Starting phenix.real_space_refine on Tue Dec 31 15:59:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cez_16614/12_2024/8cez_16614.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cez_16614/12_2024/8cez_16614.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cez_16614/12_2024/8cez_16614.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cez_16614/12_2024/8cez_16614.map" model { file = "/net/cci-nas-00/data/ceres_data/8cez_16614/12_2024/8cez_16614.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cez_16614/12_2024/8cez_16614.cif" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 180 5.16 5 C 21588 2.51 5 N 6048 2.21 5 O 6528 1.98 5 H 33900 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 59 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 68244 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 5687 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 16, 'TRANS': 350} Chain: "B" Number of atoms: 5687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 5687 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 16, 'TRANS': 350} Chain: "C" Number of atoms: 5687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 5687 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 16, 'TRANS': 350} Chain: "D" Number of atoms: 5687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 5687 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 16, 'TRANS': 350} Chain: "E" Number of atoms: 5687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 5687 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 16, 'TRANS': 350} Chain: "F" Number of atoms: 5687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 5687 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 16, 'TRANS': 350} Chain: "G" Number of atoms: 5687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 5687 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 16, 'TRANS': 350} Chain: "H" Number of atoms: 5687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 5687 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 16, 'TRANS': 350} Chain: "I" Number of atoms: 5687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 5687 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 16, 'TRANS': 350} Chain: "J" Number of atoms: 5687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 5687 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 16, 'TRANS': 350} Chain: "K" Number of atoms: 5687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 5687 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 16, 'TRANS': 350} Chain: "L" Number of atoms: 5687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 5687 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 16, 'TRANS': 350} Time building chain proxies: 24.21, per 1000 atoms: 0.35 Number of scatterers: 68244 At special positions: 0 Unit cell: (154.1, 154.1, 125.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 180 16.00 O 6528 8.00 N 6048 7.00 C 21588 6.00 H 33900 1.00 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: 13.51 Conformation dependent library (CDL) restraints added in 4.3 seconds 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8088 Finding SS restraints... Secondary structure from input PDB file: 164 helices and 36 sheets defined 42.3% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.04 Creating SS restraints... Processing helix chain 'A' and resid 53 through 59 Processing helix chain 'A' and resid 60 through 76 Processing helix chain 'A' and resid 97 through 105 Processing helix chain 'A' and resid 112 through 127 Processing helix chain 'A' and resid 195 through 200 Processing helix chain 'A' and resid 200 through 220 Processing helix chain 'A' and resid 242 through 248 Processing helix chain 'A' and resid 249 through 251 No H-bonds generated for 'chain 'A' and resid 249 through 251' Processing helix chain 'A' and resid 279 through 294 removed outlier: 3.735A pdb=" N PHE A 294 " --> pdb=" O GLU A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 303 removed outlier: 3.887A pdb=" N GLY A 303 " --> pdb=" O HIS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 326 Processing helix chain 'A' and resid 327 through 342 Processing helix chain 'A' and resid 366 through 378 removed outlier: 3.697A pdb=" N ALA A 370 " --> pdb=" O ALA A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 390 removed outlier: 3.510A pdb=" N THR A 389 " --> pdb=" O GLU A 385 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASP A 390 " --> pdb=" O MET A 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 59 Processing helix chain 'B' and resid 60 through 76 Processing helix chain 'B' and resid 97 through 105 Processing helix chain 'B' and resid 112 through 127 Processing helix chain 'B' and resid 195 through 200 Processing helix chain 'B' and resid 200 through 220 Processing helix chain 'B' and resid 242 through 248 Processing helix chain 'B' and resid 249 through 251 No H-bonds generated for 'chain 'B' and resid 249 through 251' Processing helix chain 'B' and resid 279 through 294 removed outlier: 3.535A pdb=" N ARG B 284 " --> pdb=" O MET B 280 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE B 294 " --> pdb=" O GLU B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 303 removed outlier: 3.551A pdb=" N GLY B 303 " --> pdb=" O HIS B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 326 Processing helix chain 'B' and resid 327 through 342 Processing helix chain 'B' and resid 366 through 378 Processing helix chain 'B' and resid 382 through 390 removed outlier: 3.504A pdb=" N THR B 389 " --> pdb=" O GLU B 385 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP B 390 " --> pdb=" O MET B 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 59 Processing helix chain 'C' and resid 60 through 76 Processing helix chain 'C' and resid 97 through 105 Processing helix chain 'C' and resid 112 through 127 Processing helix chain 'C' and resid 195 through 200 Processing helix chain 'C' and resid 200 through 220 Processing helix chain 'C' and resid 241 through 248 removed outlier: 4.289A pdb=" N GLU C 245 " --> pdb=" O SER C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 294 removed outlier: 3.804A pdb=" N PHE C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 303 removed outlier: 3.724A pdb=" N GLY C 303 " --> pdb=" O HIS C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 326 Processing helix chain 'C' and resid 327 through 342 Processing helix chain 'C' and resid 366 through 378 removed outlier: 3.544A pdb=" N ALA C 370 " --> pdb=" O ALA C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 390 removed outlier: 3.594A pdb=" N THR C 389 " --> pdb=" O GLU C 385 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP C 390 " --> pdb=" O MET C 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 59 Processing helix chain 'D' and resid 60 through 76 Processing helix chain 'D' and resid 97 through 105 Processing helix chain 'D' and resid 112 through 127 Processing helix chain 'D' and resid 195 through 200 Processing helix chain 'D' and resid 200 through 220 Processing helix chain 'D' and resid 242 through 248 Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 279 through 294 removed outlier: 3.737A pdb=" N PHE D 294 " --> pdb=" O GLU D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 303 removed outlier: 3.888A pdb=" N GLY D 303 " --> pdb=" O HIS D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 326 Processing helix chain 'D' and resid 327 through 342 Processing helix chain 'D' and resid 366 through 378 removed outlier: 3.698A pdb=" N ALA D 370 " --> pdb=" O ALA D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 390 removed outlier: 3.516A pdb=" N THR D 389 " --> pdb=" O GLU D 385 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP D 390 " --> pdb=" O MET D 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 59 Processing helix chain 'E' and resid 60 through 76 Processing helix chain 'E' and resid 97 through 105 Processing helix chain 'E' and resid 112 through 127 Processing helix chain 'E' and resid 195 through 200 Processing helix chain 'E' and resid 200 through 220 Processing helix chain 'E' and resid 242 through 248 Processing helix chain 'E' and resid 249 through 251 No H-bonds generated for 'chain 'E' and resid 249 through 251' Processing helix chain 'E' and resid 279 through 294 removed outlier: 3.530A pdb=" N ARG E 284 " --> pdb=" O MET E 280 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE E 294 " --> pdb=" O GLU E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 303 removed outlier: 3.552A pdb=" N GLY E 303 " --> pdb=" O HIS E 300 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 326 Processing helix chain 'E' and resid 327 through 342 Processing helix chain 'E' and resid 366 through 378 Processing helix chain 'E' and resid 382 through 390 removed outlier: 3.505A pdb=" N THR E 389 " --> pdb=" O GLU E 385 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP E 390 " --> pdb=" O MET E 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 59 Processing helix chain 'F' and resid 60 through 76 Processing helix chain 'F' and resid 97 through 105 Processing helix chain 'F' and resid 112 through 127 Processing helix