Starting phenix.real_space_refine on Sat Sep 28 19:13:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kz3_0784/09_2024/6kz3_0784.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kz3_0784/09_2024/6kz3_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kz3_0784/09_2024/6kz3_0784.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kz3_0784/09_2024/6kz3_0784.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kz3_0784/09_2024/6kz3_0784.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kz3_0784/09_2024/6kz3_0784.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: C, B, E, D, F Time building chain proxies: 8.46, per 1000 atoms: 0.42 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: 4.76 Conformation dependent library (CDL) restraints added in 2.5 seconds 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: 2.77 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: 7.57 Time building geometry restraints manager: 5.57 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: 0.00 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: 2.380 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: 0.770 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 41.660 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.760 ------------------------------------------------------------------------------- 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= 0.395 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 : 9.64 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.17 (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 TRP 0.009 0.001 TRP B 222 HIS 0.002 0.000 HIS F 388 PHE 0.012 0.001 PHE B 253 TYR 0.010 0.001 TYR B 131 ARG 0.002 0.000 ARG A 67 *********************** 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 fitting. rotamer outliers: 18 poor density : 228 time to evaluate : 2.213 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: 0.8690 (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: 0.8397 (mtp85) cc_final: 0.8121 (ttm-80) REVERT: F 135 MET cc_start: 0.8322 (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: 0.3605 time to fit residues: 129.3726 Evaluate side-chains 164 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 155 time to evaluate : 2.311 ------------------------------------------------------------------------------- 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 222 optimal weight: 0.8980 chunk 200 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 134 optimal weight: 0.5980 chunk 106 optimal weight: 7.9990 chunk 206 optimal weight: 0.3980 chunk 80 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 154 optimal weight: 0.9980 chunk 239 optimal weight: 9.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20376 Z= 0.284 Angle : 0.627 10.560 27612 Z= 0.311 Chirality : 0.047 0.150 3228 Planarity : 0.005 0.053 3588 Dihedral : 5.445 43.352 2811 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 1.54 % Allowed : 8.88 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.31 (0.15), residues: 2622 helix: -3.91 (0.23), residues: 222 sheet: -1.84 (0.14), residues: 954 loop : -2.15 (0.16), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP F 222 HIS 0.002 0.001 HIS A 276 PHE 0.010 0.001 PHE B 253 TYR 0.011 0.001 TYR B 131 ARG 0.005 0.000 ARG D 155 *********************** 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 209 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 175 time to evaluate : 2.401 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.8292 (mtp85) cc_final: 0.7980 (ttm-80) REVERT: A 365 GLU cc_start: 0.8232 (tp30) cc_final: 0.7818 (tp30) REVERT: B 63 ARG cc_start: 0.8460 (mtp85) cc_final: 0.8163 (ttm-80) REVERT: B 325 MET cc_start: 0.8722 (ttm) cc_final: 0.8485 (ttp) REVERT: C 63 ARG cc_start: 0.8421 (mtp85) cc_final: 0.8045 (ttm-80) REVERT: C 491 MET cc_start: 0.8488 (tpp) cc_final: 0.8275 (mmp) REVERT: D 63 ARG cc_start: 0.8288 (mtp85) cc_final: 0.7982 (ttm-80) REVERT: D 365 GLU cc_start: 0.8244 (tp30) cc_final: 0.7827 (tp30) REVERT: E 63 ARG cc_start: 0.8462 (mtp85) cc_final: 0.8076 (ttm-80) REVERT: E 190 TYR cc_start: 0.8388 (t80) cc_final: 0.8118 (t80) REVERT: E 325 MET cc_start: 0.8721 (ttm) cc_final: 0.8479 (ttp) REVERT: F 63 ARG cc_start: 0.8419 (mtp85) cc_final: 0.8043 (ttm-80) REVERT: F 491 MET cc_start: 0.8476 (tpp) cc_final: 0.8264 (mmp) outliers start: 34 outliers final: 17 residues processed: 202 average time/residue: 0.3342 time to fit residues: 102.2946 Evaluate side-chains 172 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 155 time to evaluate : 2.257 ------------------------------------------------------------------------------- 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 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 287 LEU Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 434 THR 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 133 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 199 optimal weight: 2.9990 chunk 163 optimal weight: 0.2980 chunk 66 optimal weight: 1.9990 chunk 240 optimal weight: 1.9990 chunk 259 optimal weight: 1.9990 chunk 213 optimal weight: 1.9990 chunk 238 optimal weight: 8.9990 chunk 81 optimal weight: 0.5980 chunk 192 optimal weight: 0.1980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 HIS C 164 HIS F 164 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 20376 Z= 0.278 Angle : 0.598 10.178 27612 Z= 0.296 Chirality : 0.046 0.145 3228 Planarity : 0.005 0.051 3588 Dihedral : 4.963 21.753 2806 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 1.81 % Allowed : 11.68 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.16), residues: 2622 helix: -3.78 (0.24), residues: 186 sheet: -1.56 (0.15), residues: 978 loop : -1.73 (0.17), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 222 HIS 0.002 0.001 HIS A 276 PHE 0.009 0.001 PHE B 253 TYR 0.016 0.001 TYR A 131 ARG 0.002 0.000 ARG E 442 *********************** 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 fitting. rotamer outliers: 40 poor density : 177 time to evaluate : 2.162 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.8201 (mtp85) cc_final: 0.7851 (ttm-80) REVERT: A 365 GLU cc_start: 0.8266 (tp30) cc_final: 0.7841 (tp30) REVERT: B 63 ARG cc_start: 0.8492 (mtp85) cc_final: 0.8183 (ttm-80) REVERT: B 190 TYR cc_start: 0.8413 (t80) cc_final: 0.8194 (t80) REVERT: B 491 MET cc_start: 0.8770 (mmm) cc_final: 0.8548 (mmm) REVERT: C 63 ARG cc_start: 0.8329 (mtp85) cc_final: 0.7940 (ttm-80) REVERT: C 491 MET cc_start: 0.8475 (tpp) cc_final: 0.8245 (tpp) REVERT: D 63 ARG cc_start: 0.8196 (mtp85) cc_final: 0.7851 (ttm-80) REVERT: D 365 GLU cc_start: 0.8278 (tp30) cc_final: 0.7846 (tp30) REVERT: E 63 ARG cc_start: 0.8490 (mtp85) cc_final: 0.8179 (ttm-80) REVERT: E 190 TYR cc_start: 0.8412 (t80) cc_final: 0.8079 (t80) REVERT: E 491 MET cc_start: 0.8775 (mmm) cc_final: 0.8552 (mmm) REVERT: F 63 ARG cc_start: 0.8386 (mtp85) cc_final: 0.7988 (ttm-80) REVERT: F 491 MET cc_start: 0.8465 (tpp) cc_final: 0.8238 (tpp) outliers start: 40 outliers final: 15 residues processed: 210 average time/residue: 0.3145 time to fit residues: 102.2412 Evaluate side-chains 178 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 163 time to evaluate : 2.158 ------------------------------------------------------------------------------- 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 238 VAL Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 435 VAL 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 287 LEU Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 435 VAL 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 237 optimal weight: 0.9990 chunk 180 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 