Starting phenix.real_space_refine on Wed Jun 25 20:46:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9atl_43830/06_2025/9atl_43830.cif Found real_map, /net/cci-nas-00/data/ceres_data/9atl_43830/06_2025/9atl_43830.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9atl_43830/06_2025/9atl_43830.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9atl_43830/06_2025/9atl_43830.map" model { file = "/net/cci-nas-00/data/ceres_data/9atl_43830/06_2025/9atl_43830.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9atl_43830/06_2025/9atl_43830.cif" } resolution = 3.26 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 ------------------------------------------------------------------------------- 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= 0.008 sd= 0.039 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 44 5.16 5 C 18623 2.51 5 N 5555 2.21 5 O 6490 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 30712 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 2792 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 1, 'TRANS': 388} Chain: "B" Number of atoms: 2792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 2792 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 1, 'TRANS': 388} Chain: "C" Number of atoms: 2792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 2792 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 1, 'TRANS': 388} Chain: "D" Number of atoms: 2792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 2792 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 1, 'TRANS': 388} Chain: "E" Number of atoms: 2792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 2792 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 1, 'TRANS': 388} Chain: "F" Number of atoms: 2792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 2792 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 1, 'TRANS': 388} Chain: "G" Number of atoms: 2792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 2792 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 1, 'TRANS': 388} Chain: "H" Number of atoms: 2792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 2792 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 1, 'TRANS': 388} Chain: "I" Number of atoms: 2792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 2792 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 1, 'TRANS': 388} Chain: "J" Number of atoms: 2792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 2792 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 1, 'TRANS': 388} Chain: "K" Number of atoms: 2792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 2792 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 1, 'TRANS': 388} Time building chain proxies: 16.94, per 1000 atoms: 0.55 Number of scatterers: 30712 At special positions: 0 Unit cell: (183.15, 182.04, 235.32, 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 44 16.00 O 6490 8.00 N 5555 7.00 C 18623 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: 7.19 Conformation dependent library (CDL) restraints added in 3.9 seconds 8536 Ramachandran restraints generated. 4268 Oldfield, 0 Emsley, 4268 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7876 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 64 sheets defined 57.4% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.16 Creating SS restraints... Processing helix chain 'A' and resid 8 through 35 removed outlier: 3.739A pdb=" N ARG A 16 " --> pdb=" O LEU A 12 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N SER A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N LEU A 25 " --> pdb=" O SER A 21 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ALA A 26 " --> pdb=" O GLY A 22 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N THR A 27 " --> pdb=" O SER A 23 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY A 35 " --> pdb=" O ARG A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 98 removed outlier: 3.869A pdb=" N VAL A 63 " --> pdb=" O ARG A 59 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLU A 84 " --> pdb=" O GLY A 80 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLN A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 129 removed outlier: 3.867A pdb=" N GLU A 115 " --> pdb=" O ALA A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 225 removed outlier: 3.597A pdb=" N ALA A 218 " --> pdb=" O ASP A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 231 Processing helix chain 'A' and resid 254 through 256 No H-bonds generated for 'chain 'A' and resid 254 through 256' Processing helix chain 'A' and resid 298 through 349 removed outlier: 3.683A pdb=" N ALA A 302 " --> pdb=" O THR A 298 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N GLU A 307 " --> pdb=" O GLN A 303 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER A 349 " --> pdb=" O SER A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 352 No H-bonds generated for 'chain 'A' and resid 350 through 352' Processing helix chain 'A' and resid 355 through 383 removed outlier: 3.562A pdb=" N GLU A 359 " --> pdb=" O ASP A 355 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N THR A 360 " --> pdb=" O PHE A 356 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ALA A 361 " --> pdb=" O ALA A 357 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU A 362 " --> pdb=" O LYS A 358 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN A 371 " --> pdb=" O GLN A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 391 removed outlier: 3.722A pdb=" N VAL A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER A 389 " --> pdb=" O GLY A 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 35 removed outlier: 3.627A pdb=" N GLN B 15 " --> pdb=" O SER B 11 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG B 16 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N SER B 24 " --> pdb=" O THR B 20 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LEU B 25 " --> pdb=" O SER B 21 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ALA B 26 " --> pdb=" O GLY B 22 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N THR B 27 " --> pdb=" O SER B 23 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY B 35 " --> pdb=" O ARG B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 98 removed outlier: 4.128A pdb=" N VAL B 63 " --> pdb=" O ARG B 59 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU B 84 " --> pdb=" O GLY B 80 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLN B 98 " --> pdb=" O GLU B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 129 removed outlier: 3.943A pdb=" N GLU B 115 " --> pdb=" O ALA B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 170 removed outlier: 4.252A pdb=" N LEU B 170 " --> pdb=" O ALA B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 225 Processing helix chain 'B' and resid 254 through 256 No H-bonds generated for 'chain 'B' and resid 254 through 256' Processing helix chain 'B' and resid 298 through 349 removed outlier: 3.651A pdb=" N ALA B 302 " --> pdb=" O THR B 298 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N GLU B 307 " --> pdb=" O GLN B 303 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER B 349 " --> pdb=" O SER B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 383 removed outlier: 3.934A pdb=" N THR B 360 " --> pdb=" O PHE B 356 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ALA B 361 " --> pdb=" O ALA B 357 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLU B 362 " --> pdb=" O LYS B 358 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN B 371 " --> pdb=" O GLN B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 391 removed outlier: 3.894A pdb=" N VAL B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 35 removed outlier: 3.700A pdb=" N GLN C 15 " --> pdb=" O SER C 11 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG C 16 " --> pdb=" O LEU C 12 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N SER C 24 " --> pdb=" O THR C 20 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N LEU C 25 " --> pdb=" O SER C 21 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ALA C 26 " --> pdb=" O GLY C 22 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N THR C 27 " --> pdb=" O SER C 23 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY C 35 " --> pdb=" O ARG C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 98 removed outlier: 3.939A pdb=" N VAL C 63 " --> pdb=" O ARG C 59 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU C 84 " --> pdb=" O GLY C 80 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLN C 98 " --> pdb=" O GLU C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 129 removed outlier: 3.949A pdb=" N GLU C 115 " --> pdb=" O ALA C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 170 removed outlier: 4.270A pdb=" N LEU C 170 " --> pdb=" O ALA C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 225 Processing helix chain 'C' and resid 226 through 231 Processing helix chain 'C' and resid 254 through 256 No H-bonds generated for 'chain 'C' and resid 254 through 256' Processing helix chain 'C' and resid 298 through 349 removed outlier: 3.619A pdb=" N ALA C 302 " --> pdb=" O THR C 298 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N GLU C 307 " --> pdb=" O GLN C 303 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER C 349 " --> pdb=" O SER C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 352 No H-bonds generated for 'chain 'C' and resid 350 through 352' Processing helix chain 'C' and resid 355 through 383 removed outlier: 3.569A pdb=" N GLU C 359 " --> pdb=" O ASP C 355 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N THR C 360 " --> pdb=" O PHE C 356 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N ALA C 361 " --> pdb=" O ALA C 357 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU C 362 " --> pdb=" O LYS C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 391 removed outlier: 3.620A pdb=" N VAL C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU C 388 " --> pdb=" O GLN C 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 35 removed outlier: 3.775A pdb=" N GLN D 15 " --> pdb=" O SER D 11 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ARG D 16 " --> pdb=" O LEU D 12 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N SER D 24 " --> pdb=" O THR D 20 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LEU