chain 'F' and resid 195 through 200 Processing helix chain 'F' and resid 200 through 220 Processing helix chain 'F' and resid 241 through 248 removed outlier: 4.288A pdb=" N GLU F 245 " --> pdb=" O SER F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 294 removed outlier: 3.804A pdb=" N PHE F 294 " --> pdb=" O GLU F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 303 removed outlier: 3.721A pdb=" N GLY F 303 " --> pdb=" O HIS F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 326 Processing helix chain 'F' and resid 327 through 342 Processing helix chain 'F' and resid 366 through 378 removed outlier: 3.546A pdb=" N ALA F 370 " --> pdb=" O ALA F 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 390 removed outlier: 3.633A pdb=" N THR F 389 " --> pdb=" O GLU F 385 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASP F 390 " --> pdb=" O MET F 386 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 59 Processing helix chain 'G' and resid 60 through 76 Processing helix chain 'G' and resid 97 through 105 Processing helix chain 'G' and resid 112 through 127 Processing helix chain 'G' and resid 195 through 200 Processing helix chain 'G' and resid 200 through 220 Processing helix chain 'G' and resid 242 through 248 Processing helix chain 'G' and resid 249 through 251 No H-bonds generated for 'chain 'G' and resid 249 through 251' Processing helix chain 'G' and resid 279 through 294 removed outlier: 3.736A pdb=" N PHE G 294 " --> pdb=" O GLU G 290 " (cutoff:3.500A) Processing helix chain 'G' and resid 298 through 303 removed outlier: 3.887A pdb=" N GLY G 303 " --> pdb=" O HIS G 300 " (cutoff:3.500A) Processing helix chain 'G' and resid 317 through 326 Processing helix chain 'G' and resid 327 through 342 Processing helix chain 'G' and resid 366 through 378 removed outlier: 3.697A pdb=" N ALA G 370 " --> pdb=" O ALA G 366 " (cutoff:3.500A) Processing helix chain 'G' and resid 382 through 390 removed outlier: 3.587A pdb=" N THR G 389 " --> pdb=" O GLU G 385 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASP G 390 " --> pdb=" O MET G 386 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 59 Processing helix chain 'H' and resid 60 through 76 Processing helix chain 'H' and resid 97 through 105 Processing helix chain 'H' and resid 112 through 127 Processing helix chain 'H' and resid 195 through 200 Processing helix chain 'H' and resid 200 through 220 Processing helix chain 'H' and resid 242 through 248 Processing helix chain 'H' and resid 249 through 251 No H-bonds generated for 'chain 'H' and resid 249 through 251' Processing helix chain 'H' and resid 279 through 294 removed outlier: 3.535A pdb=" N ARG H 284 " --> pdb=" O MET H 280 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE H 294 " --> pdb=" O GLU H 290 " (cutoff:3.500A) Processing helix chain 'H' and resid 298 through 303 removed outlier: 3.552A pdb=" N GLY H 303 " --> pdb=" O HIS H 300 " (cutoff:3.500A) Processing helix chain 'H' and resid 317 through 326 Processing helix chain 'H' and resid 327 through 342 Processing helix chain 'H' and resid 366 through 378 Processing helix chain 'H' and resid 382 through 390 removed outlier: 3.507A pdb=" N THR H 389 " --> pdb=" O GLU H 385 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP H 390 " --> pdb=" O MET H 386 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 59 Processing helix chain 'I' and resid 60 through 76 Processing helix chain 'I' and resid 97 through 105 Processing helix chain 'I' and resid 112 through 127 Processing helix chain 'I' and resid 195 through 200 Processing helix chain 'I' and resid 200 through 220 Processing helix chain 'I' and resid 241 through 248 removed outlier: 4.289A pdb=" N GLU I 245 " --> pdb=" O SER I 241 " (cutoff:3.500A) Processing helix chain 'I' and resid 279 through 294 removed outlier: 3.804A pdb=" N PHE I 294 " --> pdb=" O GLU I 290 " (cutoff:3.500A) Processing helix chain 'I' and resid 298 through 303 removed outlier: 3.721A pdb=" N GLY I 303 " --> pdb=" O HIS I 300 " (cutoff:3.500A) Processing helix chain 'I' and resid 317 through 326 Processing helix chain 'I' and resid 327 through 342 Processing helix chain 'I' and resid 366 through 378 removed outlier: 3.546A pdb=" N ALA I 370 " --> pdb=" O ALA I 366 " (cutoff:3.500A) Processing helix chain 'I' and resid 382 through 390 removed outlier: 3.634A pdb=" N THR I 389 " --> pdb=" O GLU I 385 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASP I 390 " --> pdb=" O MET I 386 " (cutoff:3.500A) Processing helix chain 'J' and resid 53 through 59 Processing helix chain 'J' and resid 60 through 76 Processing helix chain 'J' and resid 97 through 105 Processing helix chain 'J' and resid 112 through 127 Processing helix chain 'J' and resid 195 through 200 Processing helix chain 'J' and resid 200 through 220 Processing helix chain 'J' and resid 242 through 248 Processing helix chain 'J' and resid 249 through 251 No H-bonds generated for 'chain 'J' and resid 249 through 251' Processing helix chain 'J' and resid 279 through 294 removed outlier: 3.737A pdb=" N PHE J 294 " --> pdb=" O GLU J 290 " (cutoff:3.500A) Processing helix chain 'J' and resid 298 through 303 removed outlier: 3.887A pdb=" N GLY J 303 " --> pdb=" O HIS J 300 " (cutoff:3.500A) Processing helix chain 'J' and resid 317 through 326 Processing helix chain 'J' and resid 327 through 342 Processing helix chain 'J' and resid 366 through 378 removed outlier: 3.696A pdb=" N ALA J 370 " --> pdb=" O ALA J 366 " (cutoff:3.500A) Processing helix chain 'J' and resid 382 through 390 removed outlier: 3.587A pdb=" N THR J 389 " --> pdb=" O GLU J 385 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASP J 390 " --> pdb=" O MET J 386 " (cutoff:3.500A) Processing helix chain 'K' and resid 53 through 59 Processing helix chain 'K' and resid 60 through 76 Processing helix chain 'K' and resid 97 through 105 Processing helix chain 'K' and resid 112 through 127 Processing helix chain 'K' and resid 195 through 200 Processing helix chain 'K' and resid 200 through 220 Processing helix chain 'K' and resid 242 through 248 Processing helix chain 'K' and resid 249 through 251 No H-bonds generated for 'chain 'K' and resid 249 through 251' Processing helix chain 'K' and resid 279 through 294 removed outlier: 3.535A pdb=" N ARG K 284 " --> pdb=" O MET K 280 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE K 294 " --> pdb=" O GLU K 290 " (cutoff:3.500A) Processing helix chain 'K' and resid 298 through 303 removed outlier: 3.551A pdb=" N GLY K 303 " --> pdb=" O HIS K 300 " (cutoff:3.500A) Processing helix chain 'K' and resid 317 through 326 Processing helix chain 'K' and resid 327 through 342 Processing helix chain 'K' and resid 366 through 378 Processing helix chain 'K' and resid 382 through 390 removed outlier: 3.507A pdb=" N THR K 389 " --> pdb=" O GLU K 385 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP K 390 " --> pdb=" O MET K 386 " (cutoff:3.500A) Processing helix chain 'L' and resid 53 through 59 Processing helix chain 'L' and resid 60 through 76 Processing helix chain 'L' and resid 97 through 105 Processing helix chain 'L' and resid 112 through 127 Processing helix chain 'L' and resid 195 through 200 Processing helix chain 'L' and resid 200 through 220 Processing helix chain 'L' and resid 241 through 248 removed outlier: 4.289A pdb=" N GLU L 245 " --> pdb=" O SER L 241 " (cutoff:3.500A) Processing helix chain 'L' and resid 279 through 294 removed outlier: 3.802A pdb=" N PHE L 294 " --> pdb=" O GLU L 290 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 303 removed outlier: 3.724A pdb=" N GLY L 303 " --> pdb=" O HIS L 300 " (cutoff:3.500A) Processing helix chain 'L' and resid 317 through 326 Processing helix chain 'L' and resid 327 through 342 Processing helix chain 'L' and resid 366 through 378 removed outlier: 3.544A pdb=" N ALA L 370 " --> pdb=" O ALA L 366 " (cutoff:3.500A) Processing helix chain 'L' and resid 382 through 390 removed outlier: 3.592A pdb=" N THR L 389 " --> pdb=" O GLU L 385 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP L 390 " --> pdb=" O MET L 386 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 79 through 82 Processing sheet with id=AA2, first strand: chain 'A' and resid 142 through 147 removed outlier: 6.563A pdb=" N ASP A 135 " --> pdb=" O ILE A 143 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LEU A 145 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N LEU A 133 " --> pdb=" O LEU A 145 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N TYR A 131 " --> pdb=" O PRO A 147 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 153 through 157 Processing sheet with id=AA4, first strand: chain 'B' and resid 79 through 82 Processing sheet with id=AA5, first strand: chain 'B' and resid 142 through 148 removed outlier: 6.509A pdb=" N ASP B 135 " --> pdb=" O ILE B 143 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LEU B 145 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LEU B 133 " --> pdb=" O LEU B 145 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N TYR B 131 " --> pdb=" O PRO B 147 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 153 through 157 Processing sheet with id=AA7, first