114 optimal weight: 0.9980 chunk 161 optimal weight: 2.9990 chunk 241 optimal weight: 5.9990 chunk 255 optimal weight: 0.2980 chunk 125 optimal weight: 0.5980 chunk 228 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 164 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 20376 Z= 0.242 Angle : 0.584 10.134 27612 Z= 0.287 Chirality : 0.046 0.145 3228 Planarity : 0.004 0.050 3588 Dihedral : 4.795 21.203 2802 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 1.90 % Allowed : 13.32 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.16), residues: 2622 helix: -3.24 (0.30), residues: 186 sheet: -1.32 (0.15), residues: 978 loop : -1.76 (0.17), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 222 HIS 0.002 0.001 HIS D 276 PHE 0.010 0.001 PHE B 253 TYR 0.012 0.001 TYR A 131 ARG 0.002 0.000 ARG D 86 *********************** 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 fitting. rotamer outliers: 42 poor density : 165 time to evaluate : 2.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.8186 (mtp85) cc_final: 0.7830 (ttm-80) REVERT: A 365 GLU cc_start: 0.8264 (tp30) cc_final: 0.7832 (tp30) REVERT: A 491 MET cc_start: 0.8806 (mmt) cc_final: 0.8443 (mmp) REVERT: B 63 ARG cc_start: 0.8475 (mtp85) cc_final: 0.8177 (ttm-80) REVERT: B 98 MET cc_start: 0.8358 (ttm) cc_final: 0.8094 (ttt) REVERT: B 190 TYR cc_start: 0.8289 (t80) cc_final: 0.8088 (t80) REVERT: C 63 ARG cc_start: 0.8284 (mtp85) cc_final: 0.7925 (ttm-80) REVERT: C 491 MET cc_start: 0.8436 (tpp) cc_final: 0.8168 (tpp) REVERT: D 63 ARG cc_start: 0.8183 (mtp85) cc_final: 0.7831 (ttm-80) REVERT: D 365 GLU cc_start: 0.8271 (tp30) cc_final: 0.7838 (tp30) REVERT: D 491 MET cc_start: 0.8798 (mmt) cc_final: 0.8429 (mmp) REVERT: E 63 ARG cc_start: 0.8475 (mtp85) cc_final: 0.8178 (ttm-80) REVERT: F 63 ARG cc_start: 0.8306 (mtp85) cc_final: 0.7947 (ttm-80) REVERT: F 491 MET cc_start: 0.8425 (tpp) cc_final: 0.8158 (tpp) outliers start: 42 outliers final: 22 residues processed: 197 average time/residue: 0.3256 time to fit residues: 98.6233 Evaluate side-chains 183 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 161 time to evaluate : 2.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 163 ILE 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 287 LEU Chi-restraints excluded: chain B residue 356 SER 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 D residue 162 MET Chi-restraints excluded: chain D residue 163 ILE 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 212 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 190 optimal weight: 0.0770 chunk 105 optimal weight: 0.5980 chunk 217 optimal weight: 0.8980 chunk 176 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 130 optimal weight: 0.0020 chunk 229 optimal weight: 0.0050 chunk 64 optimal weight: 0.5980 overall best weight: 0.2560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 20376 Z= 0.141 Angle : 0.564 10.639 27612 Z= 0.271 Chirality : 0.045 0.144 3228 Planarity : 0.004 0.048 3588 Dihedral : 4.358 20.073 2802 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.00 % Favored : 91.00 % Rotamer: Outliers : 1.45 % Allowed : 15.40 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.16), residues: 2622 helix: -3.09 (0.31), residues: 186 sheet: -1.00 (0.16), residues: 978 loop : -1.58 (0.17), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 222 HIS 0.001 0.000 HIS A 144 PHE 0.008 0.001 PHE F 108 TYR 0.008 0.001 TYR D 68 ARG 0.003 0.000 ARG D 86 *********************** 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 213 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 181 time to evaluate : 2.