Starting phenix.real_space_refine on Mon Sep 14 11:24:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9s34_54521/09_2026/9s34_54521.cif Found real_map, /net/cci-nas-00/data/ceres_data/9s34_54521/09_2026/9s34_54521.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9s34_54521/09_2026/9s34_54521.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9s34_54521/09_2026/9s34_54521.map" model { file = "/net/cci-nas-00/data/ceres_data/9s34_54521/09_2026/9s34_54521.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9s34_54521/09_2026/9s34_54521.cif" } resolution = 3.15 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= 0.037 sd= 0.130 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 112 5.16 5 C 18781 2.51 5 N 4886 2.21 5 O 5621 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 182 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29400 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2356 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 14, 'TRANS': 285} Chain: "H" Number of atoms: 1844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1844 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 8, 'TRANS': 228} Restraints were copied for chains: B, C, D, E, F, G, N, I, J, K, L, M Time building chain proxies: 3.99, per 1000 atoms: 0.14 Number of scatterers: 29400 At special positions: 0 Unit cell: (139.69, 137.4, 123.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 112 16.00 O 5621 8.00 N 4886 7.00 C 18781 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.20 Conformation dependent library (CDL) restraints added in 1.3 seconds 7462 Ramachandran restraints generated. 3731 Oldfield, 0 Emsley, 3731 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7042 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 21 sheets defined 43.8% alpha, 15.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 37 through 53 Processing helix chain 'A' and resid 86 through 93 Processing helix chain 'A' and resid 98 through 111 Processing helix chain 'A' and resid 113 through 126 Processing helix chain 'A' and resid 131 through 137 Processing helix chain 'A' and resid 140 through 147 removed outlier: 3.506A pdb=" N GLU A 144 " --> pdb=" O GLU A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 150 No H-bonds generated for 'chain 'A' and resid 148 through 150' Processing helix chain 'A' and resid 151 through 158 Processing helix chain 'A' and resid 178 through 193 Processing helix chain 'A' and resid 205 through 210 removed outlier: 3.513A pdb=" N LEU A 209 " --> pdb=" O ASP A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 219 removed outlier: 3.529A pdb=" N LEU A 219 " --> pdb=" O GLY A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 224 Processing helix chain 'A' and resid 239 through 244 Processing helix chain 'A' and resid 255 through 266 Processing helix chain 'B' and resid 37 through 53 Processing helix chain 'B' and resid 86 through 93 Processing helix chain 'B' and resid 98 through 111 Processing helix chain 'B' and resid 113 through 126 Processing helix chain 'B' and resid 131 through 137 Processing helix chain 'B' and resid 140 through 147 removed outlier: 3.506A pdb=" N GLU B 144 " --> pdb=" O GLU B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 150 No H-bonds generated for 'chain 'B' and resid 148 through 150' Processing helix chain 'B' and resid 151 through 158 Processing helix chain 'B' and resid 178 through 193 Processing helix chain 'B' and resid 205 through 210 removed outlier: 3.513A pdb=" N LEU B 209 " --> pdb=" O ASP B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 219 removed outlier: 3.529A pdb=" N LEU B 219 " --> pdb=" O GLY B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 224 Processing helix chain 'B' and resid 239 through 244 Processing helix chain 'B' and resid 255 through 266 Processing helix chain 'C' and resid 37 through 53 Processing helix chain 'C' and resid 86 through 93 Processing helix chain 'C' and resid 98 through 111 Processing helix chain 'C' and resid 113 through 126 Processing helix chain 'C' and resid 131 through 137 Processing helix chain 'C' and resid 140 through 147 removed outlier: 3.507A pdb=" N GLU C 144 " --> pdb=" O GLU C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 150 No H-bonds generated for 'chain 'C' and resid 148 through 150' Processing helix chain 'C' and resid 151 through 158 Processing helix chain 'C' and resid 178 through 193 Processing helix chain 'C' and resid 205 through 210 removed outlier: 3.513A pdb=" N LEU C 209 " --> pdb=" O ASP C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 219 removed outlier: 3.530A pdb=" N LEU C 219 " --> pdb=" O GLY C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 224 Processing helix chain 'C' and resid 239 through 244 Processing helix chain 'C' and resid 255 through 266 Processing helix chain 'D' and resid 37 through 53 Processing helix chain 'D' and resid 86 through 93 Processing helix chain 'D' and resid 98 through 111 Processing helix chain 'D' and resid 113 through 126 Processing helix chain 'D' and resid 131 through 137 Processing helix chain 'D' and resid 140 through 147 removed outlier: 3.506A pdb=" N GLU D 144 " --> pdb=" O GLU D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 150 No H-bonds generated for 'chain 'D' and resid 148 through 150' Processing helix chain 'D' and resid 151 through 158 Processing helix chain 'D' and resid 178 through 193 Processing helix chain 'D' and resid 205 through 210 removed outlier: 3.514A pdb=" N LEU D 209 " --> pdb=" O ASP D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 219 removed outlier: 3.529A pdb=" N LEU D 219 " --> pdb=" O GLY D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 224 Processing helix chain 'D' and resid 239 through 244 Processing helix chain 'D' and resid 255 through 266 Processing helix chain 'E' and resid 37 through 53 Processing helix chain 'E' and resid 86 through 93 Processing helix chain 'E' and resid 98 through 111 Processing helix chain 'E' and resid 113 through 126 Processing helix chain 'E' and resid 131 through 137 Processing helix chain 'E' and resid 140 through 147 removed outlier: 3.506A pdb=" N GLU E 144 " --> pdb=" O GLU E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 150 No H-bonds generated for 'chain 'E' and resid 148 through 150' Processing helix chain 'E' and resid 151 through 158 Processing helix chain 'E' and resid 178 through 193 Processing helix chain 'E' and resid 205 through 210 removed outlier: 3.512A pdb=" N LEU E 209 " --> pdb=" O ASP E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 219 removed outlier: 3.529A pdb=" N LEU E 219 " --> pdb=" O GLY E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 219 through 224 Processing helix chain 'E' and resid 239 through 244 Processing helix chain 'E' and resid 255 through 266 Processing helix chain 'F' and resid 37 through 53 Processing helix chain 'F' and resid 86 through 93 Processing helix chain 'F' and resid 98 through 111 Processing helix chain 'F' and resid 113 through 126 Processing helix chain 'F' and resid 131 through 137 Processing helix chain 'F' and resid 140 through 147 removed outlier: 3.507A pdb=" N GLU F 144 " --> pdb=" O GLU F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 150 No H-bonds generated for 'chain 'F' and resid 148 through 150' Processing helix chain 'F' and resid 151 through 158 Processing helix chain 'F' and resid 178 through 193 Processing helix chain 'F' and resid 205 through 210 removed outlier: 3.514A pdb=" N LEU F 209 " --> pdb=" O ASP F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 212 through 219 removed outlier: 3.529A pdb=" N LEU F 219 " --> pdb=" O GLY F 215 " (cutoff:3.500A) Processing helix chain 'F' and resid 219 through 224 Processing helix chain 'F' and resid 239 through 244 Processing helix chain 'F' and resid 255 through 266 Processing helix chain 'G' and resid 37 through 53 Processing helix chain 'G' and resid 86 through 93 Processing helix chain 'G' and resid 98 through 111 Processing helix chain 'G' and resid 113 through 126 Processing helix chain 'G' and resid 131 through 137 Processing helix chain 'G' and resid 140 through 147 removed outlier: 3.506A pdb=" N GLU G 144 " --> pdb=" O GLU G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 150 No H-bonds generated for 'chain 'G' and resid 148 through 150' Processing helix chain 'G' and resid 151 through 158 Processing helix chain 'G' and resid 178 through 193 Processing helix chain 'G' and resid 205 through 210 removed outlier: 3.513A pdb=" N LEU G 209 " --> pdb=" O ASP G 205 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 219 removed outlier: 3.529A pdb=" N LEU G 219 " --> pdb=" O GLY G 215 " (cutoff:3.500A) Processing helix chain 'G' and resid 219 through 224 Processing helix chain 'G' and resid 239 through 244 Processing helix chain 'G' and resid 255 through 266 Processing helix chain 'H' and resid 23 through 35 Processing helix chain 'H' and resid 83 through 106 Processing helix chain 'H' and resid 110 through 125 Processing helix chain 'H' and resid 169 through 181 Processing helix chain 'H' and resid 186 through 202 removed outlier: 3.653A pdb=" N THR H 201 " --> pdb=" O ALA H 197 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET H 202 " --> pdb=" O LEU H 198 " (cutoff:3.500A) Processing helix chain 'H' and resid 226 through 244 Processing helix chain 'N' and resid 23 through 35 Processing helix chain 'N' and resid 83 through 106 Processing helix chain 'N' and resid 110 through 125 Processing helix chain 'N' and resid 169 through 181 Processing helix chain 'N' and resid 186 through 202 removed outlier: 3.652A pdb=" N THR N 201 " --> pdb=" O ALA N 197 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET N 202 " --> pdb=" O LEU N 198 " (cutoff:3.500A) Processing helix chain 'N' and resid 226 through 244 Processing helix chain 'I' and resid 23 through 35 Processing helix chain 'I' and resid 83 through 106 Processing helix chain 'I' and resid 110 through 125 Processing helix chain 'I' and resid 169 through 181 Processing helix chain 'I' and resid 186 through 202 removed outlier: 3.654A pdb=" N THR I 201 " --> pdb=" O ALA I 197 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET I 202 " --> pdb=" O LEU I 198 " (cutoff:3.500A) Processing helix chain 'I' and resid 226 through 244 Processing helix chain 'J' and resid 23 through 35 Processing helix chain 'J' and resid 83 through 106 Processing helix chain 'J' and resid 110 through 125 Processing helix chain 'J' and resid 169 through 181 Processing helix chain 'J' and resid 186 through 202 removed outlier: 3.653A pdb=" N THR J 201 " --> pdb=" O ALA J 197 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET J 202 " --> pdb=" O LEU J 198 " (cutoff:3.500A) Processing helix chain 'J' and resid 226 through 244 Processing helix chain 'K' and resid 23 through 35 Processing helix chain 'K' and resid 83 through 106 Processing helix chain 'K' and resid 110 through 125 Processing helix chain 'K' and resid 169 through 181 Processing helix chain 'K' and resid 186 through 202 removed outlier: 3.654A pdb=" N THR K 201 " --> pdb=" O ALA K 197 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET K 202 " --> pdb=" O LEU K 198 " (cutoff:3.500A) Processing helix chain 'K' and resid 226 through 244 Processing helix chain 'L' and resid 23 through 35 Processing helix chain 'L' and resid 83 through 106 Processing helix chain 'L' and resid 110 through 125 Processing helix chain 'L' and resid 169 through 181 Processing helix chain 'L' and resid 186 through 202 removed outlier: 3.654A pdb=" N THR L 201 " --> pdb=" O ALA L 197 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET L 202 " --> pdb=" O LEU L 198 " (cutoff:3.500A) Processing helix chain 'L' and resid 226 through 244 Processing helix chain 'M' and resid 23 through 35 Processing helix chain 'M' and resid 83 through 106 Processing helix chain 'M' and resid 110 through 125 Processing helix chain 'M' and resid 169 through 181 Processing helix chain 'M' and resid 186 through 202 removed outlier: 3.653A