D 25 " --> pdb=" O SER D 21 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ALA D 26 " --> pdb=" O GLY D 22 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N THR D 27 " --> pdb=" O SER D 23 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY D 35 " --> pdb=" O ARG D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 98 removed outlier: 3.812A pdb=" N VAL D 63 " --> pdb=" O ARG D 59 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLU D 84 " --> pdb=" O GLY D 80 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLN D 98 " --> pdb=" O GLU D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 129 removed outlier: 3.968A pdb=" N GLU D 115 " --> pdb=" O ALA D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 170 removed outlier: 4.308A pdb=" N LEU D 170 " --> pdb=" O ALA D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 225 removed outlier: 3.552A pdb=" N LYS D 217 " --> pdb=" O ALA D 213 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA D 218 " --> pdb=" O ASP D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 231 Processing helix chain 'D' and resid 254 through 256 No H-bonds generated for 'chain 'D' and resid 254 through 256' Processing helix chain 'D' and resid 298 through 349 removed outlier: 3.660A pdb=" N ALA D 302 " --> pdb=" O THR D 298 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N GLU D 307 " --> pdb=" O GLN D 303 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER D 349 " --> pdb=" O SER D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 383 removed outlier: 3.554A pdb=" N GLU D 359 " --> pdb=" O ASP D 355 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N THR D 360 " --> pdb=" O PHE D 356 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ALA D 361 " --> pdb=" O ALA D 357 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU D 362 " --> pdb=" O LYS D 358 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN D 371 " --> pdb=" O GLN D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 391 removed outlier: 4.213A pdb=" N LEU D 390 " --> pdb=" O GLY D 386 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU D 391 " --> pdb=" O VAL D 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 386 through 391' Processing helix chain 'E' and resid 8 through 24 removed outlier: 3.757A pdb=" N GLN E 15 " --> pdb=" O SER E 11 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG E 16 " --> pdb=" O LEU E 12 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N SER E 24 " --> pdb=" O THR E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 35 removed outlier: 3.650A pdb=" N GLY E 35 " --> pdb=" O ARG E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 98 removed outlier: 3.788A pdb=" N VAL E 63 " --> pdb=" O ARG E 59 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU E 84 " --> pdb=" O GLY E 80 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLN E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 129 removed outlier: 3.811A pdb=" N GLU E 115 " --> pdb=" O ALA E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 170 removed outlier: 4.206A pdb=" N LEU E 170 " --> pdb=" O ALA E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 225 removed outlier: 3.526A pdb=" N LYS E 217 " --> pdb=" O ALA E 213 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA E 218 " --> pdb=" O ASP E 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 231 Processing helix chain 'E' and resid 254 through 256 No H-bonds generated for 'chain 'E' and resid 254 through 256' Processing helix chain 'E' and resid 298 through 349 removed outlier: 3.621A pdb=" N ALA E 302 " --> pdb=" O THR E 298 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLU E 307 " --> pdb=" O GLN E 303 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER E 349 " --> pdb=" O SER E 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 355 through 383 removed outlier: 3.990A pdb=" N THR E 360 " --> pdb=" O PHE E 356 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ALA E 361 " --> pdb=" O ALA E 357 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU E 362 " --> pdb=" O LYS E 358 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN E 371 " --> pdb=" O GLN E 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 391 removed outlier: 3.642A pdb=" N VAL E 387 " --> pdb=" O PRO E 384 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER E 389 " --> pdb=" O GLY E 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 35 removed outlier: 3.577A pdb=" N GLN F 15 " --> pdb=" O SER F 11 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG F 16 " --> pdb=" O LEU F 12 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N SER F 24 " --> pdb=" O THR F 20 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N LEU F 25 " --> pdb=" O SER F 21 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ALA F 26 " --> pdb=" O GLY F 22 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N THR F 27 " --> pdb=" O SER F 23 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY F 35 " --> pdb=" O ARG F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 98 removed outlier: 3.559A pdb=" N ILE F 50 " --> pdb=" O ALA F 46 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL F 63 " --> pdb=" O ARG F 59 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU F 84 " --> pdb=" O GLY F 80 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLN F 98 " --> pdb=" O GLU F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 129 removed outlier: 3.965A pdb=" N GLU F 115 " --> pdb=" O ALA F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 170 removed outlier: 4.168A pdb=" N LEU F 170 " --> pdb=" O ALA F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 225 removed outlier: 3.592A pdb=" N LYS F 217 " --> pdb=" O ALA F 213 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA F 218 " --> pdb=" O ASP F 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 231 Processing helix chain 'F' and resid 254 through 256 No H-bonds generated for 'chain 'F' and resid 254 through 256' Processing helix chain 'F' and resid 298 through 349 removed outlier: 3.675A pdb=" N ALA F 302 " --> pdb=" O THR F 298 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N GLU F 307 " --> pdb=" O GLN F 303 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER F 349 " --> pdb=" O SER F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 352 No H-bonds generated for 'chain 'F' and resid 350 through 352' Processing helix chain 'F' and resid 355 through 383 removed outlier: 3.557A pdb=" N GLU F 359 " --> pdb=" O ASP F 355 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N THR F 360 " --> pdb=" O PHE F 356 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ALA F 361 " --> pdb=" O ALA F 357 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU F 362 " --> pdb=" O LYS F 358 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN F 371 " --> pdb=" O GLN F 367 " (cutoff:3.500A) Processing helix chain 'F' and resid 384 through 391 removed outlier: 3.622A pdb=" N VAL F 387 " --> pdb=" O PRO F 384 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER F 389 " --> pdb=" O GLY F 386 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 35 removed outlier: 3.637A pdb=" N GLN G 15 " --> pdb=" O SER G 11 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG G 16 " --> pdb=" O LEU G 12 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N SER G 24 " --> pdb=" O THR G 20 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N LEU G 25 " --> pdb=" O SER G 21 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ALA G 26 " --> pdb=" O GLY G 22 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N THR G 27 " --> pdb=" O SER G 23 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY G 35 " --> pdb=" O ARG G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 98 removed outlier: 3.858A pdb=" N VAL G 63 " --> pdb=" O ARG G 59 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLU G 84 " --> pdb=" O GLY G 80 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLN G 98 " --> pdb=" O GLU G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 105 through 129 removed outlier: 3.967A pdb=" N GLU G 115 " --> pdb=" O ALA G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 225 removed outlier: 3.604A pdb=" N LYS G 217 " --> pdb=" O ALA G 213 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA G 218 " --> pdb=" O ASP G 214 " (cutoff:3.500A) Processing helix chain 'G' and resid 226 through 231 Processing helix chain 'G' and resid 254 through 256 No H-bonds generated for 'chain 'G' and resid 254 through 256' Processing helix chain 'G' and resid 298 through 349 removed outlier: 3.545A pdb=" N ALA G 302 " --> pdb=" O THR G 298 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N GLU G 307 " --> pdb=" O GLN G 303 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER G 349 " --> pdb=" O SER G 345 " (cutoff:3.500A) Processing helix chain 'G' and resid 350 through 352 No H-bonds generated for 'chain 'G' and resid 350 through 352' Processing helix chain 'G' and resid 355 through 383 removed outlier: 3.739A pdb=" N THR G 360 " --> pdb=" O PHE G 356 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ALA G 361 " --> pdb=" O ALA G 357 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLU G 362 " --> pdb=" O LYS G 358 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU G 363 " --> pdb=" O GLU G 359 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN G 371 " --> pdb=" O GLN G 367 " (cutoff:3.500A) Processing helix chain 'G' and resid 384 through 391 removed outlier: 3.642A pdb=" N VAL G 387 " --> pdb=" O PRO G 384 " (cutoff:3.500A) Processing helix chain 'H' and resid 8 through 34 removed outlier: 3.565A pdb=" N GLN H 15 " --> pdb=" O SER H 11 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG H 16 " --> pdb=" O LEU H 12 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N SER H 24 " --> pdb=" O THR H 20 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N LEU H 25 " --> pdb=" O SER H 21 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ALA H 26 " --> pdb=" O GLY H 22 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N THR H 27 " --> pdb=" O SER H 23 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 98 removed outlier: 3.743A pdb=" N VAL H 63 " --> pdb=" O ARG H 59 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU H 84 " --> pdb=" O