Starting phenix.real_space_refine on Fri Aug 7 20:52:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9skl_54968/08_2026/9skl_54968.cif Found real_map, /net/cci-nas-00/data/ceres_data/9skl_54968/08_2026/9skl_54968.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9skl_54968/08_2026/9skl_54968.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9skl_54968/08_2026/9skl_54968.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9skl_54968/08_2026/9skl_54968.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9skl_54968/08_2026/9skl_54968.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 15003 2.51 5 N 3879 2.21 5 O 4455 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23391 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2599 Classifications: {'peptide': 330} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 316} Chain: "B" Number of atoms: 2599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2599 Classifications: {'peptide': 330} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 316} Chain: "C" Number of atoms: 2599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2599 Classifications: {'peptide': 330} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 316} Chain: "D" Number of atoms: 2599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2599 Classifications: {'peptide': 330} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 316} Chain: "E" Number of atoms: 2599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2599 Classifications: {'peptide': 330} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 316} Chain: "F" Number of atoms: 2599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2599 Classifications: {'peptide': 330} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 316} Chain: "G" Number of atoms: 2599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2599 Classifications: {'peptide': 330} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 316} Chain: "H" Number of atoms: 2599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2599 Classifications: {'peptide': 330} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 316} Chain: "I" Number of atoms: 2599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2599 Classifications: {'peptide': 330} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 316} Time building chain proxies: 5.99, per 1000 atoms: 0.26 Number of scatterers: 23391 At special positions: 0 Unit cell: (142.416, 142.416, 157.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 4455 8.00 N 3879 7.00 C 15003 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.96 Conformation dependent library (CDL) restraints added in 1.3 seconds 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5706 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 9 sheets defined 69.3% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 28 through 39 Processing helix chain 'A' and resid 39 through 61 removed outlier: 3.567A pdb=" N VAL A 46 " --> pdb=" O THR A 42 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE A 48 " --> pdb=" O MET A 44 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ALA A 49 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE A 57 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER A 58 " --> pdb=" O GLY A 54 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 78 Processing helix chain 'A' and resid 79 through 91 removed outlier: 3.530A pdb=" N SER A 85 " --> pdb=" O GLU A 81 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N LYS A 88 " --> pdb=" O LYS A 84 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N LEU A 89 " --> pdb=" O SER A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 112 Processing helix chain 'A' and resid 113 through 124 Processing helix chain 'A' and resid 124 through 134 Processing helix chain 'A' and resid 140 through 150 Processing helix chain 'A' and resid 180 through 251 removed outlier: 3.559A pdb=" N VAL A 207 " --> pdb=" O SER A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 259 removed outlier: 3.869A pdb=" N SER A 258 " --> pdb=" O PRO A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 287 removed outlier: 4.008A pdb=" N GLY A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 311 Processing helix chain 'A' and resid 337 through 348 removed outlier: 3.654A pdb=" N ALA A 346 " --> pdb=" O VAL A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 356 removed outlier: 3.906A pdb=" N ALA A 353 " --> pdb=" O GLY A 349 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY A 356 " --> pdb=" O VAL A 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 39 Processing helix chain 'B' and resid 39 through 61 removed outlier: 3.589A pdb=" N VAL B 46 " --> pdb=" O THR B 42 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE B 48 " --> pdb=" O MET B 44 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ALA B 49 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE B 57 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER B 58 " --> pdb=" O GLY B 54 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N PHE B 59 " --> pdb=" O LEU B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 78 Processing helix chain 'B' and resid 79 through 91 removed outlier: 3.518A pdb=" N SER B 85 " --> pdb=" O GLU B 81 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LYS B 88 " --> pdb=" O LYS B 84 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N LEU B 89 " --> pdb=" O SER B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 112 Processing helix chain 'B' and resid 113 through 124 Processing helix chain 'B' and resid 124 through 134 Processing helix chain 'B' and resid 140 through 150 Processing helix chain 'B' and resid 180 through 251 removed outlier: 3.553A pdb=" N VAL B 207 " --> pdb=" O SER B 203 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS B 230 " --> pdb=" O ARG B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 287 removed outlier: 3.962A pdb=" N GLY B 277 " --> pdb=" O LEU B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 311 Processing helix chain 'B' and resid 337 through 348 removed outlier: 3.568A pdb=" N ALA B 346 " --> pdb=" O VAL B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 356 removed outlier: 3.964A pdb=" N ALA B 353 " --> pdb=" O GLY B 349 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY B 356 " --> pdb=" O VAL B 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 39 Processing helix chain 'C' and resid 39 through 61 removed outlier: 3.581A pdb=" N VAL C 46 " --> pdb=" O THR C 42 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE C 48 " --> pdb=" O MET C 44 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ALA C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA C 53 " --> pdb=" O ALA C 49 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE C 57 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER C 58 " --> pdb=" O GLY C 54 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 78 Processing helix chain 'C' and resid 79 through 91 removed outlier: 3.514A pdb=" N SER C 85 " --> pdb=" O GLU C 81 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LYS C 88 " --> pdb=" O LYS C 84 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LEU C 89 " --> pdb=" O SER C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 112 Processing helix chain 'C' and resid 113 through 124 Processing helix chain 'C' and resid 124 through 134 removed outlier: 3.511A pdb=" N GLN C 130 " --> pdb=" O TYR C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 150 Processing helix chain 'C' and resid 180 through 251 removed outlier: 3.538A pdb=" N VAL C 207 " --> pdb=" O