strand: chain 'C' and resid 79 through 82 Processing sheet with id=AA8, first strand: chain 'C' and resid 142 through 147 removed outlier: 6.501A pdb=" N ASP C 135 " --> pdb=" O ILE C 143 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LEU C 145 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N LEU C 133 " --> pdb=" O LEU C 145 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N TYR C 131 " --> pdb=" O PRO C 147 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 153 through 157 Processing sheet with id=AB1, first strand: chain 'D' and resid 79 through 82 Processing sheet with id=AB2, first strand: chain 'D' and resid 142 through 147 removed outlier: 6.566A pdb=" N ASP D 135 " --> pdb=" O ILE D 143 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LEU D 145 " --> pdb=" O LEU D 133 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N LEU D 133 " --> pdb=" O LEU D 145 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N TYR D 131 " --> pdb=" O PRO D 147 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 153 through 157 Processing sheet with id=AB4, first strand: chain 'E' and resid 79 through 82 Processing sheet with id=AB5, first strand: chain 'E' and resid 142 through 148 removed outlier: 6.509A pdb=" N ASP E 135 " --> pdb=" O ILE E 143 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LEU E 145 " --> pdb=" O LEU E 133 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LEU E 133 " --> pdb=" O LEU E 145 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N TYR E 131 " --> pdb=" O PRO E 147 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 153 through 157 Processing sheet with id=AB7, first strand: chain 'F' and resid 79 through 82 Processing sheet with id=AB8, first strand: chain 'F' and resid 142 through 147 removed outlier: 6.505A pdb=" N ASP F 135 " --> pdb=" O ILE F 143 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU F 145 " --> pdb=" O LEU F 133 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N LEU F 133 " --> pdb=" O LEU F 145 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N TYR F 131 " --> pdb=" O PRO F 147 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 153 through 157 Processing sheet with id=AC1, first strand: chain 'G' and resid 79 through 82 Processing sheet with id=AC2, first strand: chain 'G' and resid 142 through 147 removed outlier: 6.566A pdb=" N ASP G 135 " --> pdb=" O ILE G 143 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU G 145 " --> pdb=" O LEU G 133 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N LEU G 133 " --> pdb=" O LEU G 145 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N TYR G 131 " --> pdb=" O PRO G 147 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 153 through 157 Processing sheet with id=AC4, first strand: chain 'H' and resid 79 through 82 Processing sheet with id=AC5, first strand: chain 'H' and resid 142 through 148 removed outlier: 6.507A pdb=" N ASP H 135 " --> pdb=" O ILE H 143 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU H 145 " --> pdb=" O LEU H 133 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N LEU H 133 " --> pdb=" O LEU H 145 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N TYR H 131 " --> pdb=" O PRO H 147 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 153 through 157 Processing sheet with id=AC7, first strand: chain 'I' and resid 79 through 82 Processing sheet with id=AC8, first strand: chain 'I' and resid 142 through 147 removed outlier: 6.503A pdb=" N ASP I 135 " --> pdb=" O ILE I 143 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LEU I 145 " --> pdb=" O LEU I 133 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N LEU I 133 " --> pdb=" O LEU I 145 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N TYR I 131 " --> pdb=" O PRO I 147 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 153 through 157 Processing sheet with id=AD1, first strand: chain 'J' and resid 79 through 82 Processing sheet with id=AD2, first strand: chain 'J' and resid 142 through 147 removed outlier: 6.564A pdb=" N ASP J 135 " --> pdb=" O ILE J 143 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU J 145 " --> pdb=" O LEU J 133 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N LEU J 133 " --> pdb=" O LEU J 145 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N TYR J 131 " --> pdb=" O PRO J 147 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 153 through 157 Processing sheet with id=AD4, first strand: chain 'K' and resid 79 through 82 Processing sheet with id=AD5, first strand: chain 'K' and resid 142 through 148 removed outlier: 6.507A pdb=" N ASP K 135 " --> pdb=" O ILE K 143 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LEU K 145 " --> pdb=" O LEU K 133 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LEU K 133 " --> pdb=" O LEU K 145 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N TYR K 131 " --> pdb=" O PRO K 147 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 153 through 157 Processing sheet with id=AD7, first strand: chain 'L' and resid 79 through 82 Processing sheet with id=AD8, first strand: chain 'L' and resid 142 through 147 removed outlier: 6.506A pdb=" N ASP L 135 " --> pdb=" O ILE L 143 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LEU L 145 " --> pdb=" O LEU L 133 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N LEU L 133 " --> pdb=" O LEU L 145 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N TYR L 131 " --> pdb=" O PRO L 147 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 153 through 157 1368 hydrogen bonds defined for protein. 3984 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: 23.77 Time building geometry restraints manager: 16.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 33852 1.03 - 1.23: 188 1.23 - 1.42: 14632 1.42 - 1.62: 19956 1.62 - 1.81: 312 Bond restraints: 68940 Sorted by residual: bond pdb=" CG PRO H 32 " pdb=" CD PRO H 32 " ideal model delta sigma weight residual 1.503 1.428 0.075 3.40e-02 8.65e+02 4.88e+00 bond pdb=" CG PRO B 32 " pdb=" CD PRO B 32 " ideal model delta sigma weight residual 1.503 1.428 0.075 3.40e-02 8.65e+02 4.88e+00 bond pdb=" CG PRO G 32 " pdb=" CD PRO G 32 " ideal model delta sigma weight residual 1.503 1.447 0.056 3.40e-02 8.65e+02 2.73e+00 bond pdb=" CG PRO J 32 " pdb=" CD PRO J 32 " ideal model delta sigma weight residual 1.503 1.447 0.056 3.40e-02 8.65e+02 2.68e+00 bond pdb=" CG PRO A 32 " pdb=" CD PRO A 32 " ideal model delta sigma weight residual 1.503 1.447 0.056 3.40e-02 8.65e+02 2.67e+00 ... (remaining 68935 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 120664 1.51 - 3.02: 3352 3.02 - 4.54: 260 4.54 - 6.05: 26 6.05 - 7.56: 30 Bond angle restraints: 124332 Sorted by residual: angle pdb=" CA PRO B 32 " pdb=" N PRO B 32 " pdb=" CD PRO B 32 " ideal model delta sigma weight residual 112.00 105.29 6.71 1.40e+00 5.10e-01 2.30e+01 angle pdb=" CA PRO H 32 " pdb=" N PRO H 32 " pdb=" CD PRO H 32 " ideal model delta sigma weight residual 112.00 105.29 6.71 1.40e+00 5.10e-01 2.30e+01 angle pdb=" N PRO H 32 " pdb=" CD PRO H 32 " pdb=" CG PRO H 32 " ideal model delta sigma weight residual 103.20 96.12 7.08 1.50e+00 4.44e-01 2.23e+01 angle pdb=" N PRO B 32 " pdb=" CD PRO B 32 " pdb=" CG PRO B 32 " ideal model delta sigma weight residual 103.20 96.12 7.08 1.50e+00 4.44e-01 2.23e+01 angle pdb=" N ALA E 366 " pdb=" CA ALA E 366 " pdb=" C ALA E 366 " ideal model delta sigma weight residual 114.04 108.34 5.70 1.24e+00 6.50e-01 2.12e+01 ... (remaining 124327 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.77: 28974 16.77 - 33.54: 2606 33.54 - 50.31: 689 50.31 - 67.08: 211 67.08 - 83.86: 28 Dihedral angle restraints: 32508 sinusoidal: 17868 harmonic: 14640 Sorted by residual: dihedral pdb=" CA LYS E 257 " pdb=" C LYS E 257 " pdb=" N ARG E 258 " pdb=" CA ARG E 258 " ideal model delta harmonic sigma weight residual 180.00 152.67 27.33 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA LYS K 257 " pdb=" C LYS K 257 " pdb=" N ARG K 258 " pdb=" CA ARG K 258 " ideal model delta harmonic sigma weight residual 180.00 152.67 27.33 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA LYS B 257 " pdb=" C LYS B 257 " pdb=" N ARG B 258 " pdb=" CA ARG B 258 " ideal model delta harmonic sigma weight residual 180.00 152.69 27.31 0 5.00e+00 4.00e-02 2.98e+01 ... (remaining 32505 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 2566 0.026 - 0.053: 1578 0.053 - 0.079: 624 0.079 - 0.106: 165 0.106 - 0.132: 191 Chirality restraints: 5124 Sorted by residual: chirality pdb=" CA ILE E 261 " pdb=" N ILE E 261 " pdb=" C ILE E 261 " pdb=" CB ILE E 261 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.36e-01 chirality pdb=" CA ILE B 261 " pdb=" N ILE B 261 " pdb=" C ILE B 261 " pdb=" CB ILE B 261 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.26e-01 chirality pdb=" CA ILE L 261 " pdb=" N ILE L 261 " pdb=" C ILE L 261 " pdb=" CB ILE L 261 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.26e-01 ... (remaining 5121 not shown) Planarity restraints: 10440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU G 395 " 0.041 5.00e-02 4.00e+02 6.25e-02 6.25e+00 pdb=" N PRO G 396 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO G 396 