GLY H 80 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLN H 98 " --> pdb=" O GLU H 94 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 129 removed outlier: 3.785A pdb=" N GLU H 115 " --> pdb=" O ALA H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 170 removed outlier: 4.303A pdb=" N LEU H 170 " --> pdb=" O ALA H 167 " (cutoff:3.500A) Processing helix chain 'H' and resid 211 through 225 Processing helix chain 'H' and resid 226 through 231 Processing helix chain 'H' and resid 254 through 256 No H-bonds generated for 'chain 'H' and resid 254 through 256' Processing helix chain 'H' and resid 298 through 349 removed outlier: 3.627A pdb=" N ALA H 302 " --> pdb=" O THR H 298 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N GLU H 307 " --> pdb=" O GLN H 303 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER H 349 " --> pdb=" O SER H 345 " (cutoff:3.500A) Processing helix chain 'H' and resid 355 through 383 removed outlier: 3.612A pdb=" N GLU H 359 " --> pdb=" O ASP H 355 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N THR H 360 " --> pdb=" O PHE H 356 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ALA H 361 " --> pdb=" O ALA H 357 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU H 362 " --> pdb=" O LYS H 358 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN H 371 " --> pdb=" O GLN H 367 " (cutoff:3.500A) Processing helix chain 'H' and resid 384 through 391 removed outlier: 3.676A pdb=" N VAL H 387 " --> pdb=" O PRO H 384 " (cutoff:3.500A) Processing helix chain 'I' and resid 8 through 35 removed outlier: 3.567A pdb=" N GLN I 15 " --> pdb=" O SER I 11 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG I 16 " --> pdb=" O LEU I 12 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N SER I 24 " --> pdb=" O THR I 20 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LEU I 25 " --> pdb=" O SER I 21 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ALA I 26 " --> pdb=" O GLY I 22 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N THR I 27 " --> pdb=" O SER I 23 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLY I 35 " --> pdb=" O ARG I 31 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 98 removed outlier: 3.705A pdb=" N VAL I 63 " --> pdb=" O ARG I 59 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLU I 84 " --> pdb=" O GLY I 80 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLN I 98 " --> pdb=" O GLU I 94 " (cutoff:3.500A) Processing helix chain 'I' and resid 105 through 129 removed outlier: 3.811A pdb=" N GLU I 115 " --> pdb=" O ALA I 111 " (cutoff:3.500A) Processing helix chain 'I' and resid 166 through 170 removed outlier: 4.280A pdb=" N LEU I 170 " --> pdb=" O ALA I 167 " (cutoff:3.500A) Processing helix chain 'I' and resid 211 through 225 removed outlier: 3.750A pdb=" N ALA I 218 " --> pdb=" O ASP I 214 " (cutoff:3.500A) Processing helix chain 'I' and resid 226 through 231 Processing helix chain 'I' and resid 254 through 256 No H-bonds generated for 'chain 'I' and resid 254 through 256' Processing helix chain 'I' and resid 298 through 349 removed outlier: 3.761A pdb=" N ALA I 302 " --> pdb=" O THR I 298 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLU I 307 " --> pdb=" O GLN I 303 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER I 349 " --> pdb=" O SER I 345 " (cutoff:3.500A) Processing helix chain 'I' and resid 350 through 352 No H-bonds generated for 'chain 'I' and resid 350 through 352' Processing helix chain 'I' and resid 355 through 383 removed outlier: 3.744A pdb=" N THR I 360 " --> pdb=" O PHE I 356 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ALA I 361 " --> pdb=" O ALA I 357 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLU I 362 " --> pdb=" O LYS I 358 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU I 363 " --> pdb=" O GLU I 359 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN I 371 " --> pdb=" O GLN I 367 " (cutoff:3.500A) Processing helix chain 'I' and resid 384 through 391 removed outlier: 3.633A pdb=" N VAL I 387 " --> pdb=" O PRO I 384 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER I 389 " --> pdb=" O GLY I 386 " (cutoff:3.500A) Processing helix chain 'J' and resid 8 through 35 removed outlier: 3.687A pdb=" N ARG J 16 " --> pdb=" O LEU J 12 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N SER J 24 " --> pdb=" O THR J 20 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N LEU J 25 " --> pdb=" O SER J 21 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ALA J 26 " --> pdb=" O GLY J 22 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N THR J 27 " --> pdb=" O SER J 23 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY J 35 " --> pdb=" O ARG J 31 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 98 removed outlier: 3.562A pdb=" N ILE J 50 " --> pdb=" O ALA J 46 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL J 63 " --> pdb=" O ARG J 59 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU J 84 " --> pdb=" O GLY J 80 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLN J 98 " --> pdb=" O GLU J 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 105 through 129 removed outlier: 3.821A pdb=" N GLU J 115 " --> pdb=" O ALA J 111 " (cutoff:3.500A) Processing helix chain 'J' and resid 166 through 170 removed outlier: 4.192A pdb=" N LEU J 170 " --> pdb=" O ALA J 167 " (cutoff:3.500A) Processing helix chain 'J' and resid 211 through 225 removed outlier: 3.659A pdb=" N ALA J 218 " --> pdb=" O ASP J 214 " (cutoff:3.500A) Processing helix chain 'J' and resid 226 through 231 Processing helix chain 'J' and resid 254 through 256 No H-bonds generated for 'chain 'J' and resid 254 through 256' Processing helix chain 'J' and resid 298 through 349 removed outlier: 3.588A pdb=" N ALA J 302 " --> pdb=" O THR J 298 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLU J 307 " --> pdb=" O GLN J 303 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER J 349 " --> pdb=" O SER J 345 " (cutoff:3.500A) Processing helix chain 'J' and resid 355 through 383 removed outlier: 3.616A pdb=" N GLU J 359 " --> pdb=" O ASP J 355 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N THR J 360 " --> pdb=" O PHE J 356 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N ALA J 361 " --> pdb=" O ALA J 357 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU J 362 " --> pdb=" O LYS J 358 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN J 371 " --> pdb=" O GLN J 367 " (cutoff:3.500A) Processing helix chain 'J' and resid 384 through 391 removed outlier: 3.628A pdb=" N VAL J 387 " --> pdb=" O PRO J 384 " (cutoff:3.500A) Processing helix chain 'K' and resid 8 through 35 removed outlier: 3.535A pdb=" N GLN K 15 " --> pdb=" O SER K 11 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG K 16 " --> pdb=" O LEU K 12 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN K 17 " --> pdb=" O ASN K 13 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N SER K 24 " --> pdb=" O THR K 20 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N LEU K 25 " --> pdb=" O SER K 21 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ALA K 26 " --> pdb=" O GLY K 22 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N THR K 27 " --> pdb=" O SER K 23 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY K 35 " --> pdb=" O ARG K 31 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 98 removed outlier: 3.757A pdb=" N VAL K 63 " --> pdb=" O ARG K 59 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU K 84 " --> pdb=" O GLY K 80 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN K 98 " --> pdb=" O GLU K 94 " (cutoff:3.500A) Processing helix chain 'K' and resid 105 through 129 removed outlier: 3.873A pdb=" N GLU K 115 " --> pdb=" O ALA K 111 " (cutoff:3.500A) Processing helix chain 'K' and resid 166 through 170 removed outlier: 4.142A pdb=" N LEU K 170 " --> pdb=" O ALA K 167 " (cutoff:3.500A) Processing helix chain 'K' and resid 211 through 225 Processing helix chain 'K' and resid 226 through 231 Processing helix chain 'K' and resid 254 through 256 No H-bonds generated for 'chain 'K' and resid 254 through 256' Processing helix chain 'K' and resid 298 through 349 removed outlier: 3.640A pdb=" N ALA K 302 " --> pdb=" O THR K 298 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLU K 307 " --> pdb=" O GLN K 303 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER K 349 " --> pdb=" O SER K 345 " (cutoff:3.500A) Processing helix chain 'K' and resid 350 through 352 No H-bonds generated for 'chain 'K' and resid 350 through 352' Processing helix chain 'K' and resid 355 through 383 removed outlier: 4.092A pdb=" N THR K 360 " --> pdb=" O PHE K 356 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ALA K 361 " --> pdb=" O ALA K 357 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU K 362 " --> pdb=" O LYS K 358 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN K 371 " --> pdb=" O GLN K 367 " (cutoff:3.500A) Processing helix chain 'K' and resid 384 through 390 removed outlier: 3.842A pdb=" N VAL K 387 " --> pdb=" O PRO K 384 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER K 389 " --> pdb=" O GLY K 386 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 132 Processing sheet with id=AA2, first strand: chain 'A' and resid 145 through 148 Processing sheet with id=AA3, first strand: chain 'A' and resid 173 through 175 Processing sheet with id=AA4, first strand: chain 'A' and resid 199 through 200 Processing sheet with id=AA5, first strand: chain 'A' and resid 232 through 236 Processing sheet with id=AA6, first strand: chain 'B' and resid 131 through 132 Processing sheet with id=AA7, first strand: chain 'B' and resid 145 through 148 Processing sheet with id=AA8, first strand: chain 'B' and resid 173 through 175 Processing sheet with id=AA9, first strand: chain 'B' and resid 191 through 192 removed outlier: 3.712A pdb=" N PHE B 192 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL B 204 " --> pdb=" O PHE B 192 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 199 through 200 Processing sheet with id=AB2, first strand: chain 'B' and resid 232 through 236 Processing sheet with id=AB3, first strand: chain 'C' and resid 145 through 148 Processing sheet with id=AB4, first strand: chain 'C' and resid 173 through 175 Processing sheet with id=AB5, first strand: chain 'C' and resid 204 through 205 removed outlier: 3.615A pdb=" N VAL C 204 " --> pdb=" O PHE C 192 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE C 192 " --> pdb=" O VAL C 204 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 199 through 200 Processing sheet with id=AB7, first strand: chain 'C' and resid 232 through 236 removed outlier: 3.503A pdb=" N LYS C 243 " --> pdb=" O GLU C 235 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 131 through 132 Processing sheet with id=AB9, first strand: chain 'D' and resid 145 through 148 Processing sheet with id=AC1, first strand: chain 'D' and resid 173 through 175 Processing sheet with id=AC2, first strand: chain 'D' and resid 191 through 192 removed outlier: 3.685A pdb=" N PHE D 192 " --> pdb=" O VAL D 204 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL D 204 " --> pdb=" O PHE D 192 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'D' and resid 199 through 200 Processing sheet with id=AC4, first strand: chain 'D' and resid 232 through 236 Processing sheet with id=AC5, first strand: chain 'E' and resid 131 through 132 Processing sheet with id=AC6, first strand: chain 'E' and resid 145 through 148 Processing sheet with id=AC7, first strand: chain 'E' and resid 173 through 175 Processing sheet with id=AC8, first strand: chain 'E' and resid 191 through 192 removed outlier: 3.559A pdb=" N ARG E 191 " --> pdb=" O SER E 263 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 199 through 200 Processing sheet with id=AD1, first strand: chain 'E' and resid 232 through 236 Processing sheet with id=AD2, first strand: chain 'F' and resid 131 through 132 Processing sheet with id=AD3, first strand: chain 'F' and resid 145 through 148 Processing sheet with id=AD4, first strand: chain 'F' and resid 173 through 175 Processing sheet with id=AD5, first strand: chain 'F' and resid 191 through 192 removed outlier: 3.602A pdb=" N PHE F 192 " --> pdb=" O VAL F 204 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 199 through 200 Processing sheet with id=AD7, first strand: chain 'F' and resid 232 through 236 Processing sheet with id=AD8, first strand: chain 'G' and resid 131 through 132 Processing sheet with id=AD9, first strand: chain 'G' and resid 145 through 148 Processing sheet with id=AE1, first strand: chain 'G' and resid 173 through 175 Processing sheet with id=AE2, first strand: chain 'G' and resid 191 through 192 removed outlier: 3.607A pdb=" N PHE G 192 " --> pdb=" O VAL G 204 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 199 through 200 Processing sheet with id=AE4, first strand: chain 'G' and resid 232 through 236 Processing sheet with id=AE5, first strand: chain 'H' and resid 131 through 132 Processing sheet with id=AE6, first strand: chain 'H' and resid 145 through 148 Processing sheet with id=AE7, first strand: chain 'H' and resid 173 through 175 Processing sheet with id=AE8, first strand: chain 'H' and resid 204 through 205 removed outlier: 3.637A pdb=" N VAL H 204 " --> pdb=" O PHE H 192 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE H 192 " --> pdb=" O VAL H 204 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 199 through 200 Processing sheet with id=AF1, first strand: chain 'H' and resid 232 through 236 Processing sheet with id=AF2, first strand: chain 'I' and resid 131 through 132 Processing sheet with id=AF3, first strand: chain 'I' and resid 145 through 148 Processing sheet with id=AF4, first strand: chain 'I' and resid 173 through 175 Processing sheet with id=AF5, first strand: chain 'I' and resid 191 through 192 removed outlier: 3.698A pdb=" N PHE I 192 " --> pdb=" O VAL I 204 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL I 204 " --> pdb=" O PHE I 192 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'I' and resid 199 through 200 Processing sheet with id=AF7, first strand: chain 'I' and resid 232 through 236 Processing sheet with id=AF8, first strand: chain 'J' and resid 131 through 132 Processing sheet with id=AF9, first strand: chain 'J' and resid 145 through 148 Processing sheet with id=AG1, first strand: chain 'J' and resid 173 through 175 Processing sheet with id=AG2, first strand: chain 'J' and resid 199 through 200 removed outlier: 3.676A pdb=" N PHE J 192 " --> pdb=" O VAL J 204 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL J 204 " --> pdb=" O PHE J 192 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'J' and resid 199 through 200 removed outlier: 3.605A pdb=" N ARG J 191 " --> pdb=" O SER J 263 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER J 193 " --> pdb=" O MET J 261 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'J' and resid 232 through 236 Processing sheet with id=AG5, first strand: chain 'K' and resid 131 through 132 Processing sheet with id=AG6, first strand: chain 'K' and resid 145 through 148 Processing sheet with id=AG7, first strand: chain 'K' and resid 173 through 175 Processing sheet with id=AG8, first strand: chain 'K' and resid 204 through 205 removed outlier: 3.528A pdb=" N VAL K 204 " --> pdb=" O PHE K 192 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE K 192 " --> pdb=" O VAL K 204 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'K' and resid 199 through 200 Processing sheet with id=AH1, first strand: chain 'K' and resid 232 through 236 2011 hydrogen bonds defined for protein. 5703 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: 10.07 Time building geometry restraints manager: 8.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 6422 1.33 - 1.45: 6441 1.45 - 1.57: 17904 1.57 - 1.70: 0 1.70 - 1.82: 88 Bond restraints: 30855 Sorted by residual: bond pdb=" C LEU K 12 " pdb=" O LEU K 12 " ideal model delta sigma weight residual 1.237 1.202 0.035 1.17e-02 7.31e+03 8.79e+00 bond pdb=" C ASN K 13 " pdb=" O ASN K 13 " ideal model delta sigma weight residual 1.237 1.204 0.033 1.19e-02 7.06e+03 7.73e+00 bond pdb=" C ASN I 13 " pdb=" O ASN I 13 " ideal model delta sigma weight residual 1.237 1.205 0.032 1.17e-02 7.31e+03 7.57e+00 bond pdb=" C SER I 11 " pdb=" O SER I 11 " ideal model delta sigma weight residual 1.237 1.207 0.029 1.17e-02 7.31e+03 6.27e+00 bond pdb=" CA ASN K 8 " pdb=" C ASN K 8 " ideal model delta sigma weight residual 1.526 1.493 0.033 1.35e-02 5.49e+03 6.12e+00 ... (remaining 30850 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 41391 2.47 - 4.95: 364 4.95 - 7.42: 32 7.42 - 9.89: 12 9.89 - 12.36: 1 Bond angle restraints: 41800 Sorted by residual: angle pdb=" C ALA K 14 " pdb=" N GLN K 15 " pdb=" CA GLN K 15 " ideal model delta sigma weight residual 120.28 128.03 -7.75 1.34e+00 5.57e-01 3.35e+01 angle pdb=" C ALA F 277 " pdb=" CA ALA F 277 " pdb=" CB ALA F 277 " ideal model delta sigma weight residual 115.79 109.89 5.90 1.19e+00 7.06e-01 2.46e+01 angle pdb=" C ALA H 277 " pdb=" CA ALA H 277 " pdb=" CB ALA H 277 " ideal model delta sigma weight residual 115.79 109.89 5.90 1.19e+00 7.06e-01 2.46e+01 angle pdb=" C ASN D 13 " pdb=" N ALA D 14 " pdb=" CA ALA D 14 " ideal model delta sigma weight residual 121.54 130.65 -9.11 1.91e+00 2.74e-01 2.27e+01 angle pdb=" C ALA A 14 " pdb=" N GLN A 15 " pdb=" CA GLN A 15 " ideal model delta sigma weight residual 120.44 126.58 -6.14 1.36e+00 5.41e-01 2.04e+01 ... (remaining 41795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 16533 17.95 - 35.90: 1750 35.90 - 53.84: 450 53.84 - 71.79: 75 71.79 - 89.74: 24 Dihedral angle restraints: 18832 sinusoidal: 6644 harmonic: 12188 Sorted by residual: dihedral pdb=" CA VAL C 383 " pdb=" C VAL C 383 " pdb=" N PRO C 384 " pdb=" CA PRO C 384 " ideal model delta harmonic sigma weight residual -180.00 -159.27 -20.73 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA VAL D 383 " pdb=" C VAL D 383 " pdb=" N PRO D 384 " pdb=" CA PRO D 384 " ideal model delta harmonic sigma weight residual -180.00 -160.83 -19.17 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA VAL J 383 " pdb=" C VAL J 383 " pdb=" N PRO J 384 " pdb=" CA PRO J 384 " ideal model delta harmonic sigma weight residual -180.00 -162.75 -17.25 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 18829 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 4477 0.053 - 0.105: 656 0.105 - 0.158: 92 0.158 - 0.210: 6 0.210 - 0.263: 5 Chirality restraints: 5236 Sorted by residual: chirality pdb=" CA ALA I 14 " pdb=" N ALA I 14 " pdb=" C ALA I 14 " pdb=" CB ALA I 14 " both_signs ideal model delta sigma weight residual False 2.48 2.22 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA THR A 9 " pdb=" N THR A 9 " pdb=" C THR A 9 " pdb=" CB THR A 9 " both_signs ideal model delta sigma weight residual False 2.53 2.28 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CA ASN K 13 " pdb=" N ASN K 13 " pdb=" C ASN K 13 " pdb=" CB ASN K 13 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 5233 not shown) Planarity restraints: 5511 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR E 271 " -0.010 2.00e-02 2.50e+03 2.01e-02 4.04e+00 pdb=" C THR E 271 " 0.035 2.00e-02 2.50e+03 pdb=" O THR E 271 " -0.013 2.00e-02 2.50e+03 pdb=" N TRP E 272 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR J 7 " 0.009 2.00e-02 2.50e+03 1.91e-02 3.65e+00 pdb=" C THR J 7 " -0.033 2.00e-02 2.50e+03 pdb=" O THR J 7 " 0.013 2.00e-02 2.50e+03 pdb=" N ASN J 8 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL I 296 " -0.009 2.00e-02 2.50e+03 1.83e-02 3.34e+00 pdb=" C VAL I 296 " 0.032 2.00e-02 2.50e+03 pdb=" O VAL I 296 " -0.012 2.00e-02 2.50e+03 pdb=" N SER I 297 " -0.011 2.00e-02 2.50e+03 ... (remaining 5508 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 1904 2.72 - 3.27: 31479 3.27 - 3.81: 46316 3.81 - 4.36: 49191 4.36 - 4.90: 90893 Nonbonded interactions: 219783 Sorted by model distance: nonbonded pdb=" OG SER F 349 " pdb=" OD2 ASP F 353 " model vdw 2.177 3.040 nonbonded pdb=" OG SER K 349 " pdb=" OD2 ASP K 353 " model vdw 2.179 3.040 nonbonded pdb=" OG1 THR J 180 " pdb=" OG1 THR J 282 " model vdw 2.184 3.040 nonbonded pdb=" OG1 THR A 180 " pdb=" OG1 THR A 282 " model vdw 2.185 3.040 nonbonded pdb=" OG1 THR F 180 " pdb=" OG1 THR F 282 " model vdw 2.196 3.040 ... (remaining 219778 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } 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: 2.