Starting phenix.real_space_refine on Wed Mar 4 10:53:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vx5_21430/03_2026/6vx5_21430.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vx5_21430/03_2026/6vx5_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6vx5_21430/03_2026/6vx5_21430.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vx5_21430/03_2026/6vx5_21430.map" model { file = "/net/cci-nas-00/data/ceres_data/6vx5_21430/03_2026/6vx5_21430.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vx5_21430/03_2026/6vx5_21430.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13056 Number of models: 1 Model: "" Number of chains: 6 Chain: "E" 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: "C" 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: "B" 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: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2611 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 8, 'TRANS': 306} Chain: "D" 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} Time building chain proxies: 2.78, per 1000 atoms: 0.21 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: 0.97 Conformation dependent library (CDL) restraints added in 586.7 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: 0.34 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: 1.73 Time building geometry restraints manager: 1.31 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: 4.190 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: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.800 Find NCS groups from input model: 0.190 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.570 ------------------------------------------------------------------------------- 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 : 0.574 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: 0.1155 time to fit residues: 45.6119 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 : 0.488 ------------------------------------------------------------------------------- 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 = 0.3394 r_free = 0.3394 target = 0.103875 restraints weight = 17509.957| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.75 r_work: 0.3207 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 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 4.68456 ( 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 : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 166 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8057 (mp0) REVERT: E 230 ILE cc_start: 0.8944 (mm) cc_final: 0.8698 (mm) REVERT: E 238 GLN cc_start: 0.8723 (mt0) cc_final: 0.8499 (mt0) REVERT: C 203 ASP cc_start: 0.7461 (m-30) cc_final: 0.7156 (m-30) REVERT: C 282 PHE cc_start: 0.7969 (m-80) cc_final: 0.7558 (m-80) REVERT: C 316 GLN cc_start: 0.8489 (tt0) cc_final: 0.8173 (tt0) REVERT: B 82 LEU cc_start: 0.7997 (mt) cc_final: 0.7731 (tp) REVERT: B 282 PHE cc_start: 0.7926 (m-10) cc_final: 0.7561 (m-80) REVERT: B 316 GLN cc_start: 0.8617 (tt0) cc_final: 0.7882 (tt0) REVERT: A 149 LYS cc_start: 0.9096 (mttt) cc_final: 0.8858 (mttt) REVERT: A 170 LYS cc_start: 0.8719 (mttt) cc_final: 0.8288 (mtmt) REVERT: A 230 ILE cc_start: 0.8922 (mm) cc_final: 0.8609 (mm) REVERT: A 282 PHE cc_start: 0.7902 (m-10) cc_final: 0.7355 (m-80) REVERT: D 203 ASP cc_start: 0.7567 (m-30) cc_final: 0.7266 (m-30) REVERT: D 282 PHE cc_start: 0.7839 (m-10) cc_final: 0.7413 (m-80) outliers start: 18 outliers final: 6 residues processed: 282 average time/residue: 0.1004 time to fit residues: 42.2421 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 : 0.467 ------------------------------------------------------------------------------- 