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO G 396 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU J 395 " 0.041 5.00e-02 4.00e+02 6.25e-02 6.25e+00 pdb=" N PRO J 396 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO J 396 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO J 396 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 395 " -0.041 5.00e-02 4.00e+02 6.18e-02 6.11e+00 pdb=" N PRO A 396 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 396 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 396 " -0.034 5.00e-02 4.00e+02 ... (remaining 10437 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 2816 2.16 - 2.77: 132100 2.77 - 3.38: 195118 3.38 - 3.99: 259102 3.99 - 4.60: 398483 Nonbonded interactions: 987619 Sorted by model distance: nonbonded pdb=" O LEU C 77 " pdb="HH22 ARG C 117 " model vdw 1.546 2.450 nonbonded pdb=" O LEU L 77 " pdb="HH22 ARG L 117 " model vdw 1.546 2.450 nonbonded pdb=" O LEU I 77 " pdb="HH22 ARG I 117 " model vdw 1.556 2.450 nonbonded pdb=" O LEU F 77 " pdb="HH22 ARG F 117 " model vdw 1.556 2.450 nonbonded pdb=" O LEU D 77 " pdb="HH22 ARG D 117 " model vdw 1.611 2.450 ... (remaining 987614 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.860 Extract box with map and model: 1.800 Check model and map are aligned: 0.380 Set scattering table: 0.450 Process input model: 107.960 Find NCS groups from input model: 1.810 Set up NCS constraints: 0.330 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: 0.020 Load rotamer database and sin/cos tables:11.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 126.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 35040 Z= 0.274 Angle : 0.668 7.562 47340 Z= 0.367 Chirality : 0.043 0.132 5124 Planarity : 0.005 0.063 6240 Dihedral : 13.958 83.856 13092 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.04 % Favored : 90.68 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % 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: -1.75 (0.13), residues: 4380 helix: 0.43 (0.12), residues: 1716 sheet: -1.18 (0.19), residues: 648 loop : -2.66 (0.13), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 311 HIS 0.004 0.001 HIS H 182 PHE 0.010 0.002 PHE B 186 TYR 0.006 0.001 TYR G 172 ARG 0.010 0.001 ARG D 168 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 483 time to evaluate : 3.961 Fit side-chains REVERT: A 210 MET cc_start: 0.9075 (mtm) cc_final: 0.8813 (mtm) REVERT: B 57 ILE cc_start: 0.8835 (mt) cc_final: 0.8512 (mt) REVERT: B 210 MET cc_start: 0.9081 (mtm) cc_final: 0.8853 (mtm) REVERT: C 122 MET cc_start: 0.8335 (tmm) cc_final: 0.8056 (tmt) REVERT: C 133 LEU cc_start: 0.8680 (tp) cc_final: 0.8458 (tp) REVERT: C 154 ASP cc_start: 0.7430 (t70) cc_final: 0.7220 (t70) REVERT: C 189 THR cc_start: 0.6413 (p) cc_final: 0.6084 (p) REVERT: D 210 MET cc_start: 0.9049 (mtm) cc_final: 0.8781 (mtm) REVERT: E 57 ILE cc_start: 0.8858 (mt) cc_final: 0.8531 (mt) REVERT: E 210 MET cc_start: 0.9090 (mtm) cc_final: 0.8866 (mtm) REVERT: F 154 ASP cc_start: 0.7441 (t70) cc_final: 0.7204 (t70) REVERT: F 189 THR cc_start: 0.6405 (p) cc_final: 0.6057 (p) REVERT: G 210 MET cc_start: 0.9063 (mtm) cc_final: 0.8796 (mtm) REVERT: H 57 ILE cc_start: 0.8840 (mt) cc_final: 0.8511 (mt) REVERT: H 210 MET cc_start: 0.9066 (mtm) cc_final: 0.8863 (mtm) REVERT: I 154 ASP cc_start: 0.7409 (t70) cc_final: 0.7179 (t70) REVERT: I 189 THR cc_start: 0.6405 (p) cc_final: 0.6079 (p) REVERT: J 210 MET cc_start: 0.9081 (mtm) cc_final: 0.8799 (mtm) REVERT: K 57 ILE cc_start: 0.8816 (mt) cc_final: 0.8503 (mt) REVERT: L 122 MET cc_start: 0.8310 (tmm) cc_final: 0.8056 (tmt) REVERT: L 154 ASP cc_start: 0.7426 (t70) cc_final: 0.7178 (t70) REVERT: L 189 THR cc_start: 0.6416 (p) cc_final: 0.6108 (p) outliers start: 0 outliers final: 0 residues processed: 483 average time/residue: 2.5273 time to fit residues: 1476.3577 Evaluate side-chains 385 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 385 time to evaluate : 3.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 364 optimal weight: 2.9990 chunk 327 optimal weight: 5.9990 chunk 181 optimal weight: 9.9990 chunk 111 optimal weight: 5.9990 chunk 220 optimal weight: 6.9990 chunk 174 optimal weight: 5.9990 chunk 338 optimal weight: 0.8980 chunk 131 optimal weight: 0.7980 chunk 205 optimal weight: 4.9990 chunk 252 optimal weight: 7.9990 chunk 392 optimal weight: 1.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN D 177 GLN G 177 GLN J 177 GLN L 287 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 moved from start: 0.0754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 35040 Z= 0.275 Angle : 0.616 6.621 47340 Z= 0.323 Chirality : 0.043 0.135 5124 Planarity : 0.005 0.065 6240 Dihedral : 6.052 25.157 4776 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.11 % Favored : 89.70 % Rotamer: Outliers : 0.92 % Allowed : 7.25 % Favored : 91.83 % 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: -1.70 (0.12), residues: 4380 helix: 0.60 (0.12), residues: 1704 sheet: -1.23 (0.19), residues: 648 loop : -2.71 (0.13), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 311 HIS 0.003 0.001 HIS E 182 PHE 0.011 0.002 PHE L 218 TYR 0.006 0.001 TYR G 325 ARG 0.005 0.001 ARG E 90 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 402 time to evaluate : 3.936 Fit side-chains REVERT: A 171 GLU cc_start: 0.6509 (OUTLIER) cc_final: 0.6227 (pp20) REVERT: A 177 GLN cc_start: 0.7986 (OUTLIER) cc_final: 0.7196 (mt0) REVERT: A 210 MET cc_start: 0.9075 (mtm) cc_final: 0.8816 (mtm) REVERT: B 33 ASN cc_start: 0.6904 (OUTLIER) cc_final: 0.6605 (t0) REVERT: B 57 ILE cc_start: 0.8850 (mt) cc_final: 0.8521 (mt) REVERT: B 135 ASP cc_start: 0.7334 (OUTLIER) cc_final: 0.6857 (t70) REVERT: B 210 MET cc_start: 0.9085 (mtm) cc_final: 0.8829 (mtm) REVERT: C 122 MET cc_start: 0.8445 (tmm) cc_final: 0.7907 (tmt) REVERT: C 133 LEU cc_start: 0.8704 (tp) cc_final: 0.8457 (tp) REVERT: C 189 THR cc_start: 0.6587 (p) cc_final: 0.6201 (p) REVERT: D 177 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.7208 (mt0) REVERT: D 210 MET cc_start: 0.9051 (mtm) cc_final: 0.8795 (mtm) REVERT: E 57 ILE cc_start: 0.8872 (mt) cc_final: 0.8540 (mt) REVERT: E 135 ASP cc_start: 0.7349 (OUTLIER) cc_final: 0.6860 (t70) REVERT: E 210 MET cc_start: 0.9079 (mtm) cc_final: 0.8826 (mtm) REVERT: F 122 MET cc_start: 0.8214 (tmt) cc_final: 0.7969 (tmt) REVERT: F 133 LEU cc_start: 0.8712 (tp) cc_final: 0.8451 (tp) REVERT: F 189 THR cc_start: 0.6556 (p) cc_final: 0.6155 (p) REVERT: G 177 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.7258 (mt0) REVERT: G 210 MET cc_start: 0.9049 (mtm) cc_final: 0.8797 (mtm) REVERT: H 33 ASN cc_start: 0.6908 (OUTLIER) cc_final: 0.6617 (t0) REVERT: H 57 ILE cc_start: 0.8842 (mt) cc_final: 0.8517 (mt) REVERT: H 135 ASP cc_start: 0.7410 (OUTLIER) cc_final: 0.6887 (t70) REVERT: H 210 MET cc_start: 0.9071 (mtm) cc_final: 0.8852 (mtm) REVERT: I 122 MET cc_start: 0.8197 (tmt) cc_final: 0.7946 (tmt) REVERT: I 133 LEU cc_start: 0.8705 (tp) cc_final: 0.8467 (tp) REVERT: I 189 THR cc_start: 0.6563 (p) cc_final: 0.6180 (p) REVERT: J 171 GLU cc_start: 0.6534 (OUTLIER) cc_final: 0.6216 (pp20) REVERT: J 177 GLN cc_start: 0.8005 (OUTLIER) cc_final: 0.7243 (mt0) REVERT: J 210 MET cc_start: 0.9066 (mtm) cc_final: 0.8738 (mtm) REVERT: K 57 ILE cc_start: 0.8836 (mt) cc_final: 0.8502 (mt) REVERT: L 122 MET cc_start: 0.8431 (tmm) cc_final: 0.7921 (tmt) REVERT: L 133 LEU cc_start: 0.8679 (tp) cc_final: 0.8446 (tp) REVERT: L 189 THR cc_start: 0.6624 (p) cc_final: 0.6231 (p) outliers start: 34 outliers final: 6 residues processed: 425 average time/residue: 2.2553 time to fit residues: 1186.3904 Evaluate side-chains 407 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 390 time to evaluate : 4.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 177 GLN Chi-restraints excluded: chain D residue 160 LYS Chi-restraints excluded: chain D residue 177 GLN Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain E residue 177 GLN Chi-restraints excluded: chain G residue 177 GLN Chi-restraints excluded: chain H residue 33 ASN Chi-restraints excluded: chain H residue 135 ASP Chi-restraints excluded: chain H residue 177 GLN Chi-restraints excluded: chain J residue 171 GLU Chi-restraints excluded: chain J residue 177 GLN Chi-restraints excluded: chain K residue 177 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 218 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 326 optimal weight: 5.9990 chunk 267 optimal weight: 4.9990 chunk 108 optimal weight: 7.9990 chunk 393 optimal weight: 10.0000 chunk 424 optimal weight: 3.9990 chunk 350 optimal weight: 1.9990 chunk 389 optimal weight: 2.9990 chunk 133 optimal weight: 5.9990 chunk 315 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 33 ASN G 356 ASN J 356 ASN K 33 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.0999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 35040 Z= 0.378 Angle : 0.677 6.929 47340 Z= 0.356 Chirality : 0.045 0.139 5124 Planarity : 0.006 0.068 6240 Dihedral : 6.237 25.169 4776 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.80 % Favored : 88.01 % Rotamer: Outliers : 1.13 % Allowed : 8.79 % Favored : 90.08 % 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: -1.83 (0.12), residues: 4380 helix: 0.45 (0.12), residues: 1716 sheet: -1.23 (0.19), residues: 648 loop : -2.79 (0.13), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 311 HIS 0.005 0.001 HIS E 182 PHE 0.014 0.003 PHE L 218 TYR 0.009 0.002 TYR A 325 ARG 0.006 0.001 ARG L 90 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 386 time to evaluate : 3.948 Fit side-chains REVERT: A 146 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8297 (mm) REVERT: A 210 MET cc_start: 0.9086 (mtm) cc_final: 0.8788 (mtm) REVERT: B 33 ASN cc_start: 0.6947 (OUTLIER) cc_final: 0.6653 (t0) REVERT: B 57 ILE cc_start: 0.8826 (mt) cc_final: 0.8499 (mt) REVERT: B 177 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.8084 (tt0) REVERT: B 210 MET cc_start: 0.9094 (mtm) cc_final: 0.8889 (mtm) REVERT: C 83 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7237 (tm-30) REVERT: C 133 LEU cc_start: 0.8703 (tp) cc_final: 0.8437 (tp) REVERT: D 146 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8294 (mm) REVERT: D 210 MET cc_start: 0.9056 (mtm) cc_final: 0.8764 (mtm) REVERT: E 33 ASN cc_start: 0.7005 (OUTLIER) cc_final: 0.6708 (t0) REVERT: E 57 ILE cc_start: 0.8844 (mt) cc_final: 0.8514 (mt) REVERT: F 83 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7300 (tm-30) REVERT: F 133 LEU cc_start: 0.8721 (tp) cc_final: 0.8475 (tp) REVERT: G 146 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8310 (mm) REVERT: G 210 MET cc_start: 0.9055 (mtm) cc_final: 0.8763 (mtm) REVERT: H 33 ASN cc_start: 0.6955 (OUTLIER) cc_final: 0.6664 (t0) REVERT: H 57 ILE cc_start: 0.8815 (mt) cc_final: 0.8489 (mt) REVERT: I 83 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7338 (tm-30) REVERT: I 133 LEU cc_start: 0.8703 (tp) cc_final: 0.8468 (tp) REVERT: J 146 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8310 (mm) REVERT: J 210 MET cc_start: 0.9072 (mtm) cc_final: 0.8776 (mtm) REVERT: K 33 ASN cc_start: 0.6999 (OUTLIER) cc_final: 0.6714 (t0) REVERT: K 57 ILE cc_start: 0.8807 (mt) cc_final: 0.8476 (mt) REVERT: L 83 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7246 (tm-30) REVERT: L 133 LEU cc_start: 0.8680 (tp) cc_final: 0.8436 (tp) outliers start: 42 outliers final: 19 residues processed: 411 average time/residue: 2.1665 time to fit residues: 1109.3177 Evaluate side-chains 411 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 379 time to evaluate : 4.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 177 GLN Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 160 LYS Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 153 MET Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain H residue 33 ASN Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain J residue 146 LEU Chi-restraints excluded: chain J residue 273 VAL Chi-restraints excluded: chain K residue 33 ASN Chi-restraints excluded: chain K residue 94 ASP Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 80 ASP Chi-restraints excluded: chain L residue 83 GLU Chi-restraints excluded: chain L residue 153 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 388 optimal weight: 6.9990 chunk 295 optimal weight: 3.9990 chunk 203 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 187 optimal weight: 3.9990 chunk 263 optimal weight: 5.9990 chunk 394 optimal weight: 4.9990 chunk 417 optimal weight: 8.9990 chunk 206 optimal weight: 4.9990 chunk 373 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN A 356 ASN B 149 GLN D 149 GLN D 356 ASN E 149 GLN F 149 GLN G 149 GLN H 149 GLN I 149 GLN J 149 GLN K 149 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 35040 Z= 0.378 Angle : 0.675 6.968 47340 Z= 0.354 Chirality : 0.045 0.139 5124 Planarity : 0.006 0.072 6240 Dihedral : 6.306 25.398 4776 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.32 % Allowed : 11.78 % Favored : 87.90 % Rotamer: Outliers : 1.38 % Allowed : 11.00 % Favored : 87.62 % 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: -1.89 (0.12), residues: 4380 helix: 0.41 (0.12), residues: 1716 sheet: -1.25 (0.19), residues: 648 loop : -2.83 (0.13), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP I 311 HIS 0.005 0.001 HIS H 182 PHE 0.014 0.003 PHE L 218 TYR 0.008 0.002 TYR J 325 ARG 0.006 0.001 ARG B 65 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 390 time to evaluate : 3.990 Fit side-chains REVERT: A 146 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8387 (mm) REVERT: A 171 GLU cc_start: 0.6383 (OUTLIER) cc_final: 0.6123 (pp20) REVERT: A 210 MET cc_start: 0.9085 (mtm) cc_final: 0.8844 (mtm) REVERT: B 33 ASN cc_start: 0.6969 (OUTLIER) cc_final: 0.6668 (t0) REVERT: B 57 ILE cc_start: 0.8823 (mt) cc_final: 0.8511 (mt) REVERT: B 210 MET cc_start: 0.9089 (mtm) cc_final: 0.8804 (mtm) REVERT: C 83 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7244 (tm-30) REVERT: C 133 LEU cc_start: 0.8580 (tp) cc_final: 0.8336 (tp) REVERT: D 146 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8380 (mm) REVERT: D 210 MET cc_start: 0.9057 (mtm) cc_final: 0.8809 (mtm) REVERT: E 57 ILE cc_start: 0.8852 (mt) cc_final: 0.8527 (mt) REVERT: F 83 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7301 (tm-30) REVERT: F 133 LEU cc_start: 0.8562 (tp) cc_final: 0.8309 (tp) REVERT: G 146 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8400 (mm) REVERT: G 210 MET cc_start: 0.9053 (mtm) cc_final: 0.8817 (mtm) REVERT: H 33 ASN cc_start: 0.6975 (OUTLIER) cc_final: 0.6687 (t0) REVERT: H 57 ILE cc_start: 0.8819 (mt) cc_final: 0.8502 (mt) REVERT: I 83 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7334 (tm-30) REVERT: I 133 LEU cc_start: 0.8565 (tp) cc_final: 0.8315 (tp) REVERT: J 146 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8394 (mm) REVERT: J 171 GLU cc_start: 0.6568 (OUTLIER) cc_final: 0.6282 (pp20) REVERT: J 210 MET cc_start: 0.9074 (mtm) cc_final: 0.8830 (mtm) REVERT: K 57 ILE cc_start: 0.8801 (mt) cc_final: 0.8491 (mt) REVERT: L 83 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7256 (tm-30) REVERT: L 133 LEU cc_start: 0.8562 (tp) cc_final: 0.8307 (tp) outliers start: 51 outliers final: 27 residues processed: 428 average time/residue: 2.1491 time to fit residues: 1148.1616 Evaluate side-chains 417 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 378 time to evaluate : 4.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 160 LYS Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 153 MET Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain H residue 33 ASN Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain I residue 273 VAL Chi-restraints excluded: chain J residue 146 LEU Chi-restraints excluded: chain J residue 171 GLU Chi-restraints excluded: chain J residue 273 VAL Chi-restraints excluded: chain K residue 94 ASP Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 80 ASP Chi-restraints excluded: chain L residue 83 GLU Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 153 MET Chi-restraints excluded: chain L residue 273 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 347 optimal weight: 5.9990 chunk 237 optimal weight: 7.9990 chunk 6 optimal weight: 0.7980 chunk 310 optimal weight: 4.9990 chunk 172 optimal weight: 5.9990 chunk 356 optimal weight: 7.9990 chunk 288 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 213 optimal weight: 6.9990 chunk 374 optimal weight: 6.9990 chunk 105 optimal weight: 7.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN B 352 HIS C 352 HIS E 33 ASN E 352 HIS H 352 HIS K 33 ASN K 352 HIS L 352 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.117 35040 Z= 0.474 Angle : 0.759 7.581 47340 Z= 0.399 Chirality : 0.049 0.158 5124 Planarity : 0.007 0.077 6240 Dihedral : 6.628 25.993 4776 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.37 % Allowed : 12.76 % Favored : 86.87 % Rotamer: Outliers : 1.73 % Allowed : 12.59 % Favored : 85.68 % 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: -2.14 (0.12), residues: 4380 helix: 0.18 (0.12), residues: 1704 sheet: -1.40 (0.18), residues: 672 loop : -2.94 (0.13), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP I 311 HIS 0.006 0.002 HIS H 182 PHE 0.018 0.003 PHE L 218 TYR 0.010 0.002 TYR A 325 ARG 0.008 0.001 ARG K 65 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 374 time to evaluate : 3.941 Fit side-chains REVERT: A 146 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8347 (mm) REVERT: A 171 GLU cc_start: 0.6663 (OUTLIER) cc_final: 0.6393 (pp20) REVERT: A 210 MET cc_start: 0.9058 (mtm) cc_final: 0.8797 (mtm) REVERT: A 281 MET cc_start: 0.7836 (mmp) cc_final: 0.7212 (mmp) REVERT: B 33 ASN cc_start: 0.7019 (OUTLIER) cc_final: 0.6705 (t0) REVERT: B 57 ILE cc_start: 0.8830 (mt) cc_final: 0.8526 (mt) REVERT: B 189 THR cc_start: 0.6957 (p) cc_final: 0.6547 (p) REVERT: B 210 MET cc_start: 0.9077 (mtm) cc_final: 0.8772 (mtm) REVERT: C 83 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7312 (tm-30) REVERT: D 146 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8399 (mm) REVERT: D 210 MET cc_start: 0.9030 (mtm) cc_final: 0.8776 (mtm) REVERT: D 281 MET cc_start: 0.7880 (mmp) cc_final: 0.7241 (mmp) REVERT: E 33 ASN cc_start: 0.7288 (OUTLIER) cc_final: 0.6901 (m110) REVERT: E 57 ILE cc_start: 0.8856 (mt) cc_final: 0.8553 (mt) REVERT: F 83 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7370 (tm-30) REVERT: F 120 MET cc_start: 0.9045 (mmm) cc_final: 0.8830 (mmm) REVERT: G 146 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8420 (mm) REVERT: G 210 MET cc_start: 0.9025 (mtm) cc_final: 0.8775 (mtm) REVERT: G 281 MET cc_start: 0.7899 (mmp) cc_final: 0.7232 (mmp) REVERT: H 33 ASN cc_start: 0.7012 (OUTLIER) cc_final: 0.6729 (t0) REVERT: H 57 ILE cc_start: 0.8831 (mt) cc_final: 0.8525 (mt) REVERT: I 83 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7404 (tm-30) REVERT: I 120 MET cc_start: 0.9043 (mmm) cc_final: 0.8825 (mmm) REVERT: J 146 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8416 (mm) REVERT: J 171 GLU cc_start: 0.6674 (OUTLIER) cc_final: 0.6380 (pp20) REVERT: J 210 MET cc_start: 0.9044 (mtm) cc_final: 0.8780 (mtm) REVERT: J 281 MET cc_start: 0.7862 (mmp) cc_final: 0.7208 (mmp) REVERT: K 33 ASN cc_start: 0.7293 (OUTLIER) cc_final: 0.6868 (m110) REVERT: K 57 ILE cc_start: 0.8809 (mt) cc_final: 0.8507 (mt) REVERT: K 189 THR cc_start: 0.6953 (p) cc_final: 0.6558 (p) REVERT: L 83 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7329 (tm-30) outliers start: 64 outliers final: 32 residues processed: 423 average time/residue: 2.2141 time to fit residues: 1177.2087 Evaluate side-chains 399 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 353 time to evaluate : 3.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 160 LYS Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 153 MET Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain G residue 144 SER Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain H residue 33 ASN Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain I residue 273 VAL Chi-restraints excluded: chain J residue 144 SER Chi-restraints excluded: chain J residue 146 LEU Chi-restraints excluded: chain J residue 171 GLU Chi-restraints excluded: chain J residue 273 VAL Chi-restraints excluded: chain K residue 33 ASN Chi-restraints excluded: chain K residue 94 ASP Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 80 ASP Chi-restraints excluded: chain L residue 83 GLU Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 111 MET Chi-restraints excluded: chain L residue 153 MET Chi-restraints excluded: chain L residue 273 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 140 optimal weight: 7.9990 chunk 376 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 245 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 417 optimal weight: 3.9990 chunk 346 optimal weight: 5.9990 chunk 193 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 138 optimal weight: 2.9990 chunk 219 optimal weight: 2.9990 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 352 HIS L 352 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 35040 Z= 0.376 Angle : 0.692 7.414 47340 Z= 0.363 Chirality : 0.045 0.139 5124 Planarity : 0.006 0.077 6240 Dihedral : 6.494 26.118 4776 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.37 % Allowed : 12.51 % Favored : 87.12 % Rotamer: Outliers : 1.48 % Allowed : 14.02 % Favored : 84.49 % 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: -2.06 (0.12), residues: 4380 helix: 0.30 (0.12), residues: 1716 sheet: -1.41 (0.18), residues: 672 loop : -2.94 (0.13), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP F 311 HIS 0.005 0.001 HIS H 182 PHE 0.014 0.003 PHE L 218 TYR 0.007 0.002 TYR G 325 ARG 0.006 0.001 ARG B 65 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 358 time to evaluate : 3.928 Fit side-chains REVERT: A 146 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8371 (mm) REVERT: A 171 GLU cc_start: 0.6581 (OUTLIER) cc_final: 0.6318 (pp20) REVERT: A 210 MET cc_start: 0.9058 (mtm) cc_final: 0.8735 (mtm) REVERT: A 281 MET cc_start: 0.7678 (mmp) cc_final: 0.7105 (mmp) REVERT: B 57 ILE cc_start: 0.8823 (mt) cc_final: 0.8536 (mt) REVERT: B 189 THR cc_start: 0.6900 (p) cc_final: 0.6436 (p) REVERT: B 210 MET cc_start: 0.9068 (mtm) cc_final: 0.8754 (mtm) REVERT: C 83 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7309 (tm-30) REVERT: C 177 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7910 (mt0) REVERT: D 146 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8363 (mm) REVERT: D 210 MET cc_start: 0.9031 (mtm) cc_final: 0.8717 (mtm) REVERT: D 281 MET cc_start: 0.7724 (mmp) cc_final: 0.7143 (mmp) REVERT: E 57 ILE cc_start: 0.8857 (mt) cc_final: 0.8554 (mt) REVERT: F 83 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7353 (tm-30) REVERT: F 120 MET cc_start: 0.8922 (mmm) cc_final: 0.8707 (mmm) REVERT: F 133 LEU cc_start: 0.8396 (tp) cc_final: 0.8159 (tp) REVERT: F 177 GLN cc_start: 0.8149 (OUTLIER) cc_final: 0.7932 (mt0) REVERT: G 146 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8381 (mm) REVERT: G 210 MET cc_start: 0.9028 (mtm) cc_final: 0.8710 (mtm) REVERT: G 281 MET cc_start: 0.7738 (mmp) cc_final: 0.7130 (mmp) REVERT: H 57 ILE cc_start: 0.8831 (mt) cc_final: 0.8523 (mt) REVERT: I 83 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7395 (tm-30) REVERT: I 120 MET cc_start: 0.8935 (mmm) cc_final: 0.8721 (mmm) REVERT: I 177 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.7903 (mt0) REVERT: J 146 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8373 (mm) REVERT: J 171 GLU cc_start: 0.6589 (OUTLIER) cc_final: 0.6306 (pp20) REVERT: J 210 MET cc_start: 0.9047 (mtm) cc_final: 0.8715 (mtm) REVERT: J 281 MET cc_start: 0.7692 (mmp) cc_final: 0.7105 (mmp) REVERT: K 57 ILE cc_start: 0.8806 (mt) cc_final: 0.8517 (mt) REVERT: K 189 THR cc_start: 0.6896 (p) cc_final: 0.6465 (p) REVERT: L 83 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7324 (tm-30) REVERT: L 133 LEU cc_start: 0.8367 (tp) cc_final: 0.8138 (tp) REVERT: L 177 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7881 (mt0) outliers start: 55 outliers final: 35 residues processed: 401 average time/residue: 2.1878 time to fit residues: 1089.8030 Evaluate side-chains 405 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 356 time to evaluate : 3.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 160 LYS Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 345 SER Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 153 MET Chi-restraints excluded: chain F residue 177 GLN Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain H residue 345 SER Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain I residue 177 GLN Chi-restraints excluded: chain I residue 273 VAL Chi-restraints excluded: chain J residue 146 LEU Chi-restraints excluded: chain J residue 171 GLU Chi-restraints excluded: chain J residue 273 VAL Chi-restraints excluded: chain K residue 94 ASP Chi-restraints excluded: chain K residue 273 VAL Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 80 ASP Chi-restraints excluded: chain L residue 83 GLU Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 111 MET Chi-restraints excluded: chain L residue 153 MET Chi-restraints excluded: chain L residue 177 GLN Chi-restraints excluded: chain L residue 273 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 402 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 238 optimal weight: 0.8980 chunk 305 optimal weight: 3.9990 chunk 236 optimal weight: 4.9990 chunk 351 optimal weight: 7.9990 chunk 233 optimal weight: 4.9990 chunk 416 optimal weight: 7.9990 chunk 260 optimal weight: 3.9990 chunk 253 optimal weight: 0.4980 chunk 192 optimal weight: 4.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 ASN B 352 HIS E 352 HIS H 33 ASN K 352 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 35040 Z= 0.236 Angle : 0.599 6.705 47340 Z= 0.313 Chirality : 0.042 0.130 5124 Planarity : 0.005 0.070 6240 Dihedral : 6.061 24.754 4776 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.19 % Favored : 88.54 % Rotamer: Outliers : 1.19 % Allowed : 14.37 % Favored : 84.44 % 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: -1.75 (0.12), residues: 4380 helix: 0.68 (0.12), residues: 1728 sheet: -1.37 (0.19), residues: 648 loop : -2.86 (0.13), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP K 311 HIS 0.004 0.001 HIS F 300 PHE 0.011 0.002 PHE K 247 TYR 0.007 0.001 TYR E 166 ARG 0.004 0.000 ARG L 284 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 377 time to evaluate : 3.