Starting phenix.real_space_refine on Thu Mar 5 07:07:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6kz3_0784/03_2026/6kz3_0784.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kz3_0784/03_2026/6kz3_0784.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6kz3_0784/03_2026/6kz3_0784.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kz3_0784/03_2026/6kz3_0784.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6kz3_0784/03_2026/6kz3_0784.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kz3_0784/03_2026/6kz3_0784.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 48 5.16 5 C 12702 2.51 5 N 3396 2.21 5 O 3900 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20046 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3341 Classifications: {'peptide': 441} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 416} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 3.16, per 1000 atoms: 0.16 Number of scatterers: 20046 At special positions: 0 Unit cell: (110.39, 110.39, 138.32, 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 48 16.00 O 3900 8.00 N 3396 7.00 C 12702 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.82 Conformation dependent library (CDL) restraints added in 892.3 milliseconds 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4764 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 36 sheets defined 8.4% alpha, 33.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 123 through 127 removed outlier: 3.684A pdb=" N LEU A 126 " --> pdb=" O LEU A 123 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL A 127 " --> pdb=" O ASP A 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 123 through 127' Processing helix chain 'A' and resid 209 through 212 Processing helix chain 'A' and resid 243 through 249 Processing helix chain 'A' and resid 331 through 335 Processing helix chain 'A' and resid 356 through 361 removed outlier: 3.527A pdb=" N THR A 360 " --> pdb=" O SER A 356 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY A 361 " --> pdb=" O ALA A 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 356 through 361' Processing helix chain 'A' and resid 500 through 506 removed outlier: 3.787A pdb=" N ALA A 504 " --> pdb=" O ASN A 500 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU A 506 " --> pdb=" O GLU A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 509 No H-bonds generated for 'chain 'A' and resid 507 through 509' Processing helix chain 'B' and resid 123 through 127 removed outlier: 3.684A pdb=" N LEU B 126 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL B 127 " --> pdb=" O ASP B 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 123 through 127' Processing helix chain 'B' and resid 209 through 212 Processing helix chain 'B' and resid 243 through 249 Processing helix chain 'B' and resid 331 through 335 Processing helix chain 'B' and resid 356 through 361 removed outlier: 3.527A pdb=" N THR B 360 " --> pdb=" O SER B 356 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY B 361 " --> pdb=" O ALA B 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 356 through 361' Processing helix chain 'B' and resid 500 through 506 removed outlier: 3.787A pdb=" N ALA B 504 " --> pdb=" O ASN B 500 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU B 506 " --> pdb=" O GLU B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 509 No H-bonds generated for 'chain 'B' and resid 507 through 509' Processing helix chain 'C' and resid 123 through 127 removed outlier: 3.683A pdb=" N LEU C 126 " --> pdb=" O LEU C 123 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL C 127 " --> pdb=" O ASP C 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 123 through 127' Processing helix chain 'C' and resid 209 through 212 Processing helix chain 'C' and resid 243 through 249 Processing helix chain 'C' and resid 331 through 335 Processing helix chain 'C' and resid 356 through 361 removed outlier: 3.528A pdb=" N THR C 360 " --> pdb=" O SER C 356 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY C 361 " --> pdb=" O ALA C 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 356 through 361' Processing helix chain 'C' and resid 500 through 506 removed outlier: 3.787A pdb=" N ALA C 504 " --> pdb=" O ASN C 500 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU C 506 " --> pdb=" O GLU C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 509 No H-bonds generated for 'chain 'C' and resid 507 through 509' Processing helix chain 'D' and resid 123 through 127 removed outlier: 3.684A pdb=" N LEU D 126 " --> pdb=" O LEU D 123 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL D 127 " --> pdb=" O ASP D 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 123 through 127' Processing helix chain 'D' and resid 209 through 212 Processing helix chain 'D' and resid 243 through 249 Processing helix chain 'D' and resid 331 through 335 Processing helix chain 'D' and resid 356 through 361 removed outlier: 3.527A pdb=" N THR D 360 " --> pdb=" O SER D 356 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY D 361 " --> pdb=" O ALA D 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 356 through 361' Processing helix chain 'D' and resid 500 through 506 removed outlier: 3.787A pdb=" N ALA D 504 " --> pdb=" O ASN D 500 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU D 506 " --> pdb=" O GLU D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 507 through 509 No H-bonds generated for 'chain 'D' and resid 507 through 509' Processing helix chain 'E' and resid 123 through 127 removed outlier: 3.683A pdb=" N LEU E 126 " --> pdb=" O LEU E 123 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL E 127 " --> pdb=" O ASP E 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 123 through 127' Processing helix chain 'E' and resid 209 through 212 Processing helix chain 'E' and resid 243 through 249 Processing helix chain 'E' and resid 331 through 335 Processing helix chain 'E' and resid 356 through 361 removed outlier: 3.527A pdb=" N THR E 360 " --> pdb=" O SER E 356 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY E 361 " --> pdb=" O ALA E 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 356 through 361' Processing helix chain 'E' and resid 500 through 506 removed outlier: 3.787A pdb=" N ALA E 504 " --> pdb=" O ASN E 500 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU E 506 " --> pdb=" O GLU E 502 " (cutoff:3.500A) Processing helix chain 'E' and resid 507 through 509 No H-bonds generated for 'chain 'E' and resid 507 through 509' Processing helix chain 'F' and resid 123 through 127 removed outlier: 3.683A pdb=" N LEU F 126 " --> pdb=" O LEU F 123 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL F 127 " --> pdb=" O ASP F 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 123 through 127' Processing helix chain 'F' and resid 209 through 212 Processing helix chain 'F' and resid 243 through 249 Processing helix chain 'F' and resid 331 through 335 Processing helix chain 'F' and resid 356 through 361 removed outlier: 3.528A pdb=" N THR F 360 " --> pdb=" O SER F 356 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY F 361 " --> pdb=" O ALA F 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 356 through 361' Processing helix chain 'F' and resid 500 through 506 removed outlier: 3.787A pdb=" N ALA F 504 " --> pdb=" O ASN F 500 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU F 506 " --> pdb=" O GLU F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 507 through 509 No H-bonds generated for 'chain 'F' and resid 507 through 509' Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 68 removed outlier: 6.022A pdb=" N TYR A 68 " --> pdb=" O GLU A 72 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N GLU A 72 " --> pdb=" O TYR A 68 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LYS A 91 " --> pdb=" O GLN A 77 