SER C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 259 removed outlier: 4.172A pdb=" N SER C 258 " --> pdb=" O PRO C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 287 removed outlier: 4.003A pdb=" N GLY C 277 " --> pdb=" O LEU C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 311 Processing helix chain 'C' and resid 337 through 348 removed outlier: 3.522A pdb=" N ALA C 346 " --> pdb=" O VAL C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 356 removed outlier: 3.612A pdb=" N GLY C 356 " --> pdb=" O VAL C 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 39 Processing helix chain 'D' and resid 39 through 61 removed outlier: 3.549A pdb=" N VAL D 46 " --> pdb=" O THR D 42 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE D 48 " --> pdb=" O MET D 44 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ALA D 49 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA D 53 " --> pdb=" O ALA D 49 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE D 57 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER D 58 " --> pdb=" O GLY D 54 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE D 59 " --> pdb=" O LEU D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 78 Processing helix chain 'D' and resid 79 through 91 removed outlier: 3.526A pdb=" N SER D 85 " --> pdb=" O GLU D 81 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LYS D 88 " --> pdb=" O LYS D 84 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N LEU D 89 " --> pdb=" O SER D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 112 Processing helix chain 'D' and resid 113 through 124 Processing helix chain 'D' and resid 124 through 134 Processing helix chain 'D' and resid 140 through 150 Processing helix chain 'D' and resid 157 through 161 removed outlier: 4.549A pdb=" N LYS D 161 " --> pdb=" O ASP D 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 157 through 161' Processing helix chain 'D' and resid 180 through 251 removed outlier: 3.561A pdb=" N VAL D 207 " --> pdb=" O SER D 203 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS D 230 " --> pdb=" O ARG D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 259 removed outlier: 4.186A pdb=" N SER D 258 " --> pdb=" O PRO D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 287 removed outlier: 3.990A pdb=" N GLY D 277 " --> pdb=" O LEU D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 311 Processing helix chain 'D' and resid 337 through 348 Processing helix chain 'D' and resid 349 through 356 removed outlier: 4.307A pdb=" N ALA D 353 " --> pdb=" O GLY D 349 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY D 356 " --> pdb=" O VAL D 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 39 Processing helix chain 'E' and resid 39 through 61 removed outlier: 3.557A pdb=" N VAL E 46 " --> pdb=" O THR E 42 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE E 48 " --> pdb=" O MET E 44 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ALA E 49 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA E 53 " --> pdb=" O ALA E 49 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE E 57 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER E 58 " --> pdb=" O GLY E 54 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE E 59 " --> pdb=" O LEU E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 78 Processing helix chain 'E' and resid 79 through 91 removed outlier: 3.521A pdb=" N SER E 85 " --> pdb=" O GLU E 81 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LYS E 88 " --> pdb=" O LYS E 84 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LEU E 89 " --> pdb=" O SER E 85 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL E 91 " --> pdb=" O THR E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 112 Processing helix chain 'E' and resid 113 through 124 Processing helix chain 'E' and resid 124 through 134 Processing helix chain 'E' and resid 140 through 150 Processing helix chain 'E' and resid 180 through 251 removed outlier: 3.567A pdb=" N VAL E 207 " --> pdb=" O SER E 203 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS E 230 " --> pdb=" O ARG E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 287 removed outlier: 3.952A pdb=" N GLY E 277 " --> pdb=" O LEU E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 311 Processing helix chain 'E' and resid 337 through 348 removed outlier: 3.548A pdb=" N ALA E 346 " --> pdb=" O VAL E 342 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 356 removed outlier: 3.931A pdb=" N ALA E 353 " --> pdb=" O GLY E 349 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY E 356 " --> pdb=" O VAL E 352 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 39 Processing helix chain 'F' and resid 39 through 61 removed outlier: 3.525A pdb=" N VAL F 46 " --> pdb=" O THR F 42 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE F 48 " --> pdb=" O MET F 44 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ALA F 49 " --> pdb=" O ALA F 45 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA F 53 " --> pdb=" O ALA F 49 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE F 57 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER F 58 " --> pdb=" O GLY F 54 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE F 59 " --> pdb=" O LEU F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 78 Processing helix chain 'F' and resid 79 through 91 removed outlier: 4.614A pdb=" N LYS F 88 " --> pdb=" O LYS F 84 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N LEU F 89 " --> pdb=" O SER F 85 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL F 91 " --> pdb=" O THR F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 112 Processing helix chain 'F' and resid 113 through 124 Processing helix chain 'F' and resid 124 through 134 removed outlier: 3.590A pdb=" N GLN F 130 " --> pdb=" O TYR F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 150 Processing helix chain 'F' and resid 180 through 251 removed outlier: 3.572A pdb=" N VAL F 207 " --> pdb=" O SER F 203 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS F 230 " --> pdb=" O ARG F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 259 removed outlier: 3.829A pdb=" N SER F 258 " --> pdb=" O PRO F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 287 removed outlier: 4.007A pdb=" N GLY F 277 " --> pdb=" O LEU F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 311 Processing helix chain 'F' and resid 337 through 348 removed outlier: 3.581A pdb=" N ALA F 346 " --> pdb=" O VAL F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 349 through 356 removed outlier: 3.905A pdb=" N ALA F 353 " --> pdb=" O GLY F 349 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY F 356 " --> pdb=" O VAL F 352 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 39 Processing helix chain 'G' and resid 39 through 61 removed outlier: 3.595A pdb=" N VAL G 46 " --> pdb=" O THR G 42 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE G 48 " --> pdb=" O MET G 44 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ALA G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA G 53 " --> pdb=" O ALA G 49 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE G 57 " --> pdb=" O ALA G 53 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER G 58 " --> pdb=" O GLY G 54 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N PHE G 59 " --> pdb=" O LEU G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 78 Processing helix chain 'G' and resid 79 through 91 removed outlier: 3.531A pdb=" N SER G 85 " --> pdb=" O GLU G 81 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LYS G 88 " --> pdb=" O LYS G 84 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LEU G 89 " --> pdb=" O SER G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 112 Processing helix chain 'G' and resid 113 through 124 Processing helix chain 'G' and resid 124 through 134 Processing helix chain 'G' and resid 140 through 150 Processing helix chain 'G' and resid 157 through 161 removed outlier: 4.532A pdb=" N LYS G 161 " --> pdb=" O ASP G 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 157 through 161' Processing helix chain 'G' and resid 180 through 251 removed outlier: 3.552A pdb=" N VAL G 207 " --> pdb=" O SER G 203 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS G 230 " --> pdb=" O ARG G 226 " (cutoff:3.500A) Processing helix chain 'G' and resid 255 through 259 removed outlier: 4.275A pdb=" N SER G 258 " --> pdb=" O PRO G 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 273 through 287 removed outlier: 4.086A pdb=" N GLY G 277 " --> pdb=" O LEU G 273 " (cutoff:3.500A) Processing helix chain 'G' and resid 295 through 311 Processing helix chain 'G' and resid 337 through 348 removed outlier: 3.517A pdb=" N ALA G 346 " --> pdb=" O VAL G 342 " (cutoff:3.500A) Processing helix chain 'G' and resid 350 through 356 removed outlier: 3.537A pdb=" N CYS G 354 " --> pdb=" O GLY G 350 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLY G 356 " --> pdb=" O VAL G 352 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 39 Processing helix chain 'H' and resid 39 through 61 removed outlier: 3.572A pdb=" N VAL H 46 " --> pdb=" O THR H 42 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE H 48 " --> pdb=" O MET H 44 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ALA H 49 " --> pdb=" O ALA H 45 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA H 53 " --> pdb=" O ALA H 49 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE H 57 " --> pdb=" O ALA H 53 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER H 58 " --> pdb=" O GLY H 54 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE H 59 " --> pdb=" O LEU H 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 78 Processing helix chain 'H' and resid 79 through 91 removed outlier: 3.519A pdb=" N SER H 85 " --> pdb=" O GLU H 81 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LYS H 88 " --> pdb=" O LYS H 84 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N LEU H 89 " --> pdb=" O SER H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 112 Processing helix chain 'H' and resid 113 through 124 Processing helix chain 'H' and resid 124 through 134 Processing helix chain 'H' and resid 140 through 150 Processing helix chain 'H' and resid 180 through 251 removed outlier: 3.542A pdb=" N VAL H 207 " --> pdb=" O SER H 203 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 259 removed outlier: 3.611A pdb=" N SER H 258 " --> pdb=" O PRO H 255 " (cutoff:3.500A) Processing helix chain 'H' and resid 273 through 287 removed outlier: 3.975A pdb=" N GLY H 277 " --> pdb=" O LEU H 273 " (cutoff:3.500A) Processing helix chain 'H' and resid 295 through 311 Processing helix chain 'H' and resid 337 through 348 Processing helix chain 'H' and resid 350 through 356 removed outlier: 3.611A pdb=" N CYS H 354 " --> pdb=" O GLY H 350 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY H 356 " --> pdb=" O VAL H 352 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 39 Processing helix chain 'I' and resid 39 through 61 removed outlier: 3.565A pdb=" N VAL I 46 " --> pdb=" O THR I 42 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE I 48 " --> pdb=" O MET I 44 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ALA I 49 " --> pdb=" O ALA I 45 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA I 53 " --> pdb=" O ALA I 49 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE I 57 " --> pdb=" O ALA I 53 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER I 58 " --> pdb=" O GLY I 54 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE I 59 " --> pdb=" O LEU I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 75 through 78 Processing helix chain 'I' and resid 79 through 91 removed outlier: 3.529A pdb=" N SER I 85 " --> pdb=" O GLU I 81 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LYS I 88 " --> pdb=" O LYS I 84 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N LEU I 89 " --> pdb=" O SER I 85 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL I 91 " --> pdb=" O THR I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 99 through 112 Processing helix chain 'I' and resid 113 through 124 Processing helix chain 'I' and resid 124 through 134 Processing helix chain 'I' and resid 140 through 150 Processing helix chain 'I' and resid 180 through 251 removed outlier: 3.557A pdb=" N VAL I 207 " --> pdb=" O SER I 203 " (cutoff:3.500A) Processing helix chain 'I' and resid 255 through 259 removed outlier: 4.083A pdb=" N SER I 258 " --> pdb=" O PRO I 255 " (cutoff:3.500A) Processing helix chain 'I' and resid 273 through 287 removed outlier: 4.044A pdb=" N GLY I 277 " --> pdb=" O LEU I 273 " (cutoff:3.500A) Processing helix chain 'I' and resid 295 through 311 Processing helix chain 'I' and resid 337 through 348 removed outlier: 3.524A pdb=" N ALA I 346 " --> pdb=" O VAL I 342 " (cutoff:3.500A) Processing helix chain 'I' and resid 350 through 356 removed outlier: 3.711A pdb=" N CYS I 354 " --> pdb=" O GLY I 350 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLY I 356 " --> pdb=" O VAL I 352 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 152 through 156 removed outlier: 6.128A pdb=" N VAL A 70 " --> pdb=" O GLN A 324 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 152 through 156 removed outlier: 6.081A pdb=" N VAL B 70 " --> pdb=" O GLN B 324 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 152 through 156 removed outlier: 6.031A pdb=" N VAL C 70 " --> pdb=" O GLN C 324 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 152 through 156 removed outlier: 6.041A pdb=" N VAL D 70 " --> pdb=" O GLN D 324 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 152 through 156 removed outlier: 6.019A pdb=" N VAL E 70 " --> pdb=" O GLN E 324 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 152 through 156 removed outlier: 6.020A pdb=" N VAL F 70 " --> pdb=" O GLN F 324 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 152 through 156 removed outlier: 6.034A pdb=" N VAL G 70 " --> pdb=" O GLN G 324 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 152 through 156 removed outlier: 6.039A pdb=" N VAL H 70 " --> pdb=" O GLN H 324 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 152 through 156 removed outlier: 6.014A pdb=" N VAL I 70 " --> pdb=" O GLN I 324 " (cutoff:3.500A) 1556 hydrogen bonds defined for protein. 4539 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: 4.75 Time building geometry restraints manager: 2.