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.150 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 63.230 Find NCS groups from input model: 1.320 Set up NCS constraints: 0.150 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 30855 Z= 0.280 Angle : 0.633 12.363 41800 Z= 0.373 Chirality : 0.039 0.263 5236 Planarity : 0.003 0.040 5511 Dihedral : 16.174 89.739 10956 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.83 % Favored : 94.14 % Rotamer: Outliers : 0.66 % Allowed : 16.30 % Favored : 83.04 % 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: 1.42 (0.13), residues: 4268 helix: 3.02 (0.10), residues: 2222 sheet: 0.43 (0.22), residues: 561 loop : -2.34 (0.14), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 272 PHE 0.011 0.002 PHE E 175 TYR 0.011 0.002 TYR A 281 ARG 0.007 0.001 ARG A 262 Details of bonding type rmsd hydrogen bonds : bond 0.18366 ( 2009) hydrogen bonds : angle 5.46655 ( 5703) covalent geometry : bond 0.00542 (30855) covalent geometry : angle 0.63324 (41800) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8536 Ramachandran restraints generated. 4268 Oldfield, 0 Emsley, 4268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8536 Ramachandran restraints generated. 4268 Oldfield, 0 Emsley, 4268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 3190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 173 time to evaluate : 3.376 Fit side-chains REVERT: A 261 MET cc_start: 0.8334 (mmm) cc_final: 0.7418 (mmp) REVERT: C 12 LEU cc_start: 0.9503 (OUTLIER) cc_final: 0.9301 (mt) REVERT: D 19 SER cc_start: 0.9351 (OUTLIER) cc_final: 0.9062 (p) REVERT: D 342 GLU cc_start: 0.8825 (tm-30) cc_final: 0.8480 (tt0) REVERT: F 10 MET cc_start: 0.9527 (OUTLIER) cc_final: 0.9317 (mtt) REVERT: F 197 MET cc_start: 0.9037 (mtp) cc_final: 0.8770 (mtp) REVERT: H 70 ASP cc_start: 0.8396 (m-30) cc_final: 0.8155 (t0) REVERT: J 10 MET cc_start: 0.9377 (mtt) cc_final: 0.9170 (mtp) REVERT: K 281 TYR cc_start: 0.6521 (t80) cc_final: 0.6039 (t80) outliers start: 21 outliers final: 9 residues processed: 187 average time/residue: 0.3439 time to fit residues: 113.4998 Evaluate side-chains 178 residues out of total 3190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 166 time to evaluate : 3.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain D residue 10 MET Chi-restraints excluded: chain D residue 13 ASN Chi-restraints excluded: chain D residue 19 SER Chi-restraints excluded: chain D residue 388 LEU Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain G residue 10 MET Chi-restraints excluded: chain K residue 12 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 362 optimal weight: 5.9990 chunk 325 optimal weight: 7.9990 chunk 180 optimal weight: 9.9990 chunk 111 optimal weight: 0.9990 chunk 219 optimal weight: 3.9990 chunk 173 optimal weight: 8.9990 chunk 336 optimal weight: 7.9990 chunk 130 optimal weight: 6.9990 chunk 204 optimal weight: 7.9990 chunk 250 optimal weight: 1.9990 chunk 389 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 17 ASN D 13 ASN H 8 ASN J 292 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.100192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.076581 restraints weight = 67059.269| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.92 r_work: 0.2970 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.0674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 30855 Z= 0.206 Angle : 0.498 6.113 41800 Z= 0.294 Chirality : 0.036 0.161 5236 Planarity : 0.003 0.043 5511 Dihedral : 4.359 58.476 4522 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.91 % Allowed : 16.43 % Favored : 81.66 % 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: 1.45 (0.13), residues: 4268 helix: 2.99 (0.10), residues: 2233 sheet: 0.13 (0.22), residues: 583 loop : -2.14 (0.15), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 272 PHE 0.009 0.001 PHE E 175 TYR 0.011 0.001 TYR E 233 ARG 0.003 0.000 ARG K 365 Details of bonding type rmsd hydrogen bonds : bond 0.12227 ( 2009) hydrogen bonds : angle 4.71400 ( 5703) covalent geometry : bond 0.00395 (30855) covalent geometry : angle 0.49776 (41800) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8536 Ramachandran restraints generated. 4268 Oldfield, 0 Emsley, 4268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8536 Ramachandran restraints generated. 4268 Oldfield, 0 Emsley, 4268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 3190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 185 time to evaluate : 3.297 Fit side-chains revert: symmetry clash REVERT: A 261 MET cc_start: 0.8443 (mmm) cc_final: 0.7972 (mmp) REVERT: A 351 ILE cc_start: 0.9377 (pt) cc_final: 0.9151 (pt) REVERT: C 70 ASP cc_start: 0.8591 (m-30) cc_final: 0.8340 (t0) REVERT: C 261 MET cc_start: 0.8357 (mpp) cc_final: 0.8100 (mmp) REVERT: D 342 GLU cc_start: 0.8856 (tm-30) cc_final: 0.8634 (tt0) REVERT: F 197 MET cc_start: 0.9096 (OUTLIER) cc_final: 0.8789 (mtp) REVERT: G 90 GLN cc_start: 0.9283 (OUTLIER) cc_final: 0.9031 (tt0) REVERT: G 281 TYR cc_start: 0.5744 (t80) cc_final: 0.5485 (t80) REVERT: G 385 GLN cc_start: 0.9070 (OUTLIER) cc_final: 0.8753 (mm-40) REVERT: H 70 ASP cc_start: 0.8477 (m-30) cc_final: 0.8144 (t0) outliers start: 61 outliers final: 32 residues processed: 235 average time/residue: 0.3419 time to fit residues: 141.6413 Evaluate side-chains 205 residues out of total 3190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 170 time to evaluate : 3.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 197 MET Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 90 GLN Chi-restraints excluded: chain G residue 211 THR Chi-restraints excluded: chain G residue 253 VAL Chi-restraints excluded: chain G residue 334 VAL Chi-restraints excluded: chain G residue 385 GLN Chi-restraints excluded: chain H residue 23 SER Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain I residue 347 SER Chi-restraints excluded: chain J residue 282 THR Chi-restraints excluded: chain J residue 299 VAL Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 90 GLN Chi-restraints excluded: chain K residue 211 THR Chi-restraints excluded: chain K residue 298 THR Chi-restraints excluded: chain K residue 360 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 40 optimal weight: 3.9990 chunk 231 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 288 optimal weight: 10.0000 chunk 291 optimal weight: 50.0000 chunk 203 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 416 optimal weight: 40.0000 chunk 361 optimal weight: 0.8980 chunk 140 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 292 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.103955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.080726 restraints weight = 67361.797| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.94 r_work: 0.3036 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 30855 Z= 0.170 Angle : 0.441 5.740 41800 Z= 0.262 Chirality : 0.034 0.159 5236 Planarity : 0.002 0.042 5511 Dihedral : 3.947 53.308 4501 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.10 % Allowed : 17.27 % Favored : 80.63 % 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: 1.72 (0.13), residues: 4268 helix: 3.23 (0.10), residues: 2233 sheet: 0.22 (0.22), residues: 583 loop : -2.05 (0.15), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 272 PHE 0.006 0.001 PHE F 132 TYR 0.007 0.001 TYR B 281 ARG 0.002 0.000 ARG G 53 Details of bonding type rmsd hydrogen bonds : bond 0.10564 ( 2009) hydrogen bonds : angle 4.25714 ( 5703) covalent geometry : bond 0.00271 (30855) covalent geometry : angle 0.44086 (41800) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8536 Ramachandran restraints generated. 4268 Oldfield, 0 Emsley, 4268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8536 Ramachandran restraints generated. 4268 Oldfield, 0 Emsley, 4268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 3190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 191 time to evaluate : 3.595 Fit side-chains revert: symmetry clash REVERT: A 351 ILE cc_start: 0.9357 (pt) cc_final: 0.9146 (pt) REVERT: C 70 ASP cc_start: 0.8537 (m-30) cc_final: 0.8324 (t0) REVERT: C 261 MET cc_start: 0.8177 (mpp) cc_final: 0.7857 (mmp) REVERT: C 326 ILE cc_start: 0.9336 (OUTLIER) cc_final: 0.9115 (tp) REVERT: D 342 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8397 (tt0) REVERT: F 353 ASP cc_start: 0.8390 (m-30) cc_final: 0.8137 (m-30) REVERT: G 281 TYR cc_start: 0.5565 (t80) cc_final: 0.5308 (t80) REVERT: G 385 GLN cc_start: 0.9052 (OUTLIER) cc_final: 0.8786 (mm-40) REVERT: H 70 ASP cc_start: 0.8322 (m-30) cc_final: 0.8107 (t0) outliers start: 67 outliers final: 39 residues processed: 248 average time/residue: 0.3445 time to fit residues: 151.5357 Evaluate side-chains 222 residues out of total 3190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 181 time to evaluate : 3.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 217 LYS Chi-restraints excluded: chain B residue 272 TRP Chi-restraints excluded: chain B residue 389 SER Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 272 TRP Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 272 TRP Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 272 TRP Chi-restraints excluded: chain F residue 334 VAL Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 85 ILE Chi-restraints excluded: chain G residue 253 VAL Chi-restraints excluded: chain G residue 272 TRP Chi-restraints excluded: chain G residue 334 VAL Chi-restraints excluded: chain G residue 385 GLN Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain I residue 347 SER Chi-restraints excluded: chain I residue 383 VAL Chi-restraints excluded: chain J residue 258 ILE Chi-restraints excluded: chain K residue 90 GLN Chi-restraints excluded: chain K residue 272 TRP Chi-restraints excluded: chain K residue 360 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 179 optimal weight: 10.0000 chunk 287 optimal weight: 8.9990 chunk 282 optimal weight: 8.9990 chunk 277 optimal weight: 3.9990 chunk 252 optimal weight: 40.0000 chunk 112 optimal weight: 3.9990 chunk 208 optimal weight: 6.9990 chunk 395 optimal weight: 9.9990 chunk 386 optimal weight: 4.9990 chunk 6 optimal weight: 8.9990 chunk 358 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 292 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.097372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.073470 restraints weight = 68002.944| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.93 r_work: 0.2910 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 30855 Z= 0.263 Angle : 0.560 5.668 41800 Z= 0.324 Chirality : 0.037 0.166 5236 Planarity : 0.003 0.045 5511 Dihedral : 4.204 51.501 4501 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.82 % Allowed : 17.84 % Favored : 79.34 % 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: 1.34 (0.13), residues: 4268 helix: 2.87 (0.10), residues: 2233 sheet: 0.21 (0.23), residues: 539 loop : -2.13 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP J 272 PHE 0.011 0.002 PHE E 175 TYR 0.013 0.002 TYR A 281 ARG 0.004 0.001 ARG K 365 Details of bonding type rmsd hydrogen bonds : bond 0.13364 ( 2009) hydrogen bonds : angle 4.78654 ( 5703) covalent geometry : bond 0.00568 (30855) covalent geometry : angle 0.55996 (41800) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8536 Ramachandran restraints generated. 4268 Oldfield, 0 Emsley, 4268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8536 Ramachandran restraints generated. 4268 Oldfield, 0 Emsley, 4268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 3190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 171 time to evaluate : 3.219 Fit side-chains REVERT: A 261 MET cc_start: 0.8606 (mmm) cc_final: 0.7994 (mmp) REVERT: A 351 ILE cc_start: 0.9349 (pt) cc_final: 0.9142 (pt) REVERT: C 31 ARG cc_start: 0.9049 (OUTLIER) cc_final: 0.6690 (ptm160) REVERT: C 261 MET cc_start: 0.8386 (mpp) cc_final: 0.8038 (mmp) REVERT: C 326 ILE cc_start: 0.9352 (OUTLIER) cc_final: 0.9105 (tp) REVERT: D 342 GLU cc_start: 0.8895 (tm-30) cc_final: 0.8666 (tt0) REVERT: E 5 ILE cc_start: 0.8486 (mt) cc_final: 0.8244 (mt) REVERT: G 385 GLN cc_start: 0.9066 (OUTLIER) cc_final: 0.8771 (mm-40) REVERT: H 70 ASP cc_start: 0.8540 (m-30) cc_final: 0.8277 (t0) REVERT: J 161 LYS cc_start: 0.9111 (OUTLIER) cc_final: 0.8752 (pptt) outliers start: 90 outliers final: 54 residues processed: 252 average time/residue: 0.3591 time to fit residues: 156.9288 Evaluate side-chains 217 residues out of total 3190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 159 time to evaluate : 3.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 217 LYS Chi-restraints excluded: chain B residue 272 TRP Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 31 ARG Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 272 TRP Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 272 TRP Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 272 TRP Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 143 SER Chi-restraints excluded: chain F residue 272 TRP Chi-restraints excluded: chain F residue 334 VAL Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 211 THR Chi-restraints excluded: chain G residue 253 VAL Chi-restraints excluded: chain G residue 272 TRP Chi-restraints excluded: chain G residue 334 VAL Chi-restraints excluded: chain G residue 354 THR Chi-restraints excluded: chain G residue 385 GLN Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 23 SER Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 272 TRP Chi-restraints excluded: chain H residue 299 VAL Chi-restraints excluded: chain H residue 391 LEU Chi-restraints excluded: chain I residue 19 SER Chi-restraints excluded: chain I residue 347 SER Chi-restraints excluded: chain I residue 383 VAL Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 161 LYS Chi-restraints excluded: chain J residue 272 TRP Chi-restraints excluded: chain J residue 282 THR Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 29 ILE Chi-restraints excluded: chain K residue 90 GLN Chi-restraints excluded: chain K residue 232 ILE Chi-restraints excluded: chain K residue 272 TRP Chi-restraints excluded: chain K residue 360 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 357 optimal weight: 0.8980 chunk 57 optimal weight: 0.0870 chunk 94 optimal weight: 6.9990 chunk 170 optimal weight: 10.0000 chunk 139 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 251 optimal weight: 9.9990 chunk 117 optimal weight: 10.0000 chunk 214 optimal weight: 10.0000 chunk 239 optimal weight: 0.9980 chunk 236 optimal weight: 0.8980 overall best weight: 1.5760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 292 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.104979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.082150 restraints weight = 67558.594| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.88 r_work: 0.3073 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30855 Z= 0.171 Angle : 0.463 7.005 41800 Z= 0.270 Chirality : 0.034 0.156 5236 Planarity : 0.002 0.037 5511 Dihedral : 3.943 43.362 4501 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.69 % Allowed : 18.97 % Favored : 79.34 % 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: 1.72 (0.13), residues: 4268 helix: 3.23 (0.10), residues: 2233 sheet: 0.28 (0.23), residues: 539 loop : -2.02 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP A 272 PHE 0.006 0.001 PHE B 54 TYR 0.005 0.001 TYR B 281 ARG 0.004 0.000 ARG F 53 Details of bonding type rmsd hydrogen bonds : bond 0.10480 ( 2009) hydrogen bonds : angle 4.17221 ( 5703) covalent geometry : bond 0.00266 (30855) covalent geometry : angle 0.46260 (41800) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8536 Ramachandran restraints generated. 4268 Oldfield, 0 Emsley, 4268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8536 Ramachandran restraints generated. 4268 Oldfield, 0 Emsley, 4268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 3190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 185 time to evaluate : 3.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 351 ILE cc_start: 0.9355 (pt) cc_final: 0.9155 (pt) REVERT: C 261 MET cc_start: 0.8079 (mpp) cc_final: 0.7734 (mmp) REVERT: C 326 ILE cc_start: 0.9390 (OUTLIER) cc_final: 0.9175 (tp) REVERT: D 161 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8628 (pptt) REVERT: D 271 THR cc_start: -0.0962 (OUTLIER) cc_final: -0.1170 (m) REVERT: E 5 ILE cc_start: 0.8411 (mt) cc_final: 0.8149 (mt) REVERT: F 258 ILE cc_start: 0.9093 (mm) cc_final: 0.8645 (tt) REVERT: G 281 TYR cc_start: 0.5472 (t80) cc_final: 0.5253 (t80) REVERT: G 385 GLN cc_start: 0.9038 (OUTLIER) cc_final: 0.8811 (mm-40) REVERT: J 161 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8500 (pptt) REVERT: K 85 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8400 (mt) REVERT: K 281 TYR cc_start: 0.6069 (t80) cc_final: 0.5535 (t80) outliers start: 54 outliers final: 36 residues processed: 232 average time/residue: 0.3349 time to fit residues: 138.5888 Evaluate side-chains 220 residues out of total 3190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 178 time to evaluate : 3.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 272 TRP Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 272 TRP Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 272 TRP Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 161 LYS Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 272 TRP Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 272 TRP Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 143 SER Chi-restraints excluded: chain F residue 272 TRP Chi-restraints excluded: chain F residue 334 VAL Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 85 ILE Chi-restraints excluded: chain G residue 253 VAL Chi-restraints excluded: chain G residue 272 TRP Chi-restraints excluded: chain G residue 385 GLN Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 272 TRP Chi-restraints excluded: chain I residue 272 TRP Chi-restraints excluded: chain I residue 347 SER Chi-restraints excluded: chain I residue 383 VAL Chi-restraints excluded: chain J residue 161 LYS Chi-restraints excluded: chain J residue 258 ILE Chi-restraints excluded: chain J residue 272 TRP Chi-restraints excluded: chain K residue 85 ILE Chi-restraints excluded: chain K residue 90 GLN Chi-restraints excluded: chain K residue 272 TRP Chi-restraints excluded: chain K residue 360 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 288 optimal weight: 9.9990 chunk 168 optimal weight: 8.9990 chunk 234 optimal weight: 0.9990 chunk 345 optimal weight: 1.9990 chunk 199 optimal weight: 0.0470 chunk 246 optimal weight: 1.9990 chunk 107 optimal weight: 8.9990 chunk 302 optimal weight: 0.0670 chunk 378 optimal weight: 50.0000 chunk 120 optimal weight: 10.0000 chunk 284 optimal weight: 0.8980 overall best weight: 0.8020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 113 GLN J 292 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.110507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.088131 restraints weight = 67966.994| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.95 r_work: 0.3167 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.079 30855 Z= 0.148 Angle : 0.441 10.431 41800 Z= 0.254 Chirality : 0.034 0.161 5236 Planarity : 0.002 0.039 5511 Dihedral : 3.734 26.576 4501 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.69 % Allowed : 19.15 % Favored : 79.15 % 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: 2.04 (0.14), residues: 4268 helix: 3.57 (0.10), residues: 2233 sheet: 0.16 (0.23), residues: 561 loop : -1.91 (0.16), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 272 PHE 0.009 0.001 PHE J 54 TYR 0.011 0.001 TYR E 233 ARG 0.011 0.000 ARG J 53 Details of bonding type rmsd hydrogen bonds : bond 0.08323 ( 2009) hydrogen bonds : angle 3.69628 ( 5703) covalent geometry : bond 0.00234 (30855) covalent geometry : angle 0.44059 (41800) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8536 Ramachandran restraints generated. 4268 Oldfield, 0 Emsley, 4268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8536 Ramachandran restraints generated. 4268 Oldfield, 0 Emsley, 4268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 3190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 193 time to evaluate : 3.