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 GLU cc_start: 0.6948 (tt0) cc_final: 0.6400 (pt0) REVERT: A 146 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8390 (mm) REVERT: A 210 MET cc_start: 0.9088 (mtm) cc_final: 0.8797 (mtm) REVERT: A 281 MET cc_start: 0.7530 (mmp) cc_final: 0.6995 (mmp) REVERT: A 364 ASP cc_start: 0.6628 (m-30) cc_final: 0.6385 (t0) REVERT: B 57 ILE cc_start: 0.8831 (mt) cc_final: 0.8539 (mt) REVERT: B 210 MET cc_start: 0.9065 (mtm) cc_final: 0.8756 (mtm) REVERT: C 83 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7280 (tm-30) REVERT: D 146 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8388 (mm) REVERT: D 210 MET cc_start: 0.9064 (mtm) cc_final: 0.8778 (mtm) REVERT: D 280 MET cc_start: 0.7298 (mtt) cc_final: 0.7096 (mtt) REVERT: D 281 MET cc_start: 0.7566 (mmp) cc_final: 0.7031 (mmp) REVERT: D 364 ASP cc_start: 0.6584 (m-30) cc_final: 0.6351 (t0) REVERT: E 57 ILE cc_start: 0.8855 (mt) cc_final: 0.8554 (mt) REVERT: F 83 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7326 (tm-30) REVERT: F 120 MET cc_start: 0.8930 (mmm) cc_final: 0.8633 (mmm) REVERT: F 212 ASP cc_start: 0.8195 (m-30) cc_final: 0.7814 (m-30) REVERT: G 83 GLU cc_start: 0.6955 (tt0) cc_final: 0.6274 (pt0) REVERT: G 146 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8408 (mm) REVERT: G 210 MET cc_start: 0.9060 (mtm) cc_final: 0.8774 (mtm) REVERT: G 281 MET cc_start: 0.7580 (mmp) cc_final: 0.7019 (mmp) REVERT: G 364 ASP cc_start: 0.6558 (m-30) cc_final: 0.6334 (t0) REVERT: H 57 ILE cc_start: 0.8826 (mt) cc_final: 0.8527 (mt) REVERT: I 83 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7353 (tm-30) REVERT: I 120 MET cc_start: 0.8942 (mmm) cc_final: 0.8650 (mmm) REVERT: I 212 ASP cc_start: 0.8212 (m-30) cc_final: 0.7791 (m-30) REVERT: J 83 GLU cc_start: 0.6902 (tt0) cc_final: 0.6345 (pt0) REVERT: J 146 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8402 (mm) REVERT: J 210 MET cc_start: 0.9078 (mtm) cc_final: 0.8782 (mtm) REVERT: J 281 MET cc_start: 0.7533 (mmp) cc_final: 0.6990 (mmp) REVERT: J 364 ASP cc_start: 0.6604 (m-30) cc_final: 0.6366 (t0) REVERT: K 57 ILE cc_start: 0.8811 (mt) cc_final: 0.8518 (mt) REVERT: L 83 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7299 (tm-30) outliers start: 44 outliers final: 33 residues processed: 412 average time/residue: 2.2320 time to fit residues: 1140.2124 Evaluate side-chains 408 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 367 time to evaluate : 3.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 240 ARG Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain E residue 345 SER Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 153 MET Chi-restraints excluded: chain F residue 240 ARG Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain G residue 144 SER Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain H residue 345 SER Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain I residue 240 ARG Chi-restraints excluded: chain I residue 273 VAL Chi-restraints excluded: chain J residue 144 SER Chi-restraints excluded: chain J residue 146 LEU Chi-restraints excluded: chain J residue 273 VAL Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 80 ASP Chi-restraints excluded: chain L residue 83 GLU Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 153 MET Chi-restraints excluded: chain L residue 240 ARG Chi-restraints excluded: chain L residue 273 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 257 optimal weight: 5.9990 chunk 166 optimal weight: 4.9990 chunk 248 optimal weight: 7.9990 chunk 125 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 264 optimal weight: 5.9990 chunk 283 optimal weight: 5.9990 chunk 205 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 327 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.103 35040 Z= 0.382 Angle : 0.682 7.098 47340 Z= 0.356 Chirality : 0.046 0.139 5124 Planarity : 0.006 0.075 6240 Dihedral : 6.313 25.027 4776 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.37 % Allowed : 12.72 % Favored : 86.92 % Rotamer: Outliers : 1.54 % Allowed : 15.02 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.12), residues: 4380 helix: 0.51 (0.12), residues: 1716 sheet: -1.41 (0.18), residues: 672 loop : -2.91 (0.13), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP F 311 HIS 0.005 0.001 HIS E 182 PHE 0.014 0.003 PHE F 218 TYR 0.012 0.002 TYR G 172 ARG 0.006 0.001 ARG F 117 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 366 time to evaluate : 3.968 Fit side-chains REVERT: A 83 GLU cc_start: 0.6989 (tt0) cc_final: 0.6313 (pt0) REVERT: A 146 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8429 (mm) REVERT: A 210 MET cc_start: 0.9063 (mtm) cc_final: 0.8756 (mtm) REVERT: A 281 MET cc_start: 0.7516 (mmp) cc_final: 0.6937 (mmp) REVERT: A 364 ASP cc_start: 0.6793 (m-30) cc_final: 0.6495 (t0) REVERT: B 57 ILE cc_start: 0.8838 (mt) cc_final: 0.8537 (mt) REVERT: B 210 MET cc_start: 0.9065 (mtm) cc_final: 0.8776 (mtm) REVERT: C 83 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7328 (tm-30) REVERT: C 177 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7847 (mt0) REVERT: C 240 ARG cc_start: 0.2401 (OUTLIER) cc_final: 0.2137 (ptm-80) REVERT: D 146 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8425 (mm) REVERT: D 210 MET cc_start: 0.9034 (mtm) cc_final: 0.8735 (mtm) REVERT: D 281 MET cc_start: 0.7441 (mmp) cc_final: 0.6868 (mmp) REVERT: D 364 ASP cc_start: 0.6747 (m-30) cc_final: 0.6458 (t0) REVERT: E 57 ILE cc_start: 0.8861 (mt) cc_final: 0.8555 (mt) REVERT: F 83 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7379 (tm-30) REVERT: F 120 MET cc_start: 0.8963 (mmm) cc_final: 0.8718 (mmm) REVERT: F 177 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7865 (mt0) REVERT: F 240 ARG cc_start: 0.2486 (OUTLIER) cc_final: 0.2211 (ptm-80) REVERT: G 83 GLU cc_start: 0.7001 (tt0) cc_final: 0.6266 (pt0) REVERT: G 146 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8439 (mm) REVERT: G 210 MET cc_start: 0.9030 (mtm) cc_final: 0.8730 (mtm) REVERT: G 281 MET cc_start: 0.7466 (mmp) cc_final: 0.6888 (mmp) REVERT: G 364 ASP cc_start: 0.6722 (m-30) cc_final: 0.6435 (t0) REVERT: H 57 ILE cc_start: 0.8835 (mt) cc_final: 0.8526 (mt) REVERT: I 83 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7412 (tm-30) REVERT: I 120 MET cc_start: 0.8976 (mmm) cc_final: 0.8737 (mmm) REVERT: I 177 GLN cc_start: 0.8095 (OUTLIER) cc_final: 0.7842 (mt0) REVERT: I 240 ARG cc_start: 0.2442 (OUTLIER) cc_final: 0.2164 (ptm-80) REVERT: J 83 GLU cc_start: 0.6952 (tt0) cc_final: 0.6266 (pt0) REVERT: J 146 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8434 (mm) REVERT: J 210 MET cc_start: 0.9051 (mtm) cc_final: 0.8738 (mtm) REVERT: J 281 MET cc_start: 0.7416 (mmp) cc_final: 0.6856 (mmp) REVERT: J 364 ASP cc_start: 0.6765 (m-30) cc_final: 0.6473 (t0) REVERT: K 57 ILE cc_start: 0.8816 (mt) cc_final: 0.8510 (mt) REVERT: L 83 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7339 (tm-30) REVERT: L 177 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.7815 (mt0) REVERT: L 240 ARG cc_start: 0.2346 (OUTLIER) cc_final: 0.2091 (ptm-80) outliers start: 57 outliers final: 39 residues processed: 415 average time/residue: 2.2477 time to fit residues: 1164.1390 Evaluate side-chains 420 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 365 time to evaluate : 3.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 240 ARG Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 345 SER Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 153 MET Chi-restraints excluded: chain F residue 177 GLN Chi-restraints excluded: chain F residue 240 ARG Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain G residue 144 SER Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain H residue 345 SER Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 144 SER Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain I residue 177 GLN Chi-restraints excluded: chain I residue 240 ARG Chi-restraints excluded: chain I residue 273 VAL Chi-restraints excluded: chain J residue 144 SER Chi-restraints excluded: chain J residue 146 LEU Chi-restraints excluded: chain J residue 273 VAL Chi-restraints excluded: chain K residue 94 ASP Chi-restraints excluded: chain K residue 273 VAL Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 80 ASP Chi-restraints excluded: chain L residue 83 GLU Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 153 MET Chi-restraints excluded: chain L residue 177 GLN Chi-restraints excluded: chain L residue 240 ARG Chi-restraints excluded: chain L residue 273 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 378 optimal weight: 2.9990 chunk 398 optimal weight: 4.9990 chunk 363 optimal weight: 2.9990 chunk 388 optimal weight: 5.9990 chunk 233 optimal weight: 4.9990 chunk 169 optimal weight: 5.9990 chunk 304 optimal weight: 0.9980 chunk 119 optimal weight: 4.9990 chunk 350 optimal weight: 0.4980 chunk 366 optimal weight: 0.9990 chunk 386 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 352 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 35040 Z= 0.206 Angle : 0.581 6.535 47340 Z= 0.302 Chirality : 0.041 0.129 5124 Planarity : 0.005 0.067 6240 Dihedral : 5.894 24.701 4776 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.50 % Favored : 90.30 % Rotamer: Outliers : 1.21 % Allowed : 15.45 % Favored : 83.33 % 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: -1.65 (0.13), residues: 4380 helix: 0.82 (0.13), residues: 1728 sheet: -1.37 (0.19), residues: 648 loop : -2.85 (0.13), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP K 311 HIS 0.004 0.001 HIS I 300 PHE 0.012 0.002 PHE K 247 TYR 0.008 0.001 TYR G 127 ARG 0.005 0.000 ARG A 215 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 392 time to evaluate : 4.