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ILE A 79 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N GLU A 89 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N THR A 50 " --> pdb=" O PHE A 145 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 107 through 110 Processing sheet with id=AA3, first strand: chain 'A' and resid 161 through 167 removed outlier: 6.687A pdb=" N VAL A 202 " --> pdb=" O TYR A 192 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N TYR A 192 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ASP A 204 " --> pdb=" O TYR A 190 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL A 179 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU A 178 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N PHE A 253 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N TYR A 180 " --> pdb=" O PHE A 253 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N PHE A 221 " --> pdb=" O TYR A 271 " (cutoff:3.500A) removed outlier: 8.824A pdb=" N PHE A 268 " --> pdb=" O MET A 162 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N HIS A 164 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU A 270 " --> pdb=" O HIS A 164 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLN A 166 " --> pdb=" O LEU A 270 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 227 through 229 removed outlier: 3.665A pdb=" N VAL A 227 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU B 240 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA A 229 " --> pdb=" O VAL B 238 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 238 through 240 removed outlier: 3.572A pdb=" N ALA F 229 " --> pdb=" O VAL A 238 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU A 240 " --> pdb=" O VAL F 227 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL F 227 " --> pdb=" O LEU A 240 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 340 through 344 removed outlier: 6.184A pdb=" N LEU A 300 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N GLU A 324 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU A 313 " --> pdb=" O THR A 322 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N THR A 322 " --> pdb=" O LEU A 313 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL A 321 " --> pdb=" O LEU A 287 " (cutoff:3.500A) removed outlier: 8.784A pdb=" N PHE A 377 " --> pdb=" O ILE A 282 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LYS A 284 " --> pdb=" O PHE A 377 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 393 through 399 removed outlier: 6.479A pdb=" N THR A 432 " --> pdb=" O ARG A 424 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ARG A 424 " --> pdb=" O THR A 432 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N THR A 434 " --> pdb=" O ILE A 422 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU A 411 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ILE A 483 " --> pdb=" O PRO A 410 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE A 412 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N PHE A 451 " --> pdb=" O TYR A 498 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N TYR A 495 " --> pdb=" O THR A 394 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N THR A 396 " --> pdb=" O TYR A 495 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LEU A 497 " --> pdb=" O THR A 396 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N THR A 398 " --> pdb=" O LEU A 497 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 65 through 68 removed outlier: 6.022A pdb=" N TYR B 68 " --> pdb=" O GLU B 72 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N GLU B 72 " --> pdb=" O TYR B 68 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LYS B 91 " --> pdb=" O GLN B 77 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ILE B 79 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N GLU B 89 " --> pdb=" O ILE B 79 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N THR B 50 " --> pdb=" O PHE B 145 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 107 through 110 Processing sheet with id=AB1, first strand: chain 'B' and resid 161 through 167 removed outlier: 6.687A pdb=" N VAL B 202 " --> pdb=" O TYR B 192 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N TYR B 192 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ASP B 204 " --> pdb=" O TYR B 190 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL B 179 " --> pdb=" O VAL B 186 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU B 178 " --> pdb=" O ILE B 251 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N PHE B 253 " --> pdb=" O LEU B 178 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N TYR B 180 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N PHE B 221 " --> pdb=" O TYR B 271 " (cutoff:3.500A) removed outlier: 8.824A pdb=" N PHE B 268 " --> pdb=" O MET B 162 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N HIS B 164 " --> pdb=" O PHE B 268 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU B 270 " --> pdb=" O HIS B 164 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLN B 166 " --> pdb=" O LEU B 270 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 227 through 229 removed outlier: 3.669A pdb=" N VAL B 227 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU C 240 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA B 229 " --> pdb=" O VAL C 238 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 340 through 344 removed outlier: 6.185A pdb=" N LEU B 300 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N GLU B 324 " --> pdb=" O THR B 311 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LEU B 313 " --> pdb=" O THR B 322 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N THR B 322 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL B 321 " --> pdb=" O LEU B 287 " (cutoff:3.500A) removed outlier: 8.784A pdb=" N PHE B 377 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LYS B 284 " --> pdb=" O PHE B 377 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 393 through 399 removed outlier: 6.478A pdb=" N THR B 432 " --> pdb=" O ARG B 424 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ARG B 424 " --> pdb=" O THR B 432 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N THR B 434 " --> pdb=" O ILE B 422 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU B 411 " --> pdb=" O VAL B 418 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ILE B 483 " --> pdb=" O PRO B 410 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE B 412 " --> pdb=" O ILE B 483 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N PHE B 451 " --> pdb=" O TYR B 498 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N TYR B 495 " --> pdb=" O THR B 394 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N THR B 396 " --> pdb=" O TYR B 495 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU B 497 " --> pdb=" O THR B 396 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N THR B 398 " --> pdb=" O LEU B 497 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 65 through 68 removed outlier: 6.022A pdb=" N TYR C 68 " --> pdb=" O GLU C 72 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N GLU C 72 " --> pdb=" O TYR C 68 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LYS C 91 " --> pdb=" O GLN C 77 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ILE C 79 " --> pdb=" O GLU C 89 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N GLU C 89 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N THR C 50 " --> pdb=" O PHE C 145 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 107 through 110 Processing sheet with id=AB7, first strand: chain 'C' and resid 161 through 167 removed outlier: 6.687A pdb=" N VAL C 202 " --> pdb=" O TYR C 192 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N TYR C 192 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ASP C 204 " --> pdb=" O TYR C 190 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL C 179 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LEU C 178 " --> pdb=" O ILE C 251 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N PHE C 253 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N TYR C 180 " --> pdb=" O PHE C 253 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N PHE C 221 " --> pdb=" O TYR C 271 " (cutoff:3.500A) removed outlier: 8.824A pdb=" N PHE C 268 " --> pdb=" O MET C 162 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N HIS C 164 " --> pdb=" O PHE C 268 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU C 270 " --> pdb=" O HIS C 164 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLN C 166 " --> pdb=" O LEU C 270 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 227 through 229 removed outlier: 3.676A pdb=" N VAL C 227 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU D 240 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA C 229 " --> pdb=" O VAL D 238 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 340 through 344 removed outlier: 6.185A pdb=" N LEU C 300 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLU C 324 " --> pdb=" O THR C 311 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LEU C 313 " --> pdb=" O THR C 322 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N THR C 322 " --> pdb=" O LEU C 313 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL C 321 " --> pdb=" O LEU C 287 " (cutoff:3.500A) removed outlier: 8.784A pdb=" N PHE C 377 " --> pdb=" O ILE C 282 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LYS C 284 " --> pdb=" O PHE C 377 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 393 through 399 removed outlier: 6.478A pdb=" N THR C 432 " --> pdb=" O ARG C 424 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ARG C 424 " --> pdb=" O THR C 432 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N THR C 434 " --> pdb=" O ILE C 422 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU C 411 " --> pdb=" O VAL C 418 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ILE C 483 " --> pdb=" O PRO C 410 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE C 412 " --> pdb=" O ILE C 483 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N PHE C 451 " --> pdb=" O TYR C 498 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N TYR C 495 " --> pdb=" O THR C 394 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N THR C 396 " --> pdb=" O TYR C 495 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU C 497 " --> pdb=" O THR C 396 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N THR C 398 " --> pdb=" O LEU C 497 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 65 through 68 removed outlier: 6.022A pdb=" N TYR D 68 " --> pdb=" O GLU D 72 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N GLU D 72 " --> pdb=" O TYR D 68 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LYS D 91 " --> pdb=" O GLN D 77 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ILE D 79 " --> pdb=" O GLU D 89 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N GLU D 89 " --> pdb=" O ILE D 79 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N THR D 50 " --> pdb=" O PHE D 145 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 107 through 110 Processing sheet with id=AC4, first strand: chain 'D' and resid 161 through 167 removed outlier: 6.687A pdb=" N VAL D 202 " --> pdb=" O TYR D 192 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N TYR D 192 " --> pdb=" O VAL D 202 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ASP D 204 " --> pdb=" O TYR D 190 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL D 179 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU D 178 " --> pdb=" O ILE D 251 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N PHE D 253 " --> pdb=" O LEU D 178 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N TYR D 180 " --> pdb=" O PHE D 253 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N PHE D 221 " --> pdb=" O TYR D 271 " (cutoff:3.500A) removed outlier: 8.824A pdb=" N PHE D 268 " --> pdb=" O MET D 162 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N HIS D 164 " --> pdb=" O PHE D 268 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU D 270 " --> pdb=" O HIS D 164 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLN D 166 " --> pdb=" O LEU D 270 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 227 through 229 removed outlier: 3.683A pdb=" N VAL D 227 " --> pdb=" O LEU E 240 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU E 240 " --> pdb=" O VAL D 227 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA D 229 " --> pdb=" O VAL E 238 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 340 through 344 removed outlier: 6.184A pdb=" N LEU D 300 " --> pdb=" O VAL D 307 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N GLU D 324 " --> pdb=" O THR D 311 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU D 313 " --> pdb=" O THR D 322 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N THR D 322 " --> pdb=" O LEU D 313 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL D 321 " --> pdb=" O LEU D 287 " (cutoff:3.500A) removed outlier: 8.784A pdb=" N PHE D 377 " --> pdb=" O ILE D 282 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LYS D 284 " --> pdb=" O PHE D 377 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 393 through 399 removed outlier: 6.479A pdb=" N THR D 432 " --> pdb=" O ARG D 424 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ARG D 424 " --> pdb=" O THR D 432 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N THR D 434 " --> pdb=" O ILE D 422 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU D 411 " --> pdb=" O VAL D 418 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ILE D 483 " --> pdb=" O PRO D 410 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE D 412 " --> pdb=" O ILE D 483 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N PHE D 451 " --> pdb=" O TYR D 498 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N TYR D 495 " --> pdb=" O THR D 394 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N THR D 396 " --> pdb=" O TYR D 495 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LEU D 497 " --> pdb=" O THR D 396 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N THR D 398 " --> pdb=" O LEU D 497 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 65 through 68 removed outlier: 6.022A pdb=" N TYR E 68 " --> pdb=" O GLU E 72 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N GLU E 72 " --> pdb=" O TYR E 68 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LYS E 91 " --> pdb=" O GLN E 77 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ILE E 79 " --> pdb=" O GLU E 89 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N GLU E 89 " --> pdb=" O ILE E 79 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N THR E 50 " --> pdb=" O PHE E 145 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 107 through 110 Processing sheet with id=AD1, first strand: chain 'E' and resid 161 through 167 removed outlier: 6.687A pdb=" N VAL E 202 " --> pdb=" O TYR E 192 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N TYR E 192 " --> pdb=" O VAL E 202 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ASP E 204 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL E 179 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU E 178 " --> pdb=" O ILE E 251 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N PHE E 253 " --> pdb=" O LEU E 178 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N TYR E 180 " --> pdb=" O PHE E 253 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N PHE E 221 " --> pdb=" O TYR E 271 " (cutoff:3.500A) removed outlier: 8.824A pdb=" N PHE E 268 " --> pdb=" O MET E 162 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N HIS E 164 " --> pdb=" O PHE E 268 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU E 270 " --> pdb=" O HIS E 164 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLN E 166 " --> pdb=" O LEU E 270 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 227 through 229 removed outlier: 3.678A pdb=" N VAL E 227 " --> pdb=" O LEU F 240 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU F 240 " --> pdb=" O VAL E 227 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA E 229 " --> pdb=" O VAL F 238 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 340 through 344 removed outlier: 6.185A pdb=" N LEU E 300 " --> pdb=" O VAL E 307 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLU E 324 " --> pdb=" O THR E 311 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LEU E 313 " --> pdb=" O THR E 322 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N THR E 322 " --> pdb=" O LEU E 313 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL E 321 " --> pdb=" O LEU E 287 " (cutoff:3.500A) removed outlier: 8.784A pdb=" N PHE E 377 " --> pdb=" O ILE E 282 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LYS E 284 " --> pdb=" O PHE E 377 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 393 through 399 removed outlier: 6.478A pdb=" N THR E 432 " --> pdb=" O ARG E 424 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ARG E 424 " --> pdb=" O THR E 432 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N THR E 434 " --> pdb=" O ILE E 422 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU E 411 " --> pdb=" O VAL E 418 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ILE E 483 " --> pdb=" O PRO E 410 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE E 412 " --> pdb=" O ILE E 483 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N PHE E 451 " --> pdb=" O TYR E 498 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N TYR E 495 " --> pdb=" O THR E 394 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N THR E 396 " --> pdb=" O TYR E 495 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU E 497 " --> pdb=" O THR E 396 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N THR E 398 " --> pdb=" O LEU E 497 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 65 through 68 removed outlier: 6.021A pdb=" N TYR F 68 " --> pdb=" O GLU F 72 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N GLU F 72 " --> pdb=" O TYR F 68 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LYS F 91 " --> pdb=" O GLN F 77 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ILE F 79 " --> pdb=" O GLU F 89 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N GLU F 89 " --> pdb=" O ILE F 79 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N THR F 50 " --> pdb=" O PHE F 145 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 107 through 110 Processing sheet with id=AD7, first strand: chain 'F' and resid 161 through 167 removed outlier: 6.687A pdb=" N VAL F 202 " --> pdb=" O TYR F 192 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N TYR F 192 " --> pdb=" O VAL F 202 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ASP F 204 " --> pdb=" O TYR F 190 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL F 179 " --> pdb=" O VAL F 186 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LEU F 178 " --> pdb=" O ILE F 251 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N PHE F 253 " --> pdb=" O LEU F 178 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N TYR F 180 " --> pdb=" O PHE F 253 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N PHE F 221 " --> pdb=" O TYR F 271 " (cutoff:3.500A) removed outlier: 8.824A pdb=" N PHE F 268 " --> pdb=" O MET F 162 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N HIS F 164 " --> pdb=" O PHE F 268 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU F 270 " --> pdb=" O HIS F 164 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLN F 166 " --> pdb=" O LEU F 270 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 340 through 344 removed outlier: 6.185A pdb=" N LEU F 300 " --> pdb=" O VAL F 307 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N GLU F 324 " --> pdb=" O THR F 311 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LEU F 313 " --> pdb=" O THR F 322 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N THR F 322 " --> pdb=" O LEU F 313 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL F 321 " --> pdb=" O LEU F 287 " (cutoff:3.500A) removed outlier: 8.784A pdb=" N PHE F 377 " --> pdb=" O ILE F 282 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LYS F 284 " --> pdb=" O PHE F 377 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 393 through 399 removed outlier: 6.478A pdb=" N THR F 432 " --> pdb=" O ARG F 424 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ARG F 424 " --> pdb=" O THR F 432 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N THR F 434 " --> pdb=" O ILE F 422 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU F 411 " --> pdb=" O VAL F 418 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ILE F 483 " --> pdb=" O PRO F 410 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE F 412 " --> pdb=" O ILE F 483 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N PHE F 451 " --> pdb=" O TYR F 498 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N TYR F 495 " --> pdb=" O THR F 394 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N THR F 396 " --> pdb=" O TYR F 495 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU F 497 " --> pdb=" O THR F 396 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N THR F 398 " --> pdb=" O LEU F 497 " (cutoff:3.500A) 474 hydrogen bonds defined for protein. 1080 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: 3.84 Time building geometry restraints manager: 2.44 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: 6648 1.34 - 1.45: 2299 1.45 - 1.57: 11333 1.57 - 1.69: 0 1.69 - 1.80: 96 Bond restraints: 20376 Sorted by residual: bond pdb=" C GLU D 286 " pdb=" N LEU D 287 " ideal model delta sigma weight residual 1.329 1.231 0.098 3.03e-02 1.09e+03 1.04e+01 bond pdb=" C GLU A 286 " pdb=" N LEU A 287 " ideal model delta sigma weight residual 1.329 1.231 0.098 3.03e-02 1.09e+03 1.04e+01 bond pdb=" C GLU C 286 " pdb=" N LEU C 287 " ideal model delta sigma weight residual 1.329 1.231 0.098 3.03e-02 1.09e+03 1.04e+01 bond pdb=" C GLU B 286 " pdb=" N LEU B 287 " ideal model delta sigma weight residual 1.329 1.232 0.097 3.03e-02 1.09e+03 1.03e+01 bond pdb=" C GLU F 286 " pdb=" N LEU F 287 " ideal model delta sigma weight residual 1.329 1.232 0.097 3.03e-02 1.09e+03 1.03e+01 ... (remaining 20371 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 26166 1.35 - 2.71: 1145 2.71 - 4.06: 237 4.06 - 5.42: 58 5.42 - 6.77: 6 Bond angle restraints: 27612 Sorted by residual: angle pdb=" C VAL F 421 " pdb=" N ILE F 422 " pdb=" CA ILE F 422 " ideal model delta sigma weight residual 123.16 119.01 4.15 1.06e+00 8.90e-01 1.53e+01 angle pdb=" C VAL C 421 " pdb=" N ILE C 422 " pdb=" CA ILE C 422 " ideal model delta sigma weight residual 123.16 119.01 4.15 1.06e+00 8.90e-01 1.53e+01 angle pdb=" C VAL E 421 " pdb=" N ILE E 422 " pdb=" CA ILE E 422 " ideal model delta sigma weight residual 123.16 119.02 4.14 1.06e+00 8.90e-01 1.53e+01 angle pdb=" C VAL B 421 " pdb=" N ILE B 422 " pdb=" CA ILE B 422 " ideal model delta sigma weight residual 123.16 119.02 4.14 1.06e+00 8.90e-01 1.53e+01 angle pdb=" C VAL A 421 " pdb=" N ILE A 422 " pdb=" CA ILE A 422 " ideal model delta sigma weight residual 123.16 119.03 4.13 1.06e+00 8.90e-01 1.52e+01 ... (remaining 27607 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.69: 11170 15.69 - 31.38: 951 31.38 - 47.07: 221 47.07 - 62.76: 36 62.76 - 78.45: 30 Dihedral angle restraints: 12408 sinusoidal: 4944 harmonic: 7464 Sorted by residual: dihedral pdb=" CA GLN F 420 " pdb=" C GLN F 420 " pdb=" N VAL F 421 " pdb=" CA VAL F 421 " ideal model delta harmonic sigma weight residual 180.00 160.24 