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.8151 (mtp85) cc_final: 0.7765 (ttm-80) REVERT: B 63 ARG cc_start: 0.8342 (mtp85) cc_final: 0.7978 (ttm-80) REVERT: B 98 MET cc_start: 0.8340 (ttm) cc_final: 0.8109 (ttt) REVERT: C 63 ARG cc_start: 0.8398 (mtp85) cc_final: 0.7912 (ttm-80) REVERT: C 491 MET cc_start: 0.8417 (tpp) cc_final: 0.8076 (tpp) REVERT: D 63 ARG cc_start: 0.8150 (mtp85) cc_final: 0.7764 (ttm-80) REVERT: E 63 ARG cc_start: 0.8347 (mtp85) cc_final: 0.7983 (ttm-80) REVERT: E 98 MET cc_start: 0.8246 (ttm) cc_final: 0.8031 (ttt) REVERT: F 63 ARG cc_start: 0.8391 (mtp85) cc_final: 0.7906 (ttm-80) REVERT: F 491 MET cc_start: 0.8443 (tpp) cc_final: 0.8084 (tpp) outliers start: 32 outliers final: 16 residues processed: 201 average time/residue: 0.3231 time to fit residues: 99.8825 Evaluate side-chains 177 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 161 time to evaluate : 2.449 ------------------------------------------------------------------------------- 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 162 MET Chi-restraints excluded: chain B residue 238 VAL 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 162 MET 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 85 optimal weight: 1.9990 chunk 229 optimal weight: 6.9990 chunk 50 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 255 optimal weight: 0.9980 chunk 212 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 chunk 21 optimal weight: 0.0030 chunk 84 optimal weight: 0.6980 chunk 134 optimal weight: 1.9990 overall best weight: 0.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 164 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 20376 Z= 0.319 Angle : 0.613 9.864 27612 Z= 0.299 Chirality : 0.046 0.147 3228 Planarity : 0.005 0.046 3588 Dihedral : 4.765 21.999 2802 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.73 % Favored : 90.27 % Rotamer: Outliers : 1.95 % Allowed : 15.40 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.16), residues: 2622 helix: -3.47 (0.26), residues: 186 sheet: -0.96 (0.16), residues: 978 loop : -1.34 (0.17), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 222 HIS 0.003 0.001 HIS A 276 PHE 0.013 0.001 PHE C 145 TYR 0.011 0.001 TYR A 131 ARG 0.003 0.000 ARG C 424 *********************** 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 203 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 160 time to evaluate : 2.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.8154 (mtp85) cc_final: 0.7778 (ttm-80) REVERT: A 365 GLU cc_start: 0.8264 (tp30) cc_final: 0.7834 (tp30) REVERT: A 376 GLU cc_start: 0.7841 (pm20) cc_final: 0.7610 (pm20) REVERT: B 63 ARG cc_start: 0.8389 (mtp85) cc_final: 0.8016 (ttm-80) REVERT: B 98 MET cc_start: 0.8324 (ttm) cc_final: 0.8080 (ttt) REVERT: C 63 ARG cc_start: 0.8433 (mtp85) cc_final: 0.7903 (ttm-80) REVERT: C 491 MET cc_start: 0.8489 (tpp) cc_final: 0.8194 (tpp) REVERT: D 63 ARG cc_start: 0.8152 (mtp85) cc_final: 0.7780 (ttm-80) REVERT: D 365 GLU cc_start: 0.8278 (tp30) cc_final: 0.7843 (tp30) REVERT: D 376 GLU cc_start: 0.7832 (pm20) cc_final: 0.7600 (pm20) REVERT: E 63 ARG cc_start: 0.8386 (mtp85) cc_final: 0.8011 (ttm-80) REVERT: E 98 MET cc_start: 0.8332 (ttm) cc_final: 0.8101 (ttt) REVERT: F 63 ARG cc_start: 0.8420 (mtp85) cc_final: 0.7895 (ttm-80) REVERT: F 491 MET cc_start: 0.8484 (tpp) cc_final: 0.8190 (tpp) outliers start: 43 outliers final: 28 residues processed: 195 average time/residue: 0.3171 time to fit residues: 98.1735 Evaluate side-chains 186 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 158 time to evaluate : 2.289 ------------------------------------------------------------------------------- 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 238 VAL 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 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 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 246 optimal weight: 0.0370 chunk 28 optimal weight: 0.4980 chunk 145 optimal weight: 0.0970 chunk 186 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 