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 GLU cc_start: 0.6909 (tt0) cc_final: 0.6408 (pt0) REVERT: A 146 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8390 (mm) REVERT: A 171 GLU cc_start: 0.6904 (OUTLIER) cc_final: 0.6653 (pp20) REVERT: A 172 TYR cc_start: 0.6804 (m-80) cc_final: 0.6476 (m-80) REVERT: A 210 MET cc_start: 0.9091 (mtm) cc_final: 0.8813 (mtm) REVERT: A 281 MET cc_start: 0.7478 (mmp) cc_final: 0.6973 (mmp) REVERT: A 364 ASP cc_start: 0.6625 (m-30) cc_final: 0.6383 (t0) REVERT: B 57 ILE cc_start: 0.8845 (mt) cc_final: 0.8560 (mt) REVERT: B 210 MET cc_start: 0.9065 (mtm) cc_final: 0.8769 (mtm) REVERT: C 212 ASP cc_start: 0.8150 (m-30) cc_final: 0.7792 (m-30) REVERT: D 83 GLU cc_start: 0.6734 (tt0) cc_final: 0.6423 (pt0) REVERT: D 146 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8388 (mm) REVERT: D 210 MET cc_start: 0.9066 (mtm) cc_final: 0.8793 (mtm) REVERT: D 281 MET cc_start: 0.7409 (mmp) cc_final: 0.6859 (mmp) REVERT: D 364 ASP cc_start: 0.6587 (m-30) cc_final: 0.6358 (t0) REVERT: E 57 ILE cc_start: 0.8865 (mt) cc_final: 0.8574 (mt) REVERT: F 83 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7295 (tm-30) REVERT: F 120 MET cc_start: 0.8891 (mmm) cc_final: 0.8616 (mmm) REVERT: F 212 ASP cc_start: 0.8173 (m-30) cc_final: 0.7784 (m-30) REVERT: G 83 GLU cc_start: 0.6921 (tt0) cc_final: 0.6384 (pt0) REVERT: G 146 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8395 (mm) REVERT: G 172 TYR cc_start: 0.6907 (m-80) cc_final: 0.6651 (m-80) REVERT: G 210 MET cc_start: 0.9063 (mtm) cc_final: 0.8787 (mtm) REVERT: G 281 MET cc_start: 0.7524 (mmp) cc_final: 0.6994 (mmp) REVERT: G 364 ASP cc_start: 0.6564 (m-30) cc_final: 0.6306 (t0) REVERT: H 57 ILE cc_start: 0.8839 (mt) cc_final: 0.8545 (mt) REVERT: I 120 MET cc_start: 0.8902 (mmm) cc_final: 0.8630 (mmm) REVERT: I 212 ASP cc_start: 0.8197 (m-30) cc_final: 0.7766 (m-30) REVERT: J 83 GLU cc_start: 0.6858 (tt0) cc_final: 0.6351 (pt0) REVERT: J 146 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8401 (mm) REVERT: J 171 GLU cc_start: 0.6914 (OUTLIER) cc_final: 0.6646 (pp20) REVERT: J 172 TYR cc_start: 0.6815 (m-80) cc_final: 0.6471 (m-80) REVERT: J 210 MET cc_start: 0.9079 (mtm) cc_final: 0.8795 (mtm) REVERT: J 281 MET cc_start: 0.7439 (mmp) cc_final: 0.6910 (mmp) REVERT: J 364 ASP cc_start: 0.6606 (m-30) cc_final: 0.6344 (t0) REVERT: K 57 ILE cc_start: 0.8825 (mt) cc_final: 0.8536 (mt) outliers start: 45 outliers final: 35 residues processed: 427 average time/residue: 2.1360 time to fit residues: 1139.0577 Evaluate side-chains 425 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 383 time to evaluate : 3.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 240 ARG Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain E residue 345 SER Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 153 MET Chi-restraints excluded: chain F residue 240 ARG Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain G residue 144 SER Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain H residue 345 SER Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 144 SER Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain I residue 240 ARG Chi-restraints excluded: chain I residue 273 VAL Chi-restraints excluded: chain J residue 144 SER Chi-restraints excluded: chain J residue 146 LEU Chi-restraints excluded: chain J residue 171 GLU Chi-restraints excluded: chain J residue 273 VAL Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 80 ASP Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 153 MET Chi-restraints excluded: chain L residue 240 ARG Chi-restraints excluded: chain L residue 273 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 254 optimal weight: 2.9990 chunk 410 optimal weight: 5.9990 chunk 250 optimal weight: 5.9990 chunk 194 optimal weight: 0.8980 chunk 285 optimal weight: 6.9990 chunk 430 optimal weight: 5.9990 chunk 396 optimal weight: 0.0270 chunk 342 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 264 optimal weight: 5.9990 chunk 210 optimal weight: 5.9990 overall best weight: 2.1844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 35040 Z= 0.262 Angle : 0.601 6.567 47340 Z= 0.313 Chirality : 0.042 0.134 5124 Planarity : 0.005 0.071 6240 Dihedral : 5.931 24.314 4776 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.76 % Favored : 88.15 % Rotamer: Outliers : 1.13 % Allowed : 15.78 % Favored : 83.09 % 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: -1.64 (0.12), residues: 4380 helix: 0.83 (0.12), residues: 1728 sheet: -1.34 (0.19), residues: 648 loop : -2.85 (0.13), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP K 311 HIS 0.004 0.001 HIS I 300 PHE 0.010 0.002 PHE D 218 TYR 0.009 0.001 TYR D 172 ARG 0.006 0.001 ARG D 215 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 378 time to evaluate : 4.012 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 GLU cc_start: 0.6953 (tt0) cc_final: 0.6466 (pt0) REVERT: A 146 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8338 (mm) REVERT: A 210 MET cc_start: 0.9087 (mtm) cc_final: 0.8812 (mtm) REVERT: A 281 MET cc_start: 0.7501 (mmp) cc_final: 0.7104 (mmp) REVERT: A 364 ASP cc_start: 0.6721 (m-30) cc_final: 0.6495 (t0) REVERT: B 33 ASN cc_start: 0.6842 (OUTLIER) cc_final: 0.6595 (t0) REVERT: B 57 ILE cc_start: 0.8835 (mt) cc_final: 0.8551 (mt) REVERT: B 210 MET cc_start: 0.9063 (mtm) cc_final: 0.8764 (mtm) REVERT: C 212 ASP cc_start: 0.8159 (m-30) cc_final: 0.7803 (m-30) REVERT: C 240 ARG cc_start: 0.2205 (OUTLIER) cc_final: 0.1989 (ptm-80) REVERT: D 146 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8402 (mm) REVERT: D 210 MET cc_start: 0.9063 (mtm) cc_final: 0.8793 (mtm) REVERT: D 281 MET cc_start: 0.7427 (mmp) cc_final: 0.6913 (mmp) REVERT: D 364 ASP cc_start: 0.6678 (m-30) cc_final: 0.6463 (t0) REVERT: E 57 ILE cc_start: 0.8855 (mt) cc_final: 0.8558 (mt) REVERT: F 120 MET cc_start: 0.8958 (mmm) cc_final: 0.8607 (mmm) REVERT: F 212 ASP cc_start: 0.8185 (m-30) cc_final: 0.7794 (m-30) REVERT: F 240 ARG cc_start: 0.2216 (OUTLIER) cc_final: 0.2012 (ptm-80) REVERT: G 83 GLU cc_start: 0.6965 (tt0) cc_final: 0.6447 (pt0) REVERT: G 146 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8349 (mm) REVERT: G 210 MET cc_start: 0.9057 (mtm) cc_final: 0.8787 (mtm) REVERT: G 281 MET cc_start: 0.7537 (mmp) cc_final: 0.7120 (mmp) REVERT: G 364 ASP cc_start: 0.6625 (m-30) cc_final: 0.6417 (t0) REVERT: H 33 ASN cc_start: 0.6844 (OUTLIER) cc_final: 0.6605 (t0) REVERT: H 57 ILE cc_start: 0.8830 (mt) cc_final: 0.8530 (mt) REVERT: I 120 MET cc_start: 0.8964 (mmm) cc_final: 0.8620 (mmm) REVERT: I 212 ASP cc_start: 0.8201 (m-30) cc_final: 0.7772 (m-30) REVERT: J 83 GLU cc_start: 0.6905 (tt0) cc_final: 0.6408 (pt0) REVERT: J 146 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8353 (mm) REVERT: J 210 MET cc_start: 0.9076 (mtm) cc_final: 0.8798 (mtm) REVERT: J 281 MET cc_start: 0.7386 (mmp) cc_final: 0.7001 (mmp) REVERT: J 364 ASP cc_start: 0.6672 (m-30) cc_final: 0.6423 (t0) REVERT: K 57 ILE cc_start: 0.8816 (mt) cc_final: 0.8529 (mt) REVERT: L 212 ASP cc_start: 0.8171 (m-30) cc_final: 0.7776 (m-30) outliers start: 42 outliers final: 27 residues processed: 415 average time/residue: 2.2716 time to fit residues: 1170.9110 Evaluate side-chains 406 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 371 time to evaluate : 3.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 240 ARG Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain E residue 345 SER Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 240 ARG Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain G residue 144 SER Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain H residue 33 ASN Chi-restraints excluded: chain H residue 345 SER Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 144 SER Chi-restraints excluded: chain I residue 273 VAL Chi-restraints excluded: chain J residue 144 SER Chi-restraints excluded: chain J residue 146 LEU Chi-restraints excluded: chain J residue 273 VAL Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 80 ASP Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 273 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 272 optimal weight: 2.9990 chunk 365 optimal weight: 5.9990 chunk 104 optimal weight: 8.9990 chunk 316 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 95 optimal weight: 6.9990 chunk 343 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 352 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 63 optimal weight: 8.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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 = 0.3801 r_free = 0.3801 target = 0.176188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.139224 restraints weight = 917547.756| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 6.62 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 35040 Z= 0.284 Angle : 0.617 6.666 47340 Z= 0.321 Chirality : 0.043 0.135 5124 Planarity : 0.005 0.068 6240 Dihedral : 5.977 24.552 4776 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.30 % Favored : 88.52 % Rotamer: Outliers : 1.08 % Allowed : 15.75 % Favored : 83.17 % 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 (0.12), residues: 4380 helix: 0.77 (0.12), residues: 1728 sheet: -1.36 (0.19), residues: 672 loop : -2.92 (0.13), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP K 311 HIS 0.004 0.001 HIS I 300 PHE 0.010 0.002 PHE H 218 TYR 0.007 0.001 TYR F 325 ARG 0.006 0.001 ARG D 215 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16499.00 seconds wall clock time: 284 minutes 23.14 seconds (17063.14 seconds total)