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7551 1.34 - 1.46: 3778 1.46 - 1.58: 12359 1.58 - 1.69: 0 1.69 - 1.81: 90 Bond restraints: 23778 Sorted by residual: bond pdb=" N ASP E 95 " pdb=" CA ASP E 95 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.25e-02 6.40e+03 6.45e+00 bond pdb=" N ASP G 95 " pdb=" CA ASP G 95 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.25e-02 6.40e+03 6.20e+00 bond pdb=" CA ALA F 262 " pdb=" CB ALA F 262 " ideal model delta sigma weight residual 1.530 1.504 0.026 1.69e-02 3.50e+03 2.35e+00 bond pdb=" N ALA F 262 " pdb=" CA ALA F 262 " ideal model delta sigma weight residual 1.457 1.477 -0.019 1.29e-02 6.01e+03 2.25e+00 bond pdb=" CB PRO C 62 " pdb=" CG PRO C 62 " ideal model delta sigma weight residual 1.492 1.560 -0.068 5.00e-02 4.00e+02 1.84e+00 ... (remaining 23773 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 31817 1.21 - 2.42: 217 2.42 - 3.64: 116 3.64 - 4.85: 19 4.85 - 6.06: 6 Bond angle restraints: 32175 Sorted by residual: angle pdb=" N VAL H 256 " pdb=" CA VAL H 256 " pdb=" C VAL H 256 " ideal model delta sigma weight residual 112.98 108.66 4.32 1.25e+00 6.40e-01 1.19e+01 angle pdb=" N VAL A 256 " pdb=" CA VAL A 256 " pdb=" C VAL A 256 " ideal model delta sigma weight residual 112.80 109.34 3.46 1.15e+00 7.56e-01 9.06e+00 angle pdb=" C ILE E 348 " pdb=" CA ILE E 348 " pdb=" CB ILE E 348 " ideal model delta sigma weight residual 112.46 108.56 3.90 1.33e+00 5.65e-01 8.59e+00 angle pdb=" C ILE F 348 " pdb=" CA ILE F 348 " pdb=" CB ILE F 348 " ideal model delta sigma weight residual 112.46 108.58 3.88 1.33e+00 5.65e-01 8.51e+00 angle pdb=" C ILE B 348 " pdb=" CA ILE B 348 " pdb=" CB ILE B 348 " ideal model delta sigma weight residual 112.46 108.67 3.79 1.33e+00 5.65e-01 8.14e+00 ... (remaining 32170 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 13027 17.99 - 35.97: 1242 35.97 - 53.96: 308 53.96 - 71.94: 94 71.94 - 89.93: 26 Dihedral angle restraints: 14697 sinusoidal: 5949 harmonic: 8748 Sorted by residual: dihedral pdb=" CB GLU G 83 " pdb=" CG GLU G 83 " pdb=" CD GLU G 83 " pdb=" OE1 GLU G 83 " ideal model delta sinusoidal sigma weight residual 0.00 89.93 -89.93 1 3.00e+01 1.11e-03 1.07e+01 dihedral pdb=" CB GLU B 83 " pdb=" CG GLU B 83 " pdb=" CD GLU B 83 " pdb=" OE1 GLU B 83 " ideal model delta sinusoidal sigma weight residual 0.00 -88.97 88.97 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU I 83 " pdb=" CG GLU I 83 " pdb=" CD GLU I 83 " pdb=" OE1 GLU I 83 " ideal model delta sinusoidal sigma weight residual 0.00 88.60 -88.60 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 14694 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2546 0.028 - 0.055: 807 0.055 - 0.083: 279 0.083 - 0.111: 130 0.111 - 0.138: 27 Chirality restraints: 3789 Sorted by residual: chirality pdb=" CA LEU F 347 " pdb=" N LEU F 347 " pdb=" C LEU F 347 " pdb=" CB LEU F 347 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.79e-01 chirality pdb=" CA LEU E 347 " pdb=" N LEU E 347 " pdb=" C LEU E 347 " pdb=" CB LEU E 347 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.67e-01 chirality pdb=" CA LEU B 347 " pdb=" N LEU B 347 " pdb=" C LEU B 347 " pdb=" CB LEU B 347 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.67e-01 ... (remaining 3786 not shown) Planarity restraints: 4068 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER I 124 " -0.027 5.00e-02 4.00e+02 4.12e-02 2.71e+00 pdb=" N PRO I 125 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO I 125 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO I 125 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 61 " 0.024 5.00e-02 4.00e+02 3.61e-02 2.08e+00 pdb=" N PRO C 62 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO C 62 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 62 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP I 95 " -0.006 2.00e-02 2.50e+03 1.30e-02 1.68e+00 pdb=" C ASP I 95 " 0.022 2.00e-02 2.50e+03 pdb=" O ASP I 95 " -0.009 2.00e-02 2.50e+03 pdb=" N ILE I 96 " -0.008 2.00e-02 2.50e+03 ... (remaining 4065 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2018 2.74 - 3.28: 23130 3.28 - 3.82: 37739 3.82 - 4.36: 46350 4.36 - 4.90: 78057 Nonbonded interactions: 187294 Sorted by model distance: nonbonded pdb=" NE2 GLN H 130 " pdb=" OE1 GLU H 183 " model vdw 2.205 3.120 nonbonded pdb=" O TYR H 257 " pdb=" ND2 ASN I 259 " model vdw 2.207 3.120 nonbonded pdb=" OG SER C 67 " pdb=" O SER C 328 " model vdw 2.307 3.040 nonbonded pdb=" OD2 ASP F 225 " pdb=" NH1 ARG F 301 " model vdw 2.317 3.120 nonbonded pdb=" OG SER F 67 " pdb=" O SER F 328 " model vdw 2.319 3.040 ... (remaining 187289 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: 0.01 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' } 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: 8.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.500 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.880 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9041 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 : 0.002 0.068 23778 Z= 0.083 Angle : 0.357 6.060 32175 Z= 0.197 Chirality : 0.034 0.138 3789 Planarity : 0.003 0.041 4068 Dihedral : 15.851 89.931 8991 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.92 % Allowed : 18.42 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.15), residues: 2952 helix: 1.52 (0.11), residues: 1854 sheet: 1.57 (0.33), residues: 216 loop : -0.87 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 122 TYR 0.004 0.001 TYR G 257 PHE 0.004 0.001 PHE E 318 TRP 0.004 0.000 TRP I 79 HIS 0.001 0.000 HIS C 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00184 / 0.08 (23778) covalent geometry : angle 0.35721 / 0.20 (32175) hydrogen bonds : bond 0.23308 / 15.30 ( 1556) hydrogen bonds : angle 5.52070 / 3.96 ( 4539) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 0.914 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: symmetry clash outliers start: 24 outliers final: 15 residues processed: 166 average time/residue: 0.6067 time to fit residues: 115.7586 Evaluate side-chains 122 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 323 TYR Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 323 TYR Chi-restraints excluded: chain D residue 270 SER Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain H residue 319 THR Chi-restraints excluded: chain I residue 270 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 197 optimal weight: 0.1980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 40.0000 chunk 261 optimal weight: 0.4980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.7980 chunk 111 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 261 GLN ** F 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 259 ASN H 130 GLN I 259 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.090403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.057958 restraints weight = 53414.214| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 3.33 r_work: 0.2709 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23778 Z= 0.135 Angle : 0.491 6.534 32175 Z= 0.261 Chirality : 0.036 0.163 3789 Planarity : 0.004 0.046 4068 Dihedral : 3.726 37.174 3159 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.20 % Favored : 97.76 % Rotamer: Outliers : 2.27 % Allowed : 15.69 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.34 (0.15), residues: 2952 helix: 2.51 (0.12), residues: 1881 sheet: 2.06 (0.35), residues: 216 loop : -0.88 (0.19), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 122 TYR 0.011 0.001 TYR I 257 PHE 0.010 0.001 PHE H 48 TRP 0.005 0.001 TRP E 37 HIS 0.002 0.001 HIS E 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.14 (23778) covalent geometry : angle 0.49110 / 0.26 (32175) hydrogen bonds : bond 0.06411 / 4.19 ( 1556) hydrogen bonds : angle 3.87833 / 2.78 ( 4539) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 112 time to evaluate : 0.941 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 GLU cc_start: 0.8686 (mp0) cc_final: 0.8409 (OUTLIER) REVERT: C 102 GLU cc_start: 0.8562 (mp0) cc_final: 0.8304 (OUTLIER) REVERT: C 119 GLU cc_start: 0.8751 (tp30) cc_final: 0.8446 (tp30) REVERT: C 174 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8816 (mt) REVERT: E 102 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8204 (mp0) REVERT: G 102 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8310 (mp0) REVERT: I 102 GLU cc_start: 0.8908 (mt-10) cc_final: 0.8606 (mp0) outliers start: 59 outliers final: 33 residues processed: 150 average time/residue: 0.5304 time to fit residues: 93.2310 Evaluate side-chains 136 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 102 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 323 TYR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 323 TYR Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain F residue 323 TYR Chi-restraints excluded: chain G residue 96 ILE Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 315 ASP Chi-restraints excluded: chain G residue 323 TYR Chi-restraints excluded: chain H residue 96 ILE Chi-restraints excluded: chain H residue 319 THR Chi-restraints excluded: chain I residue 96 ILE Chi-restraints excluded: chain I residue 323 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 99 optimal weight: 50.0000 chunk 245 optimal weight: 4.9990 chunk 54 optimal weight: 0.6980 chunk 220 optimal weight: 0.7980 chunk 272 optimal weight: 2.9990 chunk 160 optimal weight: 0.0970 chunk 148 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 262 optimal weight: 0.0970 chunk 69 optimal weight: 0.0070 chunk 138 optimal weight: 1.9990 overall best weight: 0.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 259 ASN I 259 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.091613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.059331 restraints weight = 53245.096| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 3.35 r_work: 0.2725 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 23778 Z= 0.111 Angle : 0.435 6.842 32175 Z= 0.229 Chirality : 0.034 0.133 3789 Planarity : 0.003 0.046 4068 Dihedral : 3.549 37.355 3151 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.37 % Favored : 97.53 % Rotamer: Outliers : 1.92 % Allowed : 16.15 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.72 (0.15), residues: 2952 helix: 2.84 (0.12), residues: 1881 sheet: 2.43 (0.36), residues: 216 loop : -0.90 (0.19), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 122 TYR 0.015 0.001 TYR I 257 PHE 0.008 0.001 PHE A 318 TRP 0.005 0.001 TRP F 37 HIS 0.001 0.000 HIS E 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.11 (23778) covalent geometry : angle 0.43508 / 0.23 (32175) hydrogen bonds : bond 0.05402 / 3.53 ( 1556) hydrogen bonds : angle 3.50138 / 2.52 ( 4539) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 111 time to evaluate : 0.946 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 ASP cc_start: 0.9220 (OUTLIER) cc_final: 0.9007 (m-30) REVERT: B 102 GLU cc_start: 0.8733 (mp0) cc_final: 0.8412 (OUTLIER) REVERT: C 102 GLU cc_start: 0.8635 (mp0) cc_final: 0.8331 (OUTLIER) REVERT: C 119 GLU cc_start: 0.8747 (tp30) cc_final: 0.8457 (tp30) REVERT: C 174 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8895 (mt) REVERT: D 119 GLU cc_start: 0.8754 (tp30) cc_final: 0.8550 (tp30) REVERT: E 102 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8202 (mp0) REVERT: F 315 ASP cc_start: 0.9256 (OUTLIER) cc_final: 0.9049 (m-30) REVERT: G 102 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8340 (mp0) REVERT: G 119 GLU cc_start: 0.8697 (tp30) cc_final: 0.8496 (tp30) REVERT: G 315 ASP cc_start: 0.9224 (OUTLIER) cc_final: 0.8987 (m-30) REVERT: I 102 GLU cc_start: 0.8900 (mt-10) cc_final: 0.8568 (mp0) outliers start: 50 outliers final: 16 residues processed: 138 average time/residue: 0.4766 time to fit residues: 78.8651 Evaluate side-chains 128 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain B residue 323 TYR Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 323 TYR Chi-restraints excluded: chain D residue 323 TYR Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 323 TYR Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain F residue 323 TYR Chi-restraints excluded: chain G residue 96 ILE Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 315 ASP Chi-restraints excluded: chain G residue 323 TYR Chi-restraints excluded: chain H residue 96 ILE Chi-restraints excluded: chain I residue 323 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 28 optimal weight: 0.0000 chunk 196 optimal weight: 8.9990 chunk 181 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 177 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 274 optimal weight: 5.9990 chunk 290 optimal weight: 0.8980 chunk 120 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 259 ASN I 259 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.090869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.058472 restraints weight = 53541.163| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 3.37 r_work: 0.2728 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 23778 Z= 0.109 Angle : 0.419 7.461 32175 Z= 0.216 Chirality : 0.034 0.135 3789 Planarity : 0.003 0.035 4068 Dihedral : 3.315 36.675 3146 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.47 % Favored : 97.43 % Rotamer: Outliers : 1.54 % Allowed : 16.03 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.91 (0.15), residues: 2952 helix: 2.95 (0.12), residues: 1890 sheet: 2.53 (0.35), residues: 216 loop : -0.77 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 122 TYR 0.032 0.001 TYR I 257 PHE 0.005 0.001 PHE H 48 TRP 0.005 0.001 TRP F 37 HIS 0.001 0.000 HIS E 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 (23778) covalent geometry : angle 0.41930 / 0.22 (32175) hydrogen bonds : bond 0.04862 / 3.18 ( 1556) hydrogen bonds : angle 3.26859 / 2.35 ( 4539) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 117 time to evaluate : 1.074 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 GLU cc_start: 0.8845 (tp30) cc_final: 0.8622 (tp30) REVERT: B 102 GLU cc_start: 0.8783 (mp0) cc_final: 0.8388 (OUTLIER) REVERT: B 119 GLU cc_start: 0.8849 (tp30) cc_final: 0.8622 (tp30) REVERT: B 254 LYS cc_start: 0.9208 (OUTLIER) cc_final: 0.8945 (mmpt) REVERT: C 102 GLU cc_start: 0.8660 (mp0) cc_final: 0.8334 (mp0) REVERT: C 119 GLU cc_start: 0.8785 (tp30) cc_final: 0.8506 (tp30) REVERT: C 174 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8865 (mt) REVERT: D 119 GLU cc_start: 0.8814 (tp30) cc_final: 0.8572 (tp30) REVERT: E 102 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8180 (mp0) REVERT: G 102 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8382 (mp0) REVERT: G 119 GLU cc_start: 0.8759 (tp30) cc_final: 0.8544 (tp30) REVERT: I 102 GLU cc_start: 0.8899 (mt-10) cc_final: 0.8601 (mp0) outliers start: 40 outliers final: 20 residues processed: 137 average time/residue: 0.5876 time to fit residues: 94.4393 Evaluate side-chains 132 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 323 TYR Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 323 TYR Chi-restraints excluded: chain D residue 323 TYR Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 323 TYR Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 323 TYR Chi-restraints excluded: chain G residue 96 ILE Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 323 TYR Chi-restraints excluded: chain H residue 96 ILE Chi-restraints excluded: chain H residue 323 TYR Chi-restraints excluded: chain I residue 96 ILE Chi-restraints excluded: chain I residue 323 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 243 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 155 optimal weight: 4.9990 chunk 154 optimal weight: 0.7980 chunk 288 optimal weight: 2.9990 chunk 37 optimal weight: 0.2980 chunk 193 optimal weight: 0.0040 chunk 121 optimal weight: 1.9990 chunk 227 optimal weight: 0.9990 chunk 282 optimal weight: 0.7980 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 