19.76 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA GLN C 420 " pdb=" C GLN C 420 " pdb=" N VAL C 421 " pdb=" CA VAL C 421 " ideal model delta harmonic sigma weight residual 180.00 160.24 19.76 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA GLN E 420 " pdb=" C GLN E 420 " pdb=" N VAL E 421 " pdb=" CA VAL E 421 " ideal model delta harmonic sigma weight residual 180.00 160.25 19.75 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 12405 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1772 0.029 - 0.059: 863 0.059 - 0.088: 267 0.088 - 0.117: 272 0.117 - 0.146: 54 Chirality restraints: 3228 Sorted by residual: chirality pdb=" CA ILE F 184 " pdb=" N ILE F 184 " pdb=" C ILE F 184 " pdb=" CB ILE F 184 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.35e-01 chirality pdb=" CA ILE C 184 " pdb=" N ILE C 184 " pdb=" C ILE C 184 " pdb=" CB ILE C 184 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.27e-01 chirality pdb=" CA ILE B 184 " pdb=" N ILE B 184 " pdb=" C ILE B 184 " pdb=" CB ILE B 184 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.20e-01 ... (remaining 3225 not shown) Planarity restraints: 3588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 195 " 0.031 5.00e-02 4.00e+02 4.67e-02 3.49e+00 pdb=" N PRO C 196 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO C 196 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 196 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN F 195 " 0.031 5.00e-02 4.00e+02 4.67e-02 3.48e+00 pdb=" N PRO F 196 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO F 196 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO F 196 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN D 195 " 0.031 5.00e-02 4.00e+02 4.66e-02 3.48e+00 pdb=" N PRO D 196 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO D 196 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 196 " 0.026 5.00e-02 4.00e+02 ... (remaining 3585 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1935 2.73 - 3.28: 19585 3.28 - 3.82: 30920 3.82 - 4.36: 38685 4.36 - 4.90: 66653 Nonbonded interactions: 157778 Sorted by model distance: nonbonded pdb=" OG1 THR E 294 " pdb=" O ASP E 296 " model vdw 2.194 3.040 nonbonded pdb=" OG1 THR B 294 " pdb=" O ASP B 296 " model vdw 2.194 3.040 nonbonded pdb=" OG1 THR D 294 " pdb=" O ASP D 296 " model vdw 2.194 3.040 nonbonded pdb=" OG1 THR A 294 " pdb=" O ASP A 296 " model vdw 2.194 3.040 nonbonded pdb=" OG1 THR C 294 " pdb=" O ASP C 296 " model vdw 2.194 3.040 ... (remaining 157773 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 2.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 17.550 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 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 : 0.006 0.098 20376 Z= 0.267 Angle : 0.676 6.770 27612 Z= 0.369 Chirality : 0.047 0.146 3228 Planarity : 0.004 0.047 3588 Dihedral : 13.186 78.448 7644 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.21 % Favored : 88.79 % Rotamer: Outliers : 0.82 % Allowed : 6.20 % Favored : 92.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.17 (0.13), residues: 2622 helix: -4.79 (0.13), residues: 186 sheet: -2.54 (0.14), residues: 816 loop : -2.73 (0.13), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 67 TYR 0.010 0.001 TYR B 131 PHE 0.012 0.001 PHE B 253 TRP 0.009 0.001 TRP B 222 HIS 0.002 0.000 HIS F 388 Details of bonding type rmsd covalent geometry : bond 0.00607 (20376) covalent geometry : angle 0.67563 (27612) hydrogen bonds : bond 0.14904 ( 474) hydrogen bonds : angle 9.46380 ( 1080) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 228 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.8246 (mtp85) cc_final: 0.7911 (ttm-80) REVERT: A 365 GLU cc_start: 0.8248 (tp30) cc_final: 0.7902 (tp30) REVERT: B 190 TYR cc_start: 0.8551 (t80) cc_final: 0.8276 (t80) REVERT: B 314 ASP cc_start: 0.7737 (m-30) cc_final: 0.7338 (m-30) REVERT: B 325 MET cc_start: 0.8691 (ttm) cc_final: 0.8421 (ttp) REVERT: C 63 ARG cc_start: 0.8404 (mtp85) cc_final: 0.8127 (ttm-80) REVERT: C 135 MET cc_start: 0.8322 (tpp) cc_final: 0.7636 (mmm) REVERT: C 190 TYR cc_start: 0.8738 (t80) cc_final: 0.8491 (t80) REVERT: C 314 ASP cc_start: 0.7808 (m-30) cc_final: 0.7427 (m-30) REVERT: D 63 ARG cc_start: 0.8248 (mtp85) cc_final: 0.7913 (ttm-80) REVERT: D 365 GLU cc_start: 0.8256 (tp30) cc_final: 0.7907 (tp30) REVERT: E 190 TYR cc_start: 0.8560 (t80) cc_final: 0.8282 (t80) REVERT: E 314 ASP cc_start: 0.7754 (m-30) cc_final: 0.7354 (m-30) REVERT: E 325 MET cc_start: 0.8730 (ttm) cc_final: 0.8404 (ttp) REVERT: F 63 ARG cc_start: 0.8398 (mtp85) cc_final: 0.8121 (ttm-80) REVERT: F 135 MET cc_start: 0.8321 (tpp) cc_final: 0.7630 (mmm) REVERT: F 190 TYR cc_start: 0.8746 (t80) cc_final: 0.8510 (t80) REVERT: F 314 ASP cc_start: 0.7815 (m-30) cc_final: 0.7174 (m-30) outliers start: 18 outliers final: 9 residues processed: 246 average time/residue: 0.1701 time to fit residues: 60.9154 Evaluate side-chains 164 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 155 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 434 THR Chi-restraints excluded: chain E residue 434 THR Chi-restraints excluded: chain F residue 434 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN B 316 ASN C 316 ASN C 420 GLN D 316 ASN E 316 ASN F 316 ASN F 420 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.111296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.075639 restraints weight = 29832.690| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 2.99 r_work: 0.2738 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 20376 Z= 0.210 Angle : 0.638 10.371 27612 Z= 0.318 Chirality : 0.047 0.149 3228 Planarity : 0.005 0.054 3588 Dihedral : 5.529 44.597 2811 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 1.49 % Allowed : 8.83 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.37 (0.15), residues: 2622 helix: -3.92 (0.23), residues: 222 sheet: -1.88 (0.14), residues: 954 loop : -2.19 (0.16), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 155 TYR 0.011 0.001 TYR B 131 PHE 0.011 0.001 PHE B 253 TRP 0.009 0.001 TRP A 222 HIS 0.003 0.001 HIS A 276 Details of bonding type rmsd covalent geometry : bond 0.00488 (20376) covalent geometry : angle 0.63803 (27612) hydrogen bonds : bond 0.03508 ( 474) hydrogen bonds : angle 7.23414 ( 1080) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 174 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.8596 (mtp85) cc_final: 0.8251 (ttm-80) REVERT: A 365 GLU cc_start: 0.8747 (tp30) cc_final: 0.8310 (tp30) REVERT: B 63 ARG cc_start: 0.8725 (mtp85) cc_final: 0.8323 (ttm-80) REVERT: B 325 MET cc_start: 0.9075 (ttm) cc_final: 0.8855 (ttp) REVERT: C 63 ARG cc_start: 0.8654 (mtp85) cc_final: 0.8346 (ttm-80) REVERT: C 135 MET cc_start: 0.8355 (tpp) cc_final: 0.8129 (tpp) REVERT: C 314 ASP cc_start: 0.8409 (m-30) cc_final: 0.8200 (m-30) REVERT: D 63 ARG cc_start: 0.8596 (mtp85) cc_final: 0.8253 (ttm-80) REVERT: D 365 GLU cc_start: 0.8742 (tp30) cc_final: 0.8298 (tp30) REVERT: E 63 ARG cc_start: 0.8711 (mtp85) cc_final: 0.8299 (ttm-80) REVERT: E 325 MET cc_start: 0.9077 (ttm) cc_final: 0.8805 (ttp) REVERT: F 63 ARG cc_start: 0.8657 (mtp85) cc_final: 0.8235 (ttm-80) REVERT: F 135 MET cc_start: 0.8369 (tpp) cc_final: 0.8130 (tpp) outliers start: 33 outliers final: 22 residues processed: 200 average time/residue: 0.1555 time to fit residues: 47.0510 Evaluate side-chains 179 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 213 ASP Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain D residue 162 MET Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 434 THR Chi-restraints excluded: chain E residue 487 ASP Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 434 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 259 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 252 optimal weight: 1.9990 chunk 200 optimal weight: 0.9980 