Starting phenix.real_space_refine on Tue Nov 18 09:43:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vx5_21430/11_2025/6vx5_21430.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vx5_21430/11_2025/6vx5_21430.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6vx5_21430/11_2025/6vx5_21430.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vx5_21430/11_2025/6vx5_21430.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vx5_21430/11_2025/6vx5_21430.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vx5_21430/11_2025/6vx5_21430.map" } resolution = 3.03 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= 0.002 sd= 0.050 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 90 5.16 5 Cl 1 4.86 5 C 8565 2.51 5 N 2140 2.21 5 O 2260 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 100 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13056 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2611 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 8, 'TRANS': 306} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D, E Time building chain proxies: 2.36, per 1000 atoms: 0.18 Number of scatterers: 13056 At special positions: 0 Unit cell: (92.96, 92.96, 109.56, 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) Cl 1 17.00 S 90 16.00 O 2260 8.00 N 2140 7.00 C 8565 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 611.2 milliseconds 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2990 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 0 sheets defined 74.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'E' and resid 28 through 44 removed outlier: 3.879A pdb=" N TRP E 33 " --> pdb=" O TYR E 29 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ARG E 34 " --> pdb=" O LYS E 30 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N GLU E 35 " --> pdb=" O LEU E 31 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N CYS E 38 " --> pdb=" O ARG E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 53 removed outlier: 3.514A pdb=" N ALA E 49 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR E 50 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG E 51 " --> pdb=" O SER E 47 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE E 52 " --> pdb=" O ALA E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 64 removed outlier: 4.193A pdb=" N TYR E 61 " --> pdb=" O GLU E 57 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS E 64 " --> pdb=" O ARG E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 99 removed outlier: 4.297A pdb=" N VAL E 78 " --> pdb=" O SER E 74 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER E 79 " --> pdb=" O LEU E 75 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY E 83 " --> pdb=" O SER E 79 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU E 88 " --> pdb=" O PHE E 84 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER E 99 " --> pdb=" O ASN E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 114 removed outlier: 3.907A pdb=" N CYS E 108 " --> pdb=" O ASP E 104 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N VAL E 109 " --> pdb=" O ALA E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 144 removed outlier: 3.516A pdb=" N ARG E 125 " --> pdb=" O GLY E 121 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ILE E 139 " --> pdb=" O SER E 135 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER E 142 " --> pdb=" O LEU E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 149 Processing helix chain 'E' and resid 153 through 160 Processing helix chain 'E' and resid 166 through 173 removed outlier: 3.560A pdb=" N LYS E 170 " --> pdb=" O GLU E 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 198 removed outlier: 3.656A pdb=" N CYS E 189 " --> pdb=" O CYS E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 230 removed outlier: 3.595A pdb=" N PHE E 217 " --> pdb=" O GLU E 213 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU E 224 " --> pdb=" O LYS E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 255 removed outlier: 3.707A pdb=" N VAL E 240 " --> pdb=" O TYR E 236 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU E 249 " --> pdb=" O TYR E 245 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU E 252 " --> pdb=" O PHE E 248 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG E 255 " --> pdb=" O CYS E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 263 removed outlier: 3.937A pdb=" N GLN E 262 " --> pdb=" O ASP E 259 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY E 263 " --> pdb=" O PRO E 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 259 through 263' Processing helix chain 'E' and resid 274 through 279 removed outlier: 3.593A pdb=" N LEU E 278 " --> pdb=" O PRO E 274 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU E 279 " --> pdb=" O ILE E 275 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 274 through 279' Processing helix chain 'E' and resid 280 through 294 removed outlier: 3.778A pdb=" N ALA E 291 " --> pdb=" O TRP E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 322 removed outlier: 3.519A pdb=" N SER E 318 " --> pdb=" O CYS E 314 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET E 319 " --> pdb=" O PHE E 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 44 removed outlier: 3.880A pdb=" N TRP C 33 " --> pdb=" O TYR C 29 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ARG C 34 " --> pdb=" O LYS C 30 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N GLU C 35 " --> pdb=" O LEU C 31 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N CYS C 38 " --> pdb=" O ARG C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 53 removed outlier: 3.514A pdb=" N ALA C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR C 50 " --> pdb=" O LEU C 46 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG C 51 " --> pdb=" O SER C 47 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE C 52 " --> pdb=" O ALA C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 64 removed outlier: 4.193A pdb=" N TYR C 61 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS C 64 " --> pdb=" O ARG C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 99 removed outlier: 4.297A pdb=" N VAL C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER C 79 " --> pdb=" O LEU C 75 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY C 83 " --> pdb=" O SER C 79 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU C 88 " --> pdb=" O PHE C 84 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER C 99 " --> pdb=" O ASN C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 114 removed outlier: 3.907A pdb=" N CYS C 108 " --> pdb=" O ASP C 104 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N VAL C 109 " --> pdb=" O ALA C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 144 removed outlier: 3.517A pdb=" N ARG C 125 " --> pdb=" O GLY C 121 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ILE C 139 " --> pdb=" O SER C 135 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER C 142 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 149 Processing helix chain 'C' and resid 153 through 160 Processing helix chain 'C' and resid 166 through 173 removed outlier: 3.560A pdb=" N LYS C 170 " --> pdb=" O GLU C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 198 removed outlier: 3.657A pdb=" N CYS C 189 " --> pdb=" O CYS C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 230 removed outlier: 3.596A pdb=" N PHE C 217 " --> pdb=" O GLU C 213 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU C 224 " --> pdb=" O LYS C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 255 removed outlier: 3.708A pdb=" N VAL C 240 " --> pdb=" O TYR C 236 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU C 249 " --> pdb=" O TYR C 245 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU C 252 " --> pdb=" O PHE C 248 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG C 255 " --> pdb=" O CYS C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 263 removed outlier: 3.937A pdb=" N GLN C 262 " --> pdb=" O ASP C 259 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY C 263 " --> pdb=" O PRO C 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 259 through 263' Processing helix chain 'C' and resid 274 through 279 removed outlier: 3.594A pdb=" N LEU C 278 " --> pdb=" O PRO C 274 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU C 279 " --> pdb=" O ILE C 275 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 274 through 279' Processing helix chain 'C' and resid 280 through 294 removed outlier: 3.778A pdb=" N ALA C 291 " --> pdb=" O TRP C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 322 removed outlier: 3.519A pdb=" N SER C 318 " --> pdb=" O CYS C 314 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET C 319 " --> pdb=" O PHE C 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 44 removed outlier: 3.880A pdb=" N TRP B 33 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ARG B 34 " --> pdb=" O LYS B 30 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N GLU B 35 " --> pdb=" O LEU B 31 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N CYS B 38 " --> pdb=" O ARG B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 53 removed outlier: 3.515A pdb=" N ALA B 49 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N TYR B 50 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG B 51 " --> pdb=" O SER B 47 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE B 52 " --> pdb=" O ALA B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 64 removed outlier: 4.193A pdb=" N TYR B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS B 64 " --> pdb=" O ARG B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 99 removed outlier: 4.297A pdb=" N VAL B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER B 79 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU B 88 " --> pdb=" O PHE B 84 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER B 99 " --> pdb=" O ASN B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 114 removed outlier: 3.907A pdb=" N CYS B 108 " --> pdb=" O ASP B 104 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N VAL B 109 " --> pdb=" O ALA B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 144 removed outlier: 3.516A pdb=" N ARG B 125 " --> pdb=" O GLY B 121 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ILE B 139 " --> pdb=" O SER B 135 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER B 142 " --> pdb=" O LEU B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 149 Processing helix chain 'B' and resid 153 through 160 Processing helix chain 'B' and resid 166 through 173 removed outlier: 3.560A pdb=" N LYS B 170 " --> pdb=" O GLU B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 198 removed outlier: 3.657A pdb=" N CYS B 189 " --> pdb=" O CYS B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 230 removed outlier: 3.595A pdb=" N PHE B 217 " --> pdb=" O GLU B 213 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU B 224 " --> pdb=" O LYS B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 255 removed outlier: 3.707A pdb=" N VAL B 240 " --> pdb=" O TYR B 236 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU B 249 " --> pdb=" O TYR B 245 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU B 252 " --> pdb=" O PHE B 248 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG B 255 " --> pdb=" O CYS B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 263 removed outlier: 3.936A pdb=" N GLN B 262 " --> pdb=" O ASP B 259 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY B 263 " --> pdb=" O PRO B 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 259 through 263' Processing helix chain 'B' and resid 274 through 279 removed outlier: 3.594A pdb=" N LEU B 278 " --> pdb=" O PRO B 274 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU B 279 " --> pdb=" O ILE B 275 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 274 through 279' Processing helix chain 'B' and resid 280 through 294 removed outlier: 3.778A pdb=" N ALA B 291 " --> pdb=" O TRP B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 322 removed outlier: 3.519A pdb=" N SER B 318 " --> pdb=" O CYS B 314 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N MET B 319 " --> pdb=" O PHE B 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 44 removed outlier: 3.879A pdb=" N TRP A 33 " --> pdb=" O TYR A 29 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ARG A 34 " --> pdb=" O LYS A 30 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N GLU A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N CYS A 38 " --> pdb=" O ARG A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 53 removed outlier: 3.515A pdb=" N ALA A 49 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N TYR A 50 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE A 52 " --> pdb=" O ALA A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 64 removed outlier: 4.194A pdb=" N TYR A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS A 64 " --> pdb=" O ARG A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 99 removed outlier: 4.297A pdb=" N VAL A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY A 83 " --> pdb=" O SER A 79 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A 88 " --> pdb=" O PHE A 84 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER A 99 " --> pdb=" O ASN A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 114 removed outlier: 3.907A pdb=" N CYS A 108 " --> pdb=" O ASP A 104 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N VAL A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 144 removed outlier: 3.517A pdb=" N ARG A 125 " --> pdb=" O GLY A 121 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ILE A 139 " --> pdb=" O SER A 135 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 149 Processing helix chain 'A' and resid 153 through 160 Processing helix chain 'A' and resid 166 through 173 removed outlier: 3.559A pdb=" N LYS A 170 " --> pdb=" O GLU A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 198 removed outlier: 3.657A pdb=" N CYS A 189 " --> pdb=" O CYS A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 230 removed outlier: 3.595A pdb=" N PHE A 217 " --> pdb=" O GLU A 213 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 224 " --> pdb=" O LYS A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 255 removed outlier: 3.707A pdb=" N VAL A 240 " --> pdb=" O TYR A 236 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU A 249 " --> pdb=" O TYR A 245 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU A 252 " --> pdb=" O PHE A 248 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG A 255 " --> pdb=" O CYS A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 263 removed outlier: 3.937A pdb=" N GLN A 262 " --> pdb=" O ASP A 259 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY A 263 " --> pdb=" O PRO A 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 259 through 263' Processing helix chain 'A' and resid 274 through 279 removed outlier: 3.594A pdb=" N LEU A 278 " --> pdb=" O PRO A 274 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU A 279 " --> pdb=" O ILE A 275 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 274 through 279' Processing helix chain 'A' and resid 280 through 294 removed outlier: 3.778A pdb=" N ALA A 291 " --> pdb=" O TRP A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 322 removed outlier: 3.520A pdb=" N SER A 318 " --> pdb=" O CYS A 314 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N MET A 319 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 44 removed outlier: 3.880A pdb=" N TRP D 33 " --> pdb=" O TYR D 29 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ARG D 34 " --> pdb=" O LYS D 30 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N GLU D 35 " --> pdb=" O LEU D 31 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N CYS D 38 " --> pdb=" O ARG D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 53 removed outlier: 3.516A pdb=" N ALA D 49 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N TYR D 50 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG D 51 " --> pdb=" O SER D 47 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE D 52 " --> pdb=" O ALA D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 64 removed outlier: 4.193A pdb=" N TYR D 61 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS D 64 " --> pdb=" O ARG D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 99 removed outlier: 4.297A pdb=" N VAL D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER D 79 " --> pdb=" O LEU D 75 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY D 83 " --> pdb=" O SER D 79 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU D 88 " --> pdb=" O PHE D 84 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER D 99 " --> pdb=" O ASN D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 114 removed outlier: 3.907A pdb=" N CYS D 108 " --> pdb=" O ASP D 104 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N VAL D 109 " --> pdb=" O ALA D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 144 removed outlier: 3.517A pdb=" N ARG D 125 " --> pdb=" O GLY D 121 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ILE D 139 " --> pdb=" O SER D 135 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N SER D 142 " --> pdb=" O LEU D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 149 Processing helix chain 'D' and resid 153 through 160 Processing helix chain 'D' and resid 166 through 173 removed outlier: 3.560A pdb=" N LYS D 170 " --> pdb=" O GLU D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 198 removed outlier: 3.657A pdb=" N CYS D 189 " --> pdb=" O CYS D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 230 removed outlier: 3.595A pdb=" N PHE D 217 " --> pdb=" O GLU D 213 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU D 224 " --> pdb=" O LYS D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 255 removed outlier: 3.707A pdb=" N VAL D 240 " --> pdb=" O TYR D 236 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU D 249 " --> pdb=" O TYR D 245 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU D 252 " --> pdb=" O PHE D 248 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG D 255 " --> pdb=" O CYS D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 263 removed outlier: 3.937A pdb=" N GLN D 262 " --> pdb=" O ASP D 259 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY D 263 " --> pdb=" O PRO D 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 259 through 263' Processing helix chain 'D' and resid 274 through 279 removed outlier: 3.594A pdb=" N LEU D 278 " --> pdb=" O PRO D 274 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU D 279 " --> pdb=" O ILE D 275 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 274 through 279' Processing helix chain 'D' and resid 280 through 294 removed outlier: 3.778A pdb=" N ALA D 291 " --> pdb=" O TRP D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 322 removed outlier: 3.520A pdb=" N SER D 318 " --> pdb=" O CYS D 314 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N MET D 319 " --> pdb=" O PHE D 315 " (cutoff:3.500A) 680 hydrogen bonds defined for protein. 2040 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.12 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3510 1.33 - 1.45: 2822 1.45 - 1.57: 6948 1.57 - 1.69: 0 1.69 - 1.81: 135 Bond restraints: 13415 Sorted by residual: bond pdb=" N VAL E 183 " pdb=" CA VAL E 183 " ideal model delta sigma weight residual 1.463 1.497 -0.034 1.20e-02 6.94e+03 7.92e+00 bond pdb=" N VAL C 183 " pdb=" CA VAL C 183 " ideal model delta sigma weight residual 1.463 1.497 -0.034 1.20e-02 6.94e+03 7.83e+00 bond pdb=" N CYS A 272 " pdb=" CA CYS A 272 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.32e-02 5.74e+03 7.82e+00 bond pdb=" N VAL D 183 " pdb=" CA VAL D 183 " ideal model delta sigma weight residual 1.463 1.496 -0.033 1.20e-02 6.94e+03 7.77e+00 bond pdb=" N CYS E 272 " pdb=" CA CYS E 272 " ideal model delta sigma weight residual 1.459 1.495 -0.037 1.32e-02 5.74e+03 7.76e+00 ... (remaining 13410 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 17318 1.60 - 3.20: 712 3.20 - 4.80: 120 4.80 - 6.40: 25 6.40 - 8.00: 15 Bond angle restraints: 18190 Sorted by residual: angle pdb=" CA VAL E 183 " pdb=" C VAL E 183 " pdb=" N PRO E 184 " ideal model delta sigma weight residual 120.83 122.81 -1.98 6.10e-01 2.69e+00 1.06e+01 angle pdb=" CA VAL D 183 " pdb=" C VAL D 183 " pdb=" N PRO D 184 " ideal model delta sigma weight residual 120.83 122.80 -1.97 6.10e-01 2.69e+00 1.05e+01 angle pdb=" CA VAL A 183 " pdb=" C VAL A 183 " pdb=" N PRO A 184 " ideal model delta sigma weight residual 120.83 122.79 -1.96 6.10e-01 2.69e+00 1.03e+01 angle pdb=" CA VAL B 183 " pdb=" C VAL B 183 " pdb=" N PRO B 184 " ideal model delta sigma weight residual 120.83 122.79 -1.96 6.10e-01 2.69e+00 1.03e+01 angle pdb=" CA VAL C 183 " pdb=" C VAL C 183 " pdb=" N PRO C 184 " ideal model delta sigma weight residual 120.83 122.77 -1.94 6.10e-01 2.69e+00 1.01e+01 ... (remaining 18185 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 7020 17.79 - 35.58: 655 35.58 - 53.37: 65 53.37 - 71.17: 25 71.17 - 88.96: 15 Dihedral angle restraints: 7780 sinusoidal: 3125 harmonic: 4655 Sorted by residual: dihedral pdb=" CA ARG B 200 " pdb=" C ARG B 200 " pdb=" N ILE B 201 " pdb=" CA ILE B 201 " ideal model delta harmonic sigma weight residual 180.00 161.84 18.16 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA ARG A 200 " pdb=" C ARG A 200 " pdb=" N ILE A 201 " pdb=" CA ILE A 201 " ideal model delta harmonic sigma weight residual 180.00 161.84 18.16 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA ARG E 200 " pdb=" C ARG E 200 " pdb=" N ILE E 201 " pdb=" CA ILE E 201 " ideal model delta harmonic sigma weight residual 180.00 161.85 18.15 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 7777 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1496 0.056 - 0.113: 403 0.113 - 0.169: 47 0.169 - 0.225: 9 0.225 - 0.281: 10 Chirality restraints: 1965 Sorted by residual: chirality pdb=" CA VAL E 273 " pdb=" N VAL E 273 " pdb=" C VAL E 273 " pdb=" CB VAL E 273 " both_signs ideal model delta sigma weight residual False 2.44 2.72 -0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CA VAL C 273 " pdb=" N VAL C 273 " pdb=" C VAL C 273 " pdb=" CB VAL C 273 " both_signs ideal model delta sigma weight residual False 2.44 2.72 -0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CA ASP C 266 " pdb=" N ASP C 266 " pdb=" C ASP C 266 " pdb=" CB ASP C 266 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.93e+00 ... (remaining 1962 not shown) Planarity restraints: 2275 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 80 " 0.017 2.00e-02 2.50e+03 1.30e-02 2.95e+00 pdb=" CG PHE A 80 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 PHE A 80 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 80 " -0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE A 80 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 80 " 0.016 2.00e-02 2.50e+03 pdb=" CZ PHE A 80 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 80 " -0.017 2.00e-02 2.50e+03 1.29e-02 2.90e+00 pdb=" CG PHE C 80 " 0.015 2.00e-02 2.50e+03 pdb=" CD1 PHE C 80 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE C 80 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 PHE C 80 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE C 80 " -0.016 2.00e-02 2.50e+03 pdb=" CZ PHE C 80 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 80 " -0.017 2.00e-02 2.50e+03 1.27e-02 2.84e+00 pdb=" CG PHE D 80 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 PHE D 80 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE D 80 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 PHE D 80 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE D 80 " -0.016 2.00e-02 2.50e+03 pdb=" CZ PHE D 80 " -0.004 2.00e-02 2.50e+03 ... (remaining 2272 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 4696 2.86 - 3.37: 12172 3.37 - 3.88: 21364 3.88 - 4.39: 26898 4.39 - 4.90: 43584 Nonbonded interactions: 108714 Sorted by model distance: nonbonded pdb=" O THR D 237 " pdb=" OG1 THR D 241 " model vdw 2.348 3.040 nonbonded pdb=" O THR E 237 " pdb=" OG1 THR E 241 " model vdw 2.348 3.040 nonbonded pdb=" O THR B 237 " pdb=" OG1 THR B 241 " model vdw 2.348 3.040 nonbonded pdb=" O THR A 237 " pdb=" OG1 THR A 241 " model vdw 2.348 3.040 nonbonded pdb=" O THR C 237 " pdb=" OG1 THR C 241 " model vdw 2.348 3.040 ... (remaining 108709 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 26 through 340) selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 4.170 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: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.230 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 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 : 0.006 0.043 13415 Z= 0.302 Angle : 0.796 8.001 18190 Z= 0.437 Chirality : 0.054 0.281 1965 Planarity : 0.004 0.035 2275 Dihedral : 14.271 88.957 4790 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % 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: -6.15 (0.13), residues: 1565 helix: -4.43 (0.06), residues: 1085 sheet: None (None), residues: 0 loop : -2.51 (0.24), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 126 TYR 0.011 0.002 TYR C 97 PHE 0.020 0.002 PHE A 80 TRP 0.012 0.002 TRP D 338 HIS 0.004 0.001 HIS E 117 Details of bonding type rmsd covalent geometry : bond 0.00642 (13415) covalent geometry : angle 0.79590 (18190) hydrogen bonds : bond 0.32231 ( 680) hydrogen bonds : angle 11.03962 ( 2040) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 0.505 Fit side-chains revert: symmetry clash REVERT: E 202 ARG cc_start: 0.8277 (mtt180) cc_final: 0.7952 (mtm-85) REVERT: C 149 LYS cc_start: 0.8906 (mttt) cc_final: 0.8615 (mttt) REVERT: C 238 GLN cc_start: 0.8634 (mt0) cc_final: 0.8356 (mt0) REVERT: B 149 LYS cc_start: 0.8921 (mttt) cc_final: 0.8683 (mttt) REVERT: B 282 PHE cc_start: 0.7657 (m-10) cc_final: 0.7406 (m-80) REVERT: B 337 TYR cc_start: 0.7801 (m-80) cc_final: 0.7415 (m-80) REVERT: A 202 ARG cc_start: 0.8198 (mtt180) cc_final: 0.7736 (mtm-85) REVERT: A 245 TYR cc_start: 0.8331 (m-80) cc_final: 0.7944 (m-80) REVERT: A 282 PHE cc_start: 0.7610 (m-10) cc_final: 0.7179 (m-80) REVERT: D 169 LYS cc_start: 0.8425 (mmtm) cc_final: 0.8073 (mptt) REVERT: D 238 GLN cc_start: 0.8692 (mt0) cc_final: 0.8432 (mt0) REVERT: D 279 LEU cc_start: 0.7656 (mp) cc_final: 0.7448 (mp) REVERT: D 282 PHE cc_start: 0.7676 (m-10) cc_final: 0.7210 (m-80) outliers start: 0 outliers final: 0 residues processed: 275 average time/residue: 0.1310 time to fit residues: 51.2499 Evaluate side-chains 229 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.1980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 0.1980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 58 GLN E 91 HIS ** E 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 ASN E 316 GLN C 58 GLN B 58 GLN B 91 HIS B 238 GLN A 58 GLN A 91 HIS ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 GLN A 296 ASN D 58 GLN D 91 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.161124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.103976 restraints weight = 17509.965| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.74 r_work: 0.3209 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13415 Z= 0.137 Angle : 0.574 8.758 18190 Z= 0.301 Chirality : 0.040 0.149 1965 Planarity : 0.004 0.031 2275 Dihedral : 4.697 18.345 1770 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.29 % Allowed : 11.04 % Favored : 87.67 % 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: -3.73 (0.17), residues: 1565 helix: -2.21 (0.12), residues: 1110 sheet: None (None), residues: 0 loop : -2.67 (0.24), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 197 TYR 0.010 0.001 TYR D 97 PHE 0.017 0.002 PHE D 276 TRP 0.015 0.001 TRP A 229 HIS 0.004 0.001 HIS D 91 Details of bonding type rmsd covalent geometry : bond 0.00284 (13415) covalent geometry : angle 0.57446 (18190) hydrogen bonds : bond 0.05668 ( 680) hydrogen bonds : angle 4.68455 ( 2040) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 273 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 166 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8058 (mp0) REVERT: E 230 ILE cc_start: 0.8945 (mm) cc_final: 0.8699 (mm) REVERT: E 238 GLN cc_start: 0.8722 (mt0) cc_final: 0.8497 (mt0) REVERT: C 203 ASP cc_start: 0.7461 (m-30) cc_final: 0.7158 (m-30) REVERT: C 282 PHE cc_start: 0.7969 (m-80) cc_final: 0.7558 (m-80) REVERT: C 316 GLN cc_start: 0.8490 (tt0) cc_final: 0.8173 (tt0) REVERT: B 82 LEU cc_start: 0.7998 (mt) cc_final: 0.7732 (tp) REVERT: B 282 PHE cc_start: 0.7927 (m-10) cc_final: 0.7562 (m-80) REVERT: B 316 GLN cc_start: 0.8616 (tt0) cc_final: 0.7881 (tt0) REVERT: A 149 LYS cc_start: 0.9094 (mttt) cc_final: 0.8857 (mttt) REVERT: A 170 LYS cc_start: 0.8721 (mttt) cc_final: 0.8290 (mtmt) REVERT: A 230 ILE cc_start: 0.8922 (mm) cc_final: 0.8609 (mm) REVERT: A 282 PHE cc_start: 0.7903 (m-10) cc_final: 0.7357 (m-80) REVERT: D 203 ASP cc_start: 0.7566 (m-30) cc_final: 0.7266 (m-30) REVERT: D 282 PHE cc_start: 0.7840 (m-10) cc_final: 0.7413 (m-80) outliers start: 18 outliers final: 6 residues processed: 282 average time/residue: 0.1127 time to fit residues: 47.0013 Evaluate side-chains 264 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 258 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 242 ILE Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain D residue 78 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 136 optimal weight: 0.0040 chunk 111 optimal weight: 0.9990 chunk 116 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 120 optimal weight: 0.0000 chunk 37 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 109 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 119 optimal weight: 0.5980 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 91 HIS ** E 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 ASN B 96 GLN B 238 GLN A 296 ASN ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 HIS D 296 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.164151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.104264 restraints weight = 17661.022| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.74 r_work: 0.3220 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13415 Z= 0.110 Angle : 0.496 7.432 18190 Z= 0.258 Chirality : 0.038 0.147 1965 Planarity : 0.003 0.031 2275 Dihedral : 4.229 16.825 1770 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.29 % Allowed : 14.34 % Favored : 84.37 % 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: -2.20 (0.19), residues: 1565 helix: -0.98 (0.14), residues: 1115 sheet: None (None), residues: 0 loop : -2.38 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 202 TYR 0.015 0.001 TYR B 247 PHE 0.027 0.001 PHE E 282 TRP 0.014 0.001 TRP D 229 HIS 0.003 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00234 (13415) covalent geometry : angle 0.49586 (18190) hydrogen bonds : bond 0.04479 ( 680) hydrogen bonds : angle 4.07136 ( 2040) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 264 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 97 TYR cc_start: 0.7919 (t80) cc_final: 0.7134 (t80) REVERT: E 166 GLU cc_start: 0.8422 (mm-30) cc_final: 0.7908 (mp0) REVERT: E 203 ASP cc_start: 0.7552 (m-30) cc_final: 0.7251 (m-30) REVERT: E 230 ILE cc_start: 0.8756 (mm) cc_final: 0.8486 (mm) REVERT: E 238 GLN cc_start: 0.8667 (mt0) cc_final: 0.8442 (mt0) REVERT: E 282 PHE cc_start: 0.7937 (m-80) cc_final: 0.7693 (m-80) REVERT: E 310 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8369 (tt) REVERT: C 103 THR cc_start: 0.8817 (p) cc_final: 0.8606 (p) REVERT: C 203 ASP cc_start: 0.7513 (m-30) cc_final: 0.7148 (m-30) REVERT: C 230 ILE cc_start: 0.8826 (mm) cc_final: 0.8570 (mm) REVERT: C 282 PHE cc_start: 0.7909 (m-80) cc_final: 0.7646 (m-80) REVERT: B 103 THR cc_start: 0.8922 (p) cc_final: 0.8709 (p) REVERT: B 149 LYS cc_start: 0.9094 (mttt) cc_final: 0.8837 (mttt) REVERT: B 230 ILE cc_start: 0.8794 (mm) cc_final: 0.8524 (mm) REVERT: B 282 PHE cc_start: 0.7803 (m-10) cc_final: 0.7433 (m-80) REVERT: B 316 GLN cc_start: 0.8577 (tt0) cc_final: 0.7814 (tt0) REVERT: A 80 PHE cc_start: 0.7216 (m-80) cc_final: 0.6980 (m-80) REVERT: A 149 LYS cc_start: 0.9042 (mttt) cc_final: 0.8820 (mttt) REVERT: A 170 LYS cc_start: 0.8613 (mttt) cc_final: 0.8234 (mtpt) REVERT: A 230 ILE cc_start: 0.8712 (mm) cc_final: 0.8330 (mm) REVERT: A 282 PHE cc_start: 0.7766 (m-10) cc_final: 0.7327 (m-80) REVERT: D 103 THR cc_start: 0.8904 (p) cc_final: 0.8665 (p) REVERT: D 203 ASP cc_start: 0.7530 (m-30) cc_final: 0.7187 (m-30) REVERT: D 234 LEU cc_start: 0.8300 (tt) cc_final: 0.8040 (tp) REVERT: D 282 PHE cc_start: 0.7626 (m-10) cc_final: 0.7297 (m-80) outliers start: 18 outliers final: 8 residues processed: 268 average time/residue: 0.1121 time to fit residues: 44.5793 Evaluate side-chains 258 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 249 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 242 ILE Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain E residue 319 MET Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain D residue 223 MET Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 319 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 24 optimal weight: 20.0000 chunk 50 optimal weight: 0.5980 chunk 98 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 chunk 134 optimal weight: 1.9990 chunk 91 optimal weight: 0.0980 chunk 51 optimal weight: 0.6980 chunk 119 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 chunk 78 optimal weight: 0.1980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 296 ASN C 96 GLN ** C 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 96 GLN A 238 GLN A 296 ASN ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 GLN D 296 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.163101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.103799 restraints weight = 17767.473| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.97 r_work: 0.3166 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13415 Z= 0.112 Angle : 0.480 7.402 18190 Z= 0.248 Chirality : 0.038 0.176 1965 Planarity : 0.002 0.032 2275 Dihedral : 4.082 15.723 1770 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.58 % Allowed : 16.27 % Favored : 82.15 % 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: -1.46 (0.20), residues: 1565 helix: -0.38 (0.15), residues: 1115 sheet: None (None), residues: 0 loop : -2.24 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 92 TYR 0.010 0.001 TYR B 247 PHE 0.022 0.001 PHE E 282 TRP 0.018 0.001 TRP D 229 HIS 0.001 0.000 HIS C 117 Details of bonding type rmsd covalent geometry : bond 0.00249 (13415) covalent geometry : angle 0.48036 (18190) hydrogen bonds : bond 0.04118 ( 680) hydrogen bonds : angle 3.89096 ( 2040) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 262 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: E 97 TYR cc_start: 0.7999 (t80) cc_final: 0.7256 (t80) REVERT: E 203 ASP cc_start: 0.7362 (m-30) cc_final: 0.7053 (m-30) REVERT: E 230 ILE cc_start: 0.8489 (mm) cc_final: 0.8181 (mm) REVERT: E 238 GLN cc_start: 0.8518 (mt0) cc_final: 0.8240 (mt0) REVERT: E 242 ILE cc_start: 0.7754 (OUTLIER) cc_final: 0.7546 (mm) REVERT: E 282 PHE cc_start: 0.7733 (m-80) cc_final: 0.7505 (m-80) REVERT: C 44 MET cc_start: 0.8682 (mtp) cc_final: 0.8324 (mmm) REVERT: C 203 ASP cc_start: 0.7532 (m-30) cc_final: 0.7131 (m-30) REVERT: C 230 ILE cc_start: 0.8534 (mm) cc_final: 0.8272 (mm) REVERT: C 282 PHE cc_start: 0.7801 (m-80) cc_final: 0.7562 (m-80) REVERT: B 203 ASP cc_start: 0.7500 (m-30) cc_final: 0.7232 (m-30) REVERT: B 230 ILE cc_start: 0.8459 (mm) cc_final: 0.8226 (mm) REVERT: B 282 PHE cc_start: 0.7624 (m-10) cc_final: 0.7347 (m-80) REVERT: B 316 GLN cc_start: 0.8268 (tt0) cc_final: 0.7440 (tt0) REVERT: A 80 PHE cc_start: 0.7108 (m-80) cc_final: 0.6908 (m-80) REVERT: A 166 GLU cc_start: 0.8419 (mm-30) cc_final: 0.7808 (mp0) REVERT: A 282 PHE cc_start: 0.7576 (m-10) cc_final: 0.7182 (m-80) REVERT: D 203 ASP cc_start: 0.7396 (m-30) cc_final: 0.7019 (m-30) REVERT: D 282 PHE cc_start: 0.7540 (m-10) cc_final: 0.7252 (m-80) outliers start: 22 outliers final: 16 residues processed: 270 average time/residue: 0.0981 time to fit residues: 40.6229 Evaluate side-chains 264 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 247 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 242 ILE Chi-restraints excluded: chain E residue 296 ASN Chi-restraints excluded: chain E residue 319 MET Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain B residue 319 MET Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 223 MET Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 319 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 132 optimal weight: 0.9980 chunk 118 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 117 optimal weight: 7.9990 chunk 123 optimal weight: 2.9990 chunk 141 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 262 GLN C 238 GLN C 262 GLN C 296 ASN B 238 GLN B 262 GLN B 296 ASN A 262 GLN A 296 ASN ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.161462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.101601 restraints weight = 17890.398| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.97 r_work: 0.3187 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 13415 Z= 0.157 Angle : 0.501 6.433 18190 Z= 0.260 Chirality : 0.040 0.142 1965 Planarity : 0.003 0.033 2275 Dihedral : 4.071 15.261 1770 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.22 % Allowed : 17.06 % Favored : 80.72 % 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: -1.09 (0.20), residues: 1565 helix: -0.14 (0.15), residues: 1125 sheet: None (None), residues: 0 loop : -2.05 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 202 TYR 0.012 0.001 TYR C 97 PHE 0.021 0.001 PHE E 276 TRP 0.019 0.001 TRP D 229 HIS 0.002 0.000 HIS B 226 Details of bonding type rmsd covalent geometry : bond 0.00364 (13415) covalent geometry : angle 0.50081 (18190) hydrogen bonds : bond 0.04290 ( 680) hydrogen bonds : angle 3.88276 ( 2040) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 248 time to evaluate : 0.526 Fit side-chains revert: symmetry clash REVERT: E 97 TYR cc_start: 0.7955 (t80) cc_final: 0.7270 (t80) REVERT: E 166 GLU cc_start: 0.8366 (mm-30) cc_final: 0.7933 (mp0) REVERT: E 230 ILE cc_start: 0.8535 (mm) cc_final: 0.8238 (mm) REVERT: E 238 GLN cc_start: 0.8552 (mt0) cc_final: 0.8298 (mt0) REVERT: E 242 ILE cc_start: 0.7795 (OUTLIER) cc_final: 0.7577 (mm) REVERT: E 282 PHE cc_start: 0.7757 (m-80) cc_final: 0.7531 (m-80) REVERT: C 44 MET cc_start: 0.8646 (mtp) cc_final: 0.8365 (mmm) REVERT: C 198 GLU cc_start: 0.8377 (mt-10) cc_final: 0.8142 (mt-10) REVERT: C 230 ILE cc_start: 0.8657 (mm) cc_final: 0.8426 (mm) REVERT: C 282 PHE cc_start: 0.7874 (m-80) cc_final: 0.7638 (m-80) REVERT: B 149 LYS cc_start: 0.8989 (mttt) cc_final: 0.8692 (mttt) REVERT: B 282 PHE cc_start: 0.7605 (m-10) cc_final: 0.7332 (m-80) REVERT: B 316 GLN cc_start: 0.8359 (tt0) cc_final: 0.7572 (tt0) REVERT: A 282 PHE cc_start: 0.7560 (m-10) cc_final: 0.7182 (m-80) REVERT: D 238 GLN cc_start: 0.8482 (mt0) cc_final: 0.8273 (mt0) REVERT: D 282 PHE cc_start: 0.7538 (m-10) cc_final: 0.7245 (m-80) outliers start: 31 outliers final: 24 residues processed: 260 average time/residue: 0.1008 time to fit residues: 39.8632 Evaluate side-chains 269 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 244 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 242 ILE Chi-restraints excluded: chain E residue 319 MET Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 296 ASN Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 238 GLN Chi-restraints excluded: chain B residue 319 MET Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 223 MET Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 223 MET Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 296 ASN Chi-restraints excluded: chain D residue 319 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 121 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 95 optimal weight: 7.9990 chunk 15 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 85 optimal weight: 9.9990 chunk 141 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 14 optimal weight: 0.0770 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 296 ASN B 238 GLN B 296 ASN A 238 GLN A 296 ASN ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 GLN D 296 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.162461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.102713 restraints weight = 17572.483| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.96 r_work: 0.3152 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13415 Z= 0.128 Angle : 0.501 10.538 18190 Z= 0.255 Chirality : 0.039 0.151 1965 Planarity : 0.003 0.033 2275 Dihedral : 4.005 14.709 1770 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.94 % Allowed : 17.35 % Favored : 80.72 % 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: -0.86 (0.20), residues: 1565 helix: 0.04 (0.15), residues: 1125 sheet: None (None), residues: 0 loop : -2.01 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 202 TYR 0.013 0.001 TYR E 85 PHE 0.024 0.001 PHE A 80 TRP 0.021 0.001 TRP D 229 HIS 0.001 0.000 HIS A 117 Details of bonding type rmsd covalent geometry : bond 0.00294 (13415) covalent geometry : angle 0.50148 (18190) hydrogen bonds : bond 0.04108 ( 680) hydrogen bonds : angle 3.81167 ( 2040) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 247 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 97 TYR cc_start: 0.7999 (t80) cc_final: 0.7349 (t80) REVERT: E 166 GLU cc_start: 0.8409 (mm-30) cc_final: 0.7823 (mp0) REVERT: E 230 ILE cc_start: 0.8484 (mm) cc_final: 0.8188 (mm) REVERT: E 242 ILE cc_start: 0.7789 (OUTLIER) cc_final: 0.7572 (mm) REVERT: E 282 PHE cc_start: 0.7758 (m-80) cc_final: 0.7532 (m-80) REVERT: C 44 MET cc_start: 0.8560 (mtp) cc_final: 0.8345 (mmm) REVERT: C 198 GLU cc_start: 0.8366 (mt-10) cc_final: 0.8141 (mt-10) REVERT: C 230 ILE cc_start: 0.8571 (mm) cc_final: 0.8325 (mm) REVERT: C 282 PHE cc_start: 0.7862 (m-80) cc_final: 0.7645 (m-80) REVERT: B 44 MET cc_start: 0.8630 (mtp) cc_final: 0.8313 (mmm) REVERT: B 282 PHE cc_start: 0.7558 (m-10) cc_final: 0.7304 (m-80) REVERT: B 316 GLN cc_start: 0.8278 (tt0) cc_final: 0.7462 (tt0) REVERT: A 44 MET cc_start: 0.8713 (mtp) cc_final: 0.8347 (mmm) REVERT: A 282 PHE cc_start: 0.7546 (m-10) cc_final: 0.7179 (m-80) REVERT: D 44 MET cc_start: 0.8529 (mtp) cc_final: 0.8216 (mmm) REVERT: D 238 GLN cc_start: 0.8620 (mt0) cc_final: 0.8410 (mt0) REVERT: D 282 PHE cc_start: 0.7512 (m-10) cc_final: 0.7244 (m-80) outliers start: 27 outliers final: 21 residues processed: 258 average time/residue: 0.0993 time to fit residues: 39.1190 Evaluate side-chains 265 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 243 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 242 ILE Chi-restraints excluded: chain E residue 296 ASN Chi-restraints excluded: chain E residue 319 MET Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 319 MET Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 223 MET Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 223 MET Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 296 ASN Chi-restraints excluded: chain D residue 319 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 128 optimal weight: 10.0000 chunk 47 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 95 optimal weight: 6.9990 chunk 58 optimal weight: 0.0030 chunk 13 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 127 optimal weight: 8.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 296 ASN C 238 GLN C 296 ASN ** C 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 ASN A 296 ASN ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 262 GLN D 296 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.162842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.103078 restraints weight = 17672.198| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.98 r_work: 0.3207 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13415 Z= 0.121 Angle : 0.491 9.778 18190 Z= 0.250 Chirality : 0.039 0.155 1965 Planarity : 0.002 0.032 2275 Dihedral : 3.939 14.674 1770 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.37 % Allowed : 17.20 % Favored : 80.43 % 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: -0.70 (0.20), residues: 1565 helix: 0.17 (0.15), residues: 1125 sheet: None (None), residues: 0 loop : -1.95 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 202 TYR 0.015 0.001 TYR E 85 PHE 0.020 0.001 PHE E 282 TRP 0.022 0.001 TRP D 229 HIS 0.001 0.000 HIS A 117 Details of bonding type rmsd covalent geometry : bond 0.00279 (13415) covalent geometry : angle 0.49125 (18190) hydrogen bonds : bond 0.04005 ( 680) hydrogen bonds : angle 3.78488 ( 2040) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 244 time to evaluate : 0.431 Fit side-chains revert: symmetry clash REVERT: E 44 MET cc_start: 0.8551 (mtp) cc_final: 0.8308 (mmm) REVERT: E 97 TYR cc_start: 0.7980 (t80) cc_final: 0.7334 (t80) REVERT: E 166 GLU cc_start: 0.8413 (mm-30) cc_final: 0.7796 (mp0) REVERT: E 210 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8134 (tt) REVERT: E 230 ILE cc_start: 0.8513 (mm) cc_final: 0.8215 (mm) REVERT: E 238 GLN cc_start: 0.8607 (mt0) cc_final: 0.8244 (mt0) REVERT: C 166 GLU cc_start: 0.8360 (mm-30) cc_final: 0.7980 (mp0) REVERT: C 198 GLU cc_start: 0.8415 (mt-10) cc_final: 0.8161 (mt-10) REVERT: C 230 ILE cc_start: 0.8617 (mm) cc_final: 0.8368 (mm) REVERT: C 282 PHE cc_start: 0.7858 (m-80) cc_final: 0.7640 (m-80) REVERT: B 44 MET cc_start: 0.8600 (mtp) cc_final: 0.8318 (mmm) REVERT: B 282 PHE cc_start: 0.7573 (m-10) cc_final: 0.7332 (m-80) REVERT: B 316 GLN cc_start: 0.8318 (tt0) cc_final: 0.7492 (tt0) REVERT: A 44 MET cc_start: 0.8682 (mtp) cc_final: 0.8344 (mmm) REVERT: A 80 PHE cc_start: 0.7035 (m-80) cc_final: 0.6720 (m-80) REVERT: A 282 PHE cc_start: 0.7519 (m-10) cc_final: 0.7162 (m-80) REVERT: D 238 GLN cc_start: 0.8633 (mt0) cc_final: 0.8323 (mt0) REVERT: D 282 PHE cc_start: 0.7533 (m-10) cc_final: 0.7254 (m-80) outliers start: 33 outliers final: 25 residues processed: 259 average time/residue: 0.0996 time to fit residues: 39.5827 Evaluate side-chains 268 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 242 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 223 MET Chi-restraints excluded: chain E residue 296 ASN Chi-restraints excluded: chain E residue 319 MET Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 296 ASN Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 319 MET Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 223 MET Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 223 MET Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 319 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 142 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 4 optimal weight: 0.9990 chunk 123 optimal weight: 0.3980 chunk 34 optimal weight: 4.9990 chunk 106 optimal weight: 0.5980 chunk 113 optimal weight: 0.0050 chunk 47 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 chunk 87 optimal weight: 0.5980 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 296 ASN C 296 ASN ** B 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 ASN A 296 ASN ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.164543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.104268 restraints weight = 17567.081| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.92 r_work: 0.3169 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13415 Z= 0.114 Angle : 0.512 10.375 18190 Z= 0.256 Chirality : 0.039 0.146 1965 Planarity : 0.002 0.032 2275 Dihedral : 3.895 14.383 1770 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.01 % Allowed : 18.14 % Favored : 79.86 % 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: -0.54 (0.21), residues: 1565 helix: 0.29 (0.15), residues: 1125 sheet: None (None), residues: 0 loop : -1.92 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 92 TYR 0.014 0.001 TYR E 85 PHE 0.037 0.001 PHE E 282 TRP 0.028 0.001 TRP B 229 HIS 0.001 0.000 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00259 (13415) covalent geometry : angle 0.51198 (18190) hydrogen bonds : bond 0.03909 ( 680) hydrogen bonds : angle 3.75057 ( 2040) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 244 time to evaluate : 0.534 Fit side-chains revert: symmetry clash REVERT: E 44 MET cc_start: 0.8531 (mtp) cc_final: 0.8311 (mmm) REVERT: E 97 TYR cc_start: 0.7971 (t80) cc_final: 0.7345 (t80) REVERT: E 166 GLU cc_start: 0.8389 (mm-30) cc_final: 0.7745 (mp0) REVERT: E 230 ILE cc_start: 0.8481 (mm) cc_final: 0.8227 (mm) REVERT: E 238 GLN cc_start: 0.8564 (mt0) cc_final: 0.8235 (mt0) REVERT: C 198 GLU cc_start: 0.8361 (mt-10) cc_final: 0.8094 (mt-10) REVERT: C 229 TRP cc_start: 0.8005 (t60) cc_final: 0.7728 (t60) REVERT: C 230 ILE cc_start: 0.8488 (mm) cc_final: 0.8181 (mm) REVERT: B 85 TYR cc_start: 0.8583 (t80) cc_final: 0.8268 (t80) REVERT: B 230 ILE cc_start: 0.8447 (mm) cc_final: 0.8188 (mm) REVERT: B 282 PHE cc_start: 0.7585 (m-10) cc_final: 0.7329 (m-80) REVERT: B 316 GLN cc_start: 0.8249 (tt0) cc_final: 0.7417 (tt0) REVERT: A 44 MET cc_start: 0.8652 (mtp) cc_final: 0.8403 (mmm) REVERT: A 80 PHE cc_start: 0.6922 (m-80) cc_final: 0.6598 (m-80) REVERT: A 282 PHE cc_start: 0.7489 (m-10) cc_final: 0.7135 (m-80) REVERT: D 282 PHE cc_start: 0.7561 (m-10) cc_final: 0.7304 (m-80) outliers start: 28 outliers final: 22 residues processed: 255 average time/residue: 0.1022 time to fit residues: 39.8634 Evaluate side-chains 259 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 237 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 223 MET Chi-restraints excluded: chain E residue 296 ASN Chi-restraints excluded: chain E residue 319 MET Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 319 MET Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 223 MET Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 223 MET Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 296 ASN Chi-restraints excluded: chain D residue 319 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 105 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 101 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 127 optimal weight: 8.9990 chunk 106 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 66 optimal weight: 7.9990 chunk 132 optimal weight: 0.8980 chunk 129 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 296 ASN C 238 GLN C 296 ASN B 238 GLN B 296 ASN A 238 GLN A 296 ASN ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.162558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.103050 restraints weight = 17623.652| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.88 r_work: 0.3156 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13415 Z= 0.147 Angle : 0.528 10.711 18190 Z= 0.264 Chirality : 0.040 0.146 1965 Planarity : 0.003 0.033 2275 Dihedral : 3.911 14.439 1770 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.15 % Allowed : 18.28 % Favored : 79.57 % 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 (0.21), residues: 1565 helix: 0.35 (0.15), residues: 1125 sheet: None (None), residues: 0 loop : -1.86 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 125 TYR 0.014 0.001 TYR E 85 PHE 0.036 0.001 PHE E 282 TRP 0.040 0.001 TRP D 229 HIS 0.001 0.000 HIS A 117 Details of bonding type rmsd covalent geometry : bond 0.00345 (13415) covalent geometry : angle 0.52795 (18190) hydrogen bonds : bond 0.04074 ( 680) hydrogen bonds : angle 3.80362 ( 2040) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 239 time to evaluate : 0.606 Fit side-chains REVERT: E 44 MET cc_start: 0.8518 (mtp) cc_final: 0.8299 (mmm) REVERT: E 97 TYR cc_start: 0.8000 (t80) cc_final: 0.7358 (t80) REVERT: E 230 ILE cc_start: 0.8501 (mm) cc_final: 0.8239 (mm) REVERT: E 238 GLN cc_start: 0.8560 (mt0) cc_final: 0.8258 (mt0) REVERT: C 198 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8122 (mt-10) REVERT: C 229 TRP cc_start: 0.8079 (t60) cc_final: 0.7813 (t60) REVERT: C 230 ILE cc_start: 0.8590 (mm) cc_final: 0.8290 (mm) REVERT: C 282 PHE cc_start: 0.7804 (m-80) cc_final: 0.7528 (m-80) REVERT: B 44 MET cc_start: 0.8484 (mmm) cc_final: 0.8268 (mmm) REVERT: B 203 ASP cc_start: 0.7539 (m-30) cc_final: 0.7315 (m-30) REVERT: B 282 PHE cc_start: 0.7578 (m-10) cc_final: 0.7343 (m-80) REVERT: B 316 GLN cc_start: 0.8304 (tt0) cc_final: 0.7456 (tt0) REVERT: A 80 PHE cc_start: 0.6950 (m-80) cc_final: 0.6615 (m-80) REVERT: A 282 PHE cc_start: 0.7494 (m-10) cc_final: 0.7144 (m-80) REVERT: D 166 GLU cc_start: 0.8353 (tt0) cc_final: 0.8133 (tm-30) REVERT: D 238 GLN cc_start: 0.8757 (mt0) cc_final: 0.8519 (mt0) REVERT: D 282 PHE cc_start: 0.7569 (m-10) cc_final: 0.7317 (m-80) outliers start: 30 outliers final: 25 residues processed: 251 average time/residue: 0.1026 time to fit residues: 39.4317 Evaluate side-chains 261 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 236 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 223 MET Chi-restraints excluded: chain E residue 296 ASN Chi-restraints excluded: chain E residue 319 MET Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 238 GLN Chi-restraints excluded: chain B residue 319 MET Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 223 MET Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 238 GLN Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 223 MET Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 296 ASN Chi-restraints excluded: chain D residue 319 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 10 optimal weight: 0.5980 chunk 57 optimal weight: 0.0770 chunk 101 optimal weight: 0.4980 chunk 41 optimal weight: 0.5980 chunk 116 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 120 optimal weight: 0.4980 chunk 22 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 chunk 128 optimal weight: 5.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 296 ASN C 296 ASN B 296 ASN A 238 GLN A 296 ASN ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.164624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.104232 restraints weight = 17746.942| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.91 r_work: 0.3171 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13415 Z= 0.116 Angle : 0.534 10.261 18190 Z= 0.264 Chirality : 0.039 0.147 1965 Planarity : 0.003 0.033 2275 Dihedral : 3.866 14.302 1770 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.65 % Allowed : 19.07 % Favored : 79.28 % 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: -0.32 (0.21), residues: 1565 helix: 0.45 (0.15), residues: 1125 sheet: None (None), residues: 0 loop : -1.83 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 92 TYR 0.017 0.001 TYR E 85 PHE 0.042 0.001 PHE E 282 TRP 0.046 0.001 TRP D 229 HIS 0.001 0.000 HIS A 117 Details of bonding type rmsd covalent geometry : bond 0.00265 (13415) covalent geometry : angle 0.53391 (18190) hydrogen bonds : bond 0.03925 ( 680) hydrogen bonds : angle 3.75874 ( 2040) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 238 time to evaluate : 0.512 Fit side-chains REVERT: E 44 MET cc_start: 0.8532 (mtp) cc_final: 0.8324 (mmm) REVERT: E 97 TYR cc_start: 0.7979 (t80) cc_final: 0.7351 (t80) REVERT: E 166 GLU cc_start: 0.8378 (mm-30) cc_final: 0.7849 (mp0) REVERT: E 230 ILE cc_start: 0.8469 (mm) cc_final: 0.8194 (mm) REVERT: E 238 GLN cc_start: 0.8534 (mt0) cc_final: 0.8231 (mt0) REVERT: C 80 PHE cc_start: 0.7345 (t80) cc_final: 0.6761 (m-80) REVERT: C 198 GLU cc_start: 0.8362 (mt-10) cc_final: 0.8067 (mt-10) REVERT: C 229 TRP cc_start: 0.7992 (t60) cc_final: 0.7741 (t60) REVERT: C 230 ILE cc_start: 0.8476 (mm) cc_final: 0.8171 (mm) REVERT: C 282 PHE cc_start: 0.7763 (m-80) cc_final: 0.7471 (m-80) REVERT: B 80 PHE cc_start: 0.7528 (t80) cc_final: 0.6797 (m-80) REVERT: B 85 TYR cc_start: 0.8605 (t80) cc_final: 0.8295 (t80) REVERT: B 203 ASP cc_start: 0.7432 (m-30) cc_final: 0.7181 (m-30) REVERT: B 282 PHE cc_start: 0.7548 (m-10) cc_final: 0.7317 (m-80) REVERT: B 316 GLN cc_start: 0.8238 (tt0) cc_final: 0.7392 (tt0) REVERT: A 44 MET cc_start: 0.8498 (mmm) cc_final: 0.8288 (mmm) REVERT: A 80 PHE cc_start: 0.6928 (m-80) cc_final: 0.6425 (m-80) REVERT: A 282 PHE cc_start: 0.7472 (m-10) cc_final: 0.7140 (m-80) REVERT: D 166 GLU cc_start: 0.8332 (tt0) cc_final: 0.8103 (tm-30) REVERT: D 238 GLN cc_start: 0.8718 (mt0) cc_final: 0.8495 (mt0) REVERT: D 282 PHE cc_start: 0.7579 (m-10) cc_final: 0.7325 (m-80) outliers start: 23 outliers final: 19 residues processed: 249 average time/residue: 0.0990 time to fit residues: 38.1212 Evaluate side-chains 254 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 235 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 296 ASN Chi-restraints excluded: chain E residue 319 MET Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 319 MET Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 223 MET Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 238 GLN Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 223 MET Chi-restraints excluded: chain D residue 319 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 60 optimal weight: 0.5980 chunk 87 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 129 optimal weight: 0.5980 chunk 52 optimal weight: 0.8980 chunk 152 optimal weight: 0.6980 chunk 92 optimal weight: 0.0980 chunk 85 optimal weight: 7.9990 chunk 81 optimal weight: 0.1980 chunk 42 optimal weight: 0.9980 chunk 101 optimal weight: 0.5980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 296 ASN C 296 ASN B 296 ASN A 296 ASN ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.163818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.105218 restraints weight = 17575.655| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.81 r_work: 0.3184 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13415 Z= 0.112 Angle : 0.526 11.081 18190 Z= 0.260 Chirality : 0.039 0.143 1965 Planarity : 0.003 0.033 2275 Dihedral : 3.837 18.611 1770 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.01 % Allowed : 19.00 % Favored : 79.00 % 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: -0.11 (0.21), residues: 1565 helix: 0.58 (0.16), residues: 1105 sheet: None (None), residues: 0 loop : -1.55 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 92 TYR 0.018 0.001 TYR E 85 PHE 0.038 0.001 PHE E 282 TRP 0.062 0.002 TRP D 229 HIS 0.001 0.000 HIS A 117 Details of bonding type rmsd covalent geometry : bond 0.00254 (13415) covalent geometry : angle 0.52591 (18190) hydrogen bonds : bond 0.03825 ( 680) hydrogen bonds : angle 3.74202 ( 2040) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3555.83 seconds wall clock time: 61 minutes 41.93 seconds (3701.93 seconds total)