET cc_start: 0.7974 (OUTLIER) cc_final: 0.7708 (tpp) REVERT: C 328 GLN cc_start: 0.8811 (tm-30) cc_final: 0.8385 (tm-30) REVERT: D 233 GLN cc_start: 0.9082 (tp40) cc_final: 0.8791 (tp40) REVERT: D 379 ARG cc_start: 0.9088 (mtm-85) cc_final: 0.8696 (mtm-85) REVERT: E 61 MET cc_start: 0.8894 (tpp) cc_final: 0.7824 (tpp) REVERT: E 118 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8498 (mtmm) REVERT: E 377 ASP cc_start: 0.9077 (t0) cc_final: 0.8589 (t0) REVERT: F 61 MET cc_start: 0.8261 (tpp) cc_final: 0.7597 (tpp) REVERT: F 227 ASP cc_start: 0.8707 (t0) cc_final: 0.8409 (t0) REVERT: F 328 GLN cc_start: 0.9366 (tp40) cc_final: 0.8969 (tm-30) REVERT: F 390 LYS cc_start: 0.8674 (mmtt) cc_final: 0.8351 (mmtm) REVERT: G 328 GLN cc_start: 0.8942 (tp40) cc_final: 0.8551 (tm-30) REVERT: G 377 ASP cc_start: 0.9226 (t0) cc_final: 0.8522 (p0) REVERT: G 379 ARG cc_start: 0.9388 (ttm-80) cc_final: 0.8962 (ttm-80) REVERT: G 387 MET cc_start: 0.8566 (tpp) cc_final: 0.8364 (tpp) REVERT: H 61 MET cc_start: 0.8178 (tpp) cc_final: 0.7764 (tpp) REVERT: H 328 GLN cc_start: 0.8552 (tm-30) cc_final: 0.8267 (tm-30) REVERT: H 373 LEU cc_start: 0.9260 (mt) cc_final: 0.9014 (mp) REVERT: H 387 MET cc_start: 0.6870 (mmp) cc_final: 0.6288 (mmm) outliers start: 54 outliers final: 37 residues processed: 200 average time/residue: 0.1899 time to fit residues: 59.9551 Evaluate side-chains 186 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 146 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 391 ARG Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 117 HIS Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 302 MET Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 391 ARG Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain E residue 118 LYS Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 416 SER Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 291 SER Chi-restraints excluded: chain F residue 438 SER Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain H residue 118 LYS Chi-restraints excluded: chain H residue 141 CYS Chi-restraints excluded: chain H residue 183 VAL Chi-restraints excluded: chain H residue 291 SER Chi-restraints excluded: chain H residue 329 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 184 optimal weight: 6.9990 chunk 164 optimal weight: 0.1980 chunk 201 optimal weight: 6.9990 chunk 243 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 chunk 129 optimal weight: 4.9990 chunk 326 optimal weight: 1.9990 chunk 212 optimal weight: 1.9990 chunk 106 optimal weight: 7.9990 chunk 162 optimal weight: 5.9990 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 435 HIS F 176 HIS H 176 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.067582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.047619 restraints weight = 87826.013| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 3.56 r_work: 0.2670 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 27752 Z= 0.129 Angle : 0.459 7.240 37776 Z= 0.238 Chirality : 0.041 0.135 4496 Planarity : 0.004 0.047 5000 Dihedral : 3.778 32.129 4070 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.42 % Allowed : 14.53 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.14), residues: 3736 helix: 1.61 (0.14), residues: 1408 sheet: -0.40 (0.21), residues: 576 loop : 0.74 (0.15), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 379 TYR 0.013 0.001 TYR E 385 PHE 0.009 0.001 PHE A 316 TRP 0.003 0.001 TRP G 361 HIS 0.003 0.001 HIS A 435 Details of bonding type rmsd covalent geometry : bond 0.00295 (27752) covalent geometry : angle 0.45948 (37776) hydrogen bonds : bond 0.03262 ( 1096) hydrogen bonds : angle 3.87627 ( 3072) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 148 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.8991 (tpp) cc_final: 0.7559 (tpp) REVERT: A 255 MET cc_start: 0.9170 (tpp) cc_final: 0.8844 (tpp) REVERT: A 328 GLN cc_start: 0.9033 (tm-30) cc_final: 0.8629 (tm-30) REVERT: A 391 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.8412 (ttp80) REVERT: B 131 ARG cc_start: 0.8527 (mtp85) cc_final: 0.8306 (mtp85) REVERT: B 357 MET cc_start: 0.9301 (ttm) cc_final: 0.9080 (ttp) REVERT: B 396 ARG cc_start: 0.8540 (ttp-110) cc_final: 0.7297 (tpt170) REVERT: B 446 TYR cc_start: 0.9185 (m-80) cc_final: 0.8960 (m-80) REVERT: C 61 MET cc_start: 0.8759 (tpp) cc_final: 0.7592 (tpp) REVERT: C 184 MET cc_start: 0.8010 (OUTLIER) cc_final: 0.7767 (tpp) REVERT: C 328 GLN cc_start: 0.8902 (tm-30) cc_final: 0.8491 (tm-30) REVERT: D 184 MET cc_start: 0.7982 (mmm) cc_final: 0.7646 (mmt) REVERT: D 233 GLN cc_start: 0.9099 (tp40) cc_final: 0.8808 (tp40) REVERT: D 379 ARG cc_start: 0.9087 (mtm-85) cc_final: 0.8788 (mtm110) REVERT: E 61 MET cc_start: 0.8911 (tpp) cc_final: 0.7867 (tpp) REVERT: E 118 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8410 (mtmm) REVERT: E 328 GLN cc_start: 0.8898 (tm-30) cc_final: 0.8697 (tm-30) REVERT: E 377 ASP cc_start: 0.9079 (t0) cc_final: 0.8587 (t0) REVERT: F 61 MET cc_start: 0.8326 (tpp) cc_final: 0.7682 (tpp) REVERT: F 328 GLN cc_start: 0.9356 (tp40) cc_final: 0.8977 (tm-30) REVERT: G 328 GLN cc_start: 0.9033 (tp40) cc_final: 0.8615 (tm-30) REVERT: G 377 ASP cc_start: 0.9109 (t0) cc_final: 0.8609 (p0) REVERT: G 379 ARG cc_start: 0.9373 (ttm-80) cc_final: 0.8771 (mtm110) REVERT: H 61 MET cc_start: 0.8208 (tpp) cc_final: 0.7816 (tpp) REVERT: H 328 GLN cc_start: 0.8586 (tm-30) cc_final: 0.8268 (tm-30) REVERT: H 387 MET cc_start: 0.7149 (mmp) cc_final: 0.6636 (mmm) outliers start: 68 outliers final: 46 residues processed: 209 average time/residue: 0.1861 time to fit residues: 61.0911 Evaluate side-chains 195 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 146 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 391 ARG Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 117 HIS Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 302 MET Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 391 ARG Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain E residue 118 LYS Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 416 SER Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 291 SER Chi-restraints excluded: chain F residue 438 SER Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 291 SER Chi-restraints excluded: chain G residue 376 ARG Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain H residue 118 LYS Chi-restraints excluded: chain H residue 131 ARG Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 141 CYS Chi-restraints excluded: chain H residue 183 VAL Chi-restraints excluded: chain H residue 291 SER Chi-restraints excluded: chain H residue 329 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 263 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 272 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 chunk 243 optimal weight: 9.9990 chunk 353 optimal weight: 0.8980 chunk 2 optimal weight: 6.9990 chunk 105 optimal weight: 10.0000 chunk 304 optimal weight: 2.9990 chunk 252 optimal weight: 2.