chunk 106 optimal weight: 9.9990 chunk 86 optimal weight: 2.9990 chunk 168 optimal weight: 0.9980 chunk 158 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 95 optimal weight: 4.9990 chunk 122 optimal weight: 0.6980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.111116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.075445 restraints weight = 30177.438| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 3.02 r_work: 0.2738 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 20376 Z= 0.205 Angle : 0.611 10.241 27612 Z= 0.303 Chirality : 0.046 0.149 3228 Planarity : 0.005 0.052 3588 Dihedral : 5.067 21.860 2806 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.73 % Favored : 90.27 % Rotamer: Outliers : 1.90 % Allowed : 11.14 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.82 (0.16), residues: 2622 helix: -3.77 (0.25), residues: 186 sheet: -1.60 (0.15), residues: 978 loop : -1.77 (0.17), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 86 TYR 0.016 0.001 TYR A 131 PHE 0.010 0.001 PHE E 108 TRP 0.009 0.002 TRP A 222 HIS 0.003 0.001 HIS D 276 Details of bonding type rmsd covalent geometry : bond 0.00476 (20376) covalent geometry : angle 0.61135 (27612) hydrogen bonds : bond 0.03107 ( 474) hydrogen bonds : angle 6.84265 ( 1080) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 175 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.8502 (mtp85) cc_final: 0.8106 (ttm-80) REVERT: A 365 GLU cc_start: 0.8766 (tp30) cc_final: 0.8564 (tp30) REVERT: B 63 ARG cc_start: 0.8758 (mtp85) cc_final: 0.8443 (ttm-80) REVERT: B 190 TYR cc_start: 0.8887 (t80) cc_final: 0.8564 (t80) REVERT: B 491 MET cc_start: 0.8844 (mmm) cc_final: 0.8582 (mmm) REVERT: C 63 ARG cc_start: 0.8637 (mtp85) cc_final: 0.8196 (ttm-80) REVERT: D 63 ARG cc_start: 0.8512 (mtp85) cc_final: 0.8123 (ttm-80) REVERT: D 365 GLU cc_start: 0.8768 (tp30) cc_final: 0.8554 (tp30) REVERT: E 63 ARG cc_start: 0.8757 (mtp85) cc_final: 0.8437 (ttm-80) REVERT: E 325 MET cc_start: 0.9086 (ttm) cc_final: 0.8886 (ttp) REVERT: E 491 MET cc_start: 0.8839 (mmm) cc_final: 0.8579 (mmm) REVERT: F 63 ARG cc_start: 0.8670 (mtp85) cc_final: 0.8346 (ttm-80) outliers start: 42 outliers final: 20 residues processed: 209 average time/residue: 0.1414 time to fit residues: 46.4153 Evaluate side-chains 187 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 167 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain D residue 162 MET Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 505 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 191 optimal weight: 0.9990 chunk 162 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 180 optimal weight: 3.9990 chunk 235 optimal weight: 0.8980 chunk 171 optimal weight: 1.9990 chunk 263 optimal weight: 0.4980 chunk 153 optimal weight: 1.9990 chunk 194 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.111861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.076137 restraints weight = 29910.215| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 3.01 r_work: 0.2746 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 20376 Z= 0.181 Angle : 0.595 10.067 27612 Z= 0.294 Chirality : 0.046 0.147 3228 Planarity : 0.005 0.050 3588 Dihedral : 4.911 21.532 2802 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.57 % Favored : 90.43 % Rotamer: Outliers : 1.81 % Allowed : 13.99 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.63 (0.16), residues: 2622 helix: -3.50 (0.26), residues: 222 sheet: -1.34 (0.15), residues: 978 loop : -1.70 (0.17), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 86 TYR 0.018 0.001 TYR C 131 PHE 0.010 0.001 PHE E 253 TRP 0.009 0.001 TRP A 222 HIS 0.003 0.001 HIS D 276 Details of bonding type rmsd covalent geometry : bond 0.00420 (20376) covalent geometry : angle 0.59460 (27612) hydrogen bonds : bond 0.02853 ( 474) hydrogen bonds : angle 6.58173 ( 1080) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 167 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.8493 (mtp85) cc_final: 0.8076 (ttm-80) REVERT: A 365 GLU cc_start: 0.8752 (tp30) cc_final: 0.8296 (tp30) REVERT: A 491 MET cc_start: 0.8839 (mmt) cc_final: 0.8580 (mmp) REVERT: B 63 ARG cc_start: 0.8762 (mtp85) cc_final: 0.8452 (ttm-80) REVERT: B 98 MET cc_start: 0.8601 (ttm) cc_final: 0.8275 (ttt) REVERT: C 63 ARG cc_start: 0.8596 (mtp85) cc_final: 0.8182 (ttm-80) REVERT: D 63 ARG cc_start: 0.8510 (mtp85) cc_final: 0.8102 (ttm-80) REVERT: D 365 GLU cc_start: 0.8752 (tp30) cc_final: 0.8293 (tp30) REVERT: D 491 MET cc_start: 0.8825 (mmt) cc_final: 0.8568 (mmp) REVERT: E 63 ARG cc_start: 0.8760 (mtp85) cc_final: 0.8445 (ttm-80) REVERT: E 98 MET cc_start: 0.8584 (ttm) cc_final: 0.8252 (ttt) REVERT: F 63 ARG cc_start: 0.8594 (mtp85) cc_final: 0.8177 (ttm-80) outliers start: 40 outliers final: 19 residues processed: 197 average time/residue: 0.1520 time to fit residues: 45.6282 Evaluate side-chains 180 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 161 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain D residue 162 MET Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 505 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 30 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 chunk 107 optimal weight: 9.9990 chunk 246 optimal weight: 0.0050 chunk 148 optimal weight: 0.1980 chunk 163 optimal weight: 0.0370 chunk 111 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 254 optimal weight: 1.9990 overall best weight: 0.3872 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.114378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.078688 restraints weight = 29668.693| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 3.03 r_work: 0.2783 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20376 Z= 0.115 Angle : 0.576 10.529 27612 Z= 0.277 Chirality : 0.045 0.146 3228 Planarity : 0.004 0.048 3588 Dihedral : 4.525 20.594 2802 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer: Outliers : 1.72 % Allowed : 15.08 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.30 (0.16), residues: 2622 helix: -3.36 (0.27), residues: 222 sheet: -1.06 (0.16), residues: 978 loop : -1.52 (0.17), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 86 TYR 0.010 0.001 TYR F 131 PHE 0.009 0.001 PHE E 253 TRP 0.008 0.001 TRP F 222 HIS 0.001 0.000 HIS D 144 Details of bonding type rmsd covalent geometry : bond 0.00259 (20376) covalent geometry : angle 0.57553 (27612) hydrogen bonds : bond 0.02558 ( 474) hydrogen bonds : angle 6.25727 ( 1080) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 185 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.8513 (mtp85) cc_final: 0.8124 (ttm-80) REVERT: A 312 LYS cc_start: 0.8954 (tttt) cc_final: 0.8696 (mtpp) REVERT: B 63 ARG cc_start: 0.8678 (mtp85) cc_final: 0.8280 (ttm-80) REVERT: B 98 MET cc_start: 0.8569 (ttm) cc_final: 0.8264 (ttt) REVERT: C 63 ARG cc_start: 0.8696 (mtp85) cc_final: 0.8169 (ttm-80) REVERT: C 145 PHE cc_start: 0.8587 (m-80) cc_final: 0.8302 (m-80) REVERT: D 63 ARG cc_start: 0.8525 (mtp85) cc_final: 0.8145 (ttm-80) REVERT: D 312 LYS cc_start: 0.8953 (tttt) cc_final: 0.8700 (mtpp) REVERT: E 63 ARG cc_start: 0.8682 (mtp85) cc_final: 0.8277 (ttm-80) REVERT: E 98 MET cc_start: 0.8566 (ttm) cc_final: 0.8256 (ttt) REVERT: E 491 MET cc_start: 0.8848 (mmm) cc_final: 0.8568 (mmm) REVERT: F 63 ARG cc_start: 0.8686 (mtp85) cc_final: 0.8129 (ttm-80) REVERT: F 145 PHE cc_start: 0.8581 (m-80) cc_final: 0.8302 (m-80) outliers start: 38 outliers final: 21 residues processed: 209 average time/residue: 0.1353 time to fit residues: 44.1616 Evaluate side-chains 183 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 162 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 162 MET Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 505 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 90 optimal weight: 1.9990 chunk 137 optimal weight: 0.0770 chunk 142 optimal weight: 0.1980 chunk 80 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 overall best weight: 1.0342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 199 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.111910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.075846 restraints weight = 29791.955| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 3.03 r_work: 0.2735 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 20376 Z= 0.230 Angle : 0.626 10.028 27612 Z= 0.305 Chirality : 0.047 0.148 3228 Planarity : 0.005 0.046 3588 Dihedral : 4.870 21.899 2802 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.61 % Favored : 90.39 % Rotamer: Outliers : 1.99 % Allowed : 15.44 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.16), residues: 2622 helix: -3.50 (0.26), residues: 186 sheet: -1.03 (0.16), residues: 978 loop : -1.39 (0.17), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 86 TYR 0.013 0.001 TYR C 131 PHE 0.010 0.001 PHE E 253 TRP 0.009 0.001 TRP A 222 HIS 0.003 0.001 HIS A 276 Details of bonding type rmsd covalent geometry : bond 0.00538 (20376) covalent geometry : angle 0.62596 (27612) hydrogen bonds : bond 0.02873 ( 474) hydrogen bonds : angle 6.47988 ( 1080) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 160 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 MET cc_start: 0.8412 (mmt) cc_final: 0.8163 (mmm) REVERT: A 63 ARG cc_start: 0.8515 (mtp85) cc_final: 0.8085 (ttm-80) REVERT: A 376 GLU cc_start: 0.8453 (pm20) cc_final: 0.8216 (pm20) REVERT: B 63 ARG cc_start: 0.8687 (mtp85) cc_final: 0.8281 (ttm-80) REVERT: B 98 MET cc_start: 0.8571 (ttm) cc_final: 0.8283 (ttt) REVERT: C 63 ARG cc_start: 0.8547 (mtp85) cc_final: 0.8110 (ttm-80) REVERT: D 54 MET cc_start: 0.8421 (mmt) cc_final: 0.8174 (mmm) REVERT: D 63 ARG cc_start: 0.8514 (mtp85) cc_final: 0.8090 (ttm-80) REVERT: D 365 GLU cc_start: 0.8736 (tp30) cc_final: 0.8531 (tp30) REVERT: D 376 GLU cc_start: 0.8460 (pm20) cc_final: 0.8223 (pm20) REVERT: E 63 ARG cc_start: 0.8671 (mtp85) cc_final: 0.8260 (ttm-80) REVERT: E 98 MET cc_start: 0.8549 (ttm) cc_final: 0.8259 (ttt) REVERT: F 63 ARG cc_start: 0.8552 (mtp85) cc_final: 0.8112 (ttm-80) outliers start: 44 outliers final: 34 residues processed: 197 average time/residue: 0.1358 time to fit residues: 42.3620 Evaluate side-chains 188 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 154 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain E residue 376 GLU Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 505 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 152 optimal weight: 0.5980 chunk 148 optimal weight: 0.5980 chunk 160 optimal weight: 0.7980 chunk 263 optimal weight: 0.3980 chunk 248 optimal weight: 1.9990 chunk 173 optimal weight: 0.2980 chunk 242 optimal weight: 0.5980 chunk 146 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 205 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.113950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.077928 restraints weight = 29860.679| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 3.04 r_work: 0.2771 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 20376 Z= 0.134 Angle : 0.594 10.410 27612 Z= 0.284 Chirality : 0.045 0.148 3228 Planarity : 0.004 0.048 3588 Dihedral : 4.590 21.022 2802 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 1.49 % Allowed : 16.17 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.16), residues: 2622 helix: -3.24 (0.27), residues: 222 sheet: -0.83 (0.16), residues: 978 loop : -1.42 (0.17), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 86 TYR 0.010 0.001 TYR C 131 PHE 0.010 0.001 PHE B 253 TRP 0.008 0.001 TRP A 222 HIS 0.002 0.001 HIS C 144 Details of bonding type rmsd covalent geometry : bond 0.00304 (20376) covalent geometry : angle 0.59439 (27612) hydrogen bonds : bond 0.02570 ( 474) hydrogen bonds : angle 6.28391 ( 1080) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 161 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 MET cc_start: 0.8392 (mmt) cc_final: 0.8140 (mmm) REVERT: A 63 ARG cc_start: 0.8500 (mtp85) cc_final: 0.8049 (ttm-80) REVERT: A 376 GLU cc_start: 0.8407 (pm20) cc_final: 0.8154 (pm20) REVERT: B 63 ARG cc_start: 0.8666 (mtp85) cc_final: 0.8280 (ttm-80) REVERT: B 98 MET cc_start: 0.8578 (ttm) cc_final: 0.8278 (ttt) REVERT: C 63 ARG cc_start: 0.8702 (mtp85) cc_final: 0.8172 (ttm-80) REVERT: C 145 PHE cc_start: 0.8716 (m-80) cc_final: 0.8398 (m-80) REVERT: D 54 MET cc_start: 0.8401 (mmt) cc_final: 0.8152 (mmm) REVERT: D 63 ARG cc_start: 0.8505 (mtp85) cc_final: 0.8061 (ttm-80) REVERT: D 365 GLU cc_start: 0.8659 (tp30) cc_final: 0.8165 (tp30) REVERT: D 376 GLU cc_start: 0.8411 (pm20) cc_final: 0.8159 (pm20) REVERT: E 63 ARG cc_start: 0.8650 (mtp85) cc_final: 0.8253 (ttm-80) REVERT: E 98 MET cc_start: 0.8568 (ttm) cc_final: 0.8265 (ttt) REVERT: F 63 ARG cc_start: 0.8699 (mtp85) cc_final: 0.8168 (ttm-80) REVERT: F 145 PHE cc_start: 0.8680 (m-80) cc_final: 0.8375 (m-80) outliers start: 33 outliers final: 29 residues processed: 186 average time/residue: 0.1388 time to fit residues: 40.7313 Evaluate side-chains 186 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 157 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 162 MET Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 376 GLU Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 505 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 199 optimal weight: 0.9990 chunk 184 optimal weight: 2.9990 chunk 245 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 219 optimal weight: 0.4980 chunk 57 optimal weight: 0.5980 chunk 234 optimal weight: 0.0270 chunk 10 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 overall best weight: 0.5640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.113304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.077161 restraints weight = 29748.853| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 3.05 r_work: 0.2766 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20376 Z= 0.146 Angle : 0.602 10.486 27612 Z= 0.289 Chirality : 0.045 0.145 3228 Planarity : 0.004 0.047 3588 Dihedral : 4.572 21.361 2802 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.27 % Favored : 90.73 % Rotamer: Outliers : 1.59 % Allowed : 16.08 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.16), residues: 2622 helix: -2.81 (0.33), residues: 186 sheet: -0.69 (0.16), residues: 966 loop : -1.47 (0.17), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 86 TYR 0.011 0.001 TYR C 131 PHE 0.009 0.001 PHE B 253 TRP 0.007 0.001 TRP A 222 HIS 0.002 0.001 HIS A 276 Details of bonding type rmsd covalent geometry : bond 0.00336 (20376) covalent geometry : angle 0.60189 (27612) hydrogen bonds : bond 0.02572 ( 474) hydrogen bonds : angle 6.26492 ( 1080) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 159 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 MET cc_start: 0.8411 (mmt) cc_final: 0.8153 (mmm) REVERT: A 63 ARG cc_start: 0.8494 (mtp85) cc_final: 0.8045 (ttm-80) REVERT: A 376 GLU cc_start: 0.8420 (pm20) cc_final: 0.8166 (pm20) REVERT: B 63 ARG cc_start: 0.8676 (mtp85) cc_final: 0.8289 (ttm-80) REVERT: B 98 MET cc_start: 0.8487 (ttm) cc_final: 0.8194 (ttt) REVERT: C 63 ARG cc_start: 0.8701 (mtp85) cc_final: 0.8168 (ttm-80) REVERT: C 145 PHE cc_start: 0.8724 (m-80) cc_final: 0.8399 (m-80) REVERT: D 54 MET cc_start: 0.8414 (mmt) cc_final: 0.8161 (mmm) REVERT: D 63 ARG cc_start: 0.8495 (mtp85) cc_final: 0.8053 (ttm-80) REVERT: D 365 GLU cc_start: 0.8643 (tp30) cc_final: 0.8140 (tp30) REVERT: D 376 GLU cc_start: 0.8430 (pm20) cc_final: 0.8179 (pm20) REVERT: E 63 ARG cc_start: 0.8670 (mtp85) cc_final: 0.8280 (ttm-80) REVERT: E 98 MET cc_start: 0.8581 (ttm) cc_final: 0.8285 (ttt) REVERT: F 63 ARG cc_start: 0.8704 (mtp85) cc_final: 0.8168 (ttm-80) REVERT: F 145 PHE cc_start: 0.8718 (m-80) cc_final: 0.8402 (m-80) outliers start: 