259 ASN I 259 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.091180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.058927 restraints weight = 53256.832| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 3.36 r_work: 0.2733 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 23778 Z= 0.100 Angle : 0.436 9.051 32175 Z= 0.220 Chirality : 0.034 0.130 3789 Planarity : 0.003 0.034 4068 Dihedral : 3.260 36.455 3146 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.64 % Favored : 97.26 % Rotamer: Outliers : 1.35 % Allowed : 16.65 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.06 (0.15), residues: 2952 helix: 3.07 (0.12), residues: 1890 sheet: 2.72 (0.34), residues: 216 loop : -0.74 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 122 TYR 0.013 0.001 TYR G 194 PHE 0.005 0.001 PHE H 48 TRP 0.004 0.000 TRP F 37 HIS 0.001 0.000 HIS E 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.10 (23778) covalent geometry : angle 0.43633 / 0.22 (32175) hydrogen bonds : bond 0.04565 / 2.99 ( 1556) hydrogen bonds : angle 3.11069 / 2.25 ( 4539) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 120 time to evaluate : 0.924 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 GLU cc_start: 0.8827 (tp30) cc_final: 0.8596 (tp30) REVERT: A 128 MET cc_start: 0.9188 (mmp) cc_final: 0.8786 (mmm) REVERT: B 102 GLU cc_start: 0.8784 (mp0) cc_final: 0.8367 (OUTLIER) REVERT: B 119 GLU cc_start: 0.8857 (tp30) cc_final: 0.8605 (tp30) REVERT: C 102 GLU cc_start: 0.8684 (mp0) cc_final: 0.8336 (mp0) REVERT: C 119 GLU cc_start: 0.8762 (tp30) cc_final: 0.8496 (tp30) REVERT: C 174 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8833 (mt) REVERT: D 119 GLU cc_start: 0.8826 (tp30) cc_final: 0.8577 (tp30) REVERT: D 128 MET cc_start: 0.9142 (mmp) cc_final: 0.8831 (mmm) REVERT: E 102 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8170 (mp0) REVERT: E 119 GLU cc_start: 0.8832 (tp30) cc_final: 0.8604 (tp30) REVERT: G 119 GLU cc_start: 0.8776 (tp30) cc_final: 0.8524 (tp30) REVERT: G 128 MET cc_start: 0.9231 (mmp) cc_final: 0.8880 (OUTLIER) REVERT: H 119 GLU cc_start: 0.8854 (tp30) cc_final: 0.8517 (tp30) REVERT: I 102 GLU cc_start: 0.8893 (mt-10) cc_final: 0.8608 (mp0) outliers start: 35 outliers final: 21 residues processed: 137 average time/residue: 0.5330 time to fit residues: 86.0635 Evaluate side-chains 130 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 323 TYR Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 323 TYR Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 323 TYR Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 323 TYR Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 323 TYR Chi-restraints excluded: chain G residue 96 ILE Chi-restraints excluded: chain G residue 323 TYR Chi-restraints excluded: chain H residue 96 ILE Chi-restraints excluded: chain H residue 323 TYR Chi-restraints excluded: chain I residue 96 ILE Chi-restraints excluded: chain I residue 323 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 98 optimal weight: 30.0000 chunk 280 optimal weight: 0.6980 chunk 269 optimal weight: 3.9990 chunk 288 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 290 optimal weight: 0.9990 chunk 158 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 213 optimal weight: 0.9980 chunk 240 optimal weight: 0.6980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 312 HIS B 314 ASN ** C 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 259 ASN I 259 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.090599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.058286 restraints weight = 53807.194| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 3.38 r_work: 0.2713 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 23778 Z= 0.115 Angle : 0.436 9.219 32175 Z= 0.220 Chirality : 0.034 0.127 3789 Planarity : 0.003 0.035 4068 Dihedral : 3.248 36.081 3146 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.54 % Favored : 97.36 % Rotamer: Outliers : 1.23 % Allowed : 16.76 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.16 (0.15), residues: 2952 helix: 3.15 (0.12), residues: 1890 sheet: 2.79 (0.33), residues: 216 loop : -0.74 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 122 TYR 0.012 0.001 TYR H 194 PHE 0.006 0.001 PHE H 48 TRP 0.004 0.000 TRP F 37 HIS 0.001 0.000 HIS E 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (23778) covalent geometry : angle 0.43629 / 0.22 (32175) hydrogen bonds : bond 0.04570 / 2.99 ( 1556) hydrogen bonds : angle 3.05647 / 2.21 ( 4539) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 108 time to evaluate : 0.979 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 GLU cc_start: 0.8844 (tp30) cc_final: 0.8604 (tp30) REVERT: B 102 GLU cc_start: 0.8808 (mp0) cc_final: 0.8486 (mp0) REVERT: B 119 GLU cc_start: 0.8865 (tp30) cc_final: 0.8616 (tp30) REVERT: C 102 GLU cc_start: 0.8710 (mp0) cc_final: 0.8317 (mp0) REVERT: C 119 GLU cc_start: 0.8771 (tp30) cc_final: 0.8504 (tp30) REVERT: C 174 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8830 (mt) REVERT: D 119 GLU cc_start: 0.8835 (tp30) cc_final: 0.8585 (tp30) REVERT: E 102 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8111 (mp0) REVERT: E 119 GLU cc_start: 0.8848 (tp30) cc_final: 0.8575 (tp30) REVERT: E 128 MET cc_start: 0.9111 (mmp) cc_final: 0.8656 (mmm) REVERT: G 102 GLU cc_start: 0.8588 (mp0) cc_final: 0.8358 (mp0) REVERT: G 119 GLU cc_start: 0.8793 (tp30) cc_final: 0.8548 (tp30) REVERT: G 128 MET cc_start: 0.9260 (mmp) cc_final: 0.8901 (OUTLIER) REVERT: H 119 GLU cc_start: 0.8874 (tp30) cc_final: 0.8649 (tp30) REVERT: I 102 GLU cc_start: 0.8923 (mt-10) cc_final: 0.8632 (mp0) outliers start: 32 outliers final: 19 residues processed: 124 average time/residue: 0.5174 time to fit residues: 75.5875 Evaluate side-chains 127 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 323 TYR Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 323 TYR Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 323 TYR Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 323 TYR Chi-restraints excluded: chain G residue 96 ILE Chi-restraints excluded: chain G residue 323 TYR Chi-restraints excluded: chain H residue 96 ILE Chi-restraints excluded: chain H residue 323 TYR Chi-restraints excluded: chain I residue 96 ILE Chi-restraints excluded: chain I residue 323 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 10 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 chunk 9 optimal weight: 0.0060 chunk 43 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 155 optimal weight: 0.5980 chunk 248 optimal weight: 0.7980 chunk 142 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 134 optimal weight: 20.0000 chunk 118 optimal weight: 0.8980 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 259 ASN I 259 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.091238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.058413 restraints weight = 53457.065| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 3.44 r_work: 0.2724 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 23778 Z= 0.102 Angle : 0.438 10.219 32175 Z= 0.218 Chirality : 0.034 0.128 3789 Planarity : 0.003 0.034 4068 Dihedral : 3.093 27.924 3142 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.68 % Favored : 97.22 % Rotamer: Outliers : 1.15 % Allowed : 16.99 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.23 (0.15), residues: 2952 helix: 3.20 (0.11), residues: 1890 sheet: 2.90 (0.33), residues: 216 loop : -0.72 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 122 TYR 0.015 0.001 TYR D 257 PHE 0.005 0.001 PHE H 48 TRP 0.004 0.000 TRP F 37 HIS 0.001 0.000 HIS B 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 (23778) covalent geometry : angle 0.43786 / 0.22 (32175) hydrogen bonds : bond 0.04388 / 2.87 ( 1556) hydrogen bonds : angle 2.97597 / 2.15 ( 4539) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 115 time to evaluate : 0.836 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 GLU cc_start: 0.8857 (tp30) cc_final: 0.8620 (tp30) REVERT: A 128 MET cc_start: 0.9226 (mmp) cc_final: 0.8776 (mmm) REVERT: B 102 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8493 (mp0) REVERT: B 119 GLU cc_start: 0.8860 (tp30) cc_final: 0.8633 (tp30) REVERT: B 205 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8332 (tp30) REVERT: B 254 LYS cc_start: 0.9210 (OUTLIER) cc_final: 0.8902 (mmpt) REVERT: C 102 GLU cc_start: 0.8732 (mp0) cc_final: 0.8303 (mp0) REVERT: C 119 GLU cc_start: 0.8763 (tp30) cc_final: 0.8505 (tp30) REVERT: C 174 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8839 (mt) REVERT: D 119 GLU cc_start: 0.8850 (tp30) cc_final: 0.8589 (tp30) REVERT: D 128 MET cc_start: 0.9129 (mmp) cc_final: 0.8838 (mmm) REVERT: E 102 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8132 (mp0) REVERT: E 119 GLU cc_start: 0.8858 (tp30) cc_final: 0.8577 (tp30) REVERT: G 102 GLU cc_start: 0.8596 (mp0) cc_final: 0.8381 (mp0) REVERT: G 119 GLU cc_start: 0.8802 (tp30) cc_final: 0.8558 (tp30) REVERT: G 128 MET cc_start: 0.9261 (mmp) cc_final: 0.8899 (OUTLIER) REVERT: H 119 GLU cc_start: 0.8892 (tp30) cc_final: 0.8657 (tp30) REVERT: I 102 GLU cc_start: 0.8917 (mt-10) cc_final: 0.8634 (mp0) REVERT: I 128 MET cc_start: 0.9240 (mmp) cc_final: 0.9004 (mmm) outliers start: 30 outliers final: 20 residues processed: 127 average time/residue: 0.5523 time to fit residues: 81.8919 Evaluate side-chains 131 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 323 TYR Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 323 TYR Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 323 TYR Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 323 TYR Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 323 TYR Chi-restraints excluded: chain G residue 96 ILE Chi-restraints excluded: chain G residue 323 TYR Chi-restraints excluded: chain H residue 96 ILE Chi-restraints excluded: chain H residue 323 TYR Chi-restraints excluded: chain I residue 96 ILE Chi-restraints excluded: chain I residue 323 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 240 optimal weight: 0.7980 chunk 187 optimal weight: 0.7980 chunk 1 optimal weight: 6.9990 chunk 168 optimal weight: 7.9990 chunk 218 optimal weight: 0.6980 chunk 188 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 235 optimal weight: 0.0030 chunk 32 optimal weight: 7.9990 chunk 275 optimal weight: 6.9990 chunk 144 optimal weight: 0.9990 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 259 ASN I 259 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.091230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.058787 restraints weight = 53277.724| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 3.42 r_work: 0.2732 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 23778 Z= 0.102 Angle : 0.453 11.133 32175 Z= 0.222 Chirality : 0.034 0.127 3789 Planarity : 0.003 0.034 4068 Dihedral : 3.100 27.706 3142 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.71 % Favored : 97.19 % Rotamer: Outliers : 1.23 % Allowed : 17.11 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.29 (0.15), residues: 2952 helix: 3.24 (0.11), residues: 1890 sheet: 2.95 (0.33), residues: 216 loop : -0.68 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 122 TYR 0.029 0.001 TYR C 257 PHE 0.005 0.001 PHE H 48 TRP 0.004 0.000 TRP A 37 HIS 0.001 0.000 HIS B 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (23778) covalent geometry : angle 0.45300 / 0.22 (32175) hydrogen bonds : bond 0.04311 / 2.82 ( 1556) hydrogen bonds : angle 2.93251 / 2.12 ( 4539) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 116 time to evaluate : 0.960 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 GLU cc_start: 0.8878 (tp30) cc_final: 0.8636 (tp30) REVERT: B 102 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8494 (mp0) REVERT: B 119 GLU cc_start: 0.8881 (tp30) cc_final: 0.8639 (tp30) REVERT: B 254 LYS cc_start: 0.9216 (OUTLIER) cc_final: 0.8912 (mmpt) REVERT: C 102 GLU cc_start: 0.8749 (mp0) cc_final: 0.8301 (mp0) REVERT: C 119 GLU cc_start: 0.8771 (tp30) cc_final: 0.8498 (tp30) REVERT: C 174 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8842 (mt) REVERT: D 119 GLU cc_start: 0.8861 (tp30) cc_final: 0.8594 (tp30) REVERT: D 128 MET cc_start: 0.9176 (mmp) cc_final: 0.8873 (mmm) REVERT: E 102 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8154 (mp0) REVERT: E 119 GLU cc_start: 0.8884 (tp30) cc_final: 0.8595 (tp30) REVERT: E 128 MET cc_start: 0.9110 (mmp) cc_final: 0.8687 (mmm) REVERT: F 119 GLU cc_start: 0.8668 (tp30) cc_final: 0.8465 (tp30) REVERT: G 102 GLU cc_start: 0.8632 (mp0) cc_final: 0.8416 (mp0) REVERT: G 119 GLU cc_start: 0.8815 (tp30) cc_final: 0.8533 (tp30) REVERT: G 128 MET cc_start: 0.9303 (mmp) cc_final: 0.8930 (OUTLIER) REVERT: G 205 GLU cc_start: 0.8553 (tt0) cc_final: 0.8342 (tp30) REVERT: H 119 GLU cc_start: 0.8909 (tp30) cc_final: 0.8666 (tp30) REVERT: I 102 GLU cc_start: 0.8936 (mt-10) cc_final: 0.8658 (mp0) REVERT: I 128 MET cc_start: 0.9266 (mmp) cc_final: 0.9033 (mmm) outliers start: 32 outliers final: 22 residues processed: 130 average time/residue: 0.5728 time to fit residues: 86.5064 Evaluate side-chains 135 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 323 TYR Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 323 TYR Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 323 TYR Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 323 TYR Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 323 TYR Chi-restraints excluded: chain G residue 96 ILE Chi-restraints excluded: chain G residue 323 TYR Chi-restraints excluded: chain H residue 96 ILE Chi-restraints excluded: chain H residue 323 TYR Chi-restraints excluded: chain I residue 96 ILE Chi-restraints excluded: chain I residue 323 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 191 optimal weight: 1.9990 chunk 149 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 chunk 190 optimal weight: 0.9990 chunk 153 optimal weight: 0.7980 chunk 160 optimal weight: 1.9990 chunk 161 optimal weight: 0.3980 chunk 20 optimal weight: 0.6980 chunk 181 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 259 ASN I 259 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.090992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.058544 restraints weight = 53556.599| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 3.43 r_work: 0.2728 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 23778 Z= 0.106 Angle : 0.459 11.650 32175 Z= 0.224 Chirality : 0.034 0.129 3789 Planarity : 0.003 0.034 4068 Dihedral : 3.094 28.387 3142 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.78 % Favored : 97.12 % Rotamer: Outliers : 1.11 % Allowed : 17.30 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.33 (0.15), residues: 2952 helix: 3.27 (0.11), residues: 1890 sheet: 2.98 (0.33), residues: 216 loop : -0.67 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 122 TYR 0.030 0.001 TYR C 257 PHE 0.005 0.001 PHE H 48 TRP 0.004 0.000 TRP B 37 HIS 0.001 0.000 HIS B 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (23778) covalent geometry : angle 0.45864 / 0.22 (32175) hydrogen bonds : bond 0.04274 / 2.80 ( 1556) hydrogen bonds : angle 2.89662 / 2.10 ( 