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.066332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.046380 restraints weight = 88526.454| |-----------------------------------------------------------------------------| r_work (start): 0.2778 rms_B_bonded: 3.54 r_work: 0.2637 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 27752 Z= 0.189 Angle : 0.505 10.063 37776 Z= 0.259 Chirality : 0.042 0.138 4496 Planarity : 0.004 0.044 5000 Dihedral : 3.985 32.448 4070 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.74 % Allowed : 14.35 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.14), residues: 3736 helix: 1.49 (0.14), residues: 1408 sheet: -0.42 (0.21), residues: 584 loop : 0.65 (0.15), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 376 TYR 0.009 0.001 TYR G 381 PHE 0.020 0.001 PHE E 128 TRP 0.003 0.001 TRP A 361 HIS 0.003 0.001 HIS E 435 Details of bonding type rmsd covalent geometry : bond 0.00433 (27752) covalent geometry : angle 0.50521 (37776) hydrogen bonds : bond 0.03634 ( 1096) hydrogen bonds : angle 4.04492 ( 3072) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 148 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.9029 (tpp) cc_final: 0.7530 (tpp) REVERT: A 149 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.6865 (mmp80) REVERT: A 255 MET cc_start: 0.9097 (tpp) cc_final: 0.8841 (tpp) REVERT: A 328 GLN cc_start: 0.9088 (tm-30) cc_final: 0.8711 (tm-30) REVERT: A 391 ARG cc_start: 0.8812 (OUTLIER) cc_final: 0.8360 (ttp80) REVERT: B 396 ARG cc_start: 0.8555 (ttp-110) cc_final: 0.7335 (tpt170) REVERT: C 61 MET cc_start: 0.8808 (tpp) cc_final: 0.7553 (tpp) REVERT: C 184 MET cc_start: 0.8040 (OUTLIER) cc_final: 0.7702 (tpp) REVERT: C 328 GLN cc_start: 0.8933 (tm-30) cc_final: 0.8462 (tm-30) REVERT: D 233 GLN cc_start: 0.9129 (tp40) cc_final: 0.8837 (tp40) REVERT: D 379 ARG cc_start: 0.9094 (mtm-85) cc_final: 0.8762 (mtm110) REVERT: E 61 MET cc_start: 0.9109 (tpp) cc_final: 0.8034 (tpp) REVERT: E 118 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8581 (mtmm) REVERT: E 377 ASP cc_start: 0.9112 (t0) cc_final: 0.8615 (t0) REVERT: F 61 MET cc_start: 0.8366 (tpp) cc_final: 0.7721 (tpp) REVERT: F 328 GLN cc_start: 0.9355 (tp40) cc_final: 0.8977 (tm-30) REVERT: G 328 GLN cc_start: 0.8957 (tp40) cc_final: 0.8503 (tm-30) REVERT: G 377 ASP cc_start: 0.9117 (t0) cc_final: 0.8432 (p0) REVERT: G 379 ARG cc_start: 0.9399 (ttm-80) cc_final: 0.8921 (ttm-80) REVERT: H 61 MET cc_start: 0.8257 (tpp) cc_final: 0.7839 (tpp) REVERT: H 328 GLN cc_start: 0.8649 (tm-30) cc_final: 0.8329 (tm-30) REVERT: H 387 MET cc_start: 0.7169 (mmp) cc_final: 0.6770 (mmm) outliers start: 77 outliers final: 56 residues processed: 218 average time/residue: 0.1960 time to fit residues: 67.9512 Evaluate side-chains 203 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 143 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 149 ARG Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 391 ARG Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 117 HIS Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain C residue 225 ASN Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 302 MET Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 391 ARG Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain E residue 118 LYS Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 291 SER Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 416 SER Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 291 SER Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain F residue 438 SER Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 291 SER Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain H residue 118 LYS Chi-restraints excluded: chain H residue 131 ARG Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain H residue 141 CYS Chi-restraints excluded: chain H residue 183 VAL Chi-restraints excluded: chain H residue 291 SER Chi-restraints excluded: chain H residue 329 