35 outliers final: 32 residues processed: 185 average time/residue: 0.1394 time to fit residues: 40.6500 Evaluate side-chains 187 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 155 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 162 MET Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain E residue 376 GLU Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 505 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 32 optimal weight: 0.0030 chunk 144 optimal weight: 0.0370 chunk 18 optimal weight: 10.0000 chunk 108 optimal weight: 1.9990 chunk 169 optimal weight: 0.9990 chunk 190 optimal weight: 1.9990 chunk 151 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 225 optimal weight: 3.9990 chunk 192 optimal weight: 0.9980 chunk 35 optimal weight: 0.0870 overall best weight: 0.3446 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 354 ASN ** 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 = 0.3525 r_free = 0.3525 target = 0.115783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.079716 restraints weight = 29447.143| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 3.05 r_work: 0.2798 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 20376 Z= 0.111 Angle : 0.589 10.869 27612 Z= 0.279 Chirality : 0.045 0.145 3228 Planarity : 0.004 0.046 3588 Dihedral : 4.375 20.458 2802 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer: Outliers : 1.45 % Allowed : 16.30 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.17), residues: 2622 helix: -2.77 (0.33), residues: 186 sheet: -0.54 (0.17), residues: 966 loop : -1.41 (0.17), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 86 TYR 0.009 0.001 TYR C 131 PHE 0.008 0.001 PHE B 253 TRP 0.008 0.001 TRP C 222 HIS 0.002 0.000 HIS F 144 Details of bonding type rmsd covalent geometry : bond 0.00249 (20376) covalent geometry : angle 0.58852 (27612) hydrogen bonds : bond 0.02436 ( 474) hydrogen bonds : angle 6.11521 ( 1080) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 164 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 MET cc_start: 0.8419 (mmt) cc_final: 0.8183 (mmm) REVERT: A 63 ARG cc_start: 0.8501 (mtp85) cc_final: 0.8050 (ttm-80) REVERT: A 376 GLU cc_start: 0.8390 (pm20) cc_final: 0.8103 (pm20) REVERT: B 63 ARG cc_start: 0.8642 (mtp85) cc_final: 0.8239 (ttm-80) REVERT: B 98 MET cc_start: 0.8452 (ttm) cc_final: 0.8206 (ttt) REVERT: C 63 ARG cc_start: 0.8687 (mtp85) cc_final: 0.8148 (ttm-80) REVERT: C 145 PHE cc_start: 0.8578 (m-80) cc_final: 0.8283 (m-80) REVERT: D 54 MET cc_start: 0.8420 (mmt) cc_final: 0.8186 (mmm) REVERT: D 63 ARG cc_start: 0.8501 (mtp85) cc_final: 0.8058 (ttm-80) REVERT: E 63 ARG cc_start: 0.8620 (mtp85) cc_final: 0.8201 (ttm-80) REVERT: E 98 MET cc_start: 0.8457 (ttm) cc_final: 0.8207 (ttt) REVERT: F 63 ARG cc_start: 0.8687 (mtp85) cc_final: 0.8144 (ttm-80) REVERT: F 145 PHE cc_start: 0.8582 (m-80) cc_final: 0.8239 (m-80) outliers start: 32 outliers final: 29 residues processed: 188 average time/residue: 0.1314 time to fit residues: 39.2211 Evaluate side-chains 188 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 159 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 162 MET Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain E residue 376 GLU Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain F residue 505 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 173 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 chunk 194 optimal weight: 0.3980 chunk 183 optimal weight: 2.9990 chunk 75 optimal weight: 0.0470 chunk 261 optimal weight: 0.3980 chunk 68 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 225 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 237 optimal weight: 0.6980 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 354 ASN ** 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 = 0.3508 r_free = 0.3508 target = 0.114664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.078781 restraints weight = 29601.286| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 3.03 r_work: 0.2790 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 20376 Z= 0.123 Angle : 0.597 10.746 27612 Z= 0.282 Chirality : 0.045 0.144 3228 Planarity : 0.004 0.046 3588 Dihedral : 4.380 20.800 2802 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 1.45 % Allowed : 16.30 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.17), residues: 2622 helix: -2.68 (0.33), residues: 186 sheet: -0.46 (0.17), residues: 966 loop : -1.38 (0.17), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 86 TYR 0.009 0.001 TYR F 131 PHE 0.008 0.001 PHE B 253 TRP 0.007 0.001 TRP A 222 HIS 0.001 0.001 HIS A 276 Details of bonding type rmsd covalent geometry : bond 0.00282 (20376) covalent geometry : angle 0.59675 (27612) hydrogen bonds : bond 0.02456 ( 474) hydrogen bonds : angle 6.09603 ( 1080) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 158 time to evaluate : 0.660 Fit side-chains revert: symmetry clash REVERT: A 54 MET cc_start: 0.8374 (mmt) cc_final: 0.8121 (mmm) REVERT: A 63 ARG cc_start: 0.8516 (mtp85) cc_final: 0.8066 (ttm-80) REVERT: A 406 ASP cc_start: 0.7846 (t0) cc_final: 0.7493 (m-30) REVERT: B 63 ARG cc_start: 0.8589 (mtp85) cc_final: 0.8170 (ttm-80) REVERT: B 98 MET cc_start: 0.8499 (ttm) cc_final: 0.8217 (ttt) REVERT: C 63 ARG cc_start: 0.8707 (mtp85) cc_final: 0.8171 (ttm-80) REVERT: C 145 PHE cc_start: 0.8592 (m-80) cc_final: 0.8294 (m-80) REVERT: D 54 MET cc_start: 0.8394 (mmt) cc_final: 0.8145 (mmm) REVERT: D 63 ARG cc_start: 0.8498 (mtp85) cc_final: 0.8067 (ttm-80) REVERT: D 406 ASP cc_start: 0.7823 (t0) cc_final: 0.7472 (m-30) REVERT: E 63 ARG cc_start: 0.8614 (mtp85) cc_final: 0.8200 (ttm-80) REVERT: E 98 MET cc_start: 0.8490 (ttm) cc_final: 0.8209 (ttt) REVERT: F 63 ARG cc_start: 0.8711 (mtp85) cc_final: 0.8173 (ttm-80) REVERT: F 145 PHE cc_start: 0.8597 (m-80) cc_final: 0.8302 (m-80) outliers start: 32 outliers final: 27 residues processed: 183 average time/residue: 0.1391 time to fit residues: 40.2406 Evaluate side-chains 183 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 156 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 162 MET Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain E residue 376 GLU Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain F residue 505 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 114 optimal weight: 0.4980 chunk 168 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 109 optimal weight: 1.9990 chunk 214 optimal weight: 1.9990 chunk 230 optimal weight: 0.9980 chunk 120 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 175 optimal weight: 2.9990 chunk 203 optimal weight: 0.0970 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 354 ASN ** 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 = 0.3504 r_free = 0.3504 target = 0.114261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.078396 restraints weight = 29690.281| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 3.04 r_work: 0.2784 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20376 Z= 0.139 Angle : 0.596 10.619 27612 Z= 0.284 Chirality : 0.045 0.145 3228 Planarity : 0.004 0.046 3588 Dihedral : 4.439 21.557 2802 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 1.40 % Allowed : 16.58 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.17), residues: 2622 helix: -3.07 (0.29), residues: 186 sheet: -0.44 (0.17), residues: 966 loop : -1.17 (0.17), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 86 TYR 0.010 0.001 TYR C 131 PHE 0.008 0.001 PHE B 253 TRP 0.007 0.001 TRP A 222 HIS 0.002 0.001 HIS A 276 Details of bonding type rmsd covalent geometry : bond 0.00320 (20376) covalent geometry : angle 0.59616 (27612) hydrogen bonds : bond 0.02514 ( 474) hydrogen bonds : angle 6.12950 ( 1080) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3772.01 seconds wall clock time: 65 minutes 30.75 seconds (3930.75 seconds total)