4539) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 114 time to evaluate : 0.954 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 GLU cc_start: 0.8889 (tp30) cc_final: 0.8642 (tp30) REVERT: A 128 MET cc_start: 0.9220 (mmp) cc_final: 0.8839 (mmm) REVERT: B 102 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8492 (mp0) REVERT: B 119 GLU cc_start: 0.8898 (tp30) cc_final: 0.8652 (tp30) REVERT: B 254 LYS cc_start: 0.9202 (OUTLIER) cc_final: 0.8896 (mmpt) REVERT: B 263 VAL cc_start: 0.4405 (OUTLIER) cc_final: 0.3762 (t) REVERT: C 102 GLU cc_start: 0.8768 (mp0) cc_final: 0.8248 (OUTLIER) REVERT: C 119 GLU cc_start: 0.8759 (tp30) cc_final: 0.8513 (tp30) REVERT: C 174 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8849 (mt) REVERT: D 119 GLU cc_start: 0.8869 (tp30) cc_final: 0.8603 (tp30) REVERT: D 128 MET cc_start: 0.9200 (mmp) cc_final: 0.8905 (mmm) REVERT: E 102 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8152 (mp0) REVERT: E 119 GLU cc_start: 0.8897 (tp30) cc_final: 0.8605 (tp30) REVERT: E 128 MET cc_start: 0.9156 (mmp) cc_final: 0.8747 (mmm) REVERT: F 119 GLU cc_start: 0.8701 (tp30) cc_final: 0.8459 (tp30) REVERT: G 102 GLU cc_start: 0.8674 (mp0) cc_final: 0.8423 (mp0) REVERT: G 119 GLU cc_start: 0.8818 (tp30) cc_final: 0.8532 (tp30) REVERT: G 128 MET cc_start: 0.9306 (mmp) cc_final: 0.8939 (OUTLIER) REVERT: G 205 GLU cc_start: 0.8544 (tt0) cc_final: 0.8331 (tp30) REVERT: H 119 GLU cc_start: 0.8911 (tp30) cc_final: 0.8667 (tp30) REVERT: I 102 GLU cc_start: 0.8946 (mt-10) cc_final: 0.8615 (mm-30) REVERT: I 128 MET cc_start: 0.9252 (mmp) cc_final: 0.9024 (mmm) outliers start: 29 outliers final: 20 residues processed: 127 average time/residue: 0.5241 time to fit residues: 78.0195 Evaluate side-chains 133 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 323 TYR Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 323 TYR Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 323 TYR Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 323 TYR Chi-restraints excluded: chain G residue 96 ILE Chi-restraints excluded: chain G residue 323 TYR Chi-restraints excluded: chain H residue 96 ILE Chi-restraints excluded: chain H residue 323 TYR Chi-restraints excluded: chain I residue 96 ILE Chi-restraints excluded: chain I residue 323 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 274 optimal weight: 0.2980 chunk 232 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 169 optimal weight: 0.5980 chunk 208 optimal weight: 0.0970 chunk 83 optimal weight: 0.7980 chunk 182 optimal weight: 0.9980 chunk 266 optimal weight: 8.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 259 ASN I 259 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.093292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.060228 restraints weight = 52893.172| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 3.39 r_work: 0.2748 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 23778 Z= 0.098 Angle : 0.464 12.152 32175 Z= 0.224 Chirality : 0.034 0.160 3789 Planarity : 0.003 0.034 4068 Dihedral : 3.100 28.593 3142 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.71 % Favored : 97.19 % Rotamer: Outliers : 1.08 % Allowed : 17.49 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.38 (0.15), residues: 2952 helix: 3.30 (0.11), residues: 1890 sheet: 3.03 (0.32), residues: 216 loop : -0.63 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 122 TYR 0.048 0.001 TYR C 257 PHE 0.005 0.000 PHE H 48 TRP 0.003 0.000 TRP F 37 HIS 0.001 0.000 HIS B 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.10 (23778) covalent geometry : angle 0.46362 / 0.22 (32175) hydrogen bonds : bond 0.04132 / 2.71 ( 1556) hydrogen bonds : angle 2.84541 / 2.06 ( 4539) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 115 time to evaluate : 0.941 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 GLU cc_start: 0.8885 (tp30) cc_final: 0.8627 (tp30) REVERT: A 128 MET cc_start: 0.9230 (mmp) cc_final: 0.8781 (mmm) REVERT: B 102 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8497 (mp0) REVERT: B 119 GLU cc_start: 0.8895 (tp30) cc_final: 0.8663 (tp30) REVERT: B 254 LYS cc_start: 0.9192 (OUTLIER) cc_final: 0.8932 (mmpt) REVERT: B 263 VAL cc_start: 0.4399 (OUTLIER) cc_final: 0.3760 (t) REVERT: C 102 GLU cc_start: 0.8746 (mp0) cc_final: 0.8258 (OUTLIER) REVERT: C 119 GLU cc_start: 0.8743 (tp30) cc_final: 0.8475 (tp30) REVERT: C 174 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8804 (mt) REVERT: D 119 GLU cc_start: 0.8866 (tp30) cc_final: 0.8598 (tp30) REVERT: D 128 MET cc_start: 0.9205 (mmp) cc_final: 0.8912 (mmm) REVERT: E 102 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8164 (mp0) REVERT: E 119 GLU cc_start: 0.8896 (tp30) cc_final: 0.8599 (tp30) REVERT: E 128 MET cc_start: 0.9163 (mmp) cc_final: 0.8760 (mmm) REVERT: F 119 GLU cc_start: 0.8685 (tp30) cc_final: 0.8448 (tp30) REVERT: G 102 GLU cc_start: 0.8670 (mp0) cc_final: 0.8430 (mp0) REVERT: G 119 GLU cc_start: 0.8811 (tp30) cc_final: 0.8514 (tp30) REVERT: G 128 MET cc_start: 0.9308 (mmp) cc_final: 0.8942 (OUTLIER) REVERT: G 205 GLU cc_start: 0.8535 (tt0) cc_final: 0.8319 (tp30) REVERT: H 119 GLU cc_start: 0.8905 (tp30) cc_final: 0.8664 (tp30) REVERT: I 102 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8594 (mm-30) REVERT: I 128 MET cc_start: 0.9245 (mmp) cc_final: 0.9021 (mmm) outliers start: 28 outliers final: 18 residues processed: 126 average time/residue: 0.5427 time to fit residues: 80.2531 Evaluate side-chains 133 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 323 TYR Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 323 TYR Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 323 TYR Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 323 TYR Chi-restraints excluded: chain G residue 96 ILE Chi-restraints excluded: chain G residue 323 TYR Chi-restraints excluded: chain H residue 96 ILE Chi-restraints excluded: chain H residue 323 TYR Chi-restraints excluded: chain I residue 323 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 105 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 chunk 133 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 165 optimal weight: 40.0000 chunk 175 optimal weight: 3.9990 chunk 274 optimal weight: 0.0050 overall best weight: 1.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 307 GLN D 241 ASN ** F 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 259 ASN I 259 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.088785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.057132 restraints weight = 54142.809| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 3.27 r_work: 0.2689 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23778 Z= 0.168 Angle : 0.494 13.480 32175 Z= 0.244 Chirality : 0.035 0.163 3789 Planarity : 0.003 0.036 4068 Dihedral : 3.179 30.182 3142 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.64 % Favored : 97.29 % Rotamer: Outliers : 0.85 % Allowed : 17.80 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.29 (0.15), residues: 2952 helix: 3.26 (0.11), residues: 1890 sheet: 2.84 (0.33), residues: 216 loop : -0.70 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 299 TYR 0.040 0.001 TYR C 257 PHE 0.006 0.001 PHE H 48 TRP 0.007 0.001 TRP F 79 HIS 0.001 0.000 HIS B 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (23778) covalent geometry : angle 0.49439 / 0.24 (32175) hydrogen bonds : bond 0.04796 / 3.13 ( 1556) hydrogen bonds : angle 3.02540 / 2.18 ( 4539) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6438.06 seconds wall clock time: 110 minutes 49.81 seconds (6649.81 seconds total)