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: 0.6980 chunk 111 optimal weight: 0.9980 chunk 116 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 120 optimal weight: 0.3980 chunk 37 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 119 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 91 HIS E 296 ASN C 194 GLN B 238 GLN A 296 ASN ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.162496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.101958 restraints weight = 17679.407| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.75 r_work: 0.3187 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13415 Z= 0.137 Angle : 0.514 6.993 18190 Z= 0.268 Chirality : 0.040 0.146 1965 Planarity : 0.003 0.030 2275 Dihedral : 4.319 16.745 1770 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.51 % Allowed : 14.41 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.26 (0.19), residues: 1565 helix: -1.05 (0.14), residues: 1120 sheet: None (None), residues: 0 loop : -2.33 (0.26), residues: 445 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 0.023 0.001 PHE E 282 TRP 0.012 0.001 TRP D 229 HIS 0.004 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00309 (13415) covalent geometry : angle 0.51385 (18190) hydrogen bonds : bond 0.04749 ( 680) hydrogen bonds : angle 4.15199 ( 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 280 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 259 time to evaluate : 0.485 Fit side-chains REVERT: E 97 TYR cc_start: 0.7948 (t80) cc_final: 0.7122 (t80) REVERT: E 230 ILE cc_start: 0.8767 (mm) cc_final: 0.8504 (mm) REVERT: E 282 PHE cc_start: 0.7922 (m-80) cc_final: 0.7677 (m-80) REVERT: E 310 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8397 (tt) REVERT: C 203 ASP cc_start: 0.7594 (m-30) cc_final: 0.7225 (m-30) REVERT: C 230 ILE cc_start: 0.8849 (mm) cc_final: 0.8625 (mm) REVERT: C 282 PHE cc_start: 0.7922 (m-80) cc_final: 0.7648 (m-80) REVERT: B 149 LYS cc_start: 0.9091 (mttt) cc_final: 0.8825 (mttt) REVERT: B 230 ILE cc_start: 0.8807 (mm) cc_final: 0.8539 (mm) REVERT: B 282 PHE cc_start: 0.7815 (m-10) cc_final: 0.7505 (m-80) REVERT: B 316 GLN cc_start: 0.8592 (tt0) cc_final: 0.7843 (tt0) REVERT: A 149 LYS cc_start: 0.9042 (mttt) cc_final: 0.8814 (mttt) REVERT: A 230 ILE cc_start: 0.8731 (mm) cc_final: 0.8330 (mm) REVERT: A 282 PHE cc_start: 0.7793 (m-10) cc_final: 0.7359 (m-80) REVERT: D 203 ASP cc_start: 0.7541 (m-30) cc_final: 0.7197 (m-30) REVERT: D 234 LEU cc_start: 0.8300 (tt) cc_final: 0.7793 (tt) REVERT: D 238 GLN cc_start: 0.8776 (mt0) cc_final: 0.8491 (mt0) REVERT: D 282 PHE cc_start: 0.7612 (m-10) cc_final: 0.7297 (m-80) outliers start: 21 outliers final: 14 residues processed: 267 average time/residue: 0.0980 time to fit residues: 39.6073 Evaluate side-chains 263 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 248 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 145 THR 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 78 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain A residue 78 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 24 optimal weight: 20.0000 chunk 50 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 104 optimal weight: 0.9980 chunk 134 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 119 optimal weight: 0.5980 chunk 137 optimal weight: 0.9980 chunk 78 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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** B 96 GLN B 296 ASN A 96 GLN A 238 GLN A 262 GLN A 296 ASN ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.161511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.101855 restraints