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 7 optimal weight: 7.9990 chunk 109 optimal weight: 10.0000 chunk 258 optimal weight: 5.9990 chunk 362 optimal weight: 9.9990 chunk 112 optimal weight: 1.9990 chunk 345 optimal weight: 7.9990 chunk 255 optimal weight: 3.9990 chunk 349 optimal weight: 0.9990 chunk 326 optimal weight: 0.9980 chunk 23 optimal weight: 7.9990 chunk 60 optimal weight: 0.1980 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.066964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.047038 restraints weight = 87857.047| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 3.54 r_work: 0.2658 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27752 Z= 0.142 Angle : 0.479 8.269 37776 Z= 0.245 Chirality : 0.042 0.139 4496 Planarity : 0.004 0.045 5000 Dihedral : 3.819 28.121 4069 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.67 % Allowed : 14.39 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.14), residues: 3736 helix: 1.61 (0.14), residues: 1408 sheet: -0.55 (0.21), residues: 576 loop : 0.68 (0.15), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 93 TYR 0.007 0.001 TYR G 381 PHE 0.009 0.001 PHE A 316 TRP 0.002 0.001 TRP C 334 HIS 0.004 0.001 HIS E 435 Details of bonding type rmsd covalent geometry : bond 0.00326 (27752) covalent geometry : angle 0.47921 (37776) hydrogen bonds : bond 0.03274 ( 1096) hydrogen bonds : angle 3.87267 ( 3072) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 146 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.8989 (tpp) cc_final: 0.8390 (tpp) REVERT: A 149 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.6989 (mmp80) REVERT: A 255 MET cc_start: 0.9087 (tpp) cc_final: 0.8837 (tpp) REVERT: A 328 GLN cc_start: 0.9102 (tm-30) cc_final: 0.8725 (tm-30) REVERT: A 391 ARG cc_start: 0.8824 (OUTLIER) cc_final: 0.8398 (ttp80) REVERT: B 131 ARG cc_start: 0.8705 (mtp85) cc_final: 0.8444 (mtp85) REVERT: B 396 ARG cc_start: 0.8471 (ttp-110) cc_final: 0.7616 (tpt170) REVERT: C 61 MET cc_start: 0.8784 (tpp) cc_final: 0.7521 (tpp) REVERT: C 184 MET cc_start: 0.7942 (OUTLIER) cc_final: 0.7626 (tpp) REVERT: C 328 GLN cc_start: 0.8937 (tm-30) cc_final: 0.8502 (tm-30) REVERT: D 233 GLN cc_start: 0.9127 (tp40) cc_final: 0.8843 (tp40) REVERT: D 379 ARG cc_start: 0.9081 (mtm-85) cc_final: 0.8796 (mtm110) REVERT: E 61 MET cc_start: 0.9067 (tpp) cc_final: 0.8008 (tpp) REVERT: E 118 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8450 (mtmm) REVERT: E 377 ASP cc_start: 0.9101 (t0) cc_final: 0.8569 (t0) REVERT: F 61 MET cc_start: 0.8359 (tpp) cc_final: 0.7741 (tpp) REVERT: F 328 GLN cc_start: 0.9342 (tp40) cc_final: 0.8987 (tm-30) REVERT: G 328 GLN cc_start: 0.8933 (tp40) cc_final: 0.8511 (tm-30) REVERT: G 377 ASP cc_start: 0.9144 (t0) cc_final: 0.8608 (p0) REVERT: G 379 ARG cc_start: 0.9409 (ttm-80) cc_final: 0.8820 (mtm110) REVERT: H 61 MET cc_start: 0.8251 (tpp) cc_final: 0.7859 (tpp) REVERT: H 328 GLN cc_start: 0.8645 (tm-30) cc_final: 0.8329 (tm-30) REVERT: H 387 MET cc_start: 0.7201 (mmp) cc_final: 0.6796 (mmm) outliers start: 75 outliers final: 62 residues processed: 213 average time/residue: 0.1889 time to fit residues: 63.6148 Evaluate side-chains 209 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 143 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 149 ARG Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 391 ARG Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 117 HIS Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain C residue 225 ASN Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 302 MET Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 391 ARG Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain E residue 118 LYS Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 291 SER Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 416 SER Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 144 VAL Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 291 SER Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain F residue 438 SER Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 291 SER Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain H residue 118 LYS Chi-restraints excluded: chain H residue 131 ARG Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain H residue 141 CYS Chi-restraints excluded: chain H residue 183 VAL Chi-restraints excluded: chain H residue 291 SER Chi-restraints excluded: chain H residue 329 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 247 optimal weight: 3.9990 chunk 25 optimal weight: 0.4980 chunk 134 optimal weight: 6.9990 chunk 68 optimal weight: 8.9990 chunk 145 optimal weight: 7.9990 chunk 306 optimal weight: 5.9990 chunk 153 optimal weight: 1.9990 chunk 190 optimal weight: 0.3980 chunk 274 optimal weight: 4.9990 chunk 290 optimal weight: 9.9990 chunk 250 optimal weight: 5.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.066162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.046278 restraints weight = 88564.232| |-----------------------------------------------------------------------------| r_work (start): 0.2774 rms_B_bonded: 3.53 r_work: 0.2633 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 27752 Z= 0.193 Angle : 0.510 9.263 37776 Z= 0.263 Chirality : 0.043 0.143 4496 Planarity : 0.004 0.045 5000 Dihedral : 3.969 28.273 4069 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.78 % Allowed : 14.57 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.14), residues: 3736 helix: 1.11 (0.13), residues: 1504 sheet: -0.53 (0.21), residues: 584 loop : 0.55 (0.16), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 379 TYR 0.008 0.001 TYR D 385 PHE 0.021 0.001 PHE E 128 TRP 0.003 0.001 TRP A 361 HIS 0.003 0.001 HIS E 435 Details of bonding type rmsd covalent geometry : bond 0.00443 (27752) covalent geometry : angle 0.51044 (37776) hydrogen bonds : bond 0.03634 ( 1096) hydrogen bonds : angle 3.99892 ( 3072) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 146 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.9028 (tpp) cc_final: 0.7875 (tpp) REVERT: A 149 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.6802 (mmm-85) REVERT: A 255 MET cc_start: 0.9115 (tpp) cc_final: 0.8879 (tpp) REVERT: A 328 GLN cc_start: 0.9128 (tm-30) cc_final: 0.8739 (tm-30) REVERT: A 391 ARG cc_start: 0.8908 (OUTLIER) cc_final: 0.8497 (ttp80) REVERT: B 131 ARG cc_start: 0.8734 (mtp85) cc_final: 0.8454 (mtp85) REVERT: B 396 ARG cc_start: 0.8499 (ttp-110) cc_final: 0.7178 (tpt170) REVERT: B 420 MET cc_start: 0.8993 (mmp) cc_final: 0.8748 (mmm) REVERT: C 61 MET cc_start: 0.8829 (tpp) cc_final: 0.7810 (tpp) REVERT: C 184 MET cc_start: 0.7957 (OUTLIER) cc_final: 0.7590 (tpp) REVERT: C 328 GLN cc_start: 0.8966 (tm-30) cc_final: 0.8509 (tm-30) REVERT: D 184 MET cc_start: 0.8166 (mmm) cc_final: 0.7809 (mmt) REVERT: D 233 GLN cc_start: 0.9119 (tp40) cc_final: 0.8815 (tp40) REVERT: E 61 MET cc_start: 0.9108 (tpp) cc_final: 0.7998 (tpp) REVERT: E 118 LYS cc_start: 0.8965 (OUTLIER) cc_final: 0.8592 (mtmm) REVERT: F 61 MET cc_start: 0.8385 (tpp) cc_final: 0.7717 (tpp) REVERT: F 328 GLN cc_start: 0.9364 (tp40) cc_final: 0.8990 (tm-30) REVERT: F 396 ARG cc_start: 0.9087 (ttp-110) cc_final: 0.8715 (ptp-170) REVERT: G 328 GLN cc_start: 0.8969 (tp40) cc_final: 0.8517 (tm-30) REVERT: G 377 ASP cc_start: 0.9143 (t0) cc_final: 0.8484 (p0) REVERT: G 379 ARG cc_start: 0.9450 (ttm-80) cc_final: 0.8968 (ttm-80) REVERT: H 61 MET cc_start: 0.8270 (tpp) cc_final: 0.7861 (tpp) REVERT: H 328 GLN cc_start: 0.8677 (tm-30) cc_final: 0.8366 (tm-30) REVERT: H 387 MET cc_start: 0.7271 (mmp) cc_final: 0.6861 (mmm) outliers start: 78 outliers final: 62 residues processed: 216 average time/residue: 0.1910 time to fit residues: 65.5209 Evaluate side-chains 209 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 143 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 149 ARG Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 391 ARG Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 117 HIS Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain C residue 225 ASN Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 302 MET Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 391 ARG Chi-restraints excluded: chain E residue 118 LYS Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 291 SER Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 416 SER Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 144 VAL Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 291 SER Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain F residue 438 SER Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 291 SER Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain H residue 118 LYS Chi-restraints excluded: chain H residue 131 ARG Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain H residue 141 CYS Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain H residue 183 VAL Chi-restraints excluded: chain H residue 291 SER Chi-restraints excluded: chain H residue 329 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 62 optimal weight: 0.6980 chunk 71 optimal weight: 5.9990 chunk 137 optimal weight: 0.7980 chunk 166 optimal weight: 0.9990 chunk 9 optimal weight: 0.1980 chunk 287 optimal weight: 7.9990 chunk 313 optimal weight: 0.0000 chunk 367 optimal weight: 0.6980 chunk 172 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 187 optimal weight: 0.2980 overall best weight: 0.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.068475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.048745 restraints weight = 87782.886| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 3.56 r_work: 0.2710 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 27752 Z= 0.085 Angle : 0.477 12.685 37776 Z= 0.238 Chirality : 0.041 0.139 4496 Planarity : 0.004 0.045 5000 Dihedral : 3.581 28.100 4069 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.60 % Allowed : 15.92 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.14), residues: 3736 helix: 1.77 (0.14), residues: 1408 sheet: -0.46 (0.22), residues: 576 loop : 0.73 (0.15), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG D 379 TYR 0.008 0.001 TYR G 381 PHE 0.009 0.001 PHE G 89 TRP 0.003 0.000 TRP E 361 HIS 0.005 0.000 HIS E 435 Details of bonding type rmsd covalent geometry : bond 0.00190 (27752) covalent geometry : angle 0.47703 (37776) hydrogen bonds : bond 0.02775 ( 1096) hydrogen bonds : angle 3.56169 ( 3072) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 152 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.8916 (tpp) cc_final: 0.8507 (tpp) REVERT: A 255 MET cc_start: 0.9067 (tpp) cc_final: 0.8827 (tpp) REVERT: A 308 MET cc_start: 0.8930 (tpp) cc_final: 0.8706 (mmm) REVERT: A 328 GLN cc_start: 0.9029 (tm-30) cc_final: 0.8818 (tm-30) REVERT: A 391 ARG cc_start: 0.8863 (OUTLIER) cc_final: 0.8495 (ttp80) REVERT: B 131 ARG cc_start: 0.8716 (mtp85) cc_final: 0.8449 (mtp85) REVERT: B 147 PHE cc_start: 0.9013 (m-80) cc_final: 0.8766 (m-80) REVERT: B 396 ARG cc_start: 0.8507 (ttp-110) cc_final: 0.7177 (tpt170) REVERT: C 61 MET cc_start: 0.8725 (tpp) cc_final: 0.8238 (tpp) REVERT: C 308 MET cc_start: 0.8892 (tpp) cc_final: 0.8474 (mmm) REVERT: C 328 GLN cc_start: 0.8838 (tm-30) cc_final: 0.8476 (tm-30) REVERT: D 61 MET cc_start: 0.8777 (tpp) cc_final: 0.8555 (tpp) REVERT: D 184 MET cc_start: 0.8080 (mmm) cc_final: 0.7753 (mmt) REVERT: D 194 VAL cc_start: 0.8638 (OUTLIER) cc_final: 0.8347 (p) REVERT: D 233 GLN cc_start: 0.9102 (tp40) cc_final: 0.8832 (tp40) REVERT: D 379 ARG cc_start: 0.9100 (mtm110) cc_final: 0.8879 (mtm-85) REVERT: E 61 MET cc_start: 0.8832 (tpp) cc_final: 0.7897 (tpp) REVERT: F 61 MET cc_start: 0.8296 (tpp) cc_final: 0.7704 (tpp) REVERT: F 328 GLN cc_start: 0.9290 (tp40) cc_final: 0.8981 (tm-30) REVERT: G 328 GLN cc_start: 0.8865 (tp40) cc_final: 0.8537 (tm-30) REVERT: G 377 ASP cc_start: 0.9193 (t0) cc_final: 0.8654 (p0) REVERT: G 379 ARG cc_start: 0.9417 (ttm-80) cc_final: 0.8840 (mtm110) REVERT: H 61 MET cc_start: 0.8141 (tpp) cc_final: 0.7785 (tpp) REVERT: H 118 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.7420 (ptpp) REVERT: H 328 GLN cc_start: 0.8666 (tm-30) cc_final: 0.8381 (tm-30) REVERT: H 387 MET cc_start: 0.7092 (mmp) cc_final: 0.6801 (mmm) outliers start: 45 outliers final: 33 residues processed: 193 average time/residue: 0.2037 time to fit residues: 62.3744 Evaluate side-chains 180 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 144 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 391 ARG Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 117 HIS Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain C residue 302 MET Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain E residue 117 HIS Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 291 SER Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 291 SER Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain H residue 118 LYS Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain H residue 183 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 249 optimal weight: 0.2980 chunk 91 optimal weight: 4.9990 chunk 328 optimal weight: 6.9990 chunk 293 optimal weight: 0.7980 chunk 70 optimal weight: 9.9990 chunk 366 optimal weight: 5.9990 chunk 139 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 261 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 122 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.068141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.048265 restraints weight = 87854.997| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 3.57 r_work: 0.2698 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 27752 Z= 0.095 Angle : 0.477 12.301 37776 Z= 0.238 Chirality : 0.041 0.177 4496 Planarity : 0.004 0.043 5000 Dihedral : 3.535 24.255 4069 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.35 % Allowed : 16.13 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.14), residues: 3736 helix: 1.78 (0.14), residues: 1408 sheet: -0.39 (0.22), residues: 576 loop : 0.76 (0.15), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 379 TYR 0.009 0.001 TYR D 446 PHE 0.023 0.001 PHE E 128 TRP 0.003 0.000 TRP D 361 HIS 0.004 0.000 HIS E 435 Details of bonding type rmsd covalent geometry : bond 0.00218 (27752) covalent geometry : angle 0.47745 (37776) hydrogen bonds : bond 0.02854 ( 1096) hydrogen bonds : angle 3.54594 ( 3072) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 148 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.8979 (tpp) cc_final: 0.8586 (tpp) REVERT: A 255 MET cc_start: 0.9125 (tpp) cc_final: 0.8899 (tpp) REVERT: A 328 GLN cc_start: 0.9038 (tm-30) cc_final: 0.8792 (tm-30) REVERT: A 391 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.8524 (ttp80) REVERT: B 131 ARG cc_start: 0.8611 (mtp85) cc_final: 0.8314 (mtp85) REVERT: B 147 PHE cc_start: 0.9017 (m-80) cc_final: 0.8786 (m-80) REVERT: B 396 ARG cc_start: 0.8524 (ttp-110) cc_final: 0.7181 (tpt170) REVERT: C 61 MET cc_start: 0.8766 (tpp) cc_final: 0.8211 (tpp) REVERT: C 184 MET cc_start: 0.7349 (tpp) cc_final: 0.6607 (tpp) REVERT: C 328 GLN cc_start: 0.8867 (tm-30) cc_final: 0.8516 (tm-30) REVERT: D 61 MET cc_start: 0.8782 (tpp) cc_final: 0.8431 (tpp) REVERT: D 184 MET cc_start: 0.8107 (mmm) cc_final: 0.7784 (mmt) REVERT: D 194 VAL cc_start: 0.8638 (OUTLIER) cc_final: 0.8343 (p) REVERT: D 233 GLN cc_start: 0.9109 (tp40) cc_final: 0.8834 (tp40) REVERT: D 379 ARG cc_start: 0.9100 (mtm110) cc_final: 0.8815 (mtm-85) REVERT: E 61 MET cc_start: 0.8880 (tpp) cc_final: 0.7934 (tpp) REVERT: F 61 MET cc_start: 0.8340 (tpp) cc_final: 0.7712 (tpp) REVERT: F 328 GLN cc_start: 0.9297 (tp40) cc_final: 0.8979 (tm-30) REVERT: G 328 GLN cc_start: 0.9021 (tp40) cc_final: 0.8670 (tm-30) REVERT: G 377 ASP cc_start: 0.9174 (t0) cc_final: 0.8537 (p0) REVERT: G 379 ARG cc_start: 0.9415 (ttm-80) cc_final: 0.8966 (ttm-80) REVERT: H 61 MET cc_start: 0.8178 (tpp) cc_final: 0.7803 (tpp) REVERT: H 118 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.7482 (ptpp) REVERT: H 328 GLN cc_start: 0.8698 (tm-30) cc_final: 0.8383 (tm-30) REVERT: H 387 MET cc_start: 0.7230 (mmp) cc_final: 0.6828 (mmm) outliers start: 38 outliers final: 33 residues processed: 183 average time/residue: 0.1868 time to fit residues: 54.0890 Evaluate side-chains 183 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 147 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 391 ARG Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 117 HIS Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain C residue 302 MET Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 291 SER Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 291 SER Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain H residue 118 LYS Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain H residue 183 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 136 optimal weight: 6.9990 chunk 168 optimal weight: 0.8980 chunk 192 optimal weight: 6.9990 chunk 103 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 96 optimal weight: 0.0470 chunk 150 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 217 optimal weight: 2.9990 overall best weight: 1.7282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.067096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.047162 restraints weight = 87661.715| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 3.54 r_work: 0.2662 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27752 Z= 0.147 Angle : 0.504 12.614 37776 Z= 0.253 Chirality : 0.042 0.160 4496 Planarity : 0.004 0.044 5000 Dihedral : 3.727 24.132 4069 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.35 % Allowed : 16.24 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.14), residues: 3736 helix: 1.65 (0.14), residues: 1408 sheet: -0.38 (0.22), residues: 584 loop : 0.69 (0.15), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 379 TYR 0.012 0.001 TYR D 446 PHE 0.010 0.001 PHE H 316 TRP 0.003 0.001 TRP E 334 HIS 0.004 0.001 HIS E 435 Details of bonding type rmsd covalent geometry : bond 0.00339 (27752) covalent geometry : angle 0.50392 (37776) hydrogen bonds : bond 0.03252 ( 1096) hydrogen bonds : angle 3.75258 ( 3072) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5404.71 seconds wall clock time: 93 minutes 37.36 seconds (5617.36 seconds total)