chunk 215 optimal weight: 0.7980 chunk 142 optimal weight: 2.9990 chunk 254 optimal weight: 2.9990 chunk 159 optimal weight: 0.6980 chunk 155 optimal weight: 0.9980 chunk 117 optimal weight: 4.9990 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 20376 Z= 0.183 Angle : 0.582 10.468 27612 Z= 0.280 Chirality : 0.045 0.146 3228 Planarity : 0.004 0.047 3588 Dihedral : 4.485 20.723 2802 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 1.36 % Allowed : 15.90 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.16), residues: 2622 helix: -2.94 (0.32), residues: 186 sheet: -0.81 (0.16), residues: 978 loop : -1.47 (0.17), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 222 HIS 0.002 0.000 HIS A 144 PHE 0.013 0.001 PHE F 145 TYR 0.009 0.001 TYR E 131 ARG 0.003 0.000 ARG A 86 *********************** 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 fitting. rotamer outliers: 30 poor density : 164 time to evaluate : 2.291 Fit side-chains REVERT: A 63 ARG cc_start: 0.8140 (mtp85) cc_final: 0.7739 (ttm-80) REVERT: A 365 GLU cc_start: 0.8208 (tp30) cc_final: 0.7743 (tp30) REVERT: A 376 GLU cc_start: 0.7795 (pm20) cc_final: 0.7545 (pm20) REVERT: B 63 ARG cc_start: 0.8363 (mtp85) cc_final: 0.8004 (ttm-80) REVERT: B 98 MET cc_start: 0.8281 (ttm) cc_final: 0.8064 (ttt) REVERT: C 63 ARG cc_start: 0.8406 (mtp85) cc_final: 0.7911 (ttm-80) REVERT: C 491 MET cc_start: 0.8532 (tpp) cc_final: 0.8168 (tpp) REVERT: D 63 ARG cc_start: 0.8134 (mtp85) cc_final: 0.7733 (ttm-80) REVERT: D 365 GLU cc_start: 0.8219 (tp30) cc_final: 0.7748 (tp30) REVERT: D 376 GLU cc_start: 0.7785 (pm20) cc_final: 0.7536 (pm20) REVERT: E 63 ARG cc_start: 0.8368 (mtp85) cc_final: 0.8007 (ttm-80) REVERT: E 98 MET cc_start: 0.8330 (ttm) cc_final: 0.8114 (ttt) REVERT: F 63 ARG cc_start: 0.8396 (mtp85) cc_final: 0.7904 (ttm-80) REVERT: F 491 MET cc_start: 0.8524 (tpp) cc_final: 0.8164 (tpp) outliers start: 30 outliers final: 26 residues processed: 186 average time/residue: 0.3039 time to fit residues: 88.8919 Evaluate side-chains 189 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 163 time to evaluate : 2.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR 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 238 VAL 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 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 157 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 chunk 151 optimal weight: 9.9990 chunk 76 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 chunk 173 optimal weight: 0.7980 chunk 125 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 200 optimal weight: 1.9990 chunk 231 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 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 : 0.005 0.038 20376 Z= 0.296 Angle : 0.617 10.162 27612 Z= 0.299 Chirality : 0.046 0.147 3228 Planarity : 0.004 0.047 3588 Dihedral : 4.708 21.832 2802 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 1.45 % Allowed : 16.17 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.16), residues: 2622 helix: -3.34 (0.27), residues: 186 sheet: -0.79 (0.16), residues: 978 loop : -1.28 (0.17), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 222 HIS 0.003 0.001 HIS D 276 PHE 0.011 0.001 PHE C 145 TYR 0.010 0.001 TYR A 131 ARG 0.003 0.000 ARG D 86 *********************** 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 191 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 159 time to evaluate : 2.325 Fit side-chains REVERT: A 63 ARG cc_start: 0.8090 (mtp85) cc_final: 0.7756 (ttm-80) REVERT: A 365 GLU cc_start: 0.8159 (tp30) cc_final: 0.7694 (tp30) REVERT: A 376 GLU cc_start: 0.7843 (pm20) cc_final: 0.7605 (pm20) REVERT: B 63 ARG cc_start: 0.8390 (mtp85) cc_final: 0.8033 (ttm-80) REVERT: B 98 MET cc_start: 0.8326 (ttm) cc_final: 0.8091 (ttt) REVERT: C 63 ARG cc_start: 0.8428 (mtp85) cc_final: 0.7899 (ttm-80) REVERT: C 491 MET cc_start: 0.8561 (tpp) cc_final: 0.8219 (tpp) REVERT: D 63 ARG cc_start: 0.8087 (mtp85) cc_final: 0.7754 (ttm-80) REVERT: D 365 GLU cc_start: 0.8174 (tp30) cc_final: 0.7706 (tp30) REVERT: D 376 GLU cc_start: 0.7832 (pm20) cc_final: 0.7595 (pm20) REVERT: E 63 ARG cc_start: 0.8386 (mtp85) cc_final: 0.8025 (ttm-80) REVERT: E 98 MET cc_start: 0.8322 (ttm) cc_final: 0.8095 (ttt) REVERT: F 63 ARG cc_start: 0.8414 (mtp85) cc_final: 0.7889 (ttm-80) REVERT: F 491 MET cc_start: 0.8550 (tpp) cc_final: 0.8213 (tpp) outliers start: 32 outliers final: 31 residues processed: 183 average time/residue: 0.3094 time to fit residues: 88.7867 Evaluate side-chains 190 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 159 time to evaluate : 2.462 ------------------------------------------------------------------------------- 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 238 VAL 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 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 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 243 optimal weight: 1.9990 chunk 222 optimal weight: 0.7980 chunk 237 optimal weight: 0.5980 chunk 142 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 chunk 186 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 214 optimal weight: 0.8980 chunk 224 optimal weight: 2.9990 chunk 236 optimal weight: 0.9990 chunk 155 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 20376 Z= 0.271 Angle : 0.617 10.091 27612 Z= 0.297 Chirality : 0.046 0.147 3228 Planarity : 0.004 0.050 3588 Dihedral : 4.697 21.398 2802 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.34 % Favored : 90.66 % Rotamer: Outliers : 1.45 % Allowed : 16.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.17), residues: 2622 helix: -3.26 (0.28), residues: 186 sheet: -0.75 (0.16), residues: 978 loop : -1.26 (0.17), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 222 HIS 0.002 0.001 HIS A 276 PHE 0.011 0.001 PHE C 145 TYR 0.010 0.001 TYR E 131 ARG 0.004 0.000 ARG A 86 *********************** 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 194 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 162 time to evaluate : 2.130 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.8117 (mtp85) cc_final: 0.7730 (ttm-80) REVERT: A 365 GLU cc_start: 0.8161 (tp30) cc_final: 0.7956 (tp30) REVERT: A 376 GLU cc_start: 0.7837 (pm20) cc_final: 0.7573 (pm20) REVERT: B 63 ARG cc_start: 0.8388 (mtp85) cc_final: 0.8022 (ttm-80) REVERT: B 98 MET cc_start: 0.8311 (ttm) cc_final: 0.8087 (ttt) REVERT: C 63 ARG cc_start: 0.8432 (mtp85) cc_final: 0.7931 (ttm-80) REVERT: C 491 MET cc_start: 0.8643 (tpp) cc_final: 0.8334 (tpp) REVERT: D 63 ARG cc_start: 0.8114 (mtp85) cc_final: 0.7729 (ttm-80) REVERT: D 365 GLU cc_start: 0.8175 (tp30) cc_final: 0.7963 (tp30) REVERT: D 376 GLU cc_start: 0.7830 (pm20) cc_final: 0.7565 (pm20) REVERT: E 63 ARG cc_start: 0.8383 (mtp85) cc_final: 0.8027 (ttm-80) REVERT: E 98 MET cc_start: 0.8311 (ttm) cc_final: 0.8093 (ttt) REVERT: F 63 ARG cc_start: 0.8410 (mtp85) cc_final: 0.7887 (ttm-80) REVERT: F 491 MET cc_start: 0.8632 (tpp) cc_final: 0.8327 (tpp) outliers start: 32 outliers final: 31 residues processed: 186 average time/residue: 0.2962 time to fit residues: 86.8371 Evaluate side-chains 191 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 160 time to evaluate : 2.392 ------------------------------------------------------------------------------- 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 238 VAL 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 250 optimal weight: 2.9990 chunk 153 optimal weight: 0.0020 chunk 118 optimal weight: 0.0030 chunk 174 optimal weight: 0.9990 chunk 263 optimal weight: 0.9990 chunk 242 optimal weight: 0.9980 chunk 209 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 chunk 161 optimal weight: 0.7980 chunk 128 optimal weight: 1.9990 chunk 166 optimal weight: 0.7980 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 20376 Z= 0.183 Angle : 0.595 10.638 27612 Z= 0.283 Chirality : 0.045 0.146 3228 Planarity : 0.004 0.049 3588 Dihedral : 4.420 21.006 2802 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 1.54 % Allowed : 16.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.17), residues: 2622 helix: -2.67 (0.33), residues: 186 sheet: -0.60 (0.16), residues: 978 loop : -1.40 (0.17), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 222 HIS 0.002 0.001 HIS A 276 PHE 0.011 0.001 PHE C 145 TYR 0.008 0.001 TYR E 131 ARG 0.004 0.000 ARG A 86 ********************** 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 202 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 168 time to evaluate : 2.288 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 MET cc_start: 0.8092 (mmt) cc_final: 0.7873 (mmm) REVERT: A 63 ARG cc_start: 0.8121 (mtp85) cc_final: 0.7728 (ttm-80) REVERT: A 365 GLU cc_start: 0.8208 (tp30) cc_final: 0.7722 (tp30) REVERT: A 376 GLU cc_start: 0.7796 (pm20) cc_final: 0.7516 (pm20) REVERT: A 406 ASP cc_start: 0.7369 (t0) cc_final: 0.7101 (m-30) REVERT: B 63 ARG cc_start: 0.8282 (mtp85) cc_final: 0.7903 (ttm-80) REVERT: C 63 ARG cc_start: 0.8398 (mtp85) cc_final: 0.7904 (ttm-80) REVERT: D 63 ARG cc_start: 0.8115 (mtp85) cc_final: 0.7725 (ttm-80) REVERT: D 365 GLU cc_start: 0.8220 (tp30) cc_final: 0.7736 (tp30) REVERT: D 376 GLU cc_start: 0.7788 (pm20) cc_final: 0.7509 (pm20) REVERT: D 406 ASP cc_start: 0.7367 (t0) cc_final: 0.7099 (m-30) REVERT: E 63 ARG cc_start: 0.8325 (mtp85) cc_final: 0.7949 (ttm-80) REVERT: E 98 MET cc_start: 0.8221 (ttm) cc_final: 0.8017 (ttt) REVERT: F 63 ARG cc_start: 0.8382 (mtp85) cc_final: 0.7890 (ttm-80) outliers start: 34 outliers final: 31 residues processed: 195 average time/residue: 0.3055 time to fit residues: 94.2074 Evaluate side-chains 195 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 164 time to evaluate : 2.405 ------------------------------------------------------------------------------- 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 238 VAL 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 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 505 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 223 optimal weight: 0.8980 chunk 64 optimal weight: 0.5980 chunk 193 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 chunk 58 optimal weight: 0.0670 chunk 209 optimal weight: 0.0040 chunk 87 optimal weight: 0.6980 chunk 215 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 184 optimal weight: 2.9990 overall best weight: 0.4330 ------------------------------------------------------------------------------- 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 = 0.3518 r_free = 0.3518 target = 0.115513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.079301 restraints weight = 29638.216| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 3.06 r_work: 0.2790 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2288 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= 0.186 Angle : 0.592 10.665 27612 Z= 0.282 Chirality : 0.045 0.145 3228 Planarity : 0.004 0.049 3588 Dihedral : 4.394 21.350 2802 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 1.54 % Allowed : 16.35 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.17), residues: 2622 helix: -1.93 (0.44), residues: 114 sheet: -0.49 (0.17), residues: 966 loop : -1.21 (0.17), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 222 HIS 0.001 0.000 HIS A 276 PHE 0.012 0.001 PHE C 145 TYR 0.008 0.001 TYR B 131 ARG 0.004 0.000 ARG D 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3687.64 seconds wall clock time: 67 minutes 0.42 seconds (4020.42 seconds total)