Starting phenix.real_space_refine on Thu Sep 18 06:10:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e4r_47518/09_2025/9e4r_47518.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e4r_47518/09_2025/9e4r_47518.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e4r_47518/09_2025/9e4r_47518.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e4r_47518/09_2025/9e4r_47518.map" model { file = "/net/cci-nas-00/data/ceres_data/9e4r_47518/09_2025/9e4r_47518.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e4r_47518/09_2025/9e4r_47518.cif" } resolution = 3.31 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= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 6 7.16 5 S 60 5.16 5 C 9384 2.51 5 N 2502 2.21 5 O 2832 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14784 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2421 Classifications: {'peptide': 311} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 294} Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 2.66, per 1000 atoms: 0.18 Number of scatterers: 14784 At special positions: 0 Unit cell: (102.83, 99.19, 95.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 6 26.01 S 60 16.00 O 2832 8.00 N 2502 7.00 C 9384 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.41 Conformation dependent library (CDL) restraints added in 711.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3396 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 30 sheets defined 39.2% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 10 through 16 Processing helix chain 'A' and resid 31 through 55 removed outlier: 3.699A pdb=" N GLU A 35 " --> pdb=" O GLY A 31 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER A 43 " --> pdb=" O ARG A 39 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N SER A 46 " --> pdb=" O CYS A 42 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N SER A 47 " --> pdb=" O SER A 43 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ARG A 55 " --> pdb=" O GLY A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 76 Processing helix chain 'A' and resid 111 through 127 removed outlier: 3.876A pdb=" N CYS A 115 " --> pdb=" O ARG A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 167 Processing helix chain 'A' and resid 172 through 176 Processing helix chain 'A' and resid 189 through 196 Processing helix chain 'A' and resid 197 through 206 Processing helix chain 'A' and resid 224 through 229 Processing helix chain 'A' and resid 265 through 278 removed outlier: 4.357A pdb=" N ILE A 269 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 290 Processing helix chain 'A' and resid 304 through 310 Processing helix chain 'B' and resid 10 through 16 Processing helix chain 'B' and resid 31 through 55 removed outlier: 3.699A pdb=" N GLU B 35 " --> pdb=" O GLY B 31 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER B 43 " --> pdb=" O ARG B 39 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N SER B 46 " --> pdb=" O CYS B 42 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N SER B 47 " --> pdb=" O SER B 43 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ARG B 55 " --> pdb=" O GLY B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 76 Processing helix chain 'B' and resid 111 through 127 removed outlier: 3.876A pdb=" N CYS B 115 " --> pdb=" O ARG B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 167 Processing helix chain 'B' and resid 172 through 176 Processing helix chain 'B' and resid 189 through 196 Processing helix chain 'B' and resid 197 through 206 Processing helix chain 'B' and resid 224 through 229 Processing helix chain 'B' and resid 265 through 278 removed outlier: 4.357A pdb=" N ILE B 269 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 290 Processing helix chain 'B' and resid 304 through 310 Processing helix chain 'C' and resid 10 through 16 Processing helix chain 'C' and resid 31 through 55 removed outlier: 3.700A pdb=" N GLU C 35 " --> pdb=" O GLY C 31 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER C 43 " --> pdb=" O ARG C 39 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N SER C 46 " --> pdb=" O CYS C 42 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N SER C 47 " --> pdb=" O SER C 43 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ARG C 55 " --> pdb=" O GLY C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 76 Processing helix chain 'C' and resid 111 through 127 removed outlier: 3.876A pdb=" N CYS C 115 " --> pdb=" O ARG C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 167 Processing helix chain 'C' and resid 172 through 176 Processing helix chain 'C' and resid 189 through 196 Processing helix chain 'C' and resid 197 through 206 Processing helix chain 'C' and resid 224 through 229 Processing helix chain 'C' and resid 265 through 278 removed outlier: 4.356A pdb=" N ILE C 269 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 290 Processing helix chain 'C' and resid 304 through 310 Processing helix chain 'D' and resid 10 through 16 Processing helix chain 'D' and resid 31 through 55 removed outlier: 3.699A pdb=" N GLU D 35 " --> pdb=" O GLY D 31 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER D 43 " --> pdb=" O ARG D 39 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE D 44 " --> pdb=" O ALA D 40 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N SER D 46 " --> pdb=" O CYS D 42 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N SER D 47 " --> pdb=" O SER D 43 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ARG D 55 " --> pdb=" O GLY D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 76 Processing helix chain 'D' and resid 111 through 127 removed outlier: 3.877A pdb=" N CYS D 115 " --> pdb=" O ARG D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 167 Processing helix chain 'D' and resid 172 through 176 Processing helix chain 'D' and resid 189 through 196 Processing helix chain 'D' and resid 197 through 206 Processing helix chain 'D' and resid 224 through 229 Processing helix chain 'D' and resid 265 through 278 removed outlier: 4.357A pdb=" N ILE D 269 " --> pdb=" O LYS D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 290 Processing helix chain 'D' and resid 304 through 310 Processing helix chain 'E' and resid 10 through 16 Processing helix chain 'E' and resid 31 through 55 removed outlier: 3.699A pdb=" N GLU E 35 " --> pdb=" O GLY E 31 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER E 43 " --> pdb=" O ARG E 39 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE E 44 " --> pdb=" O ALA E 40 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N SER E 46 " --> pdb=" O CYS E 42 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N SER E 47 " --> pdb=" O SER E 43 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ARG E 55 " --> pdb=" O GLY E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 76 Processing helix chain 'E' and resid 111 through 127 removed outlier: 3.876A pdb=" N CYS E 115 " --> pdb=" O ARG E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 167 Processing helix chain 'E' and resid 172 through 176 Processing helix chain 'E' and resid 189 through 196 Processing helix chain 'E' and resid 197 through 206 Processing helix chain 'E' and resid 224 through 229 Processing helix chain 'E' and resid 265 through 278 removed outlier: 4.357A pdb=" N ILE E 269 " --> pdb=" O LYS E 265 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 290 Processing helix chain 'E' and resid 304 through 310 Processing helix chain 'F' and resid 10 through 16 Processing helix chain 'F' and resid 31 through 55 removed outlier: 3.699A pdb=" N GLU F 35 " --> pdb=" O GLY F 31 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER F 43 " --> pdb=" O ARG F 39 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE F 44 " --> pdb=" O ALA F 40 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N SER F 46 " --> pdb=" O CYS F 42 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N SER F 47 " --> pdb=" O SER F 43 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ARG F 55 " --> pdb=" O GLY F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 76 Processing helix chain 'F' and resid 111 through 127 removed outlier: 3.876A pdb=" N CYS F 115 " --> pdb=" O ARG F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 167 Processing helix chain 'F' and resid 172 through 176 Processing helix chain 'F' and resid 189 through 196 Processing helix chain 'F' and resid 197 through 206 Processing helix chain 'F' and resid 224 through 229 Processing helix chain 'F' and resid 265 through 278 removed outlier: 4.356A pdb=" N ILE F 269 " --> pdb=" O LYS F 265 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 290 Processing helix chain 'F' and resid 304 through 310 Processing sheet with id=1, first strand: chain 'A' and resid 62 through 67 removed outlier: 6.599A pdb=" N ALA A 21 " --> pdb=" O GLN A 137 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLN A 137 " --> pdb=" O ALA A 21 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N PHE A 23 " --> pdb=" O SER A 135 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER A 135 " --> pdb=" O PHE A 23 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL A 25 " --> pdb=" O VAL A 133 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 90 through 91 removed outlier: 3.625A pdb=" N ILE A 90 " --> pdb=" O ALA A 96 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 241 through 242 Processing sheet with id=4, first strand: chain 'A' and resid 241 through 242 removed outlier: 5.177A pdb=" N PHE A 255 " --> pdb=" O HIS A 188 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR A 296 " --> pdb=" O LYS A 185 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LEU A 187 " --> pdb=" O ALA A 294 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ALA A 294 " --> pdb=" O LEU A 187 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'A' and resid 232 through 233 Processing sheet with id=6, first strand: chain 'B' and resid 62 through 67 removed outlier: 6.600A pdb=" N ALA B 21 " --> pdb=" O GLN B 137 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N GLN B 137 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N PHE B 23 " --> pdb=" O SER B 135 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER B 135 " --> pdb=" O PHE B 23 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL B 25 " --> pdb=" O VAL B 133 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'B' and resid 90 through 91 removed outlier: 3.625A pdb=" N ILE B 90 " --> pdb=" O ALA B 96 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'B' and resid 241 through 242 Processing sheet with id=9, first strand: chain 'B' and resid 241 through 242 removed outlier: 5.176A pdb=" N PHE B 255 " --> pdb=" O HIS B 188 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR B 296 " --> pdb=" O LYS B 185 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LEU B 187 " --> pdb=" O ALA B 294 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ALA B 294 " --> pdb=" O LEU B 187 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'B' and resid 232 through 233 Processing sheet with id=11, first strand: chain 'C' and resid 62 through 67 removed outlier: 6.599A pdb=" N ALA C 21 " --> pdb=" O GLN C 137 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N GLN C 137 " --> pdb=" O ALA C 21 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N PHE C 23 " --> pdb=" O SER C 135 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N SER C 135 " --> pdb=" O PHE C 23 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL C 25 " --> pdb=" O VAL C 133 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'C' and resid 90 through 91 removed outlier: 3.624A pdb=" N ILE C 90 " --> pdb=" O ALA C 96 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'C' and resid 241 through 242 Processing sheet with id=14, first strand: chain 'C' and resid 241 through 242 removed outlier: 5.176A pdb=" N PHE C 255 " --> pdb=" O HIS C 188 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR C 296 " --> pdb=" O LYS C 185 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LEU C 187 " --> pdb=" O ALA C 294 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ALA C 294 " --> pdb=" O LEU C 187 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'C' and resid 232 through 233 Processing sheet with id=16, first strand: chain 'D' and resid 62 through 67 removed outlier: 6.600A pdb=" N ALA D 21 " --> pdb=" O GLN D 137 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLN D 137 " --> pdb=" O ALA D 21 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N PHE D 23 " --> pdb=" O SER D 135 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER D 135 " --> pdb=" O PHE D 23 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL D 25 " --> pdb=" O VAL D 133 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'D' and resid 90 through 91 removed outlier: 3.625A pdb=" N ILE D 90 " --> pdb=" O ALA D 96 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'D' and resid 241 through 242 Processing sheet with id=19, first strand: chain 'D' and resid 241 through 242 removed outlier: 5.177A pdb=" N PHE D 255 " --> pdb=" O HIS D 188 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR D 296 " --> pdb=" O LYS D 185 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU D 187 " --> pdb=" O ALA D 294 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ALA D 294 " --> pdb=" O LEU D 187 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'D' and resid 232 through 233 Processing sheet with id=21, first strand: chain 'E' and resid 62 through 67 removed outlier: 6.599A pdb=" N ALA E 21 " --> pdb=" O GLN E 137 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLN E 137 " --> pdb=" O ALA E 21 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N PHE E 23 " --> pdb=" O SER E 135 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER E 135 " --> pdb=" O PHE E 23 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL E 25 " --> pdb=" O VAL E 133 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'E' and resid 90 through 91 removed outlier: 3.625A pdb=" N ILE E 90 " --> pdb=" O ALA E 96 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'E' and resid 241 through 242 Processing sheet with id=24, first strand: chain 'E' and resid 241 through 242 removed outlier: 5.177A pdb=" N PHE E 255 " --> pdb=" O HIS E 188 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR E 296 " --> pdb=" O LYS E 185 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LEU E 187 " --> pdb=" O ALA E 294 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ALA E 294 " --> pdb=" O LEU E 187 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'E' and resid 232 through 233 Processing sheet with id=26, first strand: chain 'F' and resid 62 through 67 removed outlier: 6.599A pdb=" N ALA F 21 " --> pdb=" O GLN F 137 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLN F 137 " --> pdb=" O ALA F 21 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N PHE F 23 " --> pdb=" O SER F 135 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER F 135 " --> pdb=" O PHE F 23 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL F 25 " --> pdb=" O VAL F 133 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'F' and resid 90 through 91 removed outlier: 3.623A pdb=" N ILE F 90 " --> pdb=" O ALA F 96 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'F' and resid 241 through 242 Processing sheet with id=29, first strand: chain 'F' and resid 241 through 242 removed outlier: 5.176A pdb=" N PHE F 255 " --> pdb=" O HIS F 188 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR F 296 " --> pdb=" O LYS F 185 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU F 187 " --> pdb=" O ALA F 294 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ALA F 294 " --> pdb=" O LEU F 187 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'F' and resid 232 through 233 684 hydrogen bonds defined for protein. 1818 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: 2.67 Time building geometry restraints manager: 1.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.39: 6282 1.39 - 1.55: 8736 1.55 - 1.72: 0 1.72 - 1.88: 96 1.88 - 2.04: 24 Bond restraints: 15138 Sorted by residual: bond pdb=" CA ASP A 212 " pdb=" C ASP A 212 " ideal model delta sigma weight residual 1.525 1.542 -0.017 1.63e-02 3.76e+03 1.15e+00 bond pdb=" CA ASP D 212 " pdb=" C ASP D 212 " ideal model delta sigma weight residual 1.525 1.542 -0.017 1.63e-02 3.76e+03 1.15e+00 bond pdb=" CA ASP C 212 " pdb=" C ASP C 212 " ideal model delta sigma weight residual 1.525 1.542 -0.017 1.63e-02 3.76e+03 1.12e+00 bond pdb=" CA ASP F 212 " pdb=" C ASP F 212 " ideal model delta sigma weight residual 1.525 1.542 -0.017 1.63e-02 3.76e+03 1.12e+00 bond pdb=" CA ASP B 212 " pdb=" C ASP B 212 " ideal model delta sigma weight residual 1.525 1.542 -0.017 1.63e-02 3.76e+03 1.11e+00 ... (remaining 15133 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.08: 19652 1.08 - 2.17: 675 2.17 - 3.25: 173 3.25 - 4.33: 68 4.33 - 5.42: 42 Bond angle restraints: 20610 Sorted by residual: angle pdb=" C ARG B 55 " pdb=" CA ARG B 55 " pdb=" CB ARG B 55 " ideal model delta sigma weight residual 110.67 105.25 5.42 1.92e+00 2.71e-01 7.96e+00 angle pdb=" C ARG E 55 " pdb=" CA ARG E 55 " pdb=" CB ARG E 55 " ideal model delta sigma weight residual 110.67 105.26 5.41 1.92e+00 2.71e-01 7.94e+00 angle pdb=" C ARG C 55 " pdb=" CA ARG C 55 " pdb=" CB ARG C 55 " ideal model delta sigma weight residual 110.67 105.26 5.41 1.92e+00 2.71e-01 7.93e+00 angle pdb=" C ARG D 55 " pdb=" CA ARG D 55 " pdb=" CB ARG D 55 " ideal model delta sigma weight residual 110.67 105.27 5.40 1.92e+00 2.71e-01 7.90e+00 angle pdb=" C ARG A 55 " pdb=" CA ARG A 55 " pdb=" CB ARG A 55 " ideal model delta sigma weight residual 110.67 105.28 5.39 1.92e+00 2.71e-01 7.89e+00 ... (remaining 20605 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 7945 17.82 - 35.65: 737 35.65 - 53.47: 168 53.47 - 71.30: 24 71.30 - 89.12: 30 Dihedral angle restraints: 8904 sinusoidal: 3594 harmonic: 5310 Sorted by residual: dihedral pdb=" C2A HEM F 401 " pdb=" CAA HEM F 401 " pdb=" CBA HEM F 401 " pdb=" CGA HEM F 401 " ideal model delta sinusoidal sigma weight residual -180.00 -90.88 -89.12 2 2.00e+01 2.50e-03 1.20e+01 dihedral pdb=" C2A HEM C 401 " pdb=" CAA HEM C 401 " pdb=" CBA HEM C 401 " pdb=" CGA HEM C 401 " ideal model delta sinusoidal sigma weight residual 180.00 -90.89 -89.11 2 2.00e+01 2.50e-03 1.20e+01 dihedral pdb=" C2A HEM B 401 " pdb=" CAA HEM B 401 " pdb=" CBA HEM B 401 " pdb=" CGA HEM B 401 " ideal model delta sinusoidal sigma weight residual -180.00 -90.90 -89.10 2 2.00e+01 2.50e-03 1.20e+01 ... (remaining 8901 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1385 0.032 - 0.064: 540 0.064 - 0.096: 169 0.096 - 0.128: 108 0.128 - 0.161: 12 Chirality restraints: 2214 Sorted by residual: chirality pdb=" CB THR D 166 " pdb=" CA THR D 166 " pdb=" OG1 THR D 166 " pdb=" CG2 THR D 166 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.45e-01 chirality pdb=" CB THR B 166 " pdb=" CA THR B 166 " pdb=" OG1 THR B 166 " pdb=" CG2 THR B 166 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.32e-01 chirality pdb=" CB THR F 166 " pdb=" CA THR F 166 " pdb=" OG1 THR F 166 " pdb=" CG2 THR F 166 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.29e-01 ... (remaining 2211 not shown) Planarity restraints: 2712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP B 212 " 0.010 2.00e-02 2.50e+03 2.02e-02 4.07e+00 pdb=" CG ASP B 212 " -0.035 2.00e-02 2.50e+03 pdb=" OD1 ASP B 212 " 0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP B 212 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP E 212 " -0.010 2.00e-02 2.50e+03 2.01e-02 4.03e+00 pdb=" CG ASP E 212 " 0.035 2.00e-02 2.50e+03 pdb=" OD1 ASP E 212 " -0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP E 212 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP F 212 " 0.010 2.00e-02 2.50e+03 2.01e-02 4.03e+00 pdb=" CG ASP F 212 " -0.035 2.00e-02 2.50e+03 pdb=" OD1 ASP F 212 " 0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP F 212 " 0.012 2.00e-02 2.50e+03 ... (remaining 2709 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 5300 2.86 - 3.37: 13370 3.37 - 3.88: 24789 3.88 - 4.39: 27576 4.39 - 4.90: 49289 Nonbonded interactions: 120324 Sorted by model distance: nonbonded pdb=" O ASP D 164 " pdb=" NH1 ARG D 264 " model vdw 2.353 3.120 nonbonded pdb=" O ASP C 164 " pdb=" NH1 ARG C 264 " model vdw 2.353 3.120 nonbonded pdb=" O ASP A 164 " pdb=" NH1 ARG A 264 " model vdw 2.353 3.120 nonbonded pdb=" O ASP E 164 " pdb=" NH1 ARG E 264 " model vdw 2.353 3.120 nonbonded pdb=" O ASP B 164 " pdb=" NH1 ARG B 264 " model vdw 2.353 3.120 ... (remaining 120319 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.350 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 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: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 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 : 0.003 0.045 15144 Z= 0.114 Angle : 0.570 5.417 20610 Z= 0.293 Chirality : 0.043 0.161 2214 Planarity : 0.004 0.046 2712 Dihedral : 15.255 89.121 5508 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.25 % Allowed : 13.76 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: 0.28 (0.20), residues: 1854 helix: 1.09 (0.22), residues: 630 sheet: 0.63 (0.24), residues: 456 loop : -0.81 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 55 TYR 0.004 0.001 TYR F 223 PHE 0.006 0.001 PHE C 116 TRP 0.003 0.001 TRP F 193 HIS 0.001 0.000 HIS E 106 Details of bonding type rmsd covalent geometry : bond 0.00286 (15138) covalent geometry : angle 0.57040 (20610) hydrogen bonds : bond 0.11480 ( 672) hydrogen bonds : angle 5.46445 ( 1818) Misc. bond : bond 0.02953 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 196 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 172 ASP cc_start: 0.6404 (t0) cc_final: 0.5469 (p0) REVERT: A 295 ILE cc_start: 0.8804 (pt) cc_final: 0.8546 (pt) REVERT: B 144 ASP cc_start: 0.8087 (m-30) cc_final: 0.7858 (m-30) REVERT: B 172 ASP cc_start: 0.6051 (t0) cc_final: 0.5149 (p0) REVERT: C 172 ASP cc_start: 0.6214 (t0) cc_final: 0.5348 (p0) REVERT: C 212 ASP cc_start: 0.8608 (t0) cc_final: 0.8247 (t0) REVERT: D 172 ASP cc_start: 0.6460 (t0) cc_final: 0.5475 (p0) REVERT: D 295 ILE cc_start: 0.8797 (pt) cc_final: 0.8544 (pt) REVERT: E 144 ASP cc_start: 0.8112 (m-30) cc_final: 0.7881 (m-30) REVERT: E 172 ASP cc_start: 0.6038 (t0) cc_final: 0.5142 (p0) REVERT: F 172 ASP cc_start: 0.6162 (t0) cc_final: 0.5354 (p0) REVERT: F 212 ASP cc_start: 0.8610 (t0) cc_final: 0.8250 (t0) outliers start: 4 outliers final: 0 residues processed: 200 average time/residue: 0.1385 time to fit residues: 40.1294 Evaluate side-chains 175 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 HIS E 95 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.120364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.098364 restraints weight = 20910.235| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.53 r_work: 0.3022 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.236 15144 Z= 0.283 Angle : 0.641 5.771 20610 Z= 0.324 Chirality : 0.046 0.152 2214 Planarity : 0.005 0.034 2712 Dihedral : 8.849 83.786 2082 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.69 % Allowed : 15.03 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: 0.27 (0.19), residues: 1854 helix: 1.04 (0.22), residues: 630 sheet: 0.58 (0.25), residues: 438 loop : -0.70 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 242 TYR 0.014 0.002 TYR C 180 PHE 0.021 0.002 PHE E 54 TRP 0.003 0.001 TRP E 193 HIS 0.006 0.001 HIS C 225 Details of bonding type rmsd covalent geometry : bond 0.00735 (15138) covalent geometry : angle 0.64061 (20610) hydrogen bonds : bond 0.04243 ( 672) hydrogen bonds : angle 5.10701 ( 1818) Misc. bond : bond 0.21925 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 161 time to evaluate : 0.662 Fit side-chains REVERT: A 200 GLN cc_start: 0.8401 (mm-40) cc_final: 0.8094 (tp40) REVERT: A 212 ASP cc_start: 0.8877 (t0) cc_final: 0.8423 (t0) REVERT: B 48 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7660 (mp) REVERT: B 212 ASP cc_start: 0.8868 (t0) cc_final: 0.8642 (t0) REVERT: B 252 LYS cc_start: 0.8935 (mttp) cc_final: 0.8675 (mptt) REVERT: C 32 LYS cc_start: 0.7405 (tptt) cc_final: 0.7198 (tptt) REVERT: C 212 ASP cc_start: 0.8995 (t0) cc_final: 0.8664 (t0) REVERT: C 252 LYS cc_start: 0.9005 (mttp) cc_final: 0.8801 (mptt) REVERT: D 200 GLN cc_start: 0.8396 (mm-40) cc_final: 0.8097 (tp40) REVERT: D 212 ASP cc_start: 0.8873 (t0) cc_final: 0.8422 (t0) REVERT: E 212 ASP cc_start: 0.8885 (t0) cc_final: 0.8653 (t0) REVERT: E 252 LYS cc_start: 0.8944 (mttp) cc_final: 0.8689 (mptt) REVERT: F 32 LYS cc_start: 0.7412 (tptt) cc_final: 0.7203 (tptt) REVERT: F 212 ASP cc_start: 0.9005 (t0) cc_final: 0.8671 (t0) REVERT: F 252 LYS cc_start: 0.9012 (mttp) cc_final: 0.8804 (mptt) outliers start: 11 outliers final: 8 residues processed: 172 average time/residue: 0.1518 time to fit residues: 37.1583 Evaluate side-chains 149 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 140 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain E residue 134 ASP Chi-restraints excluded: chain E residue 284 ASN Chi-restraints excluded: chain F residue 134 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 177 optimal weight: 50.0000 chunk 116 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 22 optimal weight: 0.0870 chunk 138 optimal weight: 0.7980 chunk 56 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 150 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 overall best weight: 0.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.126059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.104452 restraints weight = 20651.730| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.49 r_work: 0.3103 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.106 15144 Z= 0.107 Angle : 0.507 5.106 20610 Z= 0.252 Chirality : 0.042 0.125 2214 Planarity : 0.004 0.038 2712 Dihedral : 8.820 87.065 2082 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.27 % Allowed : 15.03 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: 0.42 (0.20), residues: 1854 helix: 1.20 (0.22), residues: 636 sheet: 0.58 (0.24), residues: 462 loop : -0.65 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 16 TYR 0.006 0.001 TYR C 223 PHE 0.015 0.001 PHE B 54 TRP 0.002 0.000 TRP A 193 HIS 0.002 0.000 HIS A 225 Details of bonding type rmsd covalent geometry : bond 0.00286 (15138) covalent geometry : angle 0.50666 (20610) hydrogen bonds : bond 0.02780 ( 672) hydrogen bonds : angle 4.54624 ( 1818) Misc. bond : bond 0.09782 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 170 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 212 ASP cc_start: 0.8603 (t0) cc_final: 0.8091 (t0) REVERT: B 16 ARG cc_start: 0.7744 (mmm-85) cc_final: 0.7426 (mtp-110) REVERT: B 88 ARG cc_start: 0.7745 (mtp85) cc_final: 0.7500 (tpp80) REVERT: B 144 ASP cc_start: 0.8243 (m-30) cc_final: 0.7822 (m-30) REVERT: B 212 ASP cc_start: 0.8674 (t0) cc_final: 0.8418 (t0) REVERT: C 212 ASP cc_start: 0.8712 (t0) cc_final: 0.8401 (t0) REVERT: D 212 ASP cc_start: 0.8594 (t0) cc_final: 0.8084 (t0) REVERT: E 16 ARG cc_start: 0.7732 (mmm-85) cc_final: 0.7411 (mtp-110) REVERT: E 88 ARG cc_start: 0.7753 (mtp85) cc_final: 0.7509 (tpp80) REVERT: E 144 ASP cc_start: 0.8261 (m-30) cc_final: 0.7837 (m-30) REVERT: E 212 ASP cc_start: 0.8675 (t0) cc_final: 0.8413 (t0) REVERT: F 212 ASP cc_start: 0.8706 (t0) cc_final: 0.8390 (t0) outliers start: 36 outliers final: 22 residues processed: 204 average time/residue: 0.1528 time to fit residues: 44.0041 Evaluate side-chains 167 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 145 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 134 ASP Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 230 SER Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 298 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 91 optimal weight: 8.9990 chunk 4 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 38 optimal weight: 4.9990 chunk 112 optimal weight: 0.4980 chunk 55 optimal weight: 0.0980 chunk 71 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 116 optimal weight: 3.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.122890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.101297 restraints weight = 20800.436| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.49 r_work: 0.3064 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.165 15144 Z= 0.162 Angle : 0.533 4.916 20610 Z= 0.267 Chirality : 0.042 0.123 2214 Planarity : 0.004 0.044 2712 Dihedral : 8.779 84.618 2082 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.59 % Allowed : 14.33 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: 0.42 (0.20), residues: 1854 helix: 1.25 (0.22), residues: 630 sheet: 0.53 (0.24), residues: 462 loop : -0.65 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 16 TYR 0.009 0.001 TYR B 223 PHE 0.016 0.001 PHE D 54 TRP 0.002 0.001 TRP C 72 HIS 0.003 0.001 HIS C 225 Details of bonding type rmsd covalent geometry : bond 0.00435 (15138) covalent geometry : angle 0.53311 (20610) hydrogen bonds : bond 0.03149 ( 672) hydrogen bonds : angle 4.59543 ( 1818) Misc. bond : bond 0.15410 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 162 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7635 (mp) REVERT: A 200 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.6947 (tm-30) REVERT: A 212 ASP cc_start: 0.8817 (t0) cc_final: 0.8238 (t0) REVERT: B 16 ARG cc_start: 0.7719 (mmm-85) cc_final: 0.7384 (mtp-110) REVERT: B 144 ASP cc_start: 0.8473 (m-30) cc_final: 0.8017 (m-30) REVERT: B 212 ASP cc_start: 0.8817 (t0) cc_final: 0.8482 (t0) REVERT: C 212 ASP cc_start: 0.8870 (t0) cc_final: 0.8527 (t0) REVERT: D 48 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7640 (mp) REVERT: D 200 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.6973 (tm-30) REVERT: D 212 ASP cc_start: 0.8823 (t0) cc_final: 0.8258 (t0) REVERT: E 16 ARG cc_start: 0.7711 (mmm-85) cc_final: 0.7374 (mtp-110) REVERT: E 144 ASP cc_start: 0.8488 (m-30) cc_final: 0.8019 (m-30) REVERT: E 212 ASP cc_start: 0.8837 (t0) cc_final: 0.8505 (t0) REVERT: F 212 ASP cc_start: 0.8878 (t0) cc_final: 0.8532 (t0) outliers start: 41 outliers final: 29 residues processed: 201 average time/residue: 0.1588 time to fit residues: 44.6859 Evaluate side-chains 185 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 152 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 200 GLN Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 134 ASP Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 230 SER Chi-restraints excluded: chain E residue 284 ASN Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 298 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 146 optimal weight: 20.0000 chunk 153 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 143 optimal weight: 0.0050 chunk 35 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 overall best weight: 1.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.123723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.102033 restraints weight = 20729.135| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.51 r_work: 0.3073 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.141 15144 Z= 0.143 Angle : 0.514 4.934 20610 Z= 0.255 Chirality : 0.042 0.129 2214 Planarity : 0.004 0.046 2712 Dihedral : 8.749 84.942 2082 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.65 % Allowed : 14.71 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: 0.47 (0.20), residues: 1854 helix: 1.26 (0.22), residues: 636 sheet: 0.51 (0.24), residues: 462 loop : -0.56 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 16 TYR 0.007 0.001 TYR D 186 PHE 0.014 0.001 PHE F 54 TRP 0.002 0.000 TRP F 72 HIS 0.003 0.001 HIS C 225 Details of bonding type rmsd covalent geometry : bond 0.00387 (15138) covalent geometry : angle 0.51353 (20610) hydrogen bonds : bond 0.02865 ( 672) hydrogen bonds : angle 4.50443 ( 1818) Misc. bond : bond 0.13332 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 169 time to evaluate : 0.613 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: A 48 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7598 (mp) REVERT: A 88 ARG cc_start: 0.7800 (mtp85) cc_final: 0.7298 (mtm-85) REVERT: A 212 ASP cc_start: 0.8788 (t0) cc_final: 0.8188 (t0) REVERT: B 16 ARG cc_start: 0.7760 (mmm-85) cc_final: 0.7449 (mtp-110) REVERT: B 88 ARG cc_start: 0.7870 (mtp85) cc_final: 0.7579 (tpp80) REVERT: B 212 ASP cc_start: 0.8811 (t0) cc_final: 0.8446 (t0) REVERT: C 88 ARG cc_start: 0.8041 (mtp85) cc_final: 0.7494 (mtm-85) REVERT: C 212 ASP cc_start: 0.8858 (t0) cc_final: 0.8498 (t0) REVERT: D 16 ARG cc_start: 0.7491 (mtp85) cc_final: 0.7191 (mmm-85) REVERT: D 48 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7597 (mp) REVERT: D 212 ASP cc_start: 0.8795 (t0) cc_final: 0.8207 (t0) REVERT: D 216 ARG cc_start: 0.7953 (mtm-85) cc_final: 0.7567 (mtp-110) REVERT: E 16 ARG cc_start: 0.7749 (mmm-85) cc_final: 0.7439 (mtp-110) REVERT: E 88 ARG cc_start: 0.7864 (mtp85) cc_final: 0.7572 (tpp80) REVERT: E 212 ASP cc_start: 0.8824 (t0) cc_final: 0.8451 (t0) REVERT: F 88 ARG cc_start: 0.8027 (mtp85) cc_final: 0.7479 (mtm-85) REVERT: F 212 ASP cc_start: 0.8867 (t0) cc_final: 0.8504 (t0) outliers start: 42 outliers final: 32 residues processed: 211 average time/residue: 0.1611 time to fit residues: 46.9873 Evaluate side-chains 194 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 160 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 134 ASP Chi-restraints excluded: chain E residue 230 SER Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 298 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 49 optimal weight: 0.9990 chunk 175 optimal weight: 5.9990 chunk 68 optimal weight: 9.9990 chunk 20 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 6 optimal weight: 10.0000 chunk 143 optimal weight: 0.7980 chunk 142 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 133 optimal weight: 0.0980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.126475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.105019 restraints weight = 20466.777| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.49 r_work: 0.3125 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 15144 Z= 0.091 Angle : 0.487 5.024 20610 Z= 0.237 Chirality : 0.041 0.129 2214 Planarity : 0.003 0.035 2712 Dihedral : 8.758 87.883 2082 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.46 % Allowed : 15.97 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: 0.66 (0.20), residues: 1854 helix: 1.47 (0.22), residues: 636 sheet: 0.50 (0.23), residues: 462 loop : -0.42 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 16 TYR 0.006 0.001 TYR E 262 PHE 0.012 0.001 PHE C 54 TRP 0.002 0.000 TRP D 193 HIS 0.001 0.000 HIS F 225 Details of bonding type rmsd covalent geometry : bond 0.00250 (15138) covalent geometry : angle 0.48715 (20610) hydrogen bonds : bond 0.02221 ( 672) hydrogen bonds : angle 4.27636 ( 1818) Misc. bond : bond 0.07572 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 191 time to evaluate : 0.661 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 16 ARG cc_start: 0.7726 (mmm-85) cc_final: 0.7114 (mtp-110) REVERT: A 88 ARG cc_start: 0.7759 (mtp85) cc_final: 0.7293 (mtm-85) REVERT: A 212 ASP cc_start: 0.8742 (t0) cc_final: 0.8125 (t0) REVERT: B 16 ARG cc_start: 0.7729 (mmm-85) cc_final: 0.7434 (mtp-110) REVERT: B 57 SER cc_start: 0.8278 (m) cc_final: 0.7763 (p) REVERT: B 144 ASP cc_start: 0.8422 (m-30) cc_final: 0.7956 (m-30) REVERT: B 212 ASP cc_start: 0.8739 (t0) cc_final: 0.8339 (t0) REVERT: C 57 SER cc_start: 0.8108 (m) cc_final: 0.7752 (p) REVERT: C 88 ARG cc_start: 0.7982 (mtp85) cc_final: 0.7532 (mtm-85) REVERT: C 212 ASP cc_start: 0.8797 (t0) cc_final: 0.8419 (t0) REVERT: D 88 ARG cc_start: 0.7773 (mtp85) cc_final: 0.7331 (mtm-85) REVERT: D 212 ASP cc_start: 0.8756 (t0) cc_final: 0.8146 (t0) REVERT: E 16 ARG cc_start: 0.7731 (mmm-85) cc_final: 0.7443 (mtp-110) REVERT: E 144 ASP cc_start: 0.8425 (m-30) cc_final: 0.7960 (m-30) REVERT: E 212 ASP cc_start: 0.8765 (t0) cc_final: 0.8360 (t0) REVERT: F 88 ARG cc_start: 0.7987 (mtp85) cc_final: 0.7532 (mtm-85) REVERT: F 212 ASP cc_start: 0.8817 (t0) cc_final: 0.8434 (t0) outliers start: 39 outliers final: 33 residues processed: 230 average time/residue: 0.1591 time to fit residues: 50.8363 Evaluate side-chains 215 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 182 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 134 ASP Chi-restraints excluded: chain E residue 230 SER Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 298 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 8 optimal weight: 7.9990 chunk 11 optimal weight: 7.9990 chunk 149 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 179 optimal weight: 0.3980 chunk 4 optimal weight: 2.9990 chunk 162 optimal weight: 0.8980 chunk 174 optimal weight: 0.5980 chunk 31 optimal weight: 10.0000 chunk 44 optimal weight: 0.9990 chunk 21 optimal weight: 7.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.125966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.104568 restraints weight = 20513.626| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.48 r_work: 0.3114 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 15144 Z= 0.113 Angle : 0.500 4.969 20610 Z= 0.247 Chirality : 0.041 0.127 2214 Planarity : 0.003 0.027 2712 Dihedral : 8.728 87.075 2082 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.40 % Allowed : 16.86 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: 0.66 (0.20), residues: 1854 helix: 1.49 (0.22), residues: 636 sheet: 0.41 (0.23), residues: 462 loop : -0.36 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 16 TYR 0.006 0.001 TYR F 186 PHE 0.013 0.001 PHE E 54 TRP 0.002 0.000 TRP A 193 HIS 0.002 0.000 HIS E 225 Details of bonding type rmsd covalent geometry : bond 0.00309 (15138) covalent geometry : angle 0.49985 (20610) hydrogen bonds : bond 0.02495 ( 672) hydrogen bonds : angle 4.30551 ( 1818) Misc. bond : bond 0.10070 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 184 time to evaluate : 0.616 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: A 16 ARG cc_start: 0.7808 (mmm-85) cc_final: 0.7168 (mtp-110) REVERT: A 88 ARG cc_start: 0.7823 (mtp85) cc_final: 0.7314 (mtm-85) REVERT: A 212 ASP cc_start: 0.8654 (t0) cc_final: 0.8009 (t0) REVERT: B 16 ARG cc_start: 0.7724 (mmm-85) cc_final: 0.7440 (mtp-110) REVERT: B 57 SER cc_start: 0.8217 (m) cc_final: 0.7726 (p) REVERT: B 88 ARG cc_start: 0.7871 (mtp85) cc_final: 0.7468 (mtm-85) REVERT: B 212 ASP cc_start: 0.8661 (t0) cc_final: 0.8188 (t0) REVERT: C 88 ARG cc_start: 0.7960 (mtp85) cc_final: 0.7470 (mtm-85) REVERT: C 212 ASP cc_start: 0.8775 (t0) cc_final: 0.8358 (t0) REVERT: D 88 ARG cc_start: 0.7813 (mtp85) cc_final: 0.7308 (mtm-85) REVERT: D 212 ASP cc_start: 0.8681 (t0) cc_final: 0.8040 (t0) REVERT: E 16 ARG cc_start: 0.7724 (mmm-85) cc_final: 0.7442 (mtp-110) REVERT: E 57 SER cc_start: 0.8452 (m) cc_final: 0.7901 (p) REVERT: E 88 ARG cc_start: 0.7895 (mtp85) cc_final: 0.7502 (mtm-85) REVERT: E 212 ASP cc_start: 0.8698 (t0) cc_final: 0.8214 (t0) REVERT: F 88 ARG cc_start: 0.7987 (mtp85) cc_final: 0.7483 (mtm-85) REVERT: F 212 ASP cc_start: 0.8797 (t0) cc_final: 0.8377 (t0) outliers start: 38 outliers final: 34 residues processed: 222 average time/residue: 0.1555 time to fit residues: 47.9475 Evaluate side-chains 212 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 178 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 134 ASP Chi-restraints excluded: chain E residue 230 SER Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 298 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 136 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 59 optimal weight: 8.9990 chunk 119 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 168 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.119804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.098029 restraints weight = 20945.115| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.52 r_work: 0.3025 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.217 15144 Z= 0.274 Angle : 0.609 5.733 20610 Z= 0.307 Chirality : 0.044 0.154 2214 Planarity : 0.004 0.035 2712 Dihedral : 8.836 85.682 2082 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.53 % Allowed : 17.17 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: 0.32 (0.19), residues: 1854 helix: 1.13 (0.22), residues: 630 sheet: 0.28 (0.24), residues: 438 loop : -0.50 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 16 TYR 0.013 0.002 TYR B 180 PHE 0.015 0.002 PHE B 54 TRP 0.003 0.001 TRP E 193 HIS 0.005 0.001 HIS C 225 Details of bonding type rmsd covalent geometry : bond 0.00712 (15138) covalent geometry : angle 0.60945 (20610) hydrogen bonds : bond 0.03904 ( 672) hydrogen bonds : angle 4.81054 ( 1818) Misc. bond : bond 0.20903 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 161 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7486 (mp) REVERT: A 210 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8681 (tp) REVERT: A 212 ASP cc_start: 0.8656 (t0) cc_final: 0.8080 (t0) REVERT: B 57 SER cc_start: 0.8419 (m) cc_final: 0.7881 (p) REVERT: B 212 ASP cc_start: 0.8663 (t0) cc_final: 0.8194 (t0) REVERT: C 212 ASP cc_start: 0.8681 (t0) cc_final: 0.8256 (t0) REVERT: D 48 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7522 (mp) REVERT: D 210 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8674 (tp) REVERT: D 212 ASP cc_start: 0.8660 (t0) cc_final: 0.8084 (t0) REVERT: E 44 ILE cc_start: 0.8572 (tp) cc_final: 0.8262 (pt) REVERT: E 57 SER cc_start: 0.8285 (m) cc_final: 0.7844 (p) REVERT: E 212 ASP cc_start: 0.8664 (t0) cc_final: 0.8203 (t0) REVERT: F 212 ASP cc_start: 0.8668 (t0) cc_final: 0.8213 (t0) outliers start: 40 outliers final: 32 residues processed: 201 average time/residue: 0.1550 time to fit residues: 43.5507 Evaluate side-chains 194 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 158 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 134 ASP Chi-restraints excluded: chain E residue 230 SER Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 210 LEU Chi-restraints excluded: chain F residue 298 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 46 optimal weight: 6.9990 chunk 116 optimal weight: 3.9990 chunk 140 optimal weight: 7.9990 chunk 69 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 143 optimal weight: 7.9990 chunk 163 optimal weight: 4.9990 chunk 183 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.120016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.098095 restraints weight = 21011.700| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.54 r_work: 0.3025 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.197 15144 Z= 0.240 Angle : 0.586 5.793 20610 Z= 0.295 Chirality : 0.044 0.149 2214 Planarity : 0.004 0.026 2712 Dihedral : 8.837 83.378 2082 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.71 % Allowed : 17.36 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: 0.19 (0.19), residues: 1854 helix: 1.05 (0.22), residues: 630 sheet: 0.19 (0.24), residues: 438 loop : -0.59 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 16 TYR 0.011 0.002 TYR E 180 PHE 0.014 0.002 PHE E 54 TRP 0.002 0.001 TRP E 193 HIS 0.004 0.001 HIS C 225 Details of bonding type rmsd covalent geometry : bond 0.00628 (15138) covalent geometry : angle 0.58632 (20610) hydrogen bonds : bond 0.03658 ( 672) hydrogen bonds : angle 4.77929 ( 1818) Misc. bond : bond 0.18892 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 164 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.8028 (mmm-85) cc_final: 0.7684 (mmm-85) REVERT: A 48 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7471 (mp) REVERT: A 210 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8681 (tp) REVERT: A 212 ASP cc_start: 0.8645 (t0) cc_final: 0.8037 (t0) REVERT: B 44 ILE cc_start: 0.8449 (tp) cc_final: 0.8180 (pt) REVERT: B 57 SER cc_start: 0.8401 (m) cc_final: 0.7844 (p) REVERT: B 88 ARG cc_start: 0.7794 (mtp85) cc_final: 0.7525 (tpp80) REVERT: B 212 ASP cc_start: 0.8669 (t0) cc_final: 0.8201 (t0) REVERT: C 57 SER cc_start: 0.8396 (m) cc_final: 0.7949 (p) REVERT: C 212 ASP cc_start: 0.8657 (t0) cc_final: 0.8210 (t0) REVERT: D 48 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7485 (mp) REVERT: D 210 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8664 (tp) REVERT: D 212 ASP cc_start: 0.8657 (t0) cc_final: 0.8055 (t0) REVERT: E 44 ILE cc_start: 0.8613 (tp) cc_final: 0.8350 (pt) REVERT: E 57 SER cc_start: 0.8329 (m) cc_final: 0.7807 (p) REVERT: E 88 ARG cc_start: 0.7798 (mtp85) cc_final: 0.7527 (tpp80) REVERT: E 212 ASP cc_start: 0.8673 (t0) cc_final: 0.8212 (t0) REVERT: F 212 ASP cc_start: 0.8657 (t0) cc_final: 0.8201 (t0) outliers start: 43 outliers final: 34 residues processed: 206 average time/residue: 0.1632 time to fit residues: 46.9643 Evaluate side-chains 197 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 159 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 134 ASP Chi-restraints excluded: chain E residue 230 SER Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 298 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 8 optimal weight: 6.9990 chunk 160 optimal weight: 0.9990 chunk 139 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 145 optimal weight: 6.9990 chunk 169 optimal weight: 0.9990 chunk 185 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 125 optimal weight: 0.0470 chunk 101 optimal weight: 6.9990 chunk 52 optimal weight: 0.9980 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.125440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.103898 restraints weight = 20582.599| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.47 r_work: 0.3103 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 15144 Z= 0.101 Angle : 0.514 5.046 20610 Z= 0.252 Chirality : 0.042 0.127 2214 Planarity : 0.004 0.050 2712 Dihedral : 8.804 86.893 2082 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.77 % Allowed : 18.75 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: 0.50 (0.20), residues: 1854 helix: 1.40 (0.23), residues: 630 sheet: 0.14 (0.23), residues: 462 loop : -0.36 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 16 TYR 0.007 0.001 TYR D 223 PHE 0.012 0.001 PHE E 5 TRP 0.003 0.000 TRP D 193 HIS 0.002 0.000 HIS C 225 Details of bonding type rmsd covalent geometry : bond 0.00270 (15138) covalent geometry : angle 0.51354 (20610) hydrogen bonds : bond 0.02401 ( 672) hydrogen bonds : angle 4.38282 ( 1818) Misc. bond : bond 0.08998 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 192 time to evaluate : 0.553 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 44 ILE cc_start: 0.8665 (tp) cc_final: 0.8339 (pt) REVERT: A 88 ARG cc_start: 0.7810 (mtp85) cc_final: 0.7353 (mtm-85) REVERT: A 134 ASP cc_start: 0.8007 (OUTLIER) cc_final: 0.7729 (p0) REVERT: A 212 ASP cc_start: 0.8763 (t0) cc_final: 0.8400 (t0) REVERT: B 44 ILE cc_start: 0.8437 (tp) cc_final: 0.8173 (pt) REVERT: B 57 SER cc_start: 0.8360 (m) cc_final: 0.7728 (p) REVERT: B 134 ASP cc_start: 0.7932 (OUTLIER) cc_final: 0.7720 (p0) REVERT: B 212 ASP cc_start: 0.8658 (t0) cc_final: 0.8142 (t0) REVERT: C 57 SER cc_start: 0.8258 (m) cc_final: 0.7804 (p) REVERT: C 88 ARG cc_start: 0.7991 (mtp85) cc_final: 0.7509 (mtm-85) REVERT: C 212 ASP cc_start: 0.8718 (t0) cc_final: 0.8241 (t0) REVERT: D 44 ILE cc_start: 0.8666 (tp) cc_final: 0.8333 (pt) REVERT: D 88 ARG cc_start: 0.7797 (mtp85) cc_final: 0.7339 (mtm-85) REVERT: D 134 ASP cc_start: 0.8010 (OUTLIER) cc_final: 0.7726 (p0) REVERT: D 212 ASP cc_start: 0.8735 (t0) cc_final: 0.8393 (t0) REVERT: E 44 ILE cc_start: 0.8680 (tp) cc_final: 0.8401 (pt) REVERT: E 57 SER cc_start: 0.8428 (m) cc_final: 0.7798 (p) REVERT: E 134 ASP cc_start: 0.7971 (OUTLIER) cc_final: 0.7745 (p0) REVERT: E 212 ASP cc_start: 0.8666 (t0) cc_final: 0.8143 (t0) REVERT: F 88 ARG cc_start: 0.8005 (mtp85) cc_final: 0.7512 (mtm-85) outliers start: 28 outliers final: 24 residues processed: 220 average time/residue: 0.1575 time to fit residues: 47.4422 Evaluate side-chains 216 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 188 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 134 ASP Chi-restraints excluded: chain E residue 230 SER Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 298 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 101 optimal weight: 6.9990 chunk 158 optimal weight: 9.9990 chunk 53 optimal weight: 20.0000 chunk 154 optimal weight: 0.5980 chunk 39 optimal weight: 0.0970 chunk 152 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 overall best weight: 2.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 GLN E 137 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.122548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.100955 restraints weight = 20743.841| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.47 r_work: 0.3065 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.151 15144 Z= 0.164 Angle : 0.540 5.015 20610 Z= 0.269 Chirality : 0.042 0.140 2214 Planarity : 0.004 0.051 2712 Dihedral : 8.795 85.647 2082 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.08 % Allowed : 18.31 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: 0.36 (0.20), residues: 1854 helix: 1.22 (0.22), residues: 636 sheet: 0.05 (0.23), residues: 462 loop : -0.36 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 16 TYR 0.008 0.001 TYR F 186 PHE 0.013 0.001 PHE E 54 TRP 0.002 0.000 TRP C 72 HIS 0.003 0.001 HIS C 225 Details of bonding type rmsd covalent geometry : bond 0.00439 (15138) covalent geometry : angle 0.54005 (20610) hydrogen bonds : bond 0.03026 ( 672) hydrogen bonds : angle 4.51960 ( 1818) Misc. bond : bond 0.14339 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3165.09 seconds wall clock time: 55 minutes 9.35 seconds (3309.35 seconds total)