weight = 17769.748| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.95 r_work: 0.3167 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13415 Z= 0.142 Angle : 0.504 6.929 18190 Z= 0.261 Chirality : 0.040 0.203 1965 Planarity : 0.003 0.031 2275 Dihedral : 4.182 15.896 1770 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.01 % Allowed : 15.84 % 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: -1.57 (0.20), residues: 1565 helix: -0.50 (0.15), residues: 1125 sheet: None (None), residues: 0 loop : -2.21 (0.26), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 202 TYR 0.012 0.001 TYR B 247 PHE 0.023 0.001 PHE E 282 TRP 0.018 0.001 TRP D 229 HIS 0.002 0.000 HIS D 91 Details of bonding type rmsd covalent geometry : bond 0.00324 (13415) covalent geometry : angle 0.50445 (18190) hydrogen bonds : bond 0.04371 ( 680) hydrogen bonds : angle 3.98154 ( 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 292 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 264 time to evaluate : 0.425 Fit side-chains revert: symmetry clash REVERT: E 97 TYR cc_start: 0.7930 (t80) cc_final: 0.7210 (t80) REVERT: E 166 GLU cc_start: 0.8403 (mm-30) cc_final: 0.7914 (mp0) REVERT: E 230 ILE cc_start: 0.8532 (mm) cc_final: 0.8246 (mm) REVERT: E 282 PHE cc_start: 0.7812 (m-80) cc_final: 0.7592 (m-80) REVERT: C 203 ASP cc_start: 0.7526 (m-30) cc_final: 0.7134 (m-30) REVERT: C 230 ILE cc_start: 0.8603 (mm) cc_final: 0.8362 (mm) REVERT: C 282 PHE cc_start: 0.7858 (m-80) cc_final: 0.7564 (m-80) REVERT: B 203 ASP cc_start: 0.7505 (m-30) cc_final: 0.7194 (m-30) REVERT: B 223 MET cc_start: 0.8586 (OUTLIER) cc_final: 0.8368 (mmm) REVERT: B 230 ILE cc_start: 0.8530 (mm) cc_final: 0.8272 (mm) REVERT: B 282 PHE cc_start: 0.7668 (m-10) cc_final: 0.7343 (m-80) REVERT: B 316 GLN cc_start: 0.8328 (tt0) cc_final: 0.7491 (tt0) REVERT: A 80 PHE cc_start: 0.7133 (m-80) cc_final: 0.6899 (m-80) REVERT: A 149 LYS cc_start: 0.8941 (mttt) cc_final: 0.8734 (mttt) REVERT: A 230 ILE cc_start: 0.8536 (mm) cc_final: 0.8151 (mm) REVERT: A 282 PHE cc_start: 0.7574 (m-10) cc_final: 0.7189 (m-80) REVERT: D 203 ASP cc_start: 0.7392 (m-30) cc_final: 0.7014 (m-30) REVERT: D 229 TRP cc_start: 0.7983 (t60) cc_final: 0.7779 (t60) REVERT: D 282 PHE cc_start: 0.7536 (m-10) cc_final: 0.7252 (m-80) outliers start: 28 outliers final: 20 residues processed: 275 average time/residue: 0.0977 time to fit residues: 40.9705 Evaluate side-chains 274 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 253 time to evaluate : 0.485 ------------------------------------------------------------------------------- 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 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 223 MET Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 145 THR 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: 0.8980 chunk 118 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.0570 chunk 6 optimal weight: 0.6980 chunk 117 optimal weight: 0.7980 chunk 123 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 262 GLN E 296 ASN C 238 GLN C 262 GLN C 296 ASN B 238 GLN B 262 GLN 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.162430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.102696 restraints weight = 17806.555| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.97 r_work: 0.3149 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13415 Z= 0.125 Angle : 0.488 7.992 18190 Z= 0.252 Chirality : 0.039 0.142 1965 Planarity : 0.002 0.031 2275 Dihedral : 4.058 15.340 1770 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.44 % Allowed : 16.92 % Favored : 80.65 % 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: -1.18 (0.20), residues: 1565 helix: -0.19 (0.15), residues: 1125 sheet: None (None), residues: 0 loop : -2.11 (0.26), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 202 TYR 0.012 0.001 TYR E 85 PHE 0.021 0.001 PHE E 282 TRP 0.013 0.001 TRP D 229 HIS 0.001 0.000 HIS D 91 Details of bonding type rmsd covalent geometry : bond 0.00284 (13415) covalent geometry : angle 0.48792 (18190) hydrogen bonds : bond 0.04158 ( 680) hydrogen bonds : angle 3.88591 ( 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 286 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 252 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 97 TYR cc_start: 0.7940 (t80) cc_final: 0.7204 (t80) REVERT: E 166 GLU cc_start: 0.8464 (mm-30) cc_final: 0.7885 (mp0) REVERT: E 230 ILE cc_start: 0.8445 (mm) cc_final: 0.8133 (mm) REVERT: E 238 GLN cc_start: 0.8622 (mt0) cc_final: 0.8376 (mt0) REVERT: E 282 PHE cc_start: 0.7772 (m-80) cc_final: 0.7554 (m-80) REVERT: C 44 MET cc_start: 0.8653 (mtp) cc_final: 0.8363 (mmm) REVERT: C 198 GLU cc_start: 0.8253 (mt-10) cc_final: 0.8013 (mt-10) REVERT: C 230 ILE cc_start: 0.8589 (mm) cc_final: 0.8353 (mm) REVERT: C 282 PHE cc_start: 0.7836 (m-80) cc_final: 0.7579 (m-80) REVERT: B 80 PHE cc_start: 0.7550 (t80) cc_final: 0.6884 (m-80) REVERT: B 149 LYS cc_start: 0.8959 (mttt) cc_final: 0.8669 (mttt) REVERT: B 223 MET cc_start: 0.8514 (OUTLIER) cc_final: 0.8313 (mmm) REVERT: B 230 ILE cc_start: 0.8513 (mm) cc_final: 0.8284 (mm) REVERT: B 282 PHE cc_start: 0.7603 (m-10) cc_final: 0.7322 (m-80) REVERT: B 316 GLN cc_start: 0.8249 (tt0) cc_final: 0.7478 (tt0) REVERT: A 80 PHE cc_start: 0.7132 (m-80) cc_final: 0.6811 (m-80) REVERT: A 166 GLU cc_start: 0.8425 (mm-30) cc_final: 0.7907 (mp0) REVERT: A 282 PHE cc_start: 0.7554 (m-10) cc_final: 0.7183 (m-80) REVERT: D 238 GLN cc_start: 0.8682 (mt0) cc_final: 0.8351 (mt0) REVERT: D 282 PHE cc_start: 0.7515 (m-10) cc_final: 0.7252 (m-80) outliers start: 34 outliers final: 23 residues processed: 264 average time/residue: 0.0931 time to fit residues: 37.6501 Evaluate side-chains 271 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 247 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 210 LEU 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 223 MET 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 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: 0.6980 chunk 95 optimal weight: 5.9990 chunk 15 optimal weight: 0.5980 chunk 78 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 85 optimal weight: 9.9990 chunk 141 optimal weight: 1.9990 chunk 111 optimal weight: 0.5980 chunk 101 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 ** C 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 238 GLN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.162157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.102854 restraints weight = 17567.825| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.86 r_work: 0.3153 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13415 Z= 0.138 Angle : 0.504 9.401 18190 Z= 0.257 Chirality : 0.040 0.144 1965 Planarity : 0.003 0.031 2275 Dihedral : 4.016 14.984 1770 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.37 % Allowed : 16.70 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.20), residues: 1565 helix: -0.03 (0.15), residues: 1125 sheet: None (None), residues: 0 loop : -2.03 (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 0.020 0.001 PHE E 282 TRP 0.020 0.001 TRP D 229 HIS 0.001 0.000 HIS D 91 Details of bonding type rmsd covalent geometry : bond 0.00320 (13415) covalent geometry : angle 0.50434 (18190) hydrogen bonds : bond 0.04160 ( 680) hydrogen bonds : angle 3.85049 ( 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 276 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 243 time to evaluate : 0.473 Fit side-chains REVERT: E 97 TYR cc_start: 0.7926 (t80) cc_final: 0.7271 (t80) REVERT: E 166 GLU cc_start: 0.8436 (mm-30) cc_final: 0.7748 (mp0) REVERT: E 230 ILE cc_start: 0.8484 (mm) cc_final: 0.8202 (mm) REVERT: E 238 GLN cc_start: 0.8624 (mt0) cc_final: 0.8412 (mt0) REVERT: E 282 PHE cc_start: 0.7733 (m-80) cc_final: 0.7513 (m-80) REVERT: C 44 MET cc_start: 0.8562 (mtp) cc_final: 0.8333 (mmm) REVERT: C 198 GLU cc_start: 0.8313 (mt-10) cc_final: 0.8069 (mt-10) REVERT: C 230 ILE cc_start: 0.8579 (mm) cc_final: 0.8346 (mm) REVERT: C 282 PHE cc_start: 0.7838 (m-80) cc_final: 0.7579 (m-80) REVERT: B 44 MET cc_start: 0.8661 (mtp) cc_final: 0.8317 (mmm) REVERT: B 80 PHE cc_start: 0.7578 (t80) cc_final: 0.6916 (m-80) REVERT: B 282 PHE cc_start: 0.7584 (m-10) cc_final: 0.7307 (m-80) REVERT: B 316 GLN cc_start: 0.8248 (tt0) cc_final: 0.7447 (tt0) REVERT: A 44 MET cc_start: 0.8726 (mtp) cc_final: 0.8373 (mmm) REVERT: A 80 PHE cc_start: 0.7193 (m-80) cc_final: 0.6900 (m-80) REVERT: A 282 PHE cc_start: 0.7542 (m-10) cc_final: 0.7180 (m-80) REVERT: D 44 MET cc_start: 0.8541 (mtp) cc_final: 0.8273 (mmm) REVERT: D 238 GLN cc_start: 0.8647 (mt0) cc_final: 0.8299 (mt0) REVERT: D 282 PHE cc_start: 0.7489 (m-10) cc_final: 0.7254 (m-80) outliers start: 33 outliers final: 28 residues processed: 257 average time/residue: 0.0938 time to fit residues: 37.1500 Evaluate side-chains 265 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 237 time to evaluate : 0.476 ------------------------------------------------------------------------------- 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 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 319 MET Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 153 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: 3.9990 chunk 47 optimal weight: 0.5980 chunk 17 optimal weight: 0.2980 chunk 16 optimal weight: 0.5980 chunk 95 optimal weight: 6.9990 chunk 58 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 15 optimal weight: 0.0970 chunk 36 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 127 optimal weight: 5.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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 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 = 0.4132 r_free = 0.4132 target = 0.163046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.103392 restraints weight = 17654.090| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.97 r_work: 0.3162 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13415 Z= 0.113 Angle : 0.492 9.865 18190 Z= 0.250 Chirality : 0.039 0.161 1965 Planarity : 0.002 0.032 2275 Dihedral : 3.937 14.707 1770 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.22 % Allowed : 17.35 % 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: -0.75 (0.20), residues: 1565 helix: 0.13 (0.15), residues: 1125 sheet: None (None), residues: 0 loop : -1.99 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 202 TYR 0.016 0.001 TYR E 85 PHE 0.020 0.001 PHE E 282 TRP 0.023 0.001 TRP D 229 HIS 0.001 0.000 HIS D 91 Details of bonding type rmsd covalent geometry : bond 0.00255 (13415) covalent geometry : angle 0.49167 (18190) hydrogen bonds : bond 0.03952 ( 680) hydrogen bonds : angle 3.78807 ( 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 276 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 245 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: E 44 MET cc_start: 0.8559 (mtp) cc_final: 0.8280 (mmm) REVERT: E 97 TYR cc_start: 0.7978 (t80) cc_final: 0.7342 (t80) REVERT: E 166 GLU cc_start: 0.8444 (mm-30) cc_final: 0.7761 (mp0) REVERT: E 230 ILE cc_start: 0.8462 (mm) cc_final: 0.8166 (mm) REVERT: E 282 PHE cc_start: 0.7770 (m-80) cc_final: 0.7537 (m-80) REVERT: C 198 GLU cc_start: 0.8338 (mt-10) cc_final: 0.8072 (mt-10) REVERT: C 230 ILE cc_start: 0.8578 (mm) cc_final: 0.8320 (mm) REVERT: C 282 PHE cc_start: 0.7849 (m-80) cc_final: 0.7622 (m-80) REVERT: B 44 MET cc_start: 0.8614 (mtp) cc_final: 0.8350 (mmm) REVERT: B 80 PHE cc_start: 0.7580 (t80) cc_final: 0.6964 (m-80) REVERT: B 282 PHE cc_start: 0.7553 (m-10) cc_final: 0.7293 (m-80) REVERT: B 316 GLN cc_start: 0.8254 (tt0) cc_final: 0.7444 (tt0) REVERT: A 44 MET cc_start: 0.8678 (mtp) cc_final: 0.8373 (mmm) REVERT: A 80 PHE cc_start: 0.7215 (m-80) cc_final: 0.6925 (m-80) REVERT: A 282 PHE cc_start: 0.7514 (m-10) cc_final: 0.7144 (m-80) REVERT: A 310 LEU cc_start: 0.8402 (tt) cc_final: 0.8169 (tt) REVERT: D 44 MET cc_start: 0.8502 (mtp) cc_final: 0.8239 (mmm) REVERT: D 238 GLN cc_start: 0.8635 (mt0) cc_final: 0.8334 (mt0) REVERT: D 282 PHE cc_start: 0.7477 (m-10) cc_final: 0.7221 (m-80) outliers start: 31 outliers final: 21 residues processed: 260 average time/residue: 0.0940 time to fit residues: 37.3983 Evaluate side-chains 260 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 239 time to evaluate : 0.472 ------------------------------------------------------------------------------- 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 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 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 319 MET 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: 6.9990 chunk 4 optimal weight: 2.9990 chunk 123 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 113 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 103 optimal weight: 0.5980 chunk 87 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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** D 296 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.162691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.103267 restraints weight = 17523.146| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.86 r_work: 0.3188 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13415 Z= 0.131 Angle : 0.511 10.515 18190 Z= 0.256 Chirality : 0.039 0.152 1965 Planarity : 0.002 0.033 2275 Dihedral : 3.913 14.573 1770 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.15 % Allowed : 17.56 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.21), residues: 1565 helix: 0.22 (0.15), residues: 1125 sheet: None (None), residues: 0 loop : -1.94 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 125 TYR 0.015 0.001 TYR E 85 PHE 0.020 0.001 PHE E 282 TRP 0.024 0.001 TRP D 229 HIS 0.001 0.000 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00305 (13415) covalent geometry : angle 0.51095 (18190) hydrogen bonds : bond 0.04011 ( 680) hydrogen bonds : angle 3.79280 ( 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: 30 poor density : 242 time to evaluate : 0.423 Fit side-chains REVERT: E 44 MET cc_start: 0.8522 (mtp) cc_final: 0.8312 (mmm) REVERT: E 97 TYR cc_start: 0.7979 (t80) cc_final: 0.7340 (t80) REVERT: E 166 GLU cc_start: 0.8461 (mm-30) cc_final: 0.7794 (mp0) REVERT: E 210 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8093 (tt) REVERT: E 230 ILE cc_start: 0.8464 (mm) cc_final: 0.8149 (mm) REVERT: E 282 PHE cc_start: 0.7741 (m-80) cc_final: 0.7520 (m-80) REVERT: C 198 GLU cc_start: 0.8355 (mt-10) cc_final: 0.8078 (mt-10) REVERT: C 230 ILE cc_start: 0.8577 (mm) cc_final: 0.8363 (mm) REVERT: C 282 PHE cc_start: 0.7864 (m-80) cc_final: 0.7650 (m-80) REVERT: B 229 TRP cc_start: 0.7973 (t60) cc_final: 0.7735 (t60) REVERT: B 230 ILE cc_start: 0.8507 (mm) cc_final: 0.8295 (mm) REVERT: B 282 PHE cc_start: 0.7555 (m-10) cc_final: 0.7309 (m-80) REVERT: B 316 GLN cc_start: 0.8266 (tt0) cc_final: 0.7438 (tt0) REVERT: A 44 MET cc_start: 0.8645 (mtp) cc_final: 0.8389 (mmm) REVERT: A 282 PHE cc_start: 0.7512 (m-10) cc_final: 0.7166 (m-80) REVERT: D 166 GLU cc_start: 0.8383 (tt0) cc_final: 0.8158 (tm-30) REVERT: D 238 GLN cc_start: 0.8649 (mt0) cc_final: 0.8408 (mt0) REVERT: D 282 PHE cc_start: 0.7486 (m-10) cc_final: 0.7234 (m-80) outliers start: 30 outliers final: 23 residues processed: 255 average time/residue: 0.0920 time to fit residues: 36.0498 Evaluate side-chains 258 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 234 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 78 VAL 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 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 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 319 MET Chi-restraints excluded: chain D residue 78 VAL 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: 0.8980 chunk 7 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 121 optimal weight: 0.6980 chunk 127 optimal weight: 8.9990 chunk 106 optimal weight: 2.9990 chunk 86 optimal weight: 0.0970 chunk 66 optimal weight: 4.9990 chunk 132 optimal weight: 0.8980 chunk 129 optimal weight: 1.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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 95 ASN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.162784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.103267 restraints weight = 17601.678| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.85 r_work: 0.3161 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13415 Z= 0.134 Angle : 0.525 10.124 18190 Z= 0.262 Chirality : 0.040 0.145 1965 Planarity : 0.003 0.031 2275 Dihedral : 3.910 14.556 1770 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.22 % Allowed : 18.14 % Favored : 79.64 % 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: -0.52 (0.21), residues: 1565 helix: 0.30 (0.15), residues: 1125 sheet: None (None), residues: 0 loop : -1.88 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 150 TYR 0.018 0.001 TYR E 85 PHE 0.027 0.001 PHE A 80 TRP 0.041 0.001 TRP D 229 HIS 0.001 0.000 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00313 (13415) covalent geometry : angle 0.52529 (18190) hydrogen bonds : bond 0.04023 ( 680) hydrogen bonds : angle 3.80669 ( 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 266 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 235 time to evaluate : 0.452 Fit side-chains REVERT: E 97 TYR cc_start: 0.7992 (t80) cc_final: 0.7345 (t80) REVERT: E 210 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8062 (tt) REVERT: E 230 ILE cc_start: 0.8465 (mm) cc_final: 0.8171 (mm) REVERT: E 282 PHE cc_start: 0.7688 (m-80) cc_final: 0.7477 (m-80) REVERT: C 198 GLU cc_start: 0.8321 (mt-10) cc_final: 0.8027 (mt-10) REVERT: C 229 TRP cc_start: 0.8033 (t60) cc_final: 0.7761 (t60) REVERT: C 230 ILE cc_start: 0.8558 (mm) cc_final: 0.8251 (mm) REVERT: C 282 PHE cc_start: 0.7825 (m-80) cc_final: 0.7607 (m-80) REVERT: B 44 MET cc_start: 0.8455 (mmm) cc_final: 0.8246 (mmm) REVERT: B 80 PHE cc_start: 0.7530 (t80) cc_final: 0.6921 (m-80) REVERT: B 203 ASP cc_start: 0.7492 (m-30) cc_final: 0.7260 (m-30) REVERT: B 282 PHE cc_start: 0.7551 (m-10) cc_final: 0.7329 (m-80) REVERT: B 316 GLN cc_start: 0.8224 (tt0) cc_final: 0.7396 (tt0) REVERT: A 80 PHE cc_start: 0.6855 (m-80) cc_final: 0.6465 (m-80) REVERT: A 282 PHE cc_start: 0.7464 (m-10) cc_final: 0.7129 (m-80) REVERT: D 166 GLU cc_start: 0.8377 (tