Starting phenix.real_space_refine on Tue May 5 11:46:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hw1_35080/05_2026/8hw1_35080.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hw1_35080/05_2026/8hw1_35080.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hw1_35080/05_2026/8hw1_35080.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hw1_35080/05_2026/8hw1_35080.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hw1_35080/05_2026/8hw1_35080.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hw1_35080/05_2026/8hw1_35080.map" } resolution = 3.13 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= 0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mg 121 5.21 5 S 55 5.16 5 C 20592 2.51 5 N 4015 2.21 5 O 4488 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 275 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29271 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1886 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 16, 'TRANS': 224} Chain: "A" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 775 Unusual residues: {'32N': 1, 'CLA': 11, 'XAT': 1} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K Time building chain proxies: 3.72, per 1000 atoms: 0.13 Number of scatterers: 29271 At special positions: 0 Unit cell: (196.62, 197.75, 67.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 55 16.00 Mg 121 11.99 O 4488 8.00 N 4015 7.00 C 20592 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=44, symmetry=0 Number of additional bonds: simple=44, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.10 Conformation dependent library (CDL) restraints added in 1.0 seconds 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4752 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 0 sheets defined 56.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 111 through 143 removed outlier: 3.862A pdb=" N SER A 115 " --> pdb=" O ASN A 111 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU A 117 " --> pdb=" O ASP A 113 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 130 " --> pdb=" O TYR A 126 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU A 133 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL A 136 " --> pdb=" O MET A 132 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL A 141 " --> pdb=" O GLY A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 156 removed outlier: 3.566A pdb=" N LEU A 156 " --> pdb=" O PRO A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 186 removed outlier: 3.574A pdb=" N LYS A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 240 removed outlier: 3.675A pdb=" N VAL A 220 " --> pdb=" O ARG A 216 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG A 221 " --> pdb=" O GLN A 217 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU A 228 " --> pdb=" O ARG A 224 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TRP A 238 " --> pdb=" O SER A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 254 removed outlier: 3.659A pdb=" N ASP A 250 " --> pdb=" O GLU A 246 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER A 254 " --> pdb=" O ASP A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 263 removed outlier: 3.625A pdb=" N THR A 262 " --> pdb=" O ASN A 259 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR A 263 " --> pdb=" O ILE A 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 259 through 263' Processing helix chain 'A' and resid 265 through 279 removed outlier: 3.567A pdb=" N VAL A 271 " --> pdb=" O GLY A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 290 removed outlier: 3.779A pdb=" N ILE A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 143 removed outlier: 3.861A pdb=" N SER B 115 " --> pdb=" O ASN B 111 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU B 117 " --> pdb=" O ASP B 113 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU B 130 " --> pdb=" O TYR B 126 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU B 133 " --> pdb=" O ARG B 129 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL B 136 " --> pdb=" O MET B 132 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL B 141 " --> pdb=" O GLY B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 156 removed outlier: 3.566A pdb=" N LEU B 156 " --> pdb=" O PRO B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 186 removed outlier: 3.574A pdb=" N LYS B 180 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG B 186 " --> pdb=" O LEU B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 240 removed outlier: 3.675A pdb=" N VAL B 220 " --> pdb=" O ARG B 216 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG B 221 " --> pdb=" O GLN B 217 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU B 228 " --> pdb=" O ARG B 224 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TRP B 238 " --> pdb=" O SER B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 254 removed outlier: 3.659A pdb=" N ASP B 250 " --> pdb=" O GLU B 246 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER B 254 " --> pdb=" O ASP B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 263 removed outlier: 3.624A pdb=" N THR B 262 " --> pdb=" O ASN B 259 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR B 263 " --> pdb=" O ILE B 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 259 through 263' Processing helix chain 'B' and resid 265 through 279 removed outlier: 3.567A pdb=" N VAL B 271 " --> pdb=" O GLY B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 290 removed outlier: 3.779A pdb=" N ILE B 283 " --> pdb=" O ALA B 279 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 143 removed outlier: 3.862A pdb=" N SER C 115 " --> pdb=" O ASN C 111 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU C 117 " --> pdb=" O ASP C 113 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU C 130 " --> pdb=" O TYR C 126 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU C 133 " --> pdb=" O ARG C 129 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL C 136 " --> pdb=" O MET C 132 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL C 141 " --> pdb=" O GLY C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 156 removed outlier: 3.567A pdb=" N LEU C 156 " --> pdb=" O PRO C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 186 removed outlier: 3.574A pdb=" N LYS C 180 " --> pdb=" O LEU C 176 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG C 186 " --> pdb=" O LEU C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 240 removed outlier: 3.675A pdb=" N VAL C 220 " --> pdb=" O ARG C 216 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG C 221 " --> pdb=" O GLN C 217 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU C 228 " --> pdb=" O ARG C 224 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TRP C 238 " --> pdb=" O SER C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 254 removed outlier: 3.659A pdb=" N ASP C 250 " --> pdb=" O GLU C 246 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER C 254 " --> pdb=" O ASP C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 263 removed outlier: 3.625A pdb=" N THR C 262 " --> pdb=" O ASN C 259 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR C 263 " --> pdb=" O ILE C 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 259 through 263' Processing helix chain 'C' and resid 265 through 279 removed outlier: 3.567A pdb=" N VAL C 271 " --> pdb=" O GLY C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 290 removed outlier: 3.779A pdb=" N ILE C 283 " --> pdb=" O ALA C 279 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 143 removed outlier: 3.862A pdb=" N SER D 115 " --> pdb=" O ASN D 111 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU D 117 " --> pdb=" O ASP D 113 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU D 130 " --> pdb=" O TYR D 126 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU D 133 " --> pdb=" O ARG D 129 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL D 136 " --> pdb=" O MET D 132 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL D 141 " --> pdb=" O GLY D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 156 removed outlier: 3.566A pdb=" N LEU D 156 " --> pdb=" O PRO D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 186 removed outlier: 3.574A pdb=" N LYS D 180 " --> pdb=" O LEU D 176 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG D 186 " --> pdb=" O LEU D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 240 removed outlier: 3.675A pdb=" N VAL D 220 " --> pdb=" O ARG D 216 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG D 221 " --> pdb=" O GLN D 217 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU D 228 " --> pdb=" O ARG D 224 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TRP D 238 " --> pdb=" O SER D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 254 removed outlier: 3.659A pdb=" N ASP D 250 " --> pdb=" O GLU D 246 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER D 254 " --> pdb=" O ASP D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 263 removed outlier: 3.625A pdb=" N THR D 262 " --> pdb=" O ASN D 259 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR D 263 " --> pdb=" O ILE D 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 259 through 263' Processing helix chain 'D' and resid 265 through 279 removed outlier: 3.567A pdb=" N VAL D 271 " --> pdb=" O GLY D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 290 removed outlier: 3.778A pdb=" N ILE D 283 " --> pdb=" O ALA D 279 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS D 290 " --> pdb=" O LEU D 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 143 removed outlier: 3.861A pdb=" N SER E 115 " --> pdb=" O ASN E 111 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU E 117 " --> pdb=" O ASP E 113 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU E 130 " --> pdb=" O TYR E 126 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU E 133 " --> pdb=" O ARG E 129 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL E 136 " --> pdb=" O MET E 132 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL E 141 " --> pdb=" O GLY E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 156 removed outlier: 3.566A pdb=" N LEU E 156 " --> pdb=" O PRO E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 186 removed outlier: 3.574A pdb=" N LYS E 180 " --> pdb=" O LEU E 176 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG E 186 " --> pdb=" O LEU E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 240 removed outlier: 3.675A pdb=" N VAL E 220 " --> pdb=" O ARG E 216 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG E 221 " --> pdb=" O GLN E 217 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU E 228 " --> pdb=" O ARG E 224 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TRP E 238 " --> pdb=" O SER E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 254 removed outlier: 3.659A pdb=" N ASP E 250 " --> pdb=" O GLU E 246 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER E 254 " --> pdb=" O ASP E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 263 removed outlier: 3.624A pdb=" N THR E 262 " --> pdb=" O ASN E 259 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR E 263 " --> pdb=" O ILE E 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 259 through 263' Processing helix chain 'E' and resid 265 through 279 removed outlier: 3.567A pdb=" N VAL E 271 " --> pdb=" O GLY E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 290 removed outlier: 3.779A pdb=" N ILE E 283 " --> pdb=" O ALA E 279 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS E 290 " --> pdb=" O LEU E 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 143 removed outlier: 3.861A pdb=" N SER F 115 " --> pdb=" O ASN F 111 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU F 117 " --> pdb=" O ASP F 113 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU F 130 " --> pdb=" O TYR F 126 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU F 133 " --> pdb=" O ARG F 129 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL F 136 " --> pdb=" O MET F 132 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL F 141 " --> pdb=" O GLY F 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 156 removed outlier: 3.566A pdb=" N LEU F 156 " --> pdb=" O PRO F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 186 removed outlier: 3.574A pdb=" N LYS F 180 " --> pdb=" O LEU F 176 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG F 186 " --> pdb=" O LEU F 182 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 240 removed outlier: 3.675A pdb=" N VAL F 220 " --> pdb=" O ARG F 216 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG F 221 " --> pdb=" O GLN F 217 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU F 228 " --> pdb=" O ARG F 224 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TRP F 238 " --> pdb=" O SER F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 254 removed outlier: 3.659A pdb=" N ASP F 250 " --> pdb=" O GLU F 246 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER F 254 " --> pdb=" O ASP F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 263 removed outlier: 3.625A pdb=" N THR F 262 " --> pdb=" O ASN F 259 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR F 263 " --> pdb=" O ILE F 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 259 through 263' Processing helix chain 'F' and resid 265 through 279 removed outlier: 3.567A pdb=" N VAL F 271 " --> pdb=" O GLY F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 290 removed outlier: 3.779A pdb=" N ILE F 283 " --> pdb=" O ALA F 279 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS F 290 " --> pdb=" O LEU F 286 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 143 removed outlier: 3.862A pdb=" N SER G 115 " --> pdb=" O ASN G 111 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU G 117 " --> pdb=" O ASP G 113 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU G 130 " --> pdb=" O TYR G 126 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU G 133 " --> pdb=" O ARG G 129 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL G 136 " --> pdb=" O MET G 132 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL G 141 " --> pdb=" O GLY G 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 152 through 156 removed outlier: 3.567A pdb=" N LEU G 156 " --> pdb=" O PRO G 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 186 removed outlier: 3.574A pdb=" N LYS G 180 " --> pdb=" O LEU G 176 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG G 186 " --> pdb=" O LEU G 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 214 through 240 removed outlier: 3.675A pdb=" N VAL G 220 " --> pdb=" O ARG G 216 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG G 221 " --> pdb=" O GLN G 217 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU G 228 " --> pdb=" O ARG G 224 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TRP G 238 " --> pdb=" O SER G 234 " (cutoff:3.500A) Processing helix chain 'G' and resid 243 through 254 removed outlier: 3.659A pdb=" N ASP G 250 " --> pdb=" O GLU G 246 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER G 254 " --> pdb=" O ASP G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 259 through 263 removed outlier: 3.625A pdb=" N THR G 262 " --> pdb=" O ASN G 259 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR G 263 " --> pdb=" O ILE G 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 259 through 263' Processing helix chain 'G' and resid 265 through 279 removed outlier: 3.567A pdb=" N VAL G 271 " --> pdb=" O GLY G 267 " (cutoff:3.500A) Processing helix chain 'G' and resid 279 through 290 removed outlier: 3.779A pdb=" N ILE G 283 " --> pdb=" O ALA G 279 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS G 290 " --> pdb=" O LEU G 286 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 143 removed outlier: 3.862A pdb=" N SER H 115 " --> pdb=" O ASN H 111 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU H 117 " --> pdb=" O ASP H 113 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU H 130 " --> pdb=" O TYR H 126 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU H 133 " --> pdb=" O ARG H 129 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL H 136 " --> pdb=" O MET H 132 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL H 141 " --> pdb=" O GLY H 137 " (cutoff:3.500A) Processing helix chain 'H' and resid 152 through 156 removed outlier: 3.567A pdb=" N LEU H 156 " --> pdb=" O PRO H 153 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 186 removed outlier: 3.574A pdb=" N LYS H 180 " --> pdb=" O LEU H 176 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG H 186 " --> pdb=" O LEU H 182 " (cutoff:3.500A) Processing helix chain 'H' and resid 214 through 240 removed outlier: 3.675A pdb=" N VAL H 220 " --> pdb=" O ARG H 216 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG H 221 " --> pdb=" O GLN H 217 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU H 228 " --> pdb=" O ARG H 224 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TRP H 238 " --> pdb=" O SER H 234 " (cutoff:3.500A) Processing helix chain 'H' and resid 243 through 254 removed outlier: 3.659A pdb=" N ASP H 250 " --> pdb=" O GLU H 246 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER H 254 " --> pdb=" O ASP H 250 " (cutoff:3.500A) Processing helix chain 'H' and resid 259 through 263 removed outlier: 3.625A pdb=" N THR H 262 " --> pdb=" O ASN H 259 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR H 263 " --> pdb=" O ILE H 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 259 through 263' Processing helix chain 'H' and resid 265 through 279 removed outlier: 3.567A pdb=" N VAL H 271 " --> pdb=" O GLY H 267 " (cutoff:3.500A) Processing helix chain 'H' and resid 279 through 290 removed outlier: 3.779A pdb=" N ILE H 283 " --> pdb=" O ALA H 279 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS H 290 " --> pdb=" O LEU H 286 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 143 removed outlier: 3.861A pdb=" N SER I 115 " --> pdb=" O ASN I 111 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU I 117 " --> pdb=" O ASP I 113 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU I 130 " --> pdb=" O TYR I 126 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU I 133 " --> pdb=" O ARG I 129 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL I 136 " --> pdb=" O MET I 132 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL I 141 " --> pdb=" O GLY I 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 152 through 156 removed outlier: 3.566A pdb=" N LEU I 156 " --> pdb=" O PRO I 153 " (cutoff:3.500A) Processing helix chain 'I' and resid 160 through 186 removed outlier: 3.575A pdb=" N LYS I 180 " --> pdb=" O LEU I 176 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG I 186 " --> pdb=" O LEU I 182 " (cutoff:3.500A) Processing helix chain 'I' and resid 214 through 240 removed outlier: 3.675A pdb=" N VAL I 220 " --> pdb=" O ARG I 216 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG I 221 " --> pdb=" O GLN I 217 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU I 228 " --> pdb=" O ARG I 224 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TRP I 238 " --> pdb=" O SER I 234 " (cutoff:3.500A) Processing helix chain 'I' and resid 243 through 254 removed outlier: 3.659A pdb=" N ASP I 250 " --> pdb=" O GLU I 246 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER I 254 " --> pdb=" O ASP I 250 " (cutoff:3.500A) Processing helix chain 'I' and resid 259 through 263 removed outlier: 3.625A pdb=" N THR I 262 " --> pdb=" O ASN I 259 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR I 263 " --> pdb=" O ILE I 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 259 through 263' Processing helix chain 'I' and resid 265 through 279 removed outlier: 3.567A pdb=" N VAL I 271 " --> pdb=" O GLY I 267 " (cutoff:3.500A) Processing helix chain 'I' and resid 279 through 290 removed outlier: 3.779A pdb=" N ILE I 283 " --> pdb=" O ALA I 279 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS I 290 " --> pdb=" O LEU I 286 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 143 removed outlier: 3.861A pdb=" N SER J 115 " --> pdb=" O ASN J 111 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU J 117 " --> pdb=" O ASP J 113 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU J 130 " --> pdb=" O TYR J 126 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU J 133 " --> pdb=" O ARG J 129 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL J 136 " --> pdb=" O MET J 132 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL J 141 " --> pdb=" O GLY J 137 " (cutoff:3.500A) Processing helix chain 'J' and resid 152 through 156 removed outlier: 3.567A pdb=" N LEU J 156 " --> pdb=" O PRO J 153 " (cutoff:3.500A) Processing helix chain 'J' and resid 160 through 186 removed outlier: 3.574A pdb=" N LYS J 180 " --> pdb=" O LEU J 176 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG J 186 " --> pdb=" O LEU J 182 " (cutoff:3.500A) Processing helix chain 'J' and resid 214 through 240 removed outlier: 3.675A pdb=" N VAL J 220 " --> pdb=" O ARG J 216 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG J 221 " --> pdb=" O GLN J 217 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU J 228 " --> pdb=" O ARG J 224 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TRP J 238 " --> pdb=" O SER J 234 " (cutoff:3.500A) Processing helix chain 'J' and resid 243 through 254 removed outlier: 3.659A pdb=" N ASP J 250 " --> pdb=" O GLU J 246 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER J 254 " --> pdb=" O ASP J 250 " (cutoff:3.500A) Processing helix chain 'J' and resid 259 through 263 removed outlier: 3.625A pdb=" N THR J 262 " --> pdb=" O ASN J 259 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR J 263 " --> pdb=" O ILE J 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 259 through 263' Processing helix chain 'J' and resid 265 through 279 removed outlier: 3.568A pdb=" N VAL J 271 " --> pdb=" O GLY J 267 " (cutoff:3.500A) Processing helix chain 'J' and resid 279 through 290 removed outlier: 3.779A pdb=" N ILE J 283 " --> pdb=" O ALA J 279 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS J 290 " --> pdb=" O LEU J 286 " (cutoff:3.500A) Processing helix chain 'K' and resid 111 through 143 removed outlier: 3.862A pdb=" N SER K 115 " --> pdb=" O ASN K 111 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU K 117 " --> pdb=" O ASP K 113 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU K 130 " --> pdb=" O TYR K 126 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU K 133 " --> pdb=" O ARG K 129 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL K 136 " --> pdb=" O MET K 132 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL K 141 " --> pdb=" O GLY K 137 " (cutoff:3.500A) Processing helix chain 'K' and resid 152 through 156 removed outlier: 3.567A pdb=" N LEU K 156 " --> pdb=" O PRO K 153 " (cutoff:3.500A) Processing helix chain 'K' and resid 160 through 186 removed outlier: 3.574A pdb=" N LYS K 180 " --> pdb=" O LEU K 176 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG K 186 " --> pdb=" O LEU K 182 " (cutoff:3.500A) Processing helix chain 'K' and resid 214 through 240 removed outlier: 3.675A pdb=" N VAL K 220 " --> pdb=" O ARG K 216 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG K 221 " --> pdb=" O GLN K 217 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU K 228 " --> pdb=" O ARG K 224 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TRP K 238 " --> pdb=" O SER K 234 " (cutoff:3.500A) Processing helix chain 'K' and resid 243 through 254 removed outlier: 3.660A pdb=" N ASP K 250 " --> pdb=" O GLU K 246 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER K 254 " --> pdb=" O ASP K 250 " (cutoff:3.500A) Processing helix chain 'K' and resid 259 through 263 removed outlier: 3.624A pdb=" N THR K 262 " --> pdb=" O ASN K 259 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR K 263 " --> pdb=" O ILE K 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 259 through 263' Processing helix chain 'K' and resid 265 through 279 removed outlier: 3.567A pdb=" N VAL K 271 " --> pdb=" O GLY K 267 " (cutoff:3.500A) Processing helix chain 'K' and resid 279 through 290 removed outlier: 3.779A pdb=" N ILE K 283 " --> pdb=" O ALA K 279 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS K 290 " --> pdb=" O LEU K 286 " (cutoff:3.500A) 946 hydrogen bonds defined for protein. 2805 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.06 Time building geometry restraints manager: 3.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.35: 8287 1.35 - 1.51: 13747 1.51 - 1.67: 8304 1.67 - 1.83: 99 1.83 - 1.99: 484 Bond restraints: 30921 Sorted by residual: bond pdb=" CAD CLA H 610 " pdb=" CBD CLA H 610 " ideal model delta sigma weight residual 1.563 1.414 0.149 2.00e-02 2.50e+03 5.56e+01 bond pdb=" CAD CLA I 610 " pdb=" CBD CLA I 610 " ideal model delta sigma weight residual 1.563 1.414 0.149 2.00e-02 2.50e+03 5.55e+01 bond pdb=" CAD CLA E 610 " pdb=" CBD CLA E 610 " ideal model delta sigma weight residual 1.563 1.414 0.149 2.00e-02 2.50e+03 5.55e+01 bond pdb=" CAD CLA B 610 " pdb=" CBD CLA B 610 " ideal model delta sigma weight residual 1.563 1.414 0.149 2.00e-02 2.50e+03 5.55e+01 bond pdb=" CAD CLA K 610 " pdb=" CBD CLA K 610 " ideal model delta sigma weight residual 1.563 1.414 0.149 2.00e-02 2.50e+03 5.54e+01 ... (remaining 30916 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.11: 41748 4.11 - 8.21: 1933 8.21 - 12.32: 110 12.32 - 16.42: 66 16.42 - 20.53: 88 Bond angle restraints: 43945 Sorted by residual: angle pdb=" NB CLA B 603 " pdb="MG CLA B 603 " pdb=" ND CLA B 603 " ideal model delta sigma weight residual 176.90 156.37 20.53 3.00e+00 1.11e-01 4.68e+01 angle pdb=" NB CLA J 603 " pdb="MG CLA J 603 " pdb=" ND CLA J 603 " ideal model delta sigma weight residual 176.90 156.39 20.51 3.00e+00 1.11e-01 4.67e+01 angle pdb=" NB CLA C 603 " pdb="MG CLA C 603 " pdb=" ND CLA C 603 " ideal model delta sigma weight residual 176.90 156.40 20.50 3.00e+00 1.11e-01 4.67e+01 angle pdb=" NB CLA E 603 " pdb="MG CLA E 603 " pdb=" ND CLA E 603 " ideal model delta sigma weight residual 176.90 156.41 20.49 3.00e+00 1.11e-01 4.67e+01 angle pdb=" NB CLA I 603 " pdb="MG CLA I 603 " pdb=" ND CLA I 603 " ideal model delta sigma weight residual 176.90 156.41 20.49 3.00e+00 1.11e-01 4.67e+01 ... (remaining 43940 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.20: 12233 20.20 - 40.40: 1616 40.40 - 60.60: 748 60.60 - 80.80: 121 80.80 - 101.00: 77 Dihedral angle restraints: 14795 sinusoidal: 7337 harmonic: 7458 Sorted by residual: dihedral pdb=" CA GLY E 145 " pdb=" C GLY E 145 " pdb=" N LYS E 146 " pdb=" CA LYS E 146 " ideal model delta harmonic sigma weight residual -180.00 -158.83 -21.17 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA GLY J 145 " pdb=" C GLY J 145 " pdb=" N LYS J 146 " pdb=" CA LYS J 146 " ideal model delta harmonic sigma weight residual 180.00 -158.83 -21.17 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA GLY B 145 " pdb=" C GLY B 145 " pdb=" N LYS B 146 " pdb=" CA LYS B 146 " ideal model delta harmonic sigma weight residual -180.00 -158.84 -21.16 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 14792 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 3051 0.087 - 0.175: 427 0.175 - 0.262: 137 0.262 - 0.349: 80 0.349 - 0.437: 23 Chirality restraints: 3718 Sorted by residual: chirality pdb=" C29 32N B 613 " pdb=" C28 32N B 613 " pdb=" C30 32N B 613 " pdb=" C34 32N B 613 " both_signs ideal model delta sigma weight residual False -2.44 -2.00 -0.44 2.00e-01 2.50e+01 4.76e+00 chirality pdb=" C29 32N I 613 " pdb=" C28 32N I 613 " pdb=" C30 32N I 613 " pdb=" C34 32N I 613 " both_signs ideal model delta sigma weight residual False -2.44 -2.00 -0.44 2.00e-01 2.50e+01 4.75e+00 chirality pdb=" C29 32N D 613 " pdb=" C28 32N D 613 " pdb=" C30 32N D 613 " pdb=" C34 32N D 613 " both_signs ideal model delta sigma weight residual False -2.44 -2.00 -0.44 2.00e-01 2.50e+01 4.73e+00 ... (remaining 3715 not shown) Planarity restraints: 5852 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1A CLA H 606 " -0.027 2.00e-02 2.50e+03 2.08e-01 6.47e+02 pdb=" C2A CLA H 606 " -0.301 2.00e-02 2.50e+03 pdb=" C4A CLA H 606 " 0.284 2.00e-02 2.50e+03 pdb=" CHA CLA H 606 " 0.213 2.00e-02 2.50e+03 pdb=" NA CLA H 606 " 0.032 2.00e-02 2.50e+03 pdb="MG CLA H 606 " -0.201 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1A CLA C 606 " 0.027 2.00e-02 2.50e+03 2.08e-01 6.47e+02 pdb=" C2A CLA C 606 " 0.301 2.00e-02 2.50e+03 pdb=" C4A CLA C 606 " -0.284 2.00e-02 2.50e+03 pdb=" CHA CLA C 606 " -0.213 2.00e-02 2.50e+03 pdb=" NA CLA C 606 " -0.032 2.00e-02 2.50e+03 pdb="MG CLA C 606 " 0.201 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1A CLA F 606 " 0.027 2.00e-02 2.50e+03 2.08e-01 6.47e+02 pdb=" C2A CLA F 606 " 0.301 2.00e-02 2.50e+03 pdb=" C4A CLA F 606 " -0.283 2.00e-02 2.50e+03 pdb=" CHA CLA F 606 " -0.213 2.00e-02 2.50e+03 pdb=" NA CLA F 606 " -0.032 2.00e-02 2.50e+03 pdb="MG CLA F 606 " 0.201 2.00e-02 2.50e+03 ... (remaining 5849 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 967 2.69 - 3.24: 24883 3.24 - 3.79: 44951 3.79 - 4.35: 58987 4.35 - 4.90: 101292 Nonbonded interactions: 231080 Sorted by model distance: nonbonded pdb=" O VAL F 271 " pdb=" OG SER F 275 " model vdw 2.137 3.040 nonbonded pdb=" O VAL K 271 " pdb=" OG SER K 275 " model vdw 2.137 3.040 nonbonded pdb=" O VAL B 271 " pdb=" OG SER B 275 " model vdw 2.137 3.040 nonbonded pdb=" O VAL I 271 " pdb=" OG SER I 275 " model vdw 2.137 3.040 nonbonded pdb=" O VAL G 271 " pdb=" OG SER G 275 " model vdw 2.138 3.040 ... (remaining 231075 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.390 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: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 21.980 Find NCS groups from input model: 0.210 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: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 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 : 0.031 0.686 30965 Z= 1.861 Angle : 1.980 20.526 43945 Z= 0.767 Chirality : 0.089 0.437 3718 Planarity : 0.029 0.208 5852 Dihedral : 22.402 100.996 10043 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.30 % Favored : 88.70 % Rotamer: Outliers : 6.74 % Allowed : 7.77 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.57 (0.15), residues: 2629 helix: -0.39 (0.14), residues: 1309 sheet: None (None), residues: 0 loop : -3.23 (0.14), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG K 116 TYR 0.008 0.001 TYR K 68 PHE 0.022 0.003 PHE I 230 TRP 0.009 0.002 TRP D 69 HIS 0.009 0.003 HIS K 193 Details of bonding type rmsd covalent geometry : bond 0.02444 (30921) covalent geometry : angle 1.98002 (43945) hydrogen bonds : bond 0.17699 ( 946) hydrogen bonds : angle 6.37413 ( 2805) Misc. bond : bond 0.51889 ( 44) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 2123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 478 time to evaluate : 0.835 Fit side-chains REVERT: A 57 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.6789 (tp30) REVERT: A 115 SER cc_start: 0.8882 (t) cc_final: 0.8646 (m) REVERT: A 132 MET cc_start: 0.8638 (mtm) cc_final: 0.8227 (mtp) REVERT: B 115 SER cc_start: 0.8821 (t) cc_final: 0.8593 (m) REVERT: B 132 MET cc_start: 0.8667 (mtm) cc_final: 0.8258 (mtp) REVERT: B 190 GLU cc_start: 0.8035 (tt0) cc_final: 0.7817 (tt0) REVERT: B 242 LYS cc_start: 0.8743 (mttm) cc_final: 0.8245 (mttt) REVERT: B 290 LYS cc_start: 0.7201 (OUTLIER) cc_final: 0.6846 (ttmt) REVERT: C 200 ASP cc_start: 0.8481 (OUTLIER) cc_final: 0.8138 (t0) REVERT: C 290 LYS cc_start: 0.7269 (OUTLIER) cc_final: 0.6951 (ttpt) REVERT: D 54 MET cc_start: 0.8292 (mtp) cc_final: 0.8024 (mtp) REVERT: D 204 LEU cc_start: 0.8701 (mt) cc_final: 0.8426 (mp) REVERT: E 59 ASP cc_start: 0.8286 (p0) cc_final: 0.8080 (p0) REVERT: E 180 LYS cc_start: 0.8673 (tptt) cc_final: 0.7886 (tptm) REVERT: E 184 ASN cc_start: 0.7965 (m-40) cc_final: 0.7682 (m-40) REVERT: E 200 ASP cc_start: 0.8440 (OUTLIER) cc_final: 0.7989 (t0) REVERT: E 227 MET cc_start: 0.9042 (mtt) cc_final: 0.8769 (mtp) REVERT: F 115 SER cc_start: 0.8836 (t) cc_final: 0.8595 (m) REVERT: F 180 LYS cc_start: 0.8883 (tptt) cc_final: 0.8679 (tptm) REVERT: F 246 GLU cc_start: 0.6896 (mp0) cc_final: 0.6534 (mp0) REVERT: G 132 MET cc_start: 0.8651 (mtm) cc_final: 0.8423 (mtm) REVERT: G 180 LYS cc_start: 0.8675 (tptt) cc_final: 0.7930 (tptm) REVERT: H 132 MET cc_start: 0.8654 (mtm) cc_final: 0.8357 (mtp) REVERT: H 180 LYS cc_start: 0.8796 (tptt) cc_final: 0.8314 (tptm) REVERT: I 102 GLN cc_start: 0.8896 (mt0) cc_final: 0.8444 (mt0) REVERT: I 115 SER cc_start: 0.8850 (t) cc_final: 0.8621 (m) REVERT: I 132 MET cc_start: 0.8622 (mtm) cc_final: 0.8417 (mtp) REVERT: I 180 LYS cc_start: 0.8568 (tptt) cc_final: 0.7772 (tptm) REVERT: I 184 ASN cc_start: 0.7911 (m-40) cc_final: 0.7665 (m110) REVERT: I 190 GLU cc_start: 0.8155 (tt0) cc_final: 0.7845 (tt0) REVERT: I 200 ASP cc_start: 0.8656 (OUTLIER) cc_final: 0.8346 (t0) REVERT: J 132 MET cc_start: 0.8588 (mtm) cc_final: 0.8217 (mtp) REVERT: J 200 ASP cc_start: 0.8560 (OUTLIER) cc_final: 0.8348 (m-30) REVERT: J 242 LYS cc_start: 0.8720 (mttm) cc_final: 0.8147 (mttt) REVERT: K 117 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8280 (mt) REVERT: K 227 MET cc_start: 0.8986 (mtt) cc_final: 0.8727 (mtm) outliers start: 143 outliers final: 43 residues processed: 557 average time/residue: 0.1953 time to fit residues: 171.8762 Evaluate side-chains 448 residues out of total 2123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 397 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 290 LYS Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 200 ASP Chi-restraints excluded: chain E residue 257 GLU Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 106 ASP Chi-restraints excluded: chain F residue 257 GLU Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 73 SER Chi-restraints excluded: chain G residue 106 ASP Chi-restraints excluded: chain G residue 257 GLU Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 257 GLU Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 106 ASP Chi-restraints excluded: chain I residue 200 ASP Chi-restraints excluded: chain I residue 257 GLU Chi-restraints excluded: chain I residue 275 SER Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain J residue 106 ASP Chi-restraints excluded: chain J residue 200 ASP Chi-restraints excluded: chain J residue 257 GLU Chi-restraints excluded: chain K residue 57 GLU Chi-restraints excluded: chain K residue 84 SER Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain K residue 257 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.8980 chunk 111 optimal weight: 0.0470 overall best weight: 1.1082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 ASN B 184 ASN B 247 ASN C 184 ASN E 236 GLN E 247 ASN F 247 ASN G 236 GLN H 184 ASN I 247 ASN J 247 ASN K 184 ASN K 247 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.132209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.101446 restraints weight = 35716.011| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.69 r_work: 0.2862 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.532 30965 Z= 0.185 Angle : 0.826 10.235 43945 Z= 0.341 Chirality : 0.059 0.411 3718 Planarity : 0.006 0.033 5852 Dihedral : 18.982 99.642 5439 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 1.79 % Allowed : 13.09 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.16), residues: 2629 helix: 0.46 (0.14), residues: 1419 sheet: None (None), residues: 0 loop : -3.21 (0.15), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 89 TYR 0.014 0.002 TYR E 112 PHE 0.014 0.002 PHE J 159 TRP 0.008 0.001 TRP E 100 HIS 0.004 0.001 HIS I 80 Details of bonding type rmsd covalent geometry : bond 0.00319 (30921) covalent geometry : angle 0.82567 (43945) hydrogen bonds : bond 0.05089 ( 946) hydrogen bonds : angle 4.05316 ( 2805) Misc. bond : bond 0.26328 ( 44) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 433 time to evaluate : 0.861 Fit side-chains REVERT: A 56 GLU cc_start: 0.6944 (mt-10) cc_final: 0.6641 (mt-10) REVERT: A 57 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.6775 (tp30) REVERT: A 106 ASP cc_start: 0.7592 (m-30) cc_final: 0.7291 (t0) REVERT: A 132 MET cc_start: 0.8764 (mtm) cc_final: 0.8321 (mtp) REVERT: B 57 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.6687 (tp30) REVERT: B 115 SER cc_start: 0.8836 (t) cc_final: 0.8564 (m) REVERT: B 132 MET cc_start: 0.8769 (mtm) cc_final: 0.8507 (mtp) REVERT: B 183 GLU cc_start: 0.7971 (tt0) cc_final: 0.7671 (tm-30) REVERT: C 57 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.6733 (tp30) REVERT: C 200 ASP cc_start: 0.8475 (OUTLIER) cc_final: 0.8093 (t0) REVERT: D 57 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7392 (tp30) REVERT: D 180 LYS cc_start: 0.8630 (tptt) cc_final: 0.8255 (tptm) REVERT: D 210 LEU cc_start: 0.8804 (mp) cc_final: 0.8453 (mt) REVERT: D 213 ASP cc_start: 0.9022 (p0) cc_final: 0.8821 (p0) REVERT: E 57 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.6903 (tp30) REVERT: E 59 ASP cc_start: 0.8382 (p0) cc_final: 0.8093 (p0) REVERT: E 180 LYS cc_start: 0.8449 (tptt) cc_final: 0.7838 (tptm) REVERT: E 200 ASP cc_start: 0.8551 (OUTLIER) cc_final: 0.8141 (t0) REVERT: E 213 ASP cc_start: 0.8982 (p0) cc_final: 0.8730 (p0) REVERT: F 57 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.6708 (tp30) REVERT: F 106 ASP cc_start: 0.7815 (m-30) cc_final: 0.7517 (t0) REVERT: F 257 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.8091 (pm20) REVERT: G 57 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7051 (tp30) REVERT: G 180 LYS cc_start: 0.8467 (tptt) cc_final: 0.7926 (tptm) REVERT: H 180 LYS cc_start: 0.8670 (tptt) cc_final: 0.8265 (tptm) REVERT: I 57 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.6858 (tp30) REVERT: I 106 ASP cc_start: 0.7739 (m-30) cc_final: 0.7412 (t0) REVERT: I 180 LYS cc_start: 0.8456 (tptt) cc_final: 0.7983 (tptm) REVERT: I 190 GLU cc_start: 0.8397 (tt0) cc_final: 0.7980 (tt0) REVERT: I 200 ASP cc_start: 0.8745 (OUTLIER) cc_final: 0.8361 (t0) REVERT: I 213 ASP cc_start: 0.8851 (p0) cc_final: 0.8613 (p0) REVERT: I 250 ASP cc_start: 0.7854 (m-30) cc_final: 0.7472 (m-30) REVERT: J 57 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.6852 (tp30) REVERT: J 106 ASP cc_start: 0.7912 (m-30) cc_final: 0.7685 (t0) REVERT: J 132 MET cc_start: 0.8820 (mtm) cc_final: 0.8586 (mtp) REVERT: J 183 GLU cc_start: 0.8148 (tm-30) cc_final: 0.7921 (tp30) REVERT: J 242 LYS cc_start: 0.8652 (mttm) cc_final: 0.7872 (mtmt) REVERT: K 111 ASN cc_start: 0.7877 (m-40) cc_final: 0.7633 (m-40) REVERT: K 142 GLU cc_start: 0.8150 (tm-30) cc_final: 0.7859 (tt0) outliers start: 38 outliers final: 5 residues processed: 456 average time/residue: 0.2020 time to fit residues: 143.9253 Evaluate side-chains 418 residues out of total 2123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 400 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 200 ASP Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 257 GLU Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain I residue 200 ASP Chi-restraints excluded: chain J residue 57 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 190 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 213 optimal weight: 5.9990 chunk 209 optimal weight: 5.9990 chunk 168 optimal weight: 10.0000 chunk 255 optimal weight: 0.6980 chunk 157 optimal weight: 9.9990 chunk 94 optimal weight: 4.9990 chunk 127 optimal weight: 5.9990 chunk 217 optimal weight: 3.9990 chunk 108 optimal weight: 9.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 184 ASN E 184 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.125371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.093751 restraints weight = 35707.267| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 1.63 r_work: 0.2697 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2554 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.525 30965 Z= 0.269 Angle : 0.907 13.675 43945 Z= 0.373 Chirality : 0.062 0.424 3718 Planarity : 0.007 0.049 5852 Dihedral : 18.289 100.993 5360 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.74 % Favored : 90.26 % Rotamer: Outliers : 1.55 % Allowed : 15.36 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.54 (0.16), residues: 2629 helix: 0.51 (0.14), residues: 1430 sheet: None (None), residues: 0 loop : -3.11 (0.16), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 221 TYR 0.015 0.002 TYR G 68 PHE 0.024 0.002 PHE C 230 TRP 0.009 0.002 TRP D 150 HIS 0.011 0.002 HIS I 80 Details of bonding type rmsd covalent geometry : bond 0.00573 (30921) covalent geometry : angle 0.90732 (43945) hydrogen bonds : bond 0.05932 ( 946) hydrogen bonds : angle 3.91848 ( 2805) Misc. bond : bond 0.25481 ( 44) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 422 time to evaluate : 0.881 Fit side-chains REVERT: A 106 ASP cc_start: 0.7561 (m-30) cc_final: 0.7144 (t0) REVERT: A 132 MET cc_start: 0.8804 (mtm) cc_final: 0.8379 (mtp) REVERT: B 115 SER cc_start: 0.8901 (t) cc_final: 0.8602 (m) REVERT: B 183 GLU cc_start: 0.8002 (tt0) cc_final: 0.7692 (tm-30) REVERT: C 200 ASP cc_start: 0.8429 (OUTLIER) cc_final: 0.7945 (t0) REVERT: C 290 LYS cc_start: 0.7303 (mtpp) cc_final: 0.6898 (ttpt) REVERT: D 254 SER cc_start: 0.8369 (p) cc_final: 0.8120 (p) REVERT: E 59 ASP cc_start: 0.8440 (p0) cc_final: 0.8168 (p0) REVERT: E 117 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8271 (tt) REVERT: E 180 LYS cc_start: 0.8372 (tptt) cc_final: 0.8042 (tptt) REVERT: E 200 ASP cc_start: 0.8422 (OUTLIER) cc_final: 0.7993 (t0) REVERT: E 227 MET cc_start: 0.9222 (mtt) cc_final: 0.8971 (mtp) REVERT: E 290 LYS cc_start: 0.7432 (mtpp) cc_final: 0.7133 (ttmt) REVERT: F 106 ASP cc_start: 0.7909 (m-30) cc_final: 0.7547 (t0) REVERT: G 180 LYS cc_start: 0.8491 (tptt) cc_final: 0.7876 (tptm) REVERT: H 180 LYS cc_start: 0.8645 (tptt) cc_final: 0.8293 (tptm) REVERT: I 102 GLN cc_start: 0.9117 (mt0) cc_final: 0.8887 (mt0) REVERT: I 106 ASP cc_start: 0.7772 (m-30) cc_final: 0.7410 (t0) REVERT: I 180 LYS cc_start: 0.8443 (tptt) cc_final: 0.7901 (tptm) REVERT: I 200 ASP cc_start: 0.8757 (OUTLIER) cc_final: 0.8340 (t0) REVERT: I 213 ASP cc_start: 0.8992 (p0) cc_final: 0.8728 (p0) REVERT: I 246 GLU cc_start: 0.6933 (mp0) cc_final: 0.6709 (mp0) REVERT: I 250 ASP cc_start: 0.7661 (m-30) cc_final: 0.7279 (m-30) REVERT: J 183 GLU cc_start: 0.8122 (tm-30) cc_final: 0.7877 (tp30) REVERT: J 254 SER cc_start: 0.8540 (p) cc_final: 0.8315 (p) outliers start: 33 outliers final: 17 residues processed: 443 average time/residue: 0.1864 time to fit residues: 133.3219 Evaluate side-chains 429 residues out of total 2123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 408 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 200 ASP Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 257 GLU Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain I residue 64 ILE Chi-restraints excluded: chain I residue 200 ASP Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain K residue 64 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 135 optimal weight: 6.9990 chunk 228 optimal weight: 10.0000 chunk 101 optimal weight: 0.0040 chunk 235 optimal weight: 10.0000 chunk 217 optimal weight: 1.9990 chunk 242 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 7 optimal weight: 0.7980 chunk 121 optimal weight: 0.0020 chunk 67 optimal weight: 9.9990 chunk 71 optimal weight: 4.9990 overall best weight: 1.5604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 102 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.132472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.101577 restraints weight = 35142.891| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 1.67 r_work: 0.2839 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.465 30965 Z= 0.164 Angle : 0.734 10.232 43945 Z= 0.304 Chirality : 0.053 0.385 3718 Planarity : 0.005 0.039 5852 Dihedral : 17.003 80.627 5333 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 1.18 % Allowed : 17.00 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.16), residues: 2629 helix: 0.92 (0.14), residues: 1430 sheet: None (None), residues: 0 loop : -2.83 (0.16), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 89 TYR 0.011 0.001 TYR E 112 PHE 0.014 0.001 PHE A 230 TRP 0.008 0.001 TRP H 100 HIS 0.004 0.001 HIS I 80 Details of bonding type rmsd covalent geometry : bond 0.00305 (30921) covalent geometry : angle 0.73367 (43945) hydrogen bonds : bond 0.04645 ( 946) hydrogen bonds : angle 3.61704 ( 2805) Misc. bond : bond 0.22626 ( 44) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 413 time to evaluate : 0.868 Fit side-chains REVERT: A 106 ASP cc_start: 0.7540 (m-30) cc_final: 0.7250 (t0) REVERT: A 132 MET cc_start: 0.8717 (mtm) cc_final: 0.8393 (mtp) REVERT: B 115 SER cc_start: 0.8820 (t) cc_final: 0.8541 (m) REVERT: C 200 ASP cc_start: 0.8392 (OUTLIER) cc_final: 0.8052 (t0) REVERT: C 290 LYS cc_start: 0.7379 (mtpp) cc_final: 0.7012 (ttpt) REVERT: D 180 LYS cc_start: 0.8748 (tptt) cc_final: 0.8403 (tptm) REVERT: D 254 SER cc_start: 0.8475 (p) cc_final: 0.8256 (p) REVERT: E 180 LYS cc_start: 0.8448 (tptt) cc_final: 0.8212 (tptt) REVERT: E 200 ASP cc_start: 0.8299 (OUTLIER) cc_final: 0.7963 (t0) REVERT: E 290 LYS cc_start: 0.7517 (mtpp) cc_final: 0.7227 (ttmt) REVERT: F 106 ASP cc_start: 0.7784 (m-30) cc_final: 0.7539 (t0) REVERT: F 115 SER cc_start: 0.9010 (t) cc_final: 0.8772 (m) REVERT: G 180 LYS cc_start: 0.8621 (tptt) cc_final: 0.8117 (tptm) REVERT: G 245 ILE cc_start: 0.8192 (mm) cc_final: 0.7921 (mp) REVERT: H 132 MET cc_start: 0.8906 (mtm) cc_final: 0.8702 (mtp) REVERT: H 180 LYS cc_start: 0.8704 (tptt) cc_final: 0.8312 (tptm) REVERT: H 200 ASP cc_start: 0.8275 (OUTLIER) cc_final: 0.7984 (t0) REVERT: H 206 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8172 (mt-10) REVERT: I 106 ASP cc_start: 0.7740 (m-30) cc_final: 0.7478 (t0) REVERT: I 115 SER cc_start: 0.8871 (t) cc_final: 0.8666 (m) REVERT: I 190 GLU cc_start: 0.8374 (tt0) cc_final: 0.8011 (tt0) REVERT: I 200 ASP cc_start: 0.8731 (OUTLIER) cc_final: 0.8318 (t0) REVERT: I 213 ASP cc_start: 0.8977 (p0) cc_final: 0.8553 (p0) REVERT: I 250 ASP cc_start: 0.7822 (m-30) cc_final: 0.7444 (m-30) REVERT: J 183 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7918 (tp30) outliers start: 25 outliers final: 15 residues processed: 427 average time/residue: 0.1920 time to fit residues: 130.7654 Evaluate side-chains 417 residues out of total 2123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 398 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 200 ASP Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain G residue 265 ASP Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 200 ASP Chi-restraints excluded: chain I residue 200 ASP Chi-restraints excluded: chain J residue 172 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 218 optimal weight: 6.9990 chunk 182 optimal weight: 9.9990 chunk 54 optimal weight: 5.9990 chunk 94 optimal weight: 9.9990 chunk 148 optimal weight: 0.3980 chunk 19 optimal weight: 8.9990 chunk 99 optimal weight: 10.0000 chunk 115 optimal weight: 7.9990 chunk 167 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 191 optimal weight: 3.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 247 ASN F 102 GLN ** J 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.128440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.097089 restraints weight = 35458.159| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 1.70 r_work: 0.2766 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2624 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.494 30965 Z= 0.219 Angle : 0.825 12.371 43945 Z= 0.338 Chirality : 0.057 0.399 3718 Planarity : 0.006 0.050 5852 Dihedral : 17.033 67.961 5330 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.85 % Favored : 90.15 % Rotamer: Outliers : 2.17 % Allowed : 17.90 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.17), residues: 2629 helix: 0.94 (0.14), residues: 1441 sheet: None (None), residues: 0 loop : -2.86 (0.16), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 221 TYR 0.011 0.002 TYR E 112 PHE 0.020 0.002 PHE B 230 TRP 0.007 0.002 TRP G 150 HIS 0.004 0.001 HIS I 80 Details of bonding type rmsd covalent geometry : bond 0.00457 (30921) covalent geometry : angle 0.82540 (43945) hydrogen bonds : bond 0.05275 ( 946) hydrogen bonds : angle 3.63245 ( 2805) Misc. bond : bond 0.23951 ( 44) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 409 time to evaluate : 0.923 Fit side-chains REVERT: A 106 ASP cc_start: 0.7558 (m-30) cc_final: 0.7226 (t0) REVERT: A 132 MET cc_start: 0.8743 (mtm) cc_final: 0.8275 (mtp) REVERT: A 290 LYS cc_start: 0.7781 (mtpp) cc_final: 0.7542 (ttpt) REVERT: B 115 SER cc_start: 0.8950 (t) cc_final: 0.8654 (m) REVERT: C 200 ASP cc_start: 0.8436 (OUTLIER) cc_final: 0.7956 (t0) REVERT: C 290 LYS cc_start: 0.7472 (mtpp) cc_final: 0.7155 (ttpt) REVERT: D 180 LYS cc_start: 0.8756 (tptt) cc_final: 0.8391 (tptm) REVERT: D 254 SER cc_start: 0.8442 (p) cc_final: 0.8198 (p) REVERT: E 59 ASP cc_start: 0.8470 (p0) cc_final: 0.8219 (p0) REVERT: E 180 LYS cc_start: 0.8464 (tptt) cc_final: 0.7906 (tptm) REVERT: E 200 ASP cc_start: 0.8317 (OUTLIER) cc_final: 0.7964 (t0) REVERT: E 290 LYS cc_start: 0.7576 (mtpp) cc_final: 0.7310 (ttmt) REVERT: F 106 ASP cc_start: 0.7758 (m-30) cc_final: 0.7495 (t0) REVERT: F 115 SER cc_start: 0.9068 (t) cc_final: 0.8839 (m) REVERT: G 180 LYS cc_start: 0.8592 (tptt) cc_final: 0.8123 (tptm) REVERT: G 245 ILE cc_start: 0.8191 (mm) cc_final: 0.7912 (mp) REVERT: H 180 LYS cc_start: 0.8744 (tptt) cc_final: 0.8341 (tptm) REVERT: H 200 ASP cc_start: 0.8321 (OUTLIER) cc_final: 0.8006 (t0) REVERT: H 206 GLU cc_start: 0.8369 (mt-10) cc_final: 0.8109 (mt-10) REVERT: I 106 ASP cc_start: 0.7801 (m-30) cc_final: 0.7484 (t0) REVERT: I 180 LYS cc_start: 0.8424 (tptt) cc_final: 0.8018 (tptm) REVERT: I 190 GLU cc_start: 0.8426 (tt0) cc_final: 0.8064 (tt0) REVERT: I 200 ASP cc_start: 0.8756 (OUTLIER) cc_final: 0.8353 (t0) REVERT: I 213 ASP cc_start: 0.9060 (p0) cc_final: 0.8715 (p0) REVERT: I 250 ASP cc_start: 0.7751 (m-30) cc_final: 0.7382 (m-30) REVERT: J 183 GLU cc_start: 0.8189 (tm-30) cc_final: 0.7949 (tp30) REVERT: J 254 SER cc_start: 0.8586 (p) cc_final: 0.8339 (p) REVERT: K 178 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7206 (mm-30) outliers start: 46 outliers final: 25 residues processed: 440 average time/residue: 0.1887 time to fit residues: 133.6164 Evaluate side-chains 432 residues out of total 2123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 402 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 200 ASP Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 265 ASP Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 200 ASP Chi-restraints excluded: chain I residue 64 ILE Chi-restraints excluded: chain I residue 200 ASP Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 187 GLU Chi-restraints excluded: chain K residue 64 ILE Chi-restraints excluded: chain K residue 178 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 77 optimal weight: 0.0670 chunk 118 optimal weight: 7.9990 chunk 153 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 238 optimal weight: 6.9990 chunk 225 optimal weight: 7.9990 chunk 251 optimal weight: 5.9990 chunk 167 optimal weight: 0.9990 chunk 22 optimal weight: 7.9990 chunk 199 optimal weight: 4.9990 overall best weight: 2.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 247 ASN E 247 ASN F 102 GLN ** J 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.129414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.098410 restraints weight = 35247.048| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 1.67 r_work: 0.2793 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.482 30965 Z= 0.214 Angle : 0.822 12.035 43945 Z= 0.341 Chirality : 0.057 0.398 3718 Planarity : 0.006 0.075 5852 Dihedral : 16.931 69.194 5330 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.59 % Favored : 90.41 % Rotamer: Outliers : 2.50 % Allowed : 18.23 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.17), residues: 2629 helix: 1.04 (0.14), residues: 1441 sheet: None (None), residues: 0 loop : -2.88 (0.16), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 221 TYR 0.012 0.002 TYR E 112 PHE 0.019 0.002 PHE B 230 TRP 0.008 0.002 TRP K 100 HIS 0.003 0.001 HIS H 193 Details of bonding type rmsd covalent geometry : bond 0.00442 (30921) covalent geometry : angle 0.82212 (43945) hydrogen bonds : bond 0.05296 ( 946) hydrogen bonds : angle 3.63951 ( 2805) Misc. bond : bond 0.23345 ( 44) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 394 time to evaluate : 0.878 Fit side-chains REVERT: A 106 ASP cc_start: 0.7535 (m-30) cc_final: 0.7242 (t0) REVERT: A 132 MET cc_start: 0.8739 (mtp) cc_final: 0.8266 (mtp) REVERT: B 115 SER cc_start: 0.8935 (t) cc_final: 0.8645 (m) REVERT: B 290 LYS cc_start: 0.7637 (mtpp) cc_final: 0.7164 (ttmt) REVERT: C 200 ASP cc_start: 0.8446 (OUTLIER) cc_final: 0.7956 (t0) REVERT: C 290 LYS cc_start: 0.7513 (mtpp) cc_final: 0.7244 (ttpt) REVERT: D 180 LYS cc_start: 0.8777 (tptt) cc_final: 0.8432 (tptm) REVERT: D 254 SER cc_start: 0.8448 (p) cc_final: 0.8190 (p) REVERT: E 59 ASP cc_start: 0.8489 (p0) cc_final: 0.8264 (p0) REVERT: E 180 LYS cc_start: 0.8453 (tptt) cc_final: 0.7930 (tptm) REVERT: E 200 ASP cc_start: 0.8322 (OUTLIER) cc_final: 0.7968 (t0) REVERT: E 290 LYS cc_start: 0.7592 (mtpp) cc_final: 0.7312 (ttmt) REVERT: F 106 ASP cc_start: 0.7727 (m-30) cc_final: 0.7497 (t0) REVERT: F 115 SER cc_start: 0.9053 (t) cc_final: 0.8831 (m) REVERT: F 180 LYS cc_start: 0.8656 (tptm) cc_final: 0.8444 (tptt) REVERT: G 180 LYS cc_start: 0.8609 (tptt) cc_final: 0.8121 (tptm) REVERT: G 245 ILE cc_start: 0.8188 (mm) cc_final: 0.7913 (mp) REVERT: H 180 LYS cc_start: 0.8727 (tptt) cc_final: 0.8357 (tptm) REVERT: I 106 ASP cc_start: 0.7758 (m-30) cc_final: 0.7525 (t0) REVERT: I 115 SER cc_start: 0.8952 (t) cc_final: 0.8733 (m) REVERT: I 180 LYS cc_start: 0.8416 (tptt) cc_final: 0.8053 (tptm) REVERT: I 200 ASP cc_start: 0.8746 (OUTLIER) cc_final: 0.8383 (t0) REVERT: I 213 ASP cc_start: 0.9066 (p0) cc_final: 0.8658 (p0) REVERT: I 246 GLU cc_start: 0.6972 (mp0) cc_final: 0.6769 (mp0) REVERT: I 250 ASP cc_start: 0.7770 (m-30) cc_final: 0.7404 (m-30) REVERT: I 290 LYS cc_start: 0.7629 (mtpp) cc_final: 0.7337 (ttpt) REVERT: J 183 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7970 (tp30) REVERT: J 254 SER cc_start: 0.8595 (p) cc_final: 0.8344 (p) REVERT: K 142 GLU cc_start: 0.8271 (tm-30) cc_final: 0.7954 (tt0) REVERT: K 178 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7190 (mm-30) outliers start: 53 outliers final: 31 residues processed: 429 average time/residue: 0.1966 time to fit residues: 134.3332 Evaluate side-chains 417 residues out of total 2123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 382 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 249 LYS Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 200 ASP Chi-restraints excluded: chain E residue 265 ASP Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 265 ASP Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain I residue 64 ILE Chi-restraints excluded: chain I residue 200 ASP Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 106 ASP Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 187 GLU Chi-restraints excluded: chain K residue 64 ILE Chi-restraints excluded: chain K residue 178 GLU Chi-restraints excluded: chain K residue 206 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 3.9990 chunk 29 optimal weight: 0.0370 chunk 245 optimal weight: 0.7980 chunk 214 optimal weight: 6.9990 chunk 260 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 247 optimal weight: 4.9990 chunk 136 optimal weight: 8.9990 chunk 192 optimal weight: 10.0000 overall best weight: 1.7664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 247 ASN F 102 GLN ** J 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.129933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.098437 restraints weight = 35363.761| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 1.69 r_work: 0.2772 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2631 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.459 30965 Z= 0.173 Angle : 0.760 11.428 43945 Z= 0.317 Chirality : 0.053 0.378 3718 Planarity : 0.006 0.074 5852 Dihedral : 16.613 67.834 5330 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.81 % Favored : 90.19 % Rotamer: Outliers : 1.84 % Allowed : 18.84 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.17), residues: 2629 helix: 1.32 (0.14), residues: 1441 sheet: None (None), residues: 0 loop : -2.81 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 221 TYR 0.011 0.001 TYR E 112 PHE 0.016 0.001 PHE A 230 TRP 0.008 0.001 TRP F 149 HIS 0.003 0.001 HIS B 193 Details of bonding type rmsd covalent geometry : bond 0.00334 (30921) covalent geometry : angle 0.76006 (43945) hydrogen bonds : bond 0.04915 ( 946) hydrogen bonds : angle 3.55843 ( 2805) Misc. bond : bond 0.22243 ( 44) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 396 time to evaluate : 0.947 Fit side-chains REVERT: A 106 ASP cc_start: 0.7603 (m-30) cc_final: 0.7264 (t0) REVERT: A 132 MET cc_start: 0.8690 (mtp) cc_final: 0.8267 (mtp) REVERT: B 115 SER cc_start: 0.8891 (t) cc_final: 0.8622 (m) REVERT: B 132 MET cc_start: 0.8726 (mtm) cc_final: 0.8428 (mtp) REVERT: B 290 LYS cc_start: 0.7742 (mtpp) cc_final: 0.7306 (ttmt) REVERT: C 200 ASP cc_start: 0.8414 (OUTLIER) cc_final: 0.7922 (t0) REVERT: C 290 LYS cc_start: 0.7468 (mtpp) cc_final: 0.7231 (ttpt) REVERT: D 180 LYS cc_start: 0.8752 (tptt) cc_final: 0.8404 (tptm) REVERT: D 254 SER cc_start: 0.8356 (p) cc_final: 0.8107 (p) REVERT: E 180 LYS cc_start: 0.8442 (tptt) cc_final: 0.7947 (tptm) REVERT: F 106 ASP cc_start: 0.7777 (m-30) cc_final: 0.7503 (t0) REVERT: F 115 SER cc_start: 0.8999 (t) cc_final: 0.8792 (m) REVERT: F 180 LYS cc_start: 0.8760 (tptm) cc_final: 0.8481 (tptt) REVERT: F 213 ASP cc_start: 0.9148 (p0) cc_final: 0.8802 (p0) REVERT: G 180 LYS cc_start: 0.8529 (tptt) cc_final: 0.8234 (tptp) REVERT: G 245 ILE cc_start: 0.8133 (mm) cc_final: 0.7863 (mp) REVERT: H 180 LYS cc_start: 0.8665 (tptt) cc_final: 0.8275 (tptm) REVERT: H 206 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8123 (mt-10) REVERT: I 106 ASP cc_start: 0.7732 (m-30) cc_final: 0.7510 (t0) REVERT: I 115 SER cc_start: 0.8901 (t) cc_final: 0.8695 (m) REVERT: I 180 LYS cc_start: 0.8387 (tptt) cc_final: 0.8037 (tptm) REVERT: I 200 ASP cc_start: 0.8702 (OUTLIER) cc_final: 0.8332 (t0) REVERT: I 213 ASP cc_start: 0.9057 (p0) cc_final: 0.8602 (p0) REVERT: I 250 ASP cc_start: 0.7738 (m-30) cc_final: 0.7360 (m-30) REVERT: I 290 LYS cc_start: 0.7565 (mtpp) cc_final: 0.7304 (ttpt) REVERT: J 183 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7939 (tp30) REVERT: J 254 SER cc_start: 0.8572 (p) cc_final: 0.8322 (p) REVERT: K 59 ASP cc_start: 0.8372 (p0) cc_final: 0.8122 (p0) REVERT: K 142 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7863 (tt0) REVERT: K 178 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.7137 (mm-30) outliers start: 39 outliers final: 26 residues processed: 424 average time/residue: 0.1926 time to fit residues: 130.6541 Evaluate side-chains 417 residues out of total 2123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 388 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 249 LYS Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 265 ASP Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain I residue 64 ILE Chi-restraints excluded: chain I residue 200 ASP Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 187 GLU Chi-restraints excluded: chain K residue 64 ILE Chi-restraints excluded: chain K residue 178 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 247 optimal weight: 3.9990 chunk 234 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 86 optimal weight: 9.9990 chunk 232 optimal weight: 8.9990 chunk 3 optimal weight: 0.4980 chunk 224 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 102 GLN ** J 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.127310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.095749 restraints weight = 35684.530| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 1.70 r_work: 0.2747 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2606 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.480 30965 Z= 0.227 Angle : 0.843 13.069 43945 Z= 0.350 Chirality : 0.057 0.395 3718 Planarity : 0.006 0.098 5852 Dihedral : 16.856 72.657 5328 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.89 % Favored : 90.11 % Rotamer: Outliers : 1.98 % Allowed : 19.27 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.17), residues: 2629 helix: 1.21 (0.14), residues: 1441 sheet: None (None), residues: 0 loop : -2.81 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 288 TYR 0.011 0.002 TYR E 112 PHE 0.022 0.002 PHE C 230 TRP 0.011 0.002 TRP K 149 HIS 0.003 0.001 HIS B 193 Details of bonding type rmsd covalent geometry : bond 0.00476 (30921) covalent geometry : angle 0.84331 (43945) hydrogen bonds : bond 0.05443 ( 946) hydrogen bonds : angle 3.61842 ( 2805) Misc. bond : bond 0.23457 ( 44) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 396 time to evaluate : 0.908 Fit side-chains REVERT: A 106 ASP cc_start: 0.7570 (m-30) cc_final: 0.7247 (t0) REVERT: A 132 MET cc_start: 0.8704 (mtp) cc_final: 0.8213 (mtp) REVERT: B 115 SER cc_start: 0.8922 (t) cc_final: 0.8621 (m) REVERT: B 132 MET cc_start: 0.8776 (mtm) cc_final: 0.8499 (mtp) REVERT: B 224 ARG cc_start: 0.9088 (OUTLIER) cc_final: 0.8747 (mtt180) REVERT: B 254 SER cc_start: 0.8490 (p) cc_final: 0.8256 (p) REVERT: B 290 LYS cc_start: 0.7710 (mtpp) cc_final: 0.7294 (ttmt) REVERT: C 200 ASP cc_start: 0.8436 (OUTLIER) cc_final: 0.7939 (t0) REVERT: C 290 LYS cc_start: 0.7563 (mtpp) cc_final: 0.7331 (ttpt) REVERT: D 180 LYS cc_start: 0.8760 (tptt) cc_final: 0.8398 (tptm) REVERT: D 254 SER cc_start: 0.8355 (p) cc_final: 0.8083 (p) REVERT: E 56 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.7017 (mt-10) REVERT: E 180 LYS cc_start: 0.8420 (tptt) cc_final: 0.7919 (tptm) REVERT: F 106 ASP cc_start: 0.7790 (m-30) cc_final: 0.7500 (t0) REVERT: F 115 SER cc_start: 0.9064 (t) cc_final: 0.8842 (m) REVERT: G 180 LYS cc_start: 0.8596 (tptt) cc_final: 0.8322 (tptp) REVERT: G 245 ILE cc_start: 0.8180 (mm) cc_final: 0.7911 (mp) REVERT: H 180 LYS cc_start: 0.8674 (tptt) cc_final: 0.8257 (tptm) REVERT: H 206 GLU cc_start: 0.8324 (mt-10) cc_final: 0.8083 (mt-10) REVERT: I 180 LYS cc_start: 0.8391 (tptt) cc_final: 0.8020 (tptm) REVERT: I 213 ASP cc_start: 0.9086 (p0) cc_final: 0.8686 (p0) REVERT: I 246 GLU cc_start: 0.6937 (mp0) cc_final: 0.6714 (mp0) REVERT: I 250 ASP cc_start: 0.7734 (m-30) cc_final: 0.7364 (m-30) REVERT: I 290 LYS cc_start: 0.7535 (mtpp) cc_final: 0.7303 (ttpt) REVERT: J 183 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7939 (tp30) REVERT: J 254 SER cc_start: 0.8597 (p) cc_final: 0.8329 (p) REVERT: K 142 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7866 (tt0) REVERT: K 254 SER cc_start: 0.8454 (p) cc_final: 0.8241 (p) outliers start: 42 outliers final: 32 residues processed: 422 average time/residue: 0.1911 time to fit residues: 129.7746 Evaluate side-chains 424 residues out of total 2123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 389 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 224 ARG Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 249 LYS Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 265 ASP Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 183 GLU Chi-restraints excluded: chain G residue 265 ASP Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain I residue 64 ILE Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 187 GLU Chi-restraints excluded: chain K residue 64 ILE Chi-restraints excluded: chain K residue 206 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 61 optimal weight: 5.9990 chunk 127 optimal weight: 7.9990 chunk 112 optimal weight: 7.9990 chunk 64 optimal weight: 0.9990 chunk 164 optimal weight: 7.9990 chunk 214 optimal weight: 5.9990 chunk 115 optimal weight: 6.9990 chunk 142 optimal weight: 3.9990 chunk 241 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 chunk 85 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 102 GLN ** J 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.125455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.094054 restraints weight = 35666.834| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 1.69 r_work: 0.2706 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2564 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.490 30965 Z= 0.268 Angle : 0.910 13.992 43945 Z= 0.377 Chirality : 0.061 0.423 3718 Planarity : 0.007 0.086 5852 Dihedral : 17.184 78.653 5326 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.38 % Favored : 89.62 % Rotamer: Outliers : 1.79 % Allowed : 19.88 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.93 (0.17), residues: 2629 helix: 1.04 (0.14), residues: 1441 sheet: None (None), residues: 0 loop : -2.89 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 288 TYR 0.011 0.002 TYR E 112 PHE 0.025 0.002 PHE C 230 TRP 0.010 0.002 TRP F 149 HIS 0.003 0.001 HIS I 80 Details of bonding type rmsd covalent geometry : bond 0.00580 (30921) covalent geometry : angle 0.91033 (43945) hydrogen bonds : bond 0.05927 ( 946) hydrogen bonds : angle 3.71434 ( 2805) Misc. bond : bond 0.23913 ( 44) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 396 time to evaluate : 0.871 Fit side-chains REVERT: A 106 ASP cc_start: 0.7585 (m-30) cc_final: 0.7257 (t0) REVERT: A 132 MET cc_start: 0.8749 (mtp) cc_final: 0.8229 (mtp) REVERT: B 115 SER cc_start: 0.8926 (t) cc_final: 0.8617 (m) REVERT: B 132 MET cc_start: 0.8789 (mtm) cc_final: 0.8513 (mtp) REVERT: B 190 GLU cc_start: 0.8474 (tt0) cc_final: 0.8246 (tt0) REVERT: B 224 ARG cc_start: 0.9139 (OUTLIER) cc_final: 0.8778 (mtt180) REVERT: B 254 SER cc_start: 0.8482 (p) cc_final: 0.8238 (p) REVERT: B 290 LYS cc_start: 0.7868 (mtpp) cc_final: 0.7496 (ttmt) REVERT: C 200 ASP cc_start: 0.8473 (OUTLIER) cc_final: 0.7958 (t0) REVERT: D 180 LYS cc_start: 0.8748 (tptt) cc_final: 0.8387 (tptm) REVERT: D 254 SER cc_start: 0.8316 (p) cc_final: 0.8051 (p) REVERT: E 56 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.7042 (mt-10) REVERT: E 180 LYS cc_start: 0.8397 (tptt) cc_final: 0.7879 (tptm) REVERT: F 106 ASP cc_start: 0.7731 (m-30) cc_final: 0.7461 (t0) REVERT: F 115 SER cc_start: 0.9071 (t) cc_final: 0.8853 (m) REVERT: F 180 LYS cc_start: 0.8716 (tptm) cc_final: 0.8500 (tptt) REVERT: G 180 LYS cc_start: 0.8512 (tptt) cc_final: 0.8084 (tptm) REVERT: G 213 ASP cc_start: 0.8996 (p0) cc_final: 0.8704 (p0) REVERT: H 180 LYS cc_start: 0.8730 (tptt) cc_final: 0.8290 (tptm) REVERT: H 206 GLU cc_start: 0.8358 (mt-10) cc_final: 0.8123 (mt-10) REVERT: I 180 LYS cc_start: 0.8413 (tptt) cc_final: 0.8052 (tptm) REVERT: I 213 ASP cc_start: 0.9097 (p0) cc_final: 0.8748 (p0) REVERT: J 183 GLU cc_start: 0.8197 (tm-30) cc_final: 0.7973 (tp30) REVERT: J 213 ASP cc_start: 0.8965 (p0) cc_final: 0.8756 (p0) REVERT: J 254 SER cc_start: 0.8583 (p) cc_final: 0.8298 (p) REVERT: K 142 GLU cc_start: 0.8217 (tm-30) cc_final: 0.7881 (tt0) REVERT: K 254 SER cc_start: 0.8407 (p) cc_final: 0.8184 (p) outliers start: 38 outliers final: 31 residues processed: 417 average time/residue: 0.1896 time to fit residues: 127.4409 Evaluate side-chains 424 residues out of total 2123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 390 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 224 ARG Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 249 LYS Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 265 ASP Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 183 GLU Chi-restraints excluded: chain G residue 265 ASP Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain I residue 64 ILE Chi-restraints excluded: chain I residue 176 LEU Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 187 GLU Chi-restraints excluded: chain K residue 64 ILE Chi-restraints excluded: chain K residue 206 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 60 optimal weight: 1.9990 chunk 263 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 151 optimal weight: 0.0570 chunk 123 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 233 optimal weight: 0.8980 chunk 239 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 126 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 overall best weight: 0.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 102 GLN ** J 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.135307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.105343 restraints weight = 34949.187| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 1.59 r_work: 0.2869 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.421 30965 Z= 0.152 Angle : 0.722 11.506 43945 Z= 0.304 Chirality : 0.050 0.366 3718 Planarity : 0.005 0.063 5852 Dihedral : 16.461 70.621 5326 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 1.27 % Allowed : 20.35 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.17), residues: 2629 helix: 1.52 (0.14), residues: 1441 sheet: None (None), residues: 0 loop : -2.83 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 129 TYR 0.010 0.001 TYR E 112 PHE 0.016 0.001 PHE K 174 TRP 0.014 0.001 TRP K 149 HIS 0.002 0.001 HIS A 171 Details of bonding type rmsd covalent geometry : bond 0.00283 (30921) covalent geometry : angle 0.72174 (43945) hydrogen bonds : bond 0.04532 ( 946) hydrogen bonds : angle 3.48644 ( 2805) Misc. bond : bond 0.20753 ( 44) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5258 Ramachandran restraints generated. 2629 Oldfield, 0 Emsley, 2629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 381 time to evaluate : 0.898 Fit side-chains REVERT: A 106 ASP cc_start: 0.7541 (m-30) cc_final: 0.7323 (t0) REVERT: A 132 MET cc_start: 0.8677 (mtp) cc_final: 0.8297 (mtp) REVERT: A 228 LEU cc_start: 0.8557 (pt) cc_final: 0.8336 (mt) REVERT: B 115 SER cc_start: 0.8776 (t) cc_final: 0.8520 (m) REVERT: B 132 MET cc_start: 0.8715 (mtm) cc_final: 0.8407 (mtp) REVERT: B 290 LYS cc_start: 0.7743 (mtpp) cc_final: 0.7428 (ttmt) REVERT: C 200 ASP cc_start: 0.8384 (OUTLIER) cc_final: 0.7903 (t0) REVERT: D 59 ASP cc_start: 0.8342 (p0) cc_final: 0.8123 (p0) REVERT: D 180 LYS cc_start: 0.8795 (tptt) cc_final: 0.8446 (tptm) REVERT: D 254 SER cc_start: 0.8422 (p) cc_final: 0.8191 (p) REVERT: F 228 LEU cc_start: 0.8766 (pt) cc_final: 0.8379 (mt) REVERT: G 180 LYS cc_start: 0.8642 (tptt) cc_final: 0.8431 (tptm) REVERT: G 228 LEU cc_start: 0.8715 (pt) cc_final: 0.8479 (mt) REVERT: G 291 LYS cc_start: 0.6821 (mmtm) cc_final: 0.6600 (mmtm) REVERT: H 180 LYS cc_start: 0.8675 (tptt) cc_final: 0.8280 (tptm) REVERT: H 290 LYS cc_start: 0.7821 (ttmt) cc_final: 0.7548 (mtpp) REVERT: I 180 LYS cc_start: 0.8451 (tptt) cc_final: 0.8123 (tptm) REVERT: I 213 ASP cc_start: 0.9031 (p0) cc_final: 0.8573 (p0) REVERT: J 228 LEU cc_start: 0.8806 (pt) cc_final: 0.8486 (mt) REVERT: J 254 SER cc_start: 0.8563 (p) cc_final: 0.8319 (p) REVERT: K 59 ASP cc_start: 0.8412 (p0) cc_final: 0.8100 (p0) REVERT: K 142 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7870 (tt0) REVERT: K 228 LEU cc_start: 0.8634 (pt) cc_final: 0.8409 (mt) outliers start: 27 outliers final: 16 residues processed: 399 average time/residue: 0.1922 time to fit residues: 123.3272 Evaluate side-chains 390 residues out of total 2123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 373 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 265 ASP Chi-restraints excluded: chain E residue 290 LYS Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain G residue 183 GLU Chi-restraints excluded: chain G residue 265 ASP Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 187 GLU Chi-restraints excluded: chain J residue 200 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 160 optimal weight: 8.9990 chunk 65 optimal weight: 6.9990 chunk 206 optimal weight: 9.9990 chunk 120 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 118 optimal weight: 8.9990 chunk 189 optimal weight: 7.9990 chunk 88 optimal weight: 8.9990 chunk 216 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 29 optimal weight: 0.4980 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 102 GLN ** J 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.125793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.094379 restraints weight = 35810.774| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 1.70 r_work: 0.2737 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2595 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.488 30965 Z= 0.270 Angle : 0.895 13.803 43945 Z= 0.372 Chirality : 0.060 0.407 3718 Planarity : 0.007 0.068 5852 Dihedral : 17.027 79.775 5326 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.76 % Favored : 89.24 % Rotamer: Outliers : 1.46 % Allowed : 20.58 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.17), residues: 2629 helix: 1.18 (0.14), residues: 1441 sheet: None (None), residues: 0 loop : -2.86 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 224 TYR 0.012 0.002 TYR G 68 PHE 0.024 0.002 PHE B 230 TRP 0.020 0.002 TRP K 149 HIS 0.003 0.001 HIS I 80 Details of bonding type rmsd covalent geometry : bond 0.00584 (30921) covalent geometry : angle 0.89527 (43945) hydrogen bonds : bond 0.05777 ( 946) hydrogen bonds : angle 3.65815 ( 2805) Misc. bond : bond 0.23855 ( 44) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7443.25 seconds wall clock time: 128 minutes 10.07 seconds (7690.07 seconds total)