pdb=" N THR M 201 " --> pdb=" O ALA M 197 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET M 202 " --> pdb=" O LEU M 198 " (cutoff:3.500A) Processing helix chain 'M' and resid 226 through 244 Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 21 removed outlier: 5.771A pdb=" N TYR A 21 " --> pdb=" O LYS A 9 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N LYS A 9 " --> pdb=" O TYR A 21 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N LEU A 250 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LYS A 31 " --> pdb=" O LEU A 250 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL A 230 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASN A 56 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N GLY A 202 " --> pdb=" O ASN A 56 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE A 58 " --> pdb=" O GLY A 202 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU A 75 " --> pdb=" O ASP A 172 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 18 through 21 removed outlier: 5.771A pdb=" N TYR B 21 " --> pdb=" O LYS B 9 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N LYS B 9 " --> pdb=" O TYR B 21 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N LEU B 250 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LYS B 31 " --> pdb=" O LEU B 250 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL B 230 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASN B 56 " --> pdb=" O ALA B 200 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N GLY B 202 " --> pdb=" O ASN B 56 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE B 58 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU B 75 " --> pdb=" O ASP B 172 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 18 through 21 removed outlier: 5.772A pdb=" N TYR C 21 " --> pdb=" O LYS C 9 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N LYS C 9 " --> pdb=" O TYR C 21 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N LEU C 250 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LYS C 31 " --> pdb=" O LEU C 250 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL C 230 " --> pdb=" O VAL C 199 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASN C 56 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N GLY C 202 " --> pdb=" O ASN C 56 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE C 58 " --> pdb=" O GLY C 202 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU C 75 " --> pdb=" O ASP C 172 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 18 through 21 removed outlier: 5.771A pdb=" N TYR D 21 " --> pdb=" O LYS D 9 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N LYS D 9 " --> pdb=" O TYR D 21 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N LEU D 250 " --> pdb=" O THR D 29 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LYS D 31 " --> pdb=" O LEU D 250 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL D 230 " --> pdb=" O VAL D 199 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASN D 56 " --> pdb=" O ALA D 200 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N GLY D 202 " --> pdb=" O ASN D 56 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE D 58 " --> pdb=" O GLY D 202 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU D 75 " --> pdb=" O ASP D 172 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 18 through 21 removed outlier: 5.771A pdb=" N TYR E 21 " --> pdb=" O LYS E 9 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N LYS E 9 " --> pdb=" O TYR E 21 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N LEU E 250 " --> pdb=" O THR E 29 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LYS E 31 " --> pdb=" O LEU E 250 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL E 230 " --> pdb=" O VAL E 199 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASN E 56 " --> pdb=" O ALA E 200 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N GLY E 202 " --> pdb=" O ASN E 56 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE E 58 " --> pdb=" O GLY E 202 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU E 75 " --> pdb=" O ASP E 172 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 18 through 21 removed outlier: 5.772A pdb=" N TYR F 21 " --> pdb=" O LYS F 9 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N LYS F 9 " --> pdb=" O TYR F 21 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N LEU F 250 " --> pdb=" O THR F 29 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LYS F 31 " --> pdb=" O LEU F 250 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL F 230 " --> pdb=" O VAL F 199 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ASN F 56 " --> pdb=" O ALA F 200 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N GLY F 202 " --> pdb=" O ASN F 56 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE F 58 " --> pdb=" O GLY F 202 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU F 75 " --> pdb=" O ASP F 172 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 18 through 21 removed outlier: 5.771A pdb=" N TYR G 21 " --> pdb=" O LYS G 9 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N LYS G 9 " --> pdb=" O TYR G 21 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N LEU G 250 " --> pdb=" O THR G 29 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LYS G 31 " --> pdb=" O LEU G 250 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL G 230 " --> pdb=" O VAL G 199 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASN G 56 " --> pdb=" O ALA G 200 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N GLY G 202 " --> pdb=" O ASN G 56 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE G 58 " --> pdb=" O GLY G 202 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU G 75 " --> pdb=" O ASP G 172 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 163 through 166 Processing sheet with id=AA9, first strand: chain 'H' and resid 70 through 71 Processing sheet with id=AB1, first strand: chain 'N' and resid 163 through 166 Processing sheet with id=AB2, first strand: chain 'N' and resid 70 through 71 Processing sheet with id=AB3, first strand: chain 'I' and resid 163 through 166 Processing sheet with id=AB4, first strand: chain 'I' and resid 70 through 71 Processing sheet with id=AB5, first strand: chain 'J' and resid 163 through 166 Processing sheet with id=AB6, first strand: chain 'J' and resid 70 through 71 Processing sheet with id=AB7, first strand: chain 'K' and resid 163 through 166 Processing sheet with id=AB8, first strand: chain 'K' and resid 70 through 71 Processing sheet with id=AB9, first strand: chain 'L' and resid 163 through 166 Processing sheet with id=AC1, first strand: chain 'L' and resid 70 through 71 Processing sheet with id=AC2, first strand: chain 'M' and resid 163 through 166 Processing sheet with id=AC3, first strand: chain 'M' and resid 70 through 71 1421 hydrogen bonds defined for protein. 4179 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.25 Time building geometry restraints manager: 3.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5135 1.32 - 1.44: 7090 1.44 - 1.56: 17462 1.56 - 1.69: 0 1.69 - 1.81: 203 Bond restraints: 29890 Sorted by residual: bond pdb=" N ILE K 14 " pdb=" CA ILE K 14 " ideal model delta sigma weight residual 1.460 1.502 -0.043 1.21e-02 6.83e+03 1.24e+01 bond pdb=" N ILE N 14 " pdb=" CA ILE N 14 " ideal model delta sigma weight residual 1.460 1.502 -0.042 1.21e-02 6.83e+03 1.23e+01 bond pdb=" N ILE L 14 " pdb=" CA ILE L 14 " ideal model delta sigma weight residual 1.460 1.502 -0.042 1.21e-02 6.83e+03 1.23e+01 bond pdb=" N ILE I 14 " pdb=" CA ILE I 14 " ideal model delta sigma weight residual 1.460 1.502 -0.042 1.21e-02 6.83e+03 1.21e+01 bond pdb=" N ILE M 14 " pdb=" CA ILE M 14 " ideal model delta sigma weight residual 1.460 1.502 -0.042 1.21e-02 6.83e+03 1.21e+01 ... (remaining 29885 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 36174 1.41 - 2.82: 3248 2.82 - 4.23: 712 4.23 - 5.64: 229 5.64 - 7.05: 41 Bond angle restraints: 40404 Sorted by residual: angle pdb=" N ARG F 236 " pdb=" CA ARG F 236 " pdb=" C ARG F 236 " ideal model delta sigma weight residual 114.31 108.43 5.88 1.29e+00 6.01e-01 2.08e+01 angle pdb=" N ARG E 236 " pdb=" CA ARG E 236 " pdb=" C ARG E 236 " ideal model delta sigma weight residual 114.31 108.44 5.87 1.29e+00 6.01e-01 2.07e+01 angle pdb=" N ARG A 236 " pdb=" CA ARG A 236 " pdb=" C ARG A 236 " ideal model delta sigma weight residual 114.31 108.46 5.85 1.29e+00 6.01e-01 2.05e+01 angle pdb=" N ARG C 236 " pdb=" CA ARG C 236 " pdb=" C ARG C 236 " ideal model delta sigma weight residual 114.31 108.46 5.85 1.29e+00 6.01e-01 2.05e+01 angle pdb=" N ARG D 236 " pdb=" CA ARG D 236 " pdb=" C ARG D 236 " ideal model delta sigma weight residual 114.31 108.47 5.84 1.29e+00 6.01e-01 2.05e+01 ... (remaining 40399 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.49: 17318 21.49 - 42.98: 840 42.98 - 64.47: 161 64.47 - 85.95: 21 85.95 - 107.44: 7 Dihedral angle restraints: 18347 sinusoidal: 7385 harmonic: 10962 Sorted by residual: dihedral pdb=" CA TYR E 204 " pdb=" C TYR E 204 " pdb=" N ASP E 205 " pdb=" CA ASP E 205 " ideal model delta harmonic sigma weight residual -180.00 -72.56 -107.44 0 5.00e+00 4.00e-02 4.62e+02 dihedral pdb=" CA TYR A 204 " pdb=" C TYR A 204 " pdb=" N ASP A 205 " pdb=" CA ASP A 205 " ideal model delta harmonic sigma weight residual -180.00 -72.58 -107.42 0 5.00e+00 4.00e-02 4.62e+02 dihedral pdb=" CA TYR G 204 " pdb=" C TYR G 204 " pdb=" N ASP G 205 " pdb=" CA ASP G 205 " ideal model delta harmonic sigma weight residual -180.00 -72.59 -107.41 0 5.00e+00 4.00e-02 4.61e+02 ... (remaining 18344 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 3506 0.060 - 0.119: 869 0.119 - 0.179: 231 0.179 - 0.238: 35 0.238 - 0.298: 7 Chirality restraints: 4648 Sorted by residual: chirality pdb=" CA ARG E 274 " pdb=" N ARG E 274 " pdb=" C ARG E 274 " pdb=" CB ARG E 274 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CA ARG G 274 " pdb=" N ARG G 274 " pdb=" C ARG G 274 " pdb=" CB ARG G 274 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" CA ARG D 274 " pdb=" N ARG D 274 " pdb=" C ARG D 274 " pdb=" CB ARG D 274 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.19e+00 ... (remaining 4645 not shown) Planarity restraints: 5187 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG J 22 " -0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C ARG J 22 " 0.060 2.00e-02 2.50e+03 pdb=" O ARG J 22 " -0.023 2.00e-02 2.50e+03 pdb=" N LEU J 23 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG M 22 " 0.017 2.00e-02 2.50e+03 3.44e-02 1.19e+01 pdb=" C ARG M 22 " -0.060 2.00e-02 2.50e+03 pdb=" O ARG M 22 " 0.022 2.00e-02 2.50e+03 pdb=" N LEU M 23 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG H 22 " -0.017 2.00e-02 2.50e+03 3.44e-02 1.18e+01 pdb=" C ARG H 22 " 0.059 2.00e-02 2.50e+03 pdb=" O ARG H 22 " -0.022 2.00e-02 2.50e+03 pdb=" N LEU H 23 " -0.020 2.00e-02 2.50e+03 ... (remaining 5184 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 10463 2.87 - 3.38: 27538 3.38 - 3.88: 49558 3.88 - 4.39: 57885 4.39 - 4.90: 98284 Nonbonded interactions: 243728 Sorted by model distance: nonbonded pdb=" O GLU K 64 " pdb=" OG SER K 65 " model vdw 2.360 3.040 nonbonded pdb=" O GLU I 64 " pdb=" OG SER I 65 " model vdw 2.361 3.040 nonbonded pdb=" O GLU H 64 " pdb=" OG SER H 65 " model vdw 2.361 3.040 nonbonded pdb=" O GLU N 64 " pdb=" OG SER N 65 " model vdw 2.361 3.040 nonbonded pdb=" O GLU M 64 " pdb=" OG SER M 65 " model vdw 2.361 3.040 ... (remaining 243723 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'N' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' } 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: 9.840 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: 0.380 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 25.230 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 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 : 0.007 0.043 29890 Z= 0.486 Angle : 0.934 7.045 40404 Z= 0.646 Chirality : 0.060 0.298 4648 Planarity : 0.008 0.113 5187 Dihedral : 12.927 107.442 11305 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 0.03 % Allowed : 8.17 % Favored : 91.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.14), residues: 3731 helix: 0.46 (0.13), residues: 1680 sheet: 0.36 (0.20), residues: 714 loop : 0.34 (0.16), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 137 TYR 0.022 0.002 TYR B 263 PHE 0.032 0.002 PHE F 211 TRP 0.019 0.006 TRP J 161 HIS 0.001 0.001 HIS E 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00677 / 0.49 (29890) covalent geometry : angle 0.93368 / 0.65 (40404) hydrogen bonds : bond 0.17641 / 11.54 ( 1421) hydrogen bonds : angle 6.88509 / 4.84 ( 4179) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7462 Ramachandran restraints generated. 3731 Oldfield, 0 Emsley, 3731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7462 Ramachandran restraints generated. 3731 Oldfield, 0 Emsley, 3731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 3157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 585 time to evaluate : 1.221 Fit side-chains REVERT: A 70 LEU cc_start: 0.7832 (mp) cc_final: 0.7571 (mt) REVERT: A 156 MET cc_start: 0.8109 (mmt) cc_final: 0.7825 (mmp) REVERT: A 164 LYS cc_start: 0.7904 (mtmm) cc_final: 0.7504 (tptp) REVERT: B 16 ASP cc_start: 0.8026 (m-30) cc_final: 0.7790 (m-30) REVERT: B 70 LEU cc_start: 0.7801 (mp) cc_final: 0.7421 (mt) REVERT: B 164 LYS cc_start: 0.7985 (mtmm) cc_final: 0.7588 (tmmt) REVERT: B 240 ASP cc_start: 0.8367 (m-30) cc_final: 0.7822 (m-30) REVERT: C 16 ASP cc_start: 0.7724 (m-30) cc_final: 0.7451 (m-30) REVERT: C 43 MET cc_start: 0.8734 (mtp) cc_final: 0.8380 (mtp) REVERT: C 70 LEU cc_start: 0.7850 (mp) cc_final: 0.7630 (mt) REVERT: C 164 LYS cc_start: 0.7796 (mtmm) cc_final: 0.7416 (tptt) REVERT: C 240 ASP cc_start: 0.8322 (m-30) cc_final: 0.8002 (t0) REVERT: C 241 GLN cc_start: 0.8427 (tt0) cc_final: 0.7812 (tt0) REVERT: C 272 PHE cc_start: 0.7990 (m-80) cc_final: 0.7743 (m-80) REVERT: D 16 ASP cc_start: 0.7912 (m-30) cc_final: 0.7631 (m-30) REVERT: D 61 ASP cc_start: 0.8089 (t0) cc_final: 0.7885 (t0) REVERT: D 156 MET cc_start: 0.8188 (mmt) cc_final: 0.7944 (mmm) REVERT: D 164 LYS cc_start: 0.8074 (mtmm) cc_final: 0.7711 (tptt) REVERT: D 224 ARG cc_start: 0.7953 (ttm-80) cc_final: 0.7646 (ttt-90) REVERT: D 242 ILE cc_start: 0.8573 (mm) cc_final: 0.8318 (mm) REVERT: E 16 ASP cc_start: 0.7796 (m-30) cc_final: 0.7489 (m-30) REVERT: E 70 LEU cc_start: 0.7884 (mp) cc_final: 0.7512 (mt) REVERT: E 164 LYS cc_start: 0.8054 (mtmm) cc_final: 0.7722 (tmtt) REVERT: E 193 LEU cc_start: 0.7985 (mt) cc_final: 0.7728 (mt) REVERT: F 13 THR cc_start: 0.7546 (p) cc_final: 0.7218 (p) REVERT: F 70 LEU cc_start: 0.7934 (mp) cc_final: 0.7719 (mt) REVERT: F 156 MET cc_start: 0.8066 (mmt) cc_final: 0.7719 (mmp) REVERT: F 164 LYS cc_start: 0.7763 (mtmm) cc_final: 0.7374 (tptt) REVERT: F 240 ASP cc_start: 0.8296 (m-30) cc_final: 0.7897 (m-30) REVERT: G 16 ASP cc_start: 0.7858 (m-30) cc_final: 0.7599 (m-30) REVERT: G 156 MET cc_start: 0.8079 (mmt) cc_final: 0.7691 (mmp) REVERT: G 164 LYS cc_start: 0.8040 (mtmm) cc_final: 0.7603 (tmmt) REVERT: H 61 ILE cc_start: 0.7308 (mt) cc_final: 0.7038 (tp) REVERT: H 92 ASN cc_start: 0.7957 (m-40) cc_final: 0.7451 (m-40) REVERT: H 146 LYS cc_start: 0.8467 (ptpp) cc_final: 0.7587 (pttt) REVERT: H 174 MET cc_start: 0.7201 (mmm) cc_final: 0.6914 (mmm) REVERT: H 179 ASP cc_start: 0.7329 (t0) cc_final: 0.7127 (m-30) REVERT: H 204 LYS cc_start: 0.7754 (tppp) cc_final: 0.7072 (tptp) REVERT: H 218 LYS cc_start: 0.8224 (mmmt) cc_final: 0.7573 (mttp) REVERT: H 228 GLU cc_start: 0.7500 (mp0) cc_final: 0.7220 (mp0) REVERT: N 22 ARG cc_start: 0.7607 (ptp-110) cc_final: 0.7082 (mtm-85) REVERT: N 55 ARG cc_start: 0.7204 (mtt90) cc_final: 0.6933 (mtt180) REVERT: N 64 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7493 (tp30) REVERT: N 92 ASN cc_start: 0.8173 (m-40) cc_final: 0.7771 (m-40) REVERT: N 146 LYS cc_start: 0.8548 (ptpp) cc_final: 0.7593 (pttt) REVERT: N 203 GLU cc_start: 0.7446 (pm20) cc_final: 0.7195 (pm20) REVERT: N 204 LYS cc_start: 0.7843 (tppp) cc_final: 0.7306 (tptt) REVERT: N 218 LYS cc_start: 0.8282 (mmmt) cc_final: 0.7610 (mttp) REVERT: I 61 ILE cc_start: 0.7478 (mt) cc_final: 0.7253 (tp) REVERT: I 92 ASN cc_start: 0.8228 (m-40) cc_final: 0.7789 (m-40) REVERT: I 146 LYS cc_start: 0.8308 (ptpp) cc_final: 0.7566 (ptmm) REVERT: I 174 MET cc_start: 0.7264 (mmm) cc_final: 0.6828 (mmt) REVERT: I 185 MET cc_start: 0.7330 (ptp) cc_final: 0.6920 (ptm) REVERT: I 202 MET cc_start: 0.7050 (mtp) cc_final: 0.6784 (mtp) REVERT: I 204 LYS cc_start: 0.7872 (tppp) cc_final: 0.7281 (tptp) REVERT: I 216 THR cc_start: 0.8290 (p) cc_final: 0.8000 (p) REVERT: J 18 SER cc_start: 0.8134 (t) cc_final: 0.7858 (p) REVERT: J 22 ARG cc_start: 0.7814 (ptp-110) cc_final: 0.7246 (mtm-85) REVERT: J 55 ARG cc_start: 0.7255 (mtt90) cc_final: 0.6998 (mtt180) REVERT: J 92 ASN cc_start: 0.8283 (m-40) cc_final: 0.7903 (m-40) REVERT: J 204 LYS cc_start: 0.7746 (tppp) cc_final: 0.7251 (tptp) REVERT: J 208 GLU cc_start: 0.7261 (mp0) cc_final: 0.7060 (mm-30) REVERT: J 221 LYS cc_start: 0.7940 (tppt) cc_final: 0.7268 (mmmt) REVERT: J 228 GLU cc_start: 0.7713 (mp0) cc_final: 0.7471 (mp0) REVERT: J 238 MET cc_start: 0.5810 (mmp) cc_final: 0.5584 (mmm) REVERT: K 22 ARG cc_start: 0.7626 (ptp-110) cc_final: 0.7346 (ttm110) REVERT: K 55 ARG cc_start: 0.7122 (mtt90) cc_final: 0.6886 (mtt180) REVERT: K 64 GLU cc_start: 0.7561 (mt-10) cc_final: 0.7240 (tp30) REVERT: K 92 ASN cc_start: 0.8250 (m-40) cc_final: 0.7735 (m-40) REVERT: K 146 LYS cc_start: 0.8270 (ptpp) cc_final: 0.7449 (pttm) REVERT: K 202 MET cc_start: 0.7052 (mtp) cc_final: 0.6815 (mtp) REVERT: K 204 LYS cc_start: 0.7986 (tppp) cc_final: 0.7411 (tptp) REVERT: K 228 GLU cc_start: 0.7566 (mp0) cc_final: 0.7292 (mp0) REVERT: L 146 LYS cc_start: 0.8390 (ptpp) cc_final: 0.7553 (ptmt) REVERT: L 182 ARG cc_start: 0.7918 (mtm110) cc_final: 0.7644 (mtm-85) REVERT: L 204 LYS cc_start: 0.7824 (tppp) cc_final: 0.7145 (tptp) REVERT: L 228 GLU cc_start: 0.7455 (mp0) cc_final: 0.7195 (mp0) REVERT: M 10 TYR cc_start: 0.6147 (m-80) cc_final: 0.5287 (m-80) REVERT: M 22 ARG cc_start: 0.7589 (ptp-110) cc_final: 0.7253 (ttm110) REVERT: M 55 ARG cc_start: 0.7058 (mtt90) cc_final: 0.6781 (mtt180) REVERT: M 61 ILE cc_start: 0.7386 (mt) cc_final: 0.7100 (tp) REVERT: M 92 ASN cc_start: 0.8271 (m-40) cc_final: 0.7761 (m-40) REVERT: M 146 LYS cc_start: 0.8537 (ptpp) cc_final: 0.7629 (pttt) REVERT: M 204 LYS cc_start: 0.7894 (tppp) cc_final: 0.7181 (tptp) REVERT: M 218 LYS cc_start: 0.8240 (mmmt) cc_final: 0.7992 (mmmt) REVERT: M 228 GLU cc_start: 0.7317 (mp0) cc_final: 0.7039 (mp0) outliers start: 1 outliers final: 0 residues processed: 586 average time/residue: 0.2525 time to fit residues: 213.1466 Evaluate side-chains 388 residues out of total 3157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 388 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 216 ASN A 241 GLN B 241 GLN C 216 ASN E 73 ASN F 73 ASN G 241 GLN H 125 HIS H 171 ASN N 171 ASN I 171 ASN J 171 ASN K 171 ASN L 171 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.093674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.079915 restraints weight = 49570.495| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.85 r_work: 0.2993 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 29890 Z= 0.155 Angle : 0.521 6.462 40404 Z= 0.274 Chirality : 0.045 0.231 4648 Planarity : 0.004 0.042 5187 Dihedral : 4.222 49.010 4123 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.19 % Allowed : 0.29 % Favored : 99.52 % Rotamer: Outliers : 1.33 % Allowed : 8.36 % Favored : 90.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.14), residues: 3731 helix: 1.63 (0.13), residues: 1666 sheet: 0.53 (0.20), residues: 721 loop : 0.64 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 224 TYR 0.022 0.002 TYR C 45 PHE 0.011 0.001 PHE M 222 TRP 0.014 0.003 TRP H 161 HIS 0.006 0.001 HIS N 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (29890) covalent geometry : angle 0.52091 / 0.27 (40404) hydrogen bonds : bond 0.04384 / 2.93 ( 1421) hydrogen bonds : angle 4.90634 / 3.48 ( 4179) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7462 Ramachandran restraints generated. 3731 Oldfield, 0 Emsley, 3731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7462 Ramachandran restraints generated. 3731 Oldfield, 0 Emsley, 3731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 3157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 406 time to evaluate : 1.084 Fit side-chains REVERT: A 70 LEU cc_start: 0.8036 (mp) cc_final: 0.7834 (mt) REVERT: A 156 MET cc_start: 0.8467 (mmt) cc_final: 0.8214 (mmp) REVERT: A 266 GLN cc_start: 0.8330 (mm110) cc_final: 0.8072 (mm110) REVERT: A 286 ARG cc_start: 0.8306 (mtp85) cc_final: 0.8085 (mtp85) REVERT: B 5 LYS cc_start: 0.8738 (mmtt) cc_final: 0.7995 (tttt) REVERT: B 16 ASP cc_start: 0.8160 (m-30) cc_final: 0.7930 (m-30) REVERT: B 70 LEU cc_start: 0.7971 (mp) cc_final: 0.7701 (mt) REVERT: B 164 LYS cc_start: 0.8264 (mtmm) cc_final: 0.7750 (tmmt) REVERT: B 240 ASP cc_start: 0.8233 (m-30) cc_final: 0.7876 (m-30) REVERT: B 241 GLN cc_start: 0.8852 (tt0) cc_final: 0.8616 (tt0) REVERT: B 292 GLU cc_start: 0.7349 (pm20) cc_final: 0.7072 (pm20) REVERT: C 5 LYS cc_start: 0.8616 (mmtt) cc_final: 0.7843 (tttt) REVERT: C 16 ASP cc_start: 0.7844 (m-30) cc_final: 0.7630 (m-30) REVERT: C 31 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8316 (mtmt) REVERT: C 164 LYS cc_start: 0.8243 (mtmm) cc_final: 0.7664 (tptt) REVERT: C 216 ASN cc_start: 0.8714 (OUTLIER) cc_final: 0.7806 (t0) REVERT: C 241 GLN cc_start: 0.8519 (tt0) cc_final: 0.8155 (tt0) REVERT: C 266 GLN cc_start: 0.8396 (mm110) cc_final: 0.7850 (mm110) REVERT: C 272 PHE cc_start: 0.8061 (m-80) cc_final: 0.7852 (m-80) REVERT: D 16 ASP cc_start: 0.8005 (m-30) cc_final: 0.7675 (m-30) REVERT: D 61 ASP cc_start: 0.8270 (t0) cc_final: 0.8042 (t0) REVERT: D 164 LYS cc_start: 0.8447 (mtmm) cc_final: 0.7943 (tptt) REVERT: D 240 ASP cc_start: 0.8278 (m-30) cc_final: 0.7828 (m-30) REVERT: D 241 GLN cc_start: 0.8916 (tt0) cc_final: 0.8703 (tt0) REVERT: D 242 ILE cc_start: 0.8628 (mm) cc_final: 0.8384 (mm) REVERT: D 292 GLU cc_start: 0.7266 (pm20) cc_final: 0.7034 (pm20) REVERT: E 156 MET cc_start: 0.8296 (mmm) cc_final: 0.7940 (mmp) REVERT: E 240 ASP cc_start: 0.8217 (m-30) cc_final: 0.8009 (m-30) REVERT: E 280 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8370 (tt0) REVERT: F 5 LYS cc_start: 0.8698 (mmtt) cc_final: 0.7924 (tttt) REVERT: F 154 ASP cc_start: 0.7982 (m-30) cc_final: 0.7666 (m-30) REVERT: F 156 MET cc_start: 0.8360 (mmt) cc_final: 0.8050 (mmp) REVERT: F 164 LYS cc_start: 0.8185 (mtmm) cc_final: 0.7632 (tptt) REVERT: F 240 ASP cc_start: 0.8267 (m-30) cc_final: 0.7865 (m-30) REVERT: F 266 GLN cc_start: 0.8297 (mm110) cc_final: 0.8086 (mm110) REVERT: G 5 LYS cc_start: 0.8692 (mmtt) cc_final: 0.7916 (tttt) REVERT: G 16 ASP cc_start: 0.7924 (m-30) cc_final: 0.7709 (m-30) REVERT: G 156 MET cc_start: 0.8347 (mmt) cc_final: 0.8016 (mmp) REVERT: G 164 LYS cc_start: 0.8418 (mtmm) cc_final: 0.7833 (tmmt) REVERT: G 240 ASP cc_start: 0.8093 (m-30) cc_final: 0.7869 (m-30) REVERT: H 92 ASN cc_start: 0.8785 (m-40) cc_final: 0.8398 (m-40) REVERT: H 146 LYS cc_start: 0.8695 (ptpp) cc_final: 0.8303 (pttt) REVERT: H 174 MET cc_start: 0.8401 (mmm) cc_final: 0.7991 (mmt) REVERT: H 204 LYS cc_start: 0.7978 (tppp) cc_final: 0.7499 (tptp) REVERT: H 228 GLU cc_start: 0.8095 (mp0) cc_final: 0.7828 (mp0) REVERT: N 22 ARG cc_start: 0.7946 (ptp-110) cc_final: 0.7676 (ttm110) REVERT: N 55 ARG cc_start: 0.7663 (mtt90) cc_final: 0.7412 (mtt180) REVERT: N 146 LYS cc_start: 0.8746 (ptpp) cc_final: 0.8301 (pttt) REVERT: N 204 LYS cc_start: 0.8198 (tppp) cc_final: 0.7674 (tptt) REVERT: I 35 ARG cc_start: 0.7960 (ttp80) cc_final: 0.7716 (mtm110) REVERT: I 146 LYS cc_start: 0.8648 (ptpp) cc_final: 0.8321 (ptmm) REVERT: I 182 ARG cc_start: 0.8414 (mtm110) cc_final: 0.8193 (mtm110) REVERT: I 185 MET cc_start: 0.8364 (ptp) cc_final: 0.8021 (ptm) REVERT: I 204 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7744 (tptp) REVERT: J 22 ARG cc_start: 0.8189 (ptp-110) cc_final: 0.7982 (ptp-110) REVERT: J 55 ARG cc_start: 0.7666 (mtt90) cc_final: 0.7377 (mtt180) REVERT: J 92 ASN cc_start: 0.8992 (m-40) cc_final: 0.8690 (m-40) REVERT: J 146 LYS cc_start: 0.8732 (ptpp) cc_final: 0.8382 (ptmm) REVERT: J 204 LYS cc_start: 0.8085 (tppp) cc_final: 0.7645 (tptt) REVERT: J 228 GLU cc_start: 0.8135 (mp0) cc_final: 0.7897 (mp0) REVERT: K 45 LYS cc_start: 0.8883 (OUTLIER) cc_final: 0.8537 (mtmm) REVERT: K 55 ARG cc_start: 0.7740 (mtt90) cc_final: 0.7457 (mtt180) REVERT: K 146 LYS cc_start: 0.8563 (ptpp) cc_final: 0.8218 (ptmm) REVERT: K 203 GLU cc_start: 0.7782 (pm20) cc_final: 0.7343 (pm20) REVERT: K 204 LYS cc_start: 0.8229 (tppp) cc_final: 0.7664 (tptp) REVERT: K 228 GLU cc_start: 0.7965 (mp0) cc_final: 0.7764 (mp0) REVERT: L 146 LYS cc_start: 0.8756 (ptpp) cc_final: 0.8385 (ptmt) REVERT: L 204 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7627 (tptp) REVERT: L 228 GLU cc_start: 0.8152 (mp0) cc_final: 0.7934 (mp0) REVERT: M 22 ARG cc_start: 0.7997 (ptp-110) cc_final: 0.7730 (ttm110) REVERT: M 45 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8545 (mtmm) REVERT: M 55 ARG cc_start: 0.7530 (mtt90) cc_final: 0.7272 (mtt180) REVERT: M 61 ILE cc_start: 0.8460 (mt) cc_final: 0.8231 (tp) REVERT: M 92 ASN cc_start: 0.8794 (m-40) cc_final: 0.8469 (m-40) REVERT: M 146 LYS cc_start: 0.8769 (ptpp) cc_final: 0.8348 (pttt) REVERT: M 204 LYS cc_start: 0.8150 (tppp) cc_final: 0.7559 (tptp) REVERT: M 228 GLU cc_start: 0.7945 (mp0) cc_final: 0.7512 (mp0) outliers start: 42 outliers final: 15 residues processed: 436 average time/residue: 0.2556 time to fit residues: 160.0581 Evaluate side-chains 384 residues out of total 3157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 363 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain C residue 31 LYS Chi-restraints excluded: chain C residue 216 ASN Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain N residue 172 THR Chi-restraints excluded: chain I residue 172 THR Chi-restraints excluded: chain I residue 204 LYS Chi-restraints excluded: chain J residue 172 THR Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 45 LYS Chi-restraints excluded: chain K residue 172 THR Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 61 ILE Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain L residue 204 LYS Chi-restraints excluded: chain M residue 45 LYS Chi-restraints excluded: chain M residue 172 THR Chi-restraints excluded: chain M residue 219 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 220 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 283 optimal weight: 0.9990 chunk 143 optimal weight: 1.9990 chunk 334 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 345 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 chunk 131 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 241 GLN C 73 ASN E 73 ASN E 259 GLN F 73 ASN G 266 GLN J 125 HIS K 125 HIS M 125 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.092370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.078659 restraints weight = 49495.774| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.86 r_work: 0.2974 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 29890 Z= 0.154 Angle : 0.493 5.734 40404 Z= 0.259 Chirality : 0.044 0.158 4648 Planarity : 0.004 0.036 5187 Dihedral : 4.446 57.034 4123 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Rotamer: Outliers : 1.17 % Allowed : 9.00 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.14), residues: 3731 helix: 1.89 (0.13), residues: 1666 sheet: 0.42 (0.20), residues: 728 loop : 0.69 (0.17), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 22 TYR 0.024 0.002 TYR F 45 PHE 0.012 0.001 PHE M 222 TRP 0.009 0.002 TRP N 161 HIS 0.005 0.001 HIS I 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.15 (29890) covalent geometry : angle 0.49340 / 0.26 (40404) hydrogen bonds : bond 0.04106 / 2.75 ( 1421) hydrogen bonds : angle 4.67156 / 3.31 ( 4179) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7462 Ramachandran restraints generated. 3731 Oldfield, 0 Emsley, 3731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7462 Ramachandran restraints generated. 3731 Oldfield, 0 Emsley, 3731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 3157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 379 time to evaluate : 1.160 Fit side-chains REVERT: A 5 LYS cc_start: 0.8744 (mmtt) cc_final: 0.7975 (tttt) REVERT: A 70 LEU cc_start: 0.8174 (mp) cc_final: 0.7972 (mt) REVERT: A 156 MET cc_start: 0.8480 (mmt) cc_final: 0.8177 (mmp) REVERT: A 266 GLN cc_start: 0.8397 (mm110) cc_final: 0.8036 (mm110) REVERT: B 5 LYS cc_start: 0.8802 (mmtt) cc_final: 0.8070 (tttp) REVERT: B 70 LEU cc_start: 0.8115 (mp) cc_final: 0.7824 (mt) REVERT: B 164 LYS cc_start: 0.8471 (mtmm) cc_final: 0.8044 (tmtt) REVERT: B 240 ASP cc_start: 0.8123 (m-30) cc_final: 0.7868 (m-30) REVERT: B 266 GLN cc_start: 0.8386 (mm110) cc_final: 0.8074 (mm-40) REVERT: B 292 GLU cc_start: 0.7370 (pm20) cc_final: 0.7112 (pm20) REVERT: C 5 LYS cc_start: 0.8609 (mmtt) cc_final: 0.7843 (tttt) REVERT: C 16 ASP cc_start: 0.7913 (m-30) cc_final: 0.7666 (m-30) REVERT: C 31 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8278 (mtmt) REVERT: C 163 MET cc_start: 0.8338 (ptp) cc_final: 0.8103 (ptm) REVERT: D 16 ASP cc_start: 0.8057 (m-30) cc_final: 0.7736 (m-30) REVERT: D 164 LYS cc_start: 0.8555 (mtmm) cc_final: 0.7952 (tptt) REVERT: D 240 ASP cc_start: 0.8223 (m-30) cc_final: 0.7915 (m-30) REVERT: D 241 GLN cc_start: 0.8934 (tt0) cc_final: 0.8710 (tt0) REVERT: D 242 ILE cc_start: 0.8628 (mm) cc_final: 0.8421 (mm) REVERT: E 70 LEU cc_start: 0.8299 (mt) cc_final: 0.8072 (tp) REVERT: E 156 MET cc_start: 0.8393 (mmm) cc_final: 0.8077 (mmp) REVERT: F 164 LYS cc_start: 0.8452 (mtmm) cc_final: 0.7824 (tptt) REVERT: F 240 ASP cc_start: 0.8184 (m-30) cc_final: 0.7902 (m-30) REVERT: G 5 LYS cc_start: 0.8679 (mmtt) cc_final: 0.7939 (tttt) REVERT: G 16 ASP cc_start: 0.7996 (m-30) cc_final: 0.7792 (m-30) REVERT: G 156 MET cc_start: 0.8428 (mmt) cc_final: 0.8100 (mmp) REVERT: G 240 ASP cc_start: 0.8064 (m-30) cc_final: 0.7840 (m-30) REVERT: H 92 ASN cc_start: 0.8747 (m-40) cc_final: 0.8346 (m-40) REVERT: H 146 LYS cc_start: 0.8680 (ptpp) cc_final: 0.8300 (pttt) REVERT: H 174 MET cc_start: 0.8450 (mmm) cc_final: 0.7929 (mmt) REVERT: H 204 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7527 (tptp) REVERT: H 228 GLU cc_start: 0.8110 (mp0) cc_final: 0.7888 (mp0) REVERT: N 12 ARG cc_start: 0.7441 (mpt180) cc_final: 0.7009 (mmt180) REVERT: N 22 ARG cc_start: 0.8216 (ptp-110) cc_final: 0.7899 (ttm110) REVERT: N 55 ARG cc_start: 0.7639 (mtt90) cc_final: 0.7369 (mtt180) REVERT: N 92 ASN cc_start: 0.8811 (m-40) cc_final: 0.8534 (m-40) REVERT: N 146 LYS cc_start: 0.8767 (ptpp) cc_final: 0.8392 (pttt) REVERT: N 204 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7601 (tptt) REVERT: I 10 TYR cc_start: 0.7299 (m-80) cc_final: 0.7047 (m-80) REVERT: I 35 ARG cc_start: 0.8085 (ttp80) cc_final: 0.7824 (mtm110) REVERT: I 146 LYS cc_start: 0.8624 (ptpp) cc_final: 0.8295 (ptmm) REVERT: I 185 MET cc_start: 0.8466 (ptp) cc_final: 0.8085 (ptm) REVERT: I 204 LYS cc_start: 0.8293 (tppp) cc_final: 0.7848 (tptp) REVERT: J 35 ARG cc_start: 0.8058 (ttp80) cc_final: 0.7803 (mtm-85) REVERT: J 92 ASN cc_start: 0.8984 (m-40) cc_final: 0.8678 (m-40) REVERT: J 146 LYS cc_start: 0.8729 (ptpp) cc_final: 0.8410 (ptmm) REVERT: J 204 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7686 (tptt) REVERT: K 35 ARG cc_start: 0.8152 (ttp80) cc_final: 0.7827 (mtm-85) REVERT: K 45 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8554 (mtmm) REVERT: K 55 ARG cc_start: 0.7684 (mtt90) cc_final: 0.7395 (mtt180) REVERT: K 146 LYS cc_start: 0.8486 (ptpp) cc_final: 0.8205 (ptmm) REVERT: K 204 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.7794 (tptp) REVERT: K 218 LYS cc_start: 0.8670 (mmpt) cc_final: 0.8392 (mmtt) REVERT: K 221 LYS cc_start: 0.8839 (tppt) cc_final: 0.8519 (mmmt) REVERT: L 22 ARG cc_start: 0.7815 (ttm110) cc_final: 0.7361 (mtm-85) REVERT: L 35 ARG cc_start: 0.8100 (ttp80) cc_final: 0.7633 (mtm110) REVERT: L 146 LYS cc_start: 0.8746 (ptpp) cc_final: 0.8374 (ptmt) REVERT: L 204 LYS cc_start: 0.8190 (tppp) cc_final: 0.7628 (tptp) REVERT: L 228 GLU cc_start: 0.8131 (mp0) cc_final: 0.7925 (mp0) REVERT: M 10 TYR cc_start: 0.7227 (m-80) cc_final: 0.6693 (m-80) REVERT: M 35 ARG cc_start: 0.8207 (ttp80) cc_final: 0.7749 (mtp-110) REVERT: M 45 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8614 (mtmm) REVERT: M 55 ARG cc_start: 0.7453 (mtt90) cc_final: 0.7172 (mtt180) REVERT: M 61 ILE cc_start: 0.8592 (mt) cc_final: 0.8362 (tp) REVERT: M 92 ASN cc_start: 0.8741 (m-40) cc_final: 0.8487 (m-40) REVERT: M 146 LYS cc_start: 0.8802 (ptpp) cc_final: 0.8411 (pttt) REVERT: M 204 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7656 (tptp) outliers start: 37 outliers final: 20 residues processed: 405 average time/residue: 0.2570 time to fit residues: 150.0533 Evaluate side-chains 379 residues out of total 3157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 351 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain C residue 31 LYS Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain G residue 97 LYS Chi-restraints excluded: chain H residue 18 SER Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 204 LYS Chi-restraints excluded: chain N residue 172 THR Chi-restraints excluded: chain N residue 204 LYS Chi-restraints excluded: chain I residue 61 ILE Chi-restraints excluded: chain I residue 172 THR Chi-restraints excluded: chain J residue 172 THR Chi-restraints excluded: chain J residue 204 LYS Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 45 LYS Chi-restraints excluded: chain K residue 172 THR Chi-restraints excluded: chain K residue 204 LYS Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 61 ILE Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain M residue 45 LYS Chi-restraints excluded: chain M residue 172 THR Chi-restraints excluded: chain M residue 185 MET Chi-restraints excluded: chain M residue 204 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 82 optimal weight: 2.9990 chunk 298 optimal weight: 0.3980 chunk 125 optimal weight: 2.9990 chunk 182 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 285 optimal weight: 0.0770 chunk 1 optimal weight: 3.9990 chunk 248 optimal weight: 1.9990 chunk 349 optimal weight: 0.9980 chunk 207 optimal weight: 4.9990 overall best weight: 1.0942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 241 GLN C 216 ASN N 71 GLN K 71 GLN L 71 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.091454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.077677 restraints weight = 49457.942| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.88 r_work: 0.2952 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 29890 Z= 0.176 Angle : 0.500 5.740 40404 Z= 0.261 Chirality : 0.044 0.216 4648 Planarity : 0.004 0.050 5187 Dihedral : 4.466 53.833 4123 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Rotamer: Outliers : 1.33 % Allowed : 9.85 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.14), residues: 3731 helix: 1.84 (0.13), residues: 1673 sheet: 0.30 (0.20), residues: 728 loop : 0.71 (0.17), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 224 TYR 0.024 0.002 TYR B 45 PHE 0.013 0.001 PHE L 222 TRP 0.008 0.002 TRP L 161 HIS 0.005 0.001 HIS I 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.18 (29890) covalent geometry : angle 0.50046 / 0.26 (40404) hydrogen bonds : bond 0.04098 / 2.75 ( 1421) hydrogen bonds : angle 4.65691 / 3.30 ( 4179) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7462 Ramachandran restraints generated. 3731 Oldfield, 0 Emsley, 3731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7462 Ramachandran restraints generated. 3731 Oldfield, 0 Emsley, 3731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 3157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 379 time to evaluate : 1.028 Fit side-chains REVERT: A 5 LYS cc_start: 0.8786 (mmtt) cc_final: 0.7961 (tttt) REVERT: A 156 MET cc_start: 0.8483 (mmt) cc_final: 0.8142 (mmp) REVERT: B 5 LYS cc_start: 0.8799 (mmtt) cc_final: 0.8022 (tttt) REVERT: B 70 LEU cc_start: 0.8202 (mp) cc_final: 0.7884 (mt) REVERT: B 266 GLN cc_start: 0.8370 (mm110) cc_final: 0.8060 (mm-40) REVERT: B 292 GLU cc_start: 0.7342 (pm20) cc_final: 0.7135 (pm20) REVERT: C 5 LYS cc_start: 0.8590 (mmtt) cc_final: 0.7863 (tttt) REVERT: C 15 ASN cc_start: 0.7910 (p0) cc_final: 0.7683 (p0) REVERT: C 16 ASP cc_start: 0.8096 (m-30) cc_final: 0.7869 (m-30) REVERT: D 16 ASP cc_start: 0.8105 (m-30) cc_final: 0.7828 (m-30) REVERT: D 61 ASP cc_start: 0.8450 (t0) cc_final: 0.8212 (t0) REVERT: D 240 ASP cc_start: 0.8215 (m-30) cc_final: 0.7913 (m-30) REVERT: D 241 GLN cc_start: 0.8886 (tt0) cc_final: 0.8654 (tt0) REVERT: E 5 LYS cc_start: 0.8596 (mmtt) cc_final: 0.7957 (tttt) REVERT: E 70 LEU cc_start: 0.8340 (mt) cc_final: 0.8139 (tp) REVERT: E 156 MET cc_start: 0.8482 (mmm) cc_final: 0.8125 (mmp) REVERT: F 154 ASP cc_start: 0.8005 (m-30) cc_final: 0.7767 (m-30) REVERT: F 164 LYS cc_start: 0.8784 (mtmm) cc_final: 0.8143 (tptt) REVERT: F 240 ASP cc_start: 0.8130 (m-30) cc_final: 0.7855 (m-30) REVERT: G 5 LYS cc_start: 0.8690 (mmtt) cc_final: 0.7962 (tttt) REVERT: G 15 ASN cc_start: 0.7916 (p0) cc_final: 0.7705 (p0) REVERT: G 156 MET cc_start: 0.8459 (mmt) cc_final: 0.8072 (mmp) REVERT: G 240 ASP cc_start: 0.8174 (m-30) cc_final: 0.7898 (m-30) REVERT: H 35 ARG cc_start: 0.8268 (ttp80) cc_final: 0.7870 (mtm-85) REVERT: H 92 ASN cc_start: 0.8748 (m-40) cc_final: 0.8346 (m-40) REVERT: H 146 LYS cc_start: 0.8668 (ptpp) cc_final: 0.8313 (pttt) REVERT: H 174 MET cc_start: 0.8385 (mmm) cc_final: 0.7800 (mmt) REVERT: H 204 LYS cc_start: 0.8026 (OUTLIER) cc_final: 0.7518 (tptp) REVERT: H 228 GLU cc_start: 0.7991 (mp0) cc_final: 0.7748 (mp0) REVERT: N 12 ARG cc_start: 0.7741 (mpt180) cc_final: 0.7369 (mmt180) REVERT: N 22 ARG cc_start: 0.8259 (ptp-110) cc_final: 0.8003 (ttm110) REVERT: N 55 ARG cc_start: 0.7630 (mtt90) cc_final: 0.7371 (mtt180) REVERT: N 92 ASN cc_start: 0.8816 (m-40) cc_final: 0.8517 (m-40) REVERT: N 146 LYS cc_start: 0.8776 (ptpp) cc_final: 0.8373 (pttt) REVERT: N 204 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7567 (tptt) REVERT: I 10 TYR cc_start: 0.7333 (m-80) cc_final: 0.7085 (m-80) REVERT: I 35 ARG cc_start: 0.8141 (ttp80) cc_final: 0.7836 (mtm110) REVERT: I 146 LYS cc_start: 0.8584 (ptpp) cc_final: 0.8231 (ptmm) REVERT: I 185 MET cc_start: 0.8447 (ptp) cc_final: 0.8088 (ptm) REVERT: I 204 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.7935 (tptp) REVERT: J 35 ARG cc_start: 0.8237 (ttp80) cc_final: 0.7989 (mtm-85) REVERT: J 92 ASN cc_start: 0.8893 (m-40) cc_final: 0.8584 (m-40) REVERT: J 146 LYS cc_start: 0.8729 (ptpp) cc_final: 0.8366 (ptmm) REVERT: J 204 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7807 (tptp) REVERT: K 45 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8621 (mtmm) REVERT: K 55 ARG cc_start: 0.7670 (mtt90) cc_final: 0.7371 (mtt180) REVERT: K 146 LYS cc_start: 0.8487 (ptpp) cc_final: 0.8129 (ptmm) REVERT: K 204 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.7796 (tptp) REVERT: K 218 LYS cc_start: 0.8670 (mmpt) cc_final: 0.8457 (mmtt) REVERT: K 221 LYS cc_start: 0.8867 (tppt) cc_final: 0.8536 (mmmt) REVERT: L 35 ARG cc_start: 0.8136 (ttp80) cc_final: 0.7794 (mtm110) REVERT: L 146 LYS cc_start: 0.8730 (ptpp) cc_final: 0.8384 (ptmt) REVERT: L 203 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7109 (pm20) REVERT: L 204 LYS cc_start: 0.8216 (tppp) cc_final: 0.7578 (tptp) REVERT: L 228 GLU cc_start: 0.8022 (mp0) cc_final: 0.7792 (mp0) REVERT: M 10 TYR cc_start: 0.7374 (m-80) cc_final: 0.6941 (m-80) REVERT: M 35 ARG cc_start: 0.8149 (ttp80) cc_final: 0.7892 (mtp-110) REVERT: M 45 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.8629 (mtmm) REVERT: M 55 ARG cc_start: 0.7417 (mtt90) cc_final: 0.7142 (mtt180) REVERT: M 61 ILE cc_start: 0.8596 (mt) cc_final: 0.8349 (tp) REVERT: M 92 ASN cc_start: 0.8738 (m-40) cc_final: 0.8465 (m-40) REVERT: M 146 LYS cc_start: 0.8742 (ptpp) cc_final: 0.8330 (pttt) REVERT: M 203 GLU cc_start: 0.7678 (pm20) cc_final: 0.7414 (pm20) REVERT: M 204 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7537 (tptp) outliers start: 42 outliers final: 29 residues processed: 411 average time/residue: 0.2438 time to fit residues: 146.3964 Evaluate side-chains 393 residues out of total 3157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 355 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain G residue 97 LYS Chi-restraints excluded: chain G residue 179 ILE Chi-restraints excluded: chain G residue 291 ILE Chi-restraints excluded: chain H residue 18 SER Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 204 LYS Chi-restraints excluded: chain N residue 172 THR Chi-restraints excluded: chain N residue 204 LYS Chi-restraints excluded: chain I residue 61 ILE Chi-restraints excluded: chain I residue 172 THR Chi-restraints excluded: chain I residue 204 LYS Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 172 THR Chi-restraints excluded: chain J residue 202 MET Chi-restraints excluded: chain J residue 204 LYS Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 45 LYS Chi-restraints excluded: chain K residue 172 THR Chi-restraints excluded: chain K residue 204 LYS Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 56 ILE Chi-restraints excluded: chain L residue 61 ILE Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain L residue 203 GLU Chi-restraints excluded: chain M residue 45 LYS Chi-restraints excluded: chain M residue 172 THR Chi-restraints excluded: chain M residue 204 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 158 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 326 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 129 optimal weight: 0.6980 chunk 264 optimal weight: 1.9990 chunk 223 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 98 optimal weight: 0.5980 chunk 266 optimal weight: 0.9980 chunk 339 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 241 GLN E 73 ASN E 266 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.092145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.078431 restraints weight = 49246.096| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 1.87 r_work: 0.2946 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 29890 Z= 0.130 Angle : 0.466 5.332 40404 Z= 0.244 Chirality : 0.043 0.157 4648 Planarity : 0.004 0.044 5187 Dihedral : 4.269 46.995 4123 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 1.27 % Allowed : 10.07 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.14), residues: 3731 helix: 1.98 (0.13), residues: 1666 sheet: 0.25 (0.19), residues: 728 loop : 0.70 (0.17), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 286 TYR 0.021 0.001 TYR E 45 PHE 0.013 0.001 PHE L 222 TRP 0.008 0.002 TRP N 161 HIS 0.003 0.001 HIS I 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (29890) covalent geometry : angle 0.46574 / 0.24 (40404) hydrogen bonds : bond 0.03716 / 2.49 ( 1421) hydrogen bonds : angle 4.51495 / 3.20 ( 4179) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7462 Ramachandran restraints generated. 3731 Oldfield, 0 Emsley, 3731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7462 Ramachandran restraints generated. 3731 Oldfield, 0 Emsley, 3731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 3157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 370 time to evaluate : 1.261 Fit side-chains REVERT: A 5 LYS cc_start: 0.8771 (mmtt) cc_final: 0.7991 (tttt) REVERT: A 156 MET cc_start: 0.8517 (mmt) cc_final: 0.8160 (mmp) REVERT: B 5 LYS cc_start: 0.8827 (mmtt) cc_final: 0.8069 (tmtt) REVERT: B 70 LEU cc_start: 0.8159 (mp) cc_final: 0.7856 (mt) REVERT: B 241 GLN cc_start: 0.8705 (tt0) cc_final: 0.8437 (tt0) REVERT: C 5 LYS cc_start: 0.8625 (mmtt) cc_final: 0.7881 (tttt) REVERT: C 15 ASN cc_start: 0.7844 (p0) cc_final: 0.7633 (p0) REVERT: C 16 ASP cc_start: 0.8054 (m-30) cc_final: 0.7825 (m-30) REVERT: C 31 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8284 (mtmt) REVERT: C 163 MET cc_start: 0.8423 (ptp) cc_final: 0.8163 (ptm) REVERT: C 294 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7875 (mp0) REVERT: D 16 ASP cc_start: 0.8083 (m-30) cc_final: 0.7801 (m-30) REVERT: D 61 ASP cc_start: 0.8415 (t0) cc_final: 0.8184 (t0) REVERT: D 240 ASP cc_start: 0.8200 (m-30) cc_final: 0.7870 (m-30) REVERT: D 241 GLN cc_start: 0.8836 (tt0) cc_final: 0.8562 (tt0) REVERT: E 5 LYS cc_start: 0.8585 (mmtt) cc_final: 0.7957 (tttt) REVERT: E 156 MET cc_start: 0.8513 (mmm) cc_final: 0.8118 (mmp) REVERT: F 75 LEU cc_start: 0.8318 (mp) cc_final: 0.8072 (mp) REVERT: F 164 LYS cc_start: 0.8801 (mtmm) cc_final: 0.8165 (tptt) REVERT: F 240 ASP cc_start: 0.8097 (m-30) cc_final: 0.7814 (m-30) REVERT: G 5 LYS cc_start: 0.8737 (mmtt) cc_final: 0.7965 (tttt) REVERT: G 156 MET cc_start: 0.8438 (mmt) cc_final: 0.8044 (mmp) REVERT: G 163 MET cc_start: 0.8520 (ptp) cc_final: 0.8299 (ptm) REVERT: G 240 ASP cc_start: 0.8168 (m-30) cc_final: 0.7818 (m-30) REVERT: H 35 ARG cc_start: 0.8233 (ttp80) cc_final: 0.7923 (mtp-110) REVERT: H 92 ASN cc_start: 0.8775 (m-40) cc_final: 0.8368 (m-40) REVERT: H 146 LYS cc_start: 0.8690 (ptpp) cc_final: 0.8306 (pttt) REVERT: H 204 LYS cc_start: 0.8060 (OUTLIER) cc_final: 0.7555 (tptp) REVERT: H 228 GLU cc_start: 0.7983 (mp0) cc_final: 0.7750 (mp0) REVERT: N 22 ARG cc_start: 0.8267 (ptp-110) cc_final: 0.8006 (ttm110) REVERT: N 55 ARG cc_start: 0.7627 (mtt90) cc_final: 0.7379 (mtt180) REVERT: N 64 GLU cc_start: 0.7922 (tt0) cc_final: 0.7616 (tp30) REVERT: N 92 ASN cc_start: 0.8810 (m-40) cc_final: 0.8509 (m-40) REVERT: N 146 LYS cc_start: 0.8790 (ptpp) cc_final: 0.8353 (pttt) REVERT: N 204 LYS cc_start: 0.8018 (OUTLIER) cc_final: 0.7585 (tptp) REVERT: I 35 ARG cc_start: 0.8118 (ttp80) cc_final: 0.7790 (mtm110) REVERT: I 185 MET cc_start: 0.8438 (ptp) cc_final: 0.8089 (ptm) REVERT: I 204 LYS cc_start: 0.8358 (tppp) cc_final: 0.7919 (tptp) REVERT: J 35 ARG cc_start: 0.8242 (ttp80) cc_final: 0.7976 (mtp-110) REVERT: J 92 ASN cc_start: 0.8887 (m-40) cc_final: 0.8609 (m-40) REVERT: J 140 MET cc_start: 0.8985 (OUTLIER) cc_final: 0.8680 (mtp) REVERT: J 146 LYS cc_start: 0.8717 (ptpp) cc_final: 0.8373 (ptmm) REVERT: J 204 LYS cc_start: 0.8172 (tppp) cc_final: 0.7815 (tptp) REVERT: K 10 TYR cc_start: 0.7175 (m-80) cc_final: 0.6923 (m-80) REVERT: K 45 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8617 (mtmm) REVERT: K 55 ARG cc_start: 0.7621 (mtt90) cc_final: 0.7333 (mtt180) REVERT: K 146 LYS cc_start: 0.8464 (ptpp) cc_final: 0.8098 (ptmm) REVERT: K 204 LYS cc_start: 0.8300 (tppp) cc_final: 0.7827 (tptp) REVERT: K 221 LYS cc_start: 0.8884 (tppt) cc_final: 0.8544 (mmmt) REVERT: L 35 ARG cc_start: 0.8103 (ttp80) cc_final: 0.7695 (mtm110) REVERT: L 146 LYS cc_start: 0.8735 (ptpp) cc_final: 0.8335 (ptmt) REVERT: L 203 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7139 (pm20) REVERT: L 204 LYS cc_start: 0.8118 (tppp) cc_final: 0.7530 (tptp) REVERT: L 228 GLU cc_start: 0.7984 (mp0) cc_final: 0.7739 (mp0) REVERT: M 45 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8614 (mtmm) REVERT: M 55 ARG cc_start: 0.7376 (mtt90) cc_final: 0.7104 (mtt180) REVERT: M 61 ILE cc_start: 0.8577 (mt) cc_final: 0.8334 (tp) REVERT: M 92 ASN cc_start: 0.8746 (m-40) cc_final: 0.8482 (m-40) REVERT: M 146 LYS cc_start: 0.8744 (ptpp) cc_final: 0.8318 (pttt) REVERT: M 204 LYS cc_start: 0.8302 (tppp) cc_final: 0.7616 (tptp) outliers start: 40 outliers final: 23 residues processed: 399 average time/residue: 0.2416 time to fit residues: 140.4857 Evaluate side-chains 384 residues out of total 3157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 354 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain C residue 31 LYS Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 52 GLU Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain G residue 97 LYS Chi-restraints excluded: chain H residue 18 SER Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 204 LYS Chi-restraints excluded: chain N residue 172 THR Chi-restraints excluded: chain N residue 204 LYS Chi-restraints excluded: chain I residue 172 THR Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 140 MET Chi-restraints excluded: chain J residue 172 THR Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 45 LYS Chi-restraints excluded: chain K residue 172 THR Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain L residue 203 GLU Chi-restraints excluded: chain M residue 45 LYS Chi-restraints excluded: chain M residue 172 THR Chi-restraints excluded: chain M residue 185 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 100 optimal weight: 0.5980 chunk 30 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 221 optimal weight: 0.8980 chunk 224 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 263 optimal weight: 0.8980 chunk 137 optimal weight: 2.9990 chunk 275 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 242 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 241 GLN B 270 GLN E 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.091886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.078106 restraints weight = 49021.675| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 1.88 r_work: 0.2935 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 29890 Z= 0.148 Angle : 0.480 5.426 40404 Z= 0.251 Chirality : 0.043 0.207 4648 Planarity : 0.004 0.042 5187 Dihedral : 4.278 46.449 4123 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 1.52 % Allowed : 9.95 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.14), residues: 3731 helix: 1.95 (0.13), residues: 1666 sheet: 0.18 (0.19), residues: 728 loop : 0.69 (0.17), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 286 TYR 0.023 0.001 TYR F 45 PHE 0.012 0.001 PHE L 222 TRP 0.009 0.001 TRP H 161 HIS 0.004 0.001 HIS I 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 (29890) covalent geometry : angle 0.47989 / 0.25 (40404) hydrogen bonds : bond 0.03784 / 2.54 ( 1421) hydrogen bonds : angle 4.51401 / 3.19 ( 4179) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7462 Ramachandran restraints generated. 3731 Oldfield, 0 Emsley, 3731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7462 Ramachandran restraints generated. 3731 Oldfield, 0 Emsley, 3731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 371 time to evaluate : 1.024 Fit side-chains REVERT: A 5 LYS cc_start: 0.8825 (mmtt) cc_final: 0.7997 (tttt) REVERT: A 156 MET cc_start: 0.8530 (mmt) cc_final: 0.8174 (mmp) REVERT: B 5 LYS cc_start: 0.8847 (mmtt) cc_final: 0.8064 (tttp) REVERT: B 15 ASN cc_start: 0.8060 (p0) cc_final: 0.7802 (p0) REVERT: B 70 LEU cc_start: 0.8197 (mp) cc_final: 0.7891 (mt) REVERT: B 241 GLN cc_start: 0.8737 (tt0) cc_final: 0.8453 (tt0) REVERT: C 5 LYS cc_start: 0.8618 (mmtt) cc_final: 0.7901 (tttt) REVERT: C 16 ASP cc_start: 0.8086 (m-30) cc_final: 0.7797 (m-30) REVERT: C 31 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8251 (mtmt) REVERT: C 163 MET cc_start: 0.8442 (ptp) cc_final: 0.8159 (ptm) REVERT: C 294 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7891 (mp0) REVERT: D 16 ASP cc_start: 0.8104 (m-30) cc_final: 0.7783 (m-30) REVERT: D 240 ASP cc_start: 0.8217 (m-30) cc_final: 0.7891 (m-30) REVERT: D 241 GLN cc_start: 0.8871 (tt0) cc_final: 0.8569 (tt0) REVERT: D 294 GLU cc_start: 0.7723 (mp0) cc_final: 0.7458 (mp0) REVERT: E 5 LYS cc_start: 0.8667 (mmtt) cc_final: 0.7971 (tttt) REVERT: E 156 MET cc_start: 0.8562 (mmm) cc_final: 0.8337 (mmp) REVERT: F 75 LEU cc_start: 0.8343 (mp) cc_final: 0.8094 (mp) REVERT: F 240 ASP cc_start: 0.8109 (m-30) cc_final: 0.7828 (m-30) REVERT: G 5 LYS cc_start: 0.8718 (mmtt) cc_final: 0.7936 (tmtt) REVERT: G 52 GLU cc_start: 0.8464 (tp30) cc_final: 0.8202 (pt0) REVERT: G 156 MET cc_start: 0.8480 (mmt) cc_final: 0.8090 (mmp) REVERT: G 240 ASP cc_start: 0.8163 (m-30) cc_final: 0.7794 (m-30) REVERT: H 35 ARG cc_start: 0.8250 (ttp80) cc_final: 0.7945 (mtp-110) REVERT: H 92 ASN cc_start: 0.8772 (m-40) cc_final: 0.8364 (m-40) REVERT: H 146 LYS cc_start: 0.8691 (ptpp) cc_final: 0.8295 (pttt) REVERT: H 204 LYS cc_start: 0.8060 (OUTLIER) cc_final: 0.7561 (tptp) REVERT: H 228 GLU cc_start: 0.7972 (mp0) cc_final: 0.7739 (mp0) REVERT: N 22 ARG cc_start: 0.8266 (ptp-110) cc_final: 0.7987 (ttm110) REVERT: N 55 ARG cc_start: 0.7633 (mtt90) cc_final: 0.7388 (mtt180) REVERT: N 64 GLU cc_start: 0.7977 (tt0) cc_final: 0.7628 (tp30) REVERT: N 92 ASN cc_start: 0.8821 (m-40) cc_final: 0.8519 (m-40) REVERT: N 146 LYS cc_start: 0.8771 (ptpp) cc_final: 0.8363 (ptmm) REVERT: N 204 LYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7616 (tptp) REVERT: I 10 TYR cc_start: 0.7190 (m-80) cc_final: 0.6857 (m-80) REVERT: I 185 MET cc_start: 0.8421 (ptp) cc_final: 0.8081 (ptm) REVERT: I 204 LYS cc_start: 0.8324 (tppp) cc_final: 0.7869 (tptp) REVERT: J 35 ARG cc_start: 0.8196 (ttp80) cc_final: 0.7991 (mtp-110) REVERT: J 92 ASN cc_start: 0.8889 (m-40) cc_final: 0.8605 (m-40) REVERT: J 146 LYS cc_start: 0.8708 (ptpp) cc_final: 0.8356 (ptmm) REVERT: J 204 LYS cc_start: 0.8168 (tppp) cc_final: 0.7794 (tptp) REVERT: K 45 LYS cc_start: 0.8949 (OUTLIER) cc_final: 0.8636 (mtmm) REVERT: K 55 ARG cc_start: 0.7627 (mtt90) cc_final: 0.7341 (mtt180) REVERT: K 204 LYS cc_start: 0.8302 (tppp) cc_final: 0.7831 (tptp) REVERT: K 221 LYS cc_start: 0.8870 (tppt) cc_final: 0.8511 (mmmt) REVERT: L 35 ARG cc_start: 0.8014 (ttp80) cc_final: 0.7650 (mtm110) REVERT: L 146 LYS cc_start: 0.8722 (ptpp) cc_final: 0.8357 (ptmt) REVERT: L 203 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7060 (pm20) REVERT: L 204 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7520 (tptp) REVERT: L 228 GLU cc_start: 0.7970 (mp0) cc_final: 0.7744 (mp0) REVERT: M 45 LYS cc_start: 0.8960 (OUTLIER) cc_final: 0.8627 (mtmm) REVERT: M 55 ARG cc_start: 0.7411 (mtt90) cc_final: 0.7137 (mtt180) REVERT: M 61 ILE cc_start: 0.8586 (mt) cc_final: 0.8332 (tp) REVERT: M 92 ASN cc_start: 0.8749 (m-40) cc_final: 0.8404 (m-40) REVERT: M 146 LYS cc_start: 0.8747 (ptpp) cc_final: 0.8316 (pttt) REVERT: M 204 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7566 (tptp) outliers start: 48 outliers final: 35 residues processed: 406 average time/residue: 0.2337 time to fit residues: 139.3277 Evaluate side-chains 394 residues out of total 3157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 351 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain C residue 31 LYS Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 52 GLU Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 274 ARG Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain G residue 97 LYS Chi-restraints excluded: chain G residue 291 ILE Chi-restraints excluded: chain H residue 18 SER Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 204 LYS Chi-restraints excluded: chain N residue 172 THR Chi-restraints excluded: chain N residue 204 LYS Chi-restraints excluded: chain I residue 172 THR Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 172 THR Chi-restraints excluded: chain J residue 202 MET Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 45 LYS Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 172 THR Chi-restraints excluded: chain L residue 56 ILE Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain L residue 203 GLU Chi-restraints excluded: chain L residue 204 LYS Chi-restraints excluded: chain M residue 45 LYS Chi-restraints excluded: chain M residue 172 THR Chi-restraints excluded: chain M residue 185 MET Chi-restraints excluded: chain M residue 202 MET Chi-restraints excluded: chain M residue 204 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 353 optimal weight: 0.9980 chunk 293 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 200 optimal weight: 2.9990 chunk 190 optimal weight: 0.8980 chunk 299 optimal weight: 3.9990 chunk 155 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 180 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 312 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 241 GLN E 73 ASN G 216 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.091648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.077993 restraints weight = 49001.866| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.84 r_work: 0.2930 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 29890 Z= 0.161 Angle : 0.490 5.822 40404 Z= 0.256 Chirality : 0.044 0.173 4648 Planarity : 0.004 0.046 5187 Dihedral : 4.333 47.221 4123 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 1.49 % Allowed : 10.29 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.14), residues: 3731 helix: 1.93 (0.13), residues: 1666 sheet: 0.09 (0.19), residues: 728 loop : 0.70 (0.17), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 286 TYR 0.023 0.002 TYR B 45 PHE 0.013 0.001 PHE L 222 TRP 0.009 0.002 TRP H 161 HIS 0.005 0.001 HIS I 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.16 (29890) covalent geometry : angle 0.49001 / 0.26 (40404) hydrogen bonds : bond 0.03858 / 2.59 ( 1421) hydrogen bonds : angle 4.56424 / 3.22 ( 4179) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7462 Ramachandran restraints generated. 3731 Oldfield, 0 Emsley, 3731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7462 Ramachandran restraints generated. 3731 Oldfield, 0 Emsley, 3731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 372 time to evaluate : 1.176 Fit side-chains REVERT: A 5 LYS cc_start: 0.8830 (mmtt) cc_final: 0.8044 (tttt) REVERT: A 156 MET cc_start: 0.8562 (mmt) cc_final: 0.8199 (mmp) REVERT: B 5 LYS cc_start: 0.8841 (mmtt) cc_final: 0.8079 (tttp) REVERT: B 15 ASN cc_start: 0.8093 (p0) cc_final: 0.7852 (p0) REVERT: B 70 LEU cc_start: 0.8249 (mp) cc_final: 0.7928 (mt) REVERT: B 241 GLN cc_start: 0.8712 (tt0) cc_final: 0.8425 (tt0) REVERT: C 16 ASP cc_start: 0.8062 (m-30) cc_final: 0.7833 (m-30) REVERT: C 31 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.8249 (mtmt) REVERT: C 163 MET cc_start: 0.8507 (ptp) cc_final: 0.8256 (ptm) REVERT: C 294 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7876 (mp0) REVERT: D 16 ASP cc_start: 0.8145 (m-30) cc_final: 0.7889 (m-30) REVERT: D 240 ASP cc_start: 0.8223 (m-30) cc_final: 0.7905 (m-30) REVERT: E 5 LYS cc_start: 0.8640 (mmtt) cc_final: 0.7997 (tmtt) REVERT: E 156 MET cc_start: 0.8595 (mmm) cc_final: 0.8374 (mmp) REVERT: E 292 GLU cc_start: 0.7176 (pm20) cc_final: 0.6969 (pm20) REVERT: F 75 LEU cc_start: 0.8198 (mp) cc_final: 0.7938 (mp) REVERT: F 240 ASP cc_start: 0.8104 (m-30) cc_final: 0.7826 (m-30) REVERT: G 5 LYS cc_start: 0.8704 (mmtt) cc_final: 0.7966 (tmtt) REVERT: G 156 MET cc_start: 0.8582 (mmt) cc_final: 0.8158 (mmp) REVERT: G 240 ASP cc_start: 0.8126 (m-30) cc_final: 0.7780 (m-30) REVERT: H 35 ARG cc_start: 0.8267 (ttp80) cc_final: 0.8004 (mtp-110) REVERT: H 92 ASN cc_start: 0.8759 (m-40) cc_final: 0.8360 (m-40) REVERT: H 146 LYS cc_start: 0.8671 (ptpp) cc_final: 0.8304 (pttt) REVERT: H 204 LYS cc_start: 0.8065 (OUTLIER) cc_final: 0.7562 (tptp) REVERT: H 228 GLU cc_start: 0.7983 (mp0) cc_final: 0.7751 (mp0) REVERT: N 22 ARG cc_start: 0.8208 (ptp-110) cc_final: 0.7929 (ttm110) REVERT: N 55 ARG cc_start: 0.7655 (mtt90) cc_final: 0.7398 (mtt180) REVERT: N 64 GLU cc_start: 0.7862 (tt0) cc_final: 0.7579 (tp30) REVERT: N 92 ASN cc_start: 0.8817 (m-40) cc_final: 0.8519 (m-40) REVERT: N 146 LYS cc_start: 0.8757 (ptpp) cc_final: 0.8385 (ptmm) REVERT: N 204 LYS cc_start: 0.7994 (OUTLIER) cc_final: 0.7641 (tptp) REVERT: I 185 MET cc_start: 0.8443 (ptp) cc_final: 0.8108 (ptm) REVERT: I 204 LYS cc_start: 0.8322 (tppp) cc_final: 0.7888 (tptp) REVERT: J 92 ASN cc_start: 0.8835 (m-40) cc_final: 0.8565 (m-40) REVERT: J 146 LYS cc_start: 0.8719 (ptpp) cc_final: 0.8380 (ptmm) REVERT: J 204 LYS cc_start: 0.8166 (tppp) cc_final: 0.7808 (tptp) REVERT: K 45 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8657 (mtmm) REVERT: K 55 ARG cc_start: 0.7646 (mtt90) cc_final: 0.7366 (mtt180) REVERT: K 204 LYS cc_start: 0.8325 (tppp) cc_final: 0.7887 (tptp) REVERT: K 221 LYS cc_start: 0.8887 (tppt) cc_final: 0.8547 (mmmt) REVERT: L 35 ARG cc_start: 0.8035 (ttp80) cc_final: 0.7693 (mtm110) REVERT: L 146 LYS cc_start: 0.8769 (ptpp) cc_final: 0.8410 (ptmt) REVERT: L 203 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.6897 (pm20) REVERT: L 204 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7514 (tptp) REVERT: L 228 GLU cc_start: 0.7998 (mp0) cc_final: 0.7780 (mp0) REVERT: M 45 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8650 (mtmm) REVERT: M 55 ARG cc_start: 0.7449 (mtt90) cc_final: 0.7166 (mtt180) REVERT: M 61 ILE cc_start: 0.8646 (mt) cc_final: 0.8391 (tp) REVERT: M 92 ASN cc_start: 0.8739 (m-40) cc_final: 0.8392 (m-40) REVERT: M 146 LYS cc_start: 0.8726 (ptpp) cc_final: 0.8339 (pttt) REVERT: M 204 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.7672 (tptp) outliers start: 47 outliers final: 34 residues processed: 405 average time/residue: 0.2269 time to fit residues: 135.6155 Evaluate side-chains 395 residues out of total 3157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 353 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain C residue 31 LYS Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 52 GLU Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 274 ARG Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain G residue 97 LYS Chi-restraints excluded: chain G residue 291 ILE Chi-restraints excluded: chain H residue 18 SER Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 204 LYS Chi-restraints excluded: chain N residue 172 THR Chi-restraints excluded: chain N residue 204 LYS Chi-restraints excluded: chain I residue 172 THR Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 172 THR Chi-restraints excluded: chain J residue 202 MET Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 45 LYS Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 172 THR Chi-restraints excluded: chain L residue 56 ILE Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain L residue 203 GLU Chi-restraints excluded: chain L residue 204 LYS Chi-restraints excluded: chain M residue 45 LYS Chi-restraints excluded: chain M residue 172 THR Chi-restraints excluded: chain M residue 185 MET Chi-restraints excluded: chain M residue 204 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 212 optimal weight: 0.9980 chunk 361 optimal weight: 2.9990 chunk 248 optimal weight: 0.9980 chunk 146 optimal weight: 0.0980 chunk 303 optimal weight: 0.1980 chunk 57 optimal weight: 0.9980 chunk 323 optimal weight: 1.9990 chunk 231 optimal weight: 0.6980 chunk 131 optimal weight: 0.8980 chunk 237 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 241 GLN D 266 GLN E 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.092601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.078840 restraints weight = 49040.463| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.87 r_work: 0.2950 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 29890 Z= 0.119 Angle : 0.469 6.372 40404 Z= 0.246 Chirality : 0.043 0.222 4648 Planarity : 0.004 0.041 5187 Dihedral : 4.165 42.449 4123 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 1.30 % Allowed : 10.71 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.14), residues: 3731 helix: 2.02 (0.13), residues: 1666 sheet: 0.11 (0.19), residues: 728 loop : 0.78 (0.18), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 286 TYR 0.026 0.001 TYR I 10 PHE 0.012 0.001 PHE H 222 TRP 0.008 0.002 TRP H 161 HIS 0.003 0.001 HIS N 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (29890) covalent geometry : angle 0.46946 / 0.25 (40404) hydrogen bonds : bond 0.03539 / 2.37 ( 1421) hydrogen bonds : angle 4.42871 / 3.13 ( 4179) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7462 Ramachandran restraints generated. 3731 Oldfield, 0 Emsley, 3731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7462 Ramachandran restraints generated. 3731 Oldfield, 0 Emsley, 3731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 3157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 373 time to evaluate : 1.101 Fit side-chains REVERT: A 5 LYS cc_start: 0.8831 (mmtt) cc_final: 0.8009 (tttt) REVERT: A 156 MET cc_start: 0.8516 (mmt) cc_final: 0.8142 (mmp) REVERT: B 5 LYS cc_start: 0.8846 (mmtt) cc_final: 0.8057 (tmtt) REVERT: B 15 ASN cc_start: 0.8041 (p0) cc_final: 0.7805 (p0) REVERT: B 70 LEU cc_start: 0.8185 (mp) cc_final: 0.7871 (mt) REVERT: B 241 GLN cc_start: 0.8860 (tt0) cc_final: 0.8593 (tt0) REVERT: C 5 LYS cc_start: 0.8640 (mmtt) cc_final: 0.7918 (tttt) REVERT: C 16 ASP cc_start: 0.8042 (m-30) cc_final: 0.7805 (m-30) REVERT: C 31 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.8270 (mtmt) REVERT: C 163 MET cc_start: 0.8484 (ptp) cc_final: 0.8222 (ptm) REVERT: C 294 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7871 (mp0) REVERT: D 16 ASP cc_start: 0.8113 (m-30) cc_final: 0.7845 (m-30) REVERT: D 240 ASP cc_start: 0.8140 (m-30) cc_final: 0.7820 (m-30) REVERT: E 5 LYS cc_start: 0.8656 (mmtt) cc_final: 0.7963 (tmtt) REVERT: E 156 MET cc_start: 0.8568 (mmm) cc_final: 0.8353 (mmp) REVERT: E 292 GLU cc_start: 0.7180 (pm20) cc_final: 0.6954 (pm20) REVERT: F 75 LEU cc_start: 0.8432 (mp) cc_final: 0.8231 (mp) REVERT: F 240 ASP cc_start: 0.8102 (m-30) cc_final: 0.7847 (m-30) REVERT: G 5 LYS cc_start: 0.8723 (mmtt) cc_final: 0.7968 (tmtt) REVERT: G 156 MET cc_start: 0.8567 (mmt) cc_final: 0.8170 (mmp) REVERT: G 240 ASP cc_start: 0.8108 (m-30) cc_final: 0.7750 (m-30) REVERT: H 35 ARG cc_start: 0.8244 (ttp80) cc_final: 0.7974 (mtm-85) REVERT: H 92 ASN cc_start: 0.8752 (m-40) cc_final: 0.8368 (m-40) REVERT: H 146 LYS cc_start: 0.8700 (ptpp) cc_final: 0.8291 (pttt) REVERT: H 204 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7594 (tptp) REVERT: H 228 GLU cc_start: 0.7975 (mp0) cc_final: 0.7751 (mp0) REVERT: N 22 ARG cc_start: 0.8175 (ptp-110) cc_final: 0.7906 (ttm110) REVERT: N 55 ARG cc_start: 0.7630 (mtt90) cc_final: 0.7389 (mtt180) REVERT: N 64 GLU cc_start: 0.7704 (tt0) cc_final: 0.7414 (tp30) REVERT: N 92 ASN cc_start: 0.8804 (m-40) cc_final: 0.8513 (m-40) REVERT: N 146 LYS cc_start: 0.8772 (ptpp) cc_final: 0.8373 (ptmm) REVERT: N 204 LYS cc_start: 0.7991 (OUTLIER) cc_final: 0.7605 (tptp) REVERT: I 22 ARG cc_start: 0.7838 (ttm110) cc_final: 0.7371 (mtm-85) REVERT: I 185 MET cc_start: 0.8392 (ptp) cc_final: 0.8062 (ptm) REVERT: I 204 LYS cc_start: 0.8296 (tppp) cc_final: 0.7846 (tptp) REVERT: J 92 ASN cc_start: 0.8871 (m-40) cc_final: 0.8594 (m-40) REVERT: J 146 LYS cc_start: 0.8735 (ptpp) cc_final: 0.8380 (ptmm) REVERT: J 204 LYS cc_start: 0.8157 (tppp) cc_final: 0.7798 (tptp) REVERT: K 45 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8679 (mtmm) REVERT: K 55 ARG cc_start: 0.7609 (mtt90) cc_final: 0.7341 (mtt180) REVERT: K 204 LYS cc_start: 0.8306 (tppp) cc_final: 0.7847 (tptp) REVERT: K 221 LYS cc_start: 0.8873 (tppt) cc_final: 0.8517 (mmmt) REVERT: L 35 ARG cc_start: 0.8014 (ttp80) cc_final: 0.7690 (mtm110) REVERT: L 146 LYS cc_start: 0.8786 (ptpp) cc_final: 0.8365 (ptmt) REVERT: L 203 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.6918 (pm20) REVERT: L 204 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7528 (tptp) REVERT: L 228 GLU cc_start: 0.8003 (mp0) cc_final: 0.7791 (mp0) REVERT: M 45 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8649 (mtmm) REVERT: M 55 ARG cc_start: 0.7459 (mtt90) cc_final: 0.7182 (mtt180) REVERT: M 61 ILE cc_start: 0.8609 (mt) cc_final: 0.8329 (tp) REVERT: M 92 ASN cc_start: 0.8776 (m-40) cc_final: 0.8418 (m-40) REVERT: M 146 LYS cc_start: 0.8744 (ptpp) cc_final: 0.8327 (pttt) REVERT: M 204 LYS cc_start: 0.8266 (tppp) cc_final: 0.7666 (tptp) outliers start: 41 outliers final: 29 residues processed: 404 average time/residue: 0.2323 time to fit residues: 138.7118 Evaluate side-chains 389 residues out of total 3157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 353 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain C residue 31 LYS Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 52 GLU Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain G residue 97 LYS Chi-restraints excluded: chain G residue 291 ILE Chi-restraints excluded: chain H residue 18 SER Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 204 LYS Chi-restraints excluded: chain N residue 172 THR Chi-restraints excluded: chain N residue 204 LYS Chi-restraints excluded: chain I residue 172 THR Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 172 THR Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 45 LYS Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 172 THR Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain L residue 203 GLU Chi-restraints excluded: chain L residue 204 LYS Chi-restraints excluded: chain M residue 45 LYS Chi-restraints excluded: chain M residue 172 THR Chi-restraints excluded: chain M residue 185 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 147 optimal weight: 0.5980 chunk 297 optimal weight: 1.9990 chunk 130 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 chunk 230 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 301 optimal weight: 0.9980 chunk 360 optimal weight: 0.9980 chunk 294 optimal weight: 0.7980 chunk 155 optimal weight: 0.5980 chunk 256 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 241 GLN E 73 ASN G 270 GLN K 25 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.092408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.078656 restraints weight = 48933.756| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 1.87 r_work: 0.2943 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 29890 Z= 0.133 Angle : 0.479 6.211 40404 Z= 0.250 Chirality : 0.043 0.197 4648 Planarity : 0.004 0.041 5187 Dihedral : 4.165 41.055 4123 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.30 % Allowed : 10.99 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.14), residues: 3731 helix: 2.01 (0.13), residues: 1666 sheet: 0.08 (0.19), residues: 728 loop : 0.79 (0.18), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 286 TYR 0.028 0.001 TYR I 10 PHE 0.012 0.001 PHE L 222 TRP 0.007 0.001 TRP H 161 HIS 0.004 0.001 HIS I 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.13 (29890) covalent geometry : angle 0.47882 / 0.25 (40404) hydrogen bonds : bond 0.03600 / 2.42 ( 1421) hydrogen bonds : angle 4.43780 / 3.14 ( 4179) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7462 Ramachandran restraints generated. 3731 Oldfield, 0 Emsley, 3731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7462 Ramachandran restraints generated. 3731 Oldfield, 0 Emsley, 3731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 3157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 362 time to evaluate : 1.138 Fit side-chains REVERT: A 5 LYS cc_start: 0.8827 (mmtt) cc_final: 0.8021 (tttt) REVERT: A 156 MET cc_start: 0.8554 (mmt) cc_final: 0.8184 (mmp) REVERT: B 5 LYS cc_start: 0.8838 (mmtt) cc_final: 0.8068 (tmtt) REVERT: B 15 ASN cc_start: 0.8014 (p0) cc_final: 0.7785 (p0) REVERT: B 70 LEU cc_start: 0.8212 (mp) cc_final: 0.7898 (mt) REVERT: B 241 GLN cc_start: 0.8842 (tt0) cc_final: 0.8555 (tt0) REVERT: C 16 ASP cc_start: 0.8056 (m-30) cc_final: 0.7825 (m-30) REVERT: C 31 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.8245 (mtmt) REVERT: C 163 MET cc_start: 0.8492 (ptp) cc_final: 0.8226 (ptm) REVERT: C 294 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7849 (mp0) REVERT: D 16 ASP cc_start: 0.8155 (m-30) cc_final: 0.7900 (m-30) REVERT: D 240 ASP cc_start: 0.8089 (m-30) cc_final: 0.7774 (m-30) REVERT: D 270 GLN cc_start: 0.8165 (mm-40) cc_final: 0.7355 (tm-30) REVERT: E 5 LYS cc_start: 0.8659 (mmtt) cc_final: 0.8000 (tmtt) REVERT: E 156 MET cc_start: 0.8590 (mmm) cc_final: 0.8372 (mmp) REVERT: E 292 GLU cc_start: 0.7158 (pm20) cc_final: 0.6934 (pm20) REVERT: F 240 ASP cc_start: 0.8081 (m-30) cc_final: 0.7830 (m-30) REVERT: G 5 LYS cc_start: 0.8728 (mmtt) cc_final: 0.7967 (tmtt) REVERT: G 156 MET cc_start: 0.8596 (mmt) cc_final: 0.8173 (mmp) REVERT: G 240 ASP cc_start: 0.8075 (m-30) cc_final: 0.7773 (m-30) REVERT: H 35 ARG cc_start: 0.8232 (ttp80) cc_final: 0.7986 (mtm-85) REVERT: H 64 GLU cc_start: 0.7634 (mt-10) cc_final: 0.7401 (tt0) REVERT: H 92 ASN cc_start: 0.8750 (m-40) cc_final: 0.8372 (m-40) REVERT: H 146 LYS cc_start: 0.8709 (ptpp) cc_final: 0.8310 (pttt) REVERT: H 204 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7592 (tptp) REVERT: H 228 GLU cc_start: 0.7961 (mp0) cc_final: 0.7738 (mp0) REVERT: N 22 ARG cc_start: 0.8169 (ptp-110) cc_final: 0.7906 (ttm110) REVERT: N 53 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.8018 (tt0) REVERT: N 55 ARG cc_start: 0.7645 (mtt90) cc_final: 0.7400 (mtt180) REVERT: N 64 GLU cc_start: 0.7757 (tt0) cc_final: 0.7465 (tp30) REVERT: N 92 ASN cc_start: 0.8801 (m-40) cc_final: 0.8586 (m-40) REVERT: N 146 LYS cc_start: 0.8783 (ptpp) cc_final: 0.8386 (ptmm) REVERT: N 204 LYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7628 (tptp) REVERT: I 22 ARG cc_start: 0.7772 (ttm110) cc_final: 0.7371 (mtm-85) REVERT: I 185 MET cc_start: 0.8411 (ptp) cc_final: 0.8083 (ptm) REVERT: I 204 LYS cc_start: 0.8274 (tppp) cc_final: 0.7805 (tptp) REVERT: J 92 ASN cc_start: 0.8842 (m-40) cc_final: 0.8566 (m-40) REVERT: J 124 MET cc_start: 0.8692 (ttm) cc_final: 0.8348 (ttm) REVERT: J 146 LYS cc_start: 0.8754 (ptpp) cc_final: 0.8399 (ptmm) REVERT: J 203 GLU cc_start: 0.7532 (pm20) cc_final: 0.7286 (pm20) REVERT: J 204 LYS cc_start: 0.8161 (tppp) cc_final: 0.7751 (tptp) REVERT: K 45 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8684 (mtmm) REVERT: K 55 ARG cc_start: 0.7603 (mtt90) cc_final: 0.7338 (mtt180) REVERT: K 204 LYS cc_start: 0.8299 (tppp) cc_final: 0.7825 (tptp) REVERT: K 221 LYS cc_start: 0.8882 (tppt) cc_final: 0.8527 (mmmt) REVERT: L 35 ARG cc_start: 0.8013 (ttp80) cc_final: 0.7698 (mtm110) REVERT: L 146 LYS cc_start: 0.8799 (ptpp) cc_final: 0.8388 (ptmt) REVERT: L 203 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.6924 (pm20) REVERT: L 204 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7521 (tptp) REVERT: L 228 GLU cc_start: 0.7978 (mp0) cc_final: 0.7772 (mp0) REVERT: M 45 LYS cc_start: 0.8972 (OUTLIER) cc_final: 0.8659 (mtmm) REVERT: M 55 ARG cc_start: 0.7444 (mtt90) cc_final: 0.7157 (mtt180) REVERT: M 61 ILE cc_start: 0.8623 (mt) cc_final: 0.8343 (tp) REVERT: M 92 ASN cc_start: 0.8775 (m-40) cc_final: 0.8423 (m-40) REVERT: M 146 LYS cc_start: 0.8757 (ptpp) cc_final: 0.8351 (pttt) REVERT: M 204 LYS cc_start: 0.8233 (tppp) cc_final: 0.7649 (tptp) outliers start: 41 outliers final: 31 residues processed: 393 average time/residue: 0.2281 time to fit residues: 132.8256 Evaluate side-chains 397 residues out of total 3157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 358 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain C residue 31 LYS Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 52 GLU Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain G residue 97 LYS Chi-restraints excluded: chain G residue 291 ILE Chi-restraints excluded: chain H residue 18 SER Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 204 LYS Chi-restraints excluded: chain N residue 53 GLU Chi-restraints excluded: chain N residue 172 THR Chi-restraints excluded: chain N residue 204 LYS Chi-restraints excluded: chain I residue 172 THR Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 172 THR Chi-restraints excluded: chain J residue 202 MET Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 45 LYS Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 172 THR Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain L residue 203 GLU Chi-restraints excluded: chain L residue 204 LYS Chi-restraints excluded: chain M residue 45 LYS Chi-restraints excluded: chain M residue 172 THR Chi-restraints excluded: chain M residue 185 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 151 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 368 optimal weight: 0.8980 chunk 134 optimal weight: 0.7980 chunk 287 optimal weight: 1.9990 chunk 347 optimal weight: 3.9990 chunk 295 optimal weight: 3.9990 chunk 132 optimal weight: 0.5980 chunk 112 optimal weight: 3.9990 chunk 344 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 241 GLN A 259 GLN G 107 GLN H 144 ASN I 144 ASN J 144 ASN K 144 ASN M 144 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.090596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.076722 restraints weight = 49009.822| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 1.87 r_work: 0.2906 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 29890 Z= 0.223 Angle : 0.544 7.317 40404 Z= 0.282 Chirality : 0.046 0.213 4648 Planarity : 0.004 0.040 5187 Dihedral : 4.539 50.935 4123 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.43 % Allowed : 11.18 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.14), residues: 3731 helix: 1.78 (0.13), residues: 1659 sheet: -0.26 (0.19), residues: 735 loop : 0.61 (0.18), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 35 TYR 0.026 0.002 TYR B 45 PHE 0.013 0.002 PHE L 222 TRP 0.007 0.001 TRP H 161 HIS 0.006 0.001 HIS N 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00562 / 0.22 (29890) covalent geometry : angle 0.54391 / 0.28 (40404) hydrogen bonds : bond 0.04234 / 2.85 ( 1421) hydrogen bonds : angle 4.72008 / 3.32 ( 4179) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7462 Ramachandran restraints generated. 3731 Oldfield, 0 Emsley, 3731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7462 Ramachandran restraints generated. 3731 Oldfield, 0 Emsley, 3731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 364 time to evaluate : 1.153 Fit side-chains REVERT: A 5 LYS cc_start: 0.8855 (mmtt) cc_final: 0.8069 (tttt) REVERT: A 156 MET cc_start: 0.8572 (mmt) cc_final: 0.8201 (mmp) REVERT: B 5 LYS cc_start: 0.8823 (mmtt) cc_final: 0.8058 (tttp) REVERT: B 15 ASN cc_start: 0.8076 (p0) cc_final: 0.7850 (p0) REVERT: B 241 GLN cc_start: 0.8856 (tt0) cc_final: 0.8544 (tt0) REVERT: C 31 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.8285 (mtmt) REVERT: C 163 MET cc_start: 0.8514 (ptp) cc_final: 0.8194 (ptm) REVERT: C 294 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7864 (mp0) REVERT: D 16 ASP cc_start: 0.8186 (m-30) cc_final: 0.7935 (m-30) REVERT: D 240 ASP cc_start: 0.8191 (m-30) cc_final: 0.7875 (m-30) REVERT: D 270 GLN cc_start: 0.8243 (mm-40) cc_final: 0.7455 (tm-30) REVERT: E 5 LYS cc_start: 0.8660 (mmtt) cc_final: 0.7975 (tmtt) REVERT: E 37 ASP cc_start: 0.7760 (m-30) cc_final: 0.7527 (m-30) REVERT: E 156 MET cc_start: 0.8652 (mmm) cc_final: 0.8413 (mmp) REVERT: E 270 GLN cc_start: 0.8049 (mm-40) cc_final: 0.7186 (tm-30) REVERT: F 168 SER cc_start: 0.9001 (t) cc_final: 0.8755 (p) REVERT: F 240 ASP cc_start: 0.8103 (m-30) cc_final: 0.7844 (m-30) REVERT: G 5 LYS cc_start: 0.8684 (mmtt) cc_final: 0.7957 (tmtt) REVERT: G 156 MET cc_start: 0.8671 (mmt) cc_final: 0.8186 (mmp) REVERT: G 240 ASP cc_start: 0.8091 (m-30) cc_final: 0.7770 (m-30) REVERT: H 35 ARG cc_start: 0.8170 (ttp80) cc_final: 0.7910 (mtp-110) REVERT: H 64 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7457 (tt0) REVERT: H 92 ASN cc_start: 0.8744 (m-40) cc_final: 0.8354 (m-40) REVERT: H 146 LYS cc_start: 0.8702 (ptpp) cc_final: 0.8293 (pttt) REVERT: H 204 LYS cc_start: 0.8026 (OUTLIER) cc_final: 0.7596 (tptp) REVERT: H 228 GLU cc_start: 0.7916 (mp0) cc_final: 0.7663 (mp0) REVERT: N 22 ARG cc_start: 0.8224 (ptp-110) cc_final: 0.7946 (ttm110) REVERT: N 53 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.8067 (tt0) REVERT: N 55 ARG cc_start: 0.7670 (mtt90) cc_final: 0.7468 (mtt180) REVERT: N 64 GLU cc_start: 0.7877 (tt0) cc_final: 0.7563 (tp30) REVERT: N 146 LYS cc_start: 0.8755 (ptpp) cc_final: 0.8342 (ptmm) REVERT: N 204 LYS cc_start: 0.8008 (OUTLIER) cc_final: 0.7636 (tptp) REVERT: I 185 MET cc_start: 0.8437 (ptp) cc_final: 0.8115 (ptm) REVERT: I 204 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7810 (tptp) REVERT: J 92 ASN cc_start: 0.8846 (m-40) cc_final: 0.8562 (m-40) REVERT: J 146 LYS cc_start: 0.8736 (ptpp) cc_final: 0.8350 (ptmm) REVERT: J 203 GLU cc_start: 0.7577 (pm20) cc_final: 0.7326 (pm20) REVERT: J 204 LYS cc_start: 0.8136 (tppp) cc_final: 0.7703 (tptp) REVERT: J 221 LYS cc_start: 0.8873 (tppt) cc_final: 0.8632 (tptt) REVERT: K 45 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.8689 (mtmm) REVERT: K 55 ARG cc_start: 0.7666 (mtt90) cc_final: 0.7315 (mtt180) REVERT: K 204 LYS cc_start: 0.8275 (tppp) cc_final: 0.7796 (tptp) REVERT: K 221 LYS cc_start: 0.8900 (tppt) cc_final: 0.8528 (mmmt) REVERT: L 35 ARG cc_start: 0.8088 (ttp80) cc_final: 0.7770 (mtm110) REVERT: L 146 LYS cc_start: 0.8827 (ptpp) cc_final: 0.8375 (pttp) REVERT: L 203 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.6945 (pm20) REVERT: L 204 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7505 (tptp) REVERT: L 228 GLU cc_start: 0.7949 (mp0) cc_final: 0.7730 (mp0) REVERT: M 45 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8662 (mtmm) REVERT: M 55 ARG cc_start: 0.7459 (mtt90) cc_final: 0.7163 (mtt180) REVERT: M 61 ILE cc_start: 0.8686 (mt) cc_final: 0.8400 (tp) REVERT: M 92 ASN cc_start: 0.8782 (m-40) cc_final: 0.8425 (m-40) REVERT: M 146 LYS cc_start: 0.8797 (ptpp) cc_final: 0.8356 (pttt) REVERT: M 204 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7602 (tptp) outliers start: 45 outliers final: 34 residues processed: 396 average time/residue: 0.2387 time to fit residues: 139.1979 Evaluate side-chains 399 residues out of total 3157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 355 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain C residue 31 LYS Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 52 GLU Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 280 GLU Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain G residue 52 GLU Chi-restraints excluded: chain G residue 97 LYS Chi-restraints excluded: chain G residue 291 ILE Chi-restraints excluded: chain H residue 18 SER Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 204 LYS Chi-restraints excluded: chain N residue 53 GLU Chi-restraints excluded: chain N residue 172 THR Chi-restraints excluded: chain N residue 204 LYS Chi-restraints excluded: chain I residue 172 THR Chi-restraints excluded: chain I residue 204 LYS Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 172 THR Chi-restraints excluded: chain J residue 202 MET Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 45 LYS Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 172 THR Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain L residue 203 GLU Chi-restraints excluded: chain L residue 204 LYS Chi-restraints excluded: chain M residue 45 LYS Chi-restraints excluded: chain M residue 172 THR Chi-restraints excluded: chain M residue 185 MET Chi-restraints excluded: chain M residue 204 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 195 optimal weight: 0.4980 chunk 43 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 220 optimal weight: 0.1980 chunk 356 optimal weight: 0.8980 chunk 228 optimal weight: 2.9990 chunk 186 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 209 optimal weight: 0.7980 chunk 227 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 241 GLN G 107 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.092283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.078490 restraints weight = 49007.292| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.87 r_work: 0.2937 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29890 Z= 0.123 Angle : 0.479 7.443 40404 Z= 0.250 Chirality : 0.043 0.192 4648 Planarity : 0.004 0.041 5187 Dihedral : 4.272 45.046 4123 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 1.30 % Allowed : 11.43 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.14), residues: 3731 helix: 1.92 (0.13), residues: 1659 sheet: -0.23 (0.19), residues: 735 loop : 0.67 (0.18), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 286 TYR 0.021 0.001 TYR E 45 PHE 0.012 0.001 PHE L 222 TRP 0.007 0.001 TRP H 161 HIS 0.003 0.001 HIS N 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 (29890) covalent geometry : angle 0.47916 / 0.25 (40404) hydrogen bonds : bond 0.03609 / 2.42 ( 1421) hydrogen bonds : angle 4.47096 / 3.16 ( 4179) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6707.55 seconds wall clock time: 116 minutes 4.20 seconds (6964.20 seconds total)