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 MET cc_start: 0.8312 (mmm) cc_final: 0.8076 (mmm) REVERT: C 261 MET cc_start: 0.7963 (mpp) cc_final: 0.7660 (mmp) REVERT: C 326 ILE cc_start: 0.9314 (OUTLIER) cc_final: 0.9100 (tp) REVERT: D 161 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8597 (pptt) REVERT: D 271 THR cc_start: -0.1187 (OUTLIER) cc_final: -0.1397 (m) REVERT: E 5 ILE cc_start: 0.8365 (mt) cc_final: 0.8102 (mt) REVERT: F 258 ILE cc_start: 0.8966 (mm) cc_final: 0.8616 (tt) REVERT: G 385 GLN cc_start: 0.9000 (OUTLIER) cc_final: 0.8770 (mm-40) REVERT: J 161 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8555 (pptt) REVERT: K 44 ASP cc_start: 0.7912 (t70) cc_final: 0.7557 (t70) REVERT: K 281 TYR cc_start: 0.5986 (t80) cc_final: 0.5383 (t80) outliers start: 54 outliers final: 31 residues processed: 238 average time/residue: 0.3432 time to fit residues: 143.0612 Evaluate side-chains 209 residues out of total 3190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 173 time to evaluate : 3.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 272 TRP Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 272 TRP Chi-restraints excluded: chain C residue 272 TRP Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 161 LYS Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 272 TRP Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 272 TRP Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 143 SER Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 272 TRP Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 272 TRP Chi-restraints excluded: chain G residue 385 GLN Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 272 TRP Chi-restraints excluded: chain I residue 272 TRP Chi-restraints excluded: chain I residue 347 SER Chi-restraints excluded: chain I residue 383 VAL Chi-restraints excluded: chain J residue 161 LYS Chi-restraints excluded: chain J residue 272 TRP Chi-restraints excluded: chain J residue 376 MET Chi-restraints excluded: chain K residue 272 TRP Chi-restraints excluded: chain K residue 298 THR Chi-restraints excluded: chain K residue 360 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 129 optimal weight: 9.9990 chunk 261 optimal weight: 40.0000 chunk 43 optimal weight: 0.9980 chunk 120 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 248 optimal weight: 7.9990 chunk 414 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 333 optimal weight: 6.9990 chunk 166 optimal weight: 8.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 382 GLN J 292 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.101922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.078684 restraints weight = 67683.118| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.90 r_work: 0.2999 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 30855 Z= 0.213 Angle : 0.526 9.215 41800 Z= 0.300 Chirality : 0.036 0.167 5236 Planarity : 0.003 0.044 5511 Dihedral : 3.878 21.500 4501 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 1.88 % Allowed : 19.25 % Favored : 78.87 % 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: 1.76 (0.13), residues: 4268 helix: 3.27 (0.10), residues: 2233 sheet: 0.35 (0.23), residues: 539 loop : -2.01 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP J 272 PHE 0.010 0.001 PHE E 175 TYR 0.011 0.001 TYR F 281 ARG 0.005 0.000 ARG J 53 Details of bonding type rmsd hydrogen bonds : bond 0.11586 ( 2009) hydrogen bonds : angle 4.34366 ( 5703) covalent geometry : bond 0.00441 (30855) covalent geometry : angle 0.52585 (41800) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8536 Ramachandran restraints generated. 4268 Oldfield, 0 Emsley, 4268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8536 Ramachandran restraints generated. 4268 Oldfield, 0 Emsley, 4268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 3190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 175 time to evaluate : 3.256 Fit side-chains revert: symmetry clash REVERT: A 261 MET cc_start: 0.8527 (mmm) cc_final: 0.8236 (mmp) REVERT: C 261 MET cc_start: 0.8264 (mpp) cc_final: 0.7907 (mmp) REVERT: C 326 ILE cc_start: 0.9421 (OUTLIER) cc_final: 0.9186 (tp) REVERT: D 161 LYS cc_start: 0.9051 (OUTLIER) cc_final: 0.8712 (pptt) REVERT: D 271 THR cc_start: -0.0984 (OUTLIER) cc_final: -0.1194 (m) REVERT: E 5 ILE cc_start: 0.8515 (mt) cc_final: 0.8226 (mt) REVERT: G 385 GLN cc_start: 0.9012 (OUTLIER) cc_final: 0.8738 (mm-40) REVERT: H 281 TYR cc_start: 0.4865 (t80) cc_final: 0.4614 (t80) REVERT: I 382 GLN cc_start: 0.8496 (mm-40) cc_final: 0.8189 (mm-40) REVERT: J 161 LYS cc_start: 0.8979 (OUTLIER) cc_final: 0.8583 (pptt) REVERT: K 44 ASP cc_start: 0.7898 (t70) cc_final: 0.7692 (t70) REVERT: K 281 TYR cc_start: 0.6240 (t80) cc_final: 0.5714 (t80) outliers start: 60 outliers final: 42 residues processed: 225 average time/residue: 0.3345 time to fit residues: 133.1022 Evaluate side-chains 216 residues out of total 3190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 169 time to evaluate : 3.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 272 TRP Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 272 TRP Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 272 TRP Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 161 LYS Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 272 TRP Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 272 TRP Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 143 SER Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 272 TRP Chi-restraints excluded: chain F residue 334 VAL Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 272 TRP Chi-restraints excluded: chain G residue 334 VAL Chi-restraints excluded: chain G residue 354 THR Chi-restraints excluded: chain G residue 385 GLN Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 272 TRP Chi-restraints excluded: chain I residue 19 SER Chi-restraints excluded: chain I residue 272 TRP Chi-restraints excluded: chain I residue 347 SER Chi-restraints excluded: chain I residue 383 VAL Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 161 LYS Chi-restraints excluded: chain J residue 258 ILE Chi-restraints excluded: chain J residue 272 TRP Chi-restraints excluded: chain K residue 90 GLN Chi-restraints excluded: chain K residue 272 TRP Chi-restraints excluded: chain K residue 360 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 345 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 140 optimal weight: 7.9990 chunk 392 optimal weight: 10.0000 chunk 350 optimal weight: 7.9990 chunk 297 optimal weight: 9.9990 chunk 184 optimal weight: 20.0000 chunk 407 optimal weight: 20.0000 chunk 268 optimal weight: 5.9990 chunk 199 optimal weight: 0.7980 chunk 269 optimal weight: 4.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 292 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.100774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.077265 restraints weight = 67748.089| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 2.94 r_work: 0.2952 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 30855 Z= 0.203 Angle : 0.503 9.036 41800 Z= 0.291 Chirality : 0.035 0.166 5236 Planarity : 0.002 0.042 5511 Dihedral : 3.906 21.140 4500 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.85 % Allowed : 19.37 % Favored : 78.78 % 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: 1.66 (0.13), residues: 4268 helix: 3.17 (0.10), residues: 2233 sheet: 0.27 (0.23), residues: 539 loop : -2.03 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP J 272 PHE 0.008 0.001 PHE J 132 TYR 0.017 0.001 TYR D 281 ARG 0.003 0.000 ARG K 365 Details of bonding type rmsd hydrogen bonds : bond 0.11690 ( 2009) hydrogen bonds : angle 4.37049 ( 5703) covalent geometry : bond 0.00401 (30855) covalent geometry : angle 0.50260 (41800) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8536 Ramachandran restraints generated. 4268 Oldfield, 0 Emsley, 4268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8536 Ramachandran restraints generated. 4268 Oldfield, 0 Emsley, 4268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 3190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 170 time to evaluate : 3.078 Fit side-chains revert: symmetry clash REVERT: A 261 MET cc_start: 0.8580 (mmm) cc_final: 0.8379 (mmm) REVERT: C 31 ARG cc_start: 0.8993 (OUTLIER) cc_final: 0.7918 (ptm160) REVERT: C 261 MET cc_start: 0.8203 (mpp) cc_final: 0.7824 (mmp) REVERT: C 326 ILE cc_start: 0.9344 (OUTLIER) cc_final: 0.9118 (tp) REVERT: D 161 LYS cc_start: 0.9068 (OUTLIER) cc_final: 0.8684 (pptt) REVERT: D 271 THR cc_start: -0.1016 (OUTLIER) cc_final: -0.1234 (m) REVERT: E 5 ILE cc_start: 0.8590 (OUTLIER) cc_final: 0.8307 (mt) REVERT: G 5 ILE cc_start: 0.8864 (OUTLIER) cc_final: 0.8516 (mt) REVERT: G 385 GLN cc_start: 0.9080 (OUTLIER) cc_final: 0.8820 (mm-40) REVERT: H 261 MET cc_start: 0.8438 (mpp) cc_final: 0.7705 (mpp) REVERT: H 281 TYR cc_start: 0.4739 (t80) cc_final: 0.4467 (t80) REVERT: J 161 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8650 (pptt) REVERT: K 44 ASP cc_start: 0.7914 (t70) cc_final: 0.7683 (t70) REVERT: K 281 TYR cc_start: 0.6156 (t80) cc_final: 0.5634 (t80) outliers start: 59 outliers final: 45 residues processed: 221 average time/residue: 0.3352 time to fit residues: 130.2047 Evaluate side-chains 222 residues out of total 3190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 169 time to evaluate : 3.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 272 TRP Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 272 TRP Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain C residue 31 ARG Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 272 TRP Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 161 LYS Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 272 TRP Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 272 TRP Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 143 SER Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 272 TRP Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 272 TRP Chi-restraints excluded: chain G residue 334 VAL Chi-restraints excluded: chain G residue 354 THR Chi-restraints excluded: chain G residue 385 GLN Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 272 TRP Chi-restraints excluded: chain I residue 19 SER Chi-restraints excluded: chain I residue 272 TRP Chi-restraints excluded: chain I residue 347 SER Chi-restraints excluded: chain I residue 383 VAL Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 161 LYS Chi-restraints excluded: chain J residue 272 TRP Chi-restraints excluded: chain K residue 90 GLN Chi-restraints excluded: chain K residue 232 ILE Chi-restraints excluded: chain K residue 272 TRP Chi-restraints excluded: chain K residue 360 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 347 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 chunk 307 optimal weight: 10.0000 chunk 146 optimal weight: 7.9990 chunk 421 optimal weight: 5.9990 chunk 182 optimal weight: 8.9990 chunk 308 optimal weight: 4.9990 chunk 278 optimal weight: 0.9990 chunk 196 optimal weight: 6.9990 chunk 258 optimal weight: 6.9990 chunk 210 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 = 0.3524 r_free = 0.3524 target = 0.102079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.078704 restraints weight = 67172.074| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.95 r_work: 0.3009 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 30855 Z= 0.181 Angle : 0.482 8.036 41800 Z= 0.279 Chirality : 0.034 0.163 5236 Planarity : 0.002 0.040 5511 Dihedral : 3.854 21.439 4500 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.76 % Allowed : 19.40 % Favored : 78.84 % 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: 1.71 (0.13), residues: 4268 helix: 3.25 (0.10), residues: 2233 sheet: 0.07 (0.23), residues: 561 loop : -1.99 (0.15), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 272 PHE 0.009 0.001 PHE J 54 TYR 0.009 0.001 TYR F 281 ARG 0.004 0.000 ARG J 53 Details of bonding type rmsd hydrogen bonds : bond 0.11115 ( 2009) hydrogen bonds : angle 4.24909 ( 5703) covalent geometry : bond 0.00324 (30855) covalent geometry : angle 0.48184 (41800) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8536 Ramachandran restraints generated. 4268 Oldfield, 0 Emsley, 4268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8536 Ramachandran restraints generated. 4268 Oldfield, 0 Emsley, 4268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 3190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 175 time to evaluate : 3.441 Fit side-chains revert: symmetry clash REVERT: A 261 MET cc_start: 0.8659 (mmm) cc_final: 0.8450 (mmm) REVERT: C 31 ARG cc_start: 0.8982 (OUTLIER) cc_final: 0.7898 (ptm160) REVERT: C 261 MET cc_start: 0.8181 (mpp) cc_final: 0.7802 (mmp) REVERT: C 326 ILE cc_start: 0.9349 (OUTLIER) cc_final: 0.9122 (tp) REVERT: D 161 LYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8676 (pptt) REVERT: D 271 THR cc_start: -0.1088 (OUTLIER) cc_final: -0.1305 (m) REVERT: E 5 ILE cc_start: 0.8599 (OUTLIER) cc_final: 0.8297 (mt) REVERT: F 3 GLN cc_start: 0.9325 (mp10) cc_final: 0.8576 (mp10) REVERT: F 258 ILE cc_start: 0.9088 (mm) cc_final: 0.8608 (tt) REVERT: G 5 ILE cc_start: 0.8878 (OUTLIER) cc_final: 0.8523 (mt) REVERT: G 385 GLN cc_start: 0.9079 (OUTLIER) cc_final: 0.8825 (mm-40) REVERT: H 261 MET cc_start: 0.8408 (mpp) cc_final: 0.7687 (mpp) REVERT: H 281 TYR cc_start: 0.4771 (t80) cc_final: 0.4478 (t80) REVERT: J 161 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8603 (pptt) REVERT: K 44 ASP cc_start: 0.7907 (t70) cc_final: 0.7554 (t70) REVERT: K 281 TYR cc_start: 0.6079 (t80) cc_final: 0.5573 (t80) outliers start: 56 outliers final: 47 residues processed: 225 average time/residue: 0.3383 time to fit residues: 134.5000 Evaluate side-chains 227 residues out of total 3190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 172 time to evaluate : 3.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 272 TRP Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 272 TRP Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain C residue 31 ARG Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 272 TRP Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 161 LYS Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 272 TRP Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 272 TRP Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 143 SER Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 272 TRP Chi-restraints excluded: chain F residue 334 VAL Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 272 TRP Chi-restraints excluded: chain G residue 334 VAL Chi-restraints excluded: chain G residue 354 THR Chi-restraints excluded: chain G residue 385 GLN Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 23 SER Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 272 TRP Chi-restraints excluded: chain I residue 19 SER Chi-restraints excluded: chain I residue 272 TRP Chi-restraints excluded: chain I residue 282 THR Chi-restraints excluded: chain I residue 347 SER Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 161 LYS Chi-restraints excluded: chain J residue 258 ILE Chi-restraints excluded: chain J residue 272 TRP Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 90 GLN Chi-restraints excluded: chain K residue 232 ILE Chi-restraints excluded: chain K residue 272 TRP Chi-restraints excluded: chain K residue 360 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 303 optimal weight: 0.6980 chunk 341 optimal weight: 0.0870 chunk 213 optimal weight: 9.9990 chunk 394 optimal weight: 10.0000 chunk 199 optimal weight: 0.0060 chunk 12 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 382 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 217 optimal weight: 2.9990 overall best weight: 1.1578 ------------------------------------------------------------------------------- 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 = 0.3633 r_free = 0.3633 target = 0.109584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.086908 restraints weight = 67243.412| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.93 r_work: 0.3148 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 30855 Z= 0.152 Angle : 0.466 9.853 41800 Z= 0.266 Chirality : 0.034 0.157 5236 Planarity : 0.002 0.037 5511 Dihedral : 3.725 22.540 4500 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.19 % Allowed : 20.09 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.00 (0.14), residues: 4268 helix: 3.54 (0.10), residues: 2233 sheet: 0.12 (0.23), residues: 561 loop : -1.91 (0.16), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 272 PHE 0.007 0.001 PHE D 54 TYR 0.014 0.001 TYR G 281 ARG 0.018 0.000 ARG D 53 Details of bonding type rmsd hydrogen bonds : bond 0.08622 ( 2009) hydrogen bonds : angle 3.77446 ( 5703) covalent geometry : bond 0.00242 (30855) covalent geometry : angle 0.46619 (41800) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8536 Ramachandran restraints generated. 4268 Oldfield, 0 Emsley, 4268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8536 Ramachandran restraints generated. 4268 Oldfield, 0 Emsley, 4268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 3190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 183 time to evaluate : 3.154 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 261 MET cc_start: 0.8636 (mmm) cc_final: 0.8426 (mmm) REVERT: C 261 MET cc_start: 0.8021 (mpp) cc_final: 0.7701 (mmp) REVERT: C 326 ILE cc_start: 0.9306 (OUTLIER) cc_final: 0.9099 (tp) REVERT: D 161 LYS cc_start: 0.8981 (OUTLIER) cc_final: 0.8585 (pptt) REVERT: D 271 THR cc_start: -0.1291 (OUTLIER) cc_final: -0.1499 (m) REVERT: F 258 ILE cc_start: 0.8940 (mm) cc_final: 0.8591 (tt) REVERT: G 5 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8373 (mt) REVERT: G 385 GLN cc_start: 0.9014 (tp40) cc_final: 0.8770 (mm-40) REVERT: H 261 MET cc_start: 0.8396 (mpp) cc_final: 0.7663 (mpp) REVERT: J 161 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8524 (pptt) REVERT: K 44 ASP cc_start: 0.7866 (t70) cc_final: 0.7507 (t70) REVERT: K 281 TYR cc_start: 0.5812 (t80) cc_final: 0.5310 (t80) outliers start: 38 outliers final: 27 residues processed: 217 average time/residue: 0.3783 time to fit residues: 145.6991 Evaluate side-chains 206 residues out of total 3190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 174 time to evaluate : 3.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 272 TRP Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 272 TRP Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 272 TRP Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 161 LYS Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 272 TRP Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 272 TRP Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 272 TRP Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 272 TRP Chi-restraints excluded: chain G residue 354 THR Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 272 TRP Chi-restraints excluded: chain I residue 272 TRP Chi-restraints excluded: chain I residue 282 THR Chi-restraints excluded: chain I residue 347 SER Chi-restraints excluded: chain J residue 161 LYS Chi-restraints excluded: chain J residue 272 TRP Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 272 TRP Chi-restraints excluded: chain K residue 360 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 126 optimal weight: 0.0570 chunk 72 optimal weight: 5.9990 chunk 364 optimal weight: 7.9990 chunk 353 optimal weight: 9.9990 chunk 275 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 294 optimal weight: 5.9990 chunk 135 optimal weight: 4.9990 chunk 388 optimal weight: 8.9990 chunk 188 optimal weight: 1.9990 chunk 255 optimal weight: 20.0000 overall best weight: 2.6104 ------------------------------------------------------------------------------- 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 = 0.3601 r_free = 0.3601 target = 0.106218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.083435 restraints weight = 67582.080| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.90 r_work: 0.3095 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30855 Z= 0.167 Angle : 0.475 10.591 41800 Z= 0.271 Chirality : 0.034 0.163 5236 Planarity : 0.002 0.042 5511 Dihedral : 3.705 21.573 4500 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.16 % Allowed : 20.41 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.96 (0.14), residues: 4268 helix: 3.50 (0.10), residues: 2233 sheet: 0.15 (0.23), residues: 561 loop : -1.95 (0.16), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 272 PHE 0.007 0.001 PHE J 132 TYR 0.016 0.001 TYR D 281 ARG 0.005 0.000 ARG D 365 Details of bonding type rmsd hydrogen bonds : bond 0.09882 ( 2009) hydrogen bonds : angle 3.96314 ( 5703) covalent geometry : bond 0.00305 (30855) covalent geometry : angle 0.47550 (41800) =============================================================================== Job complete usr+sys time: 14878.77 seconds wall clock time: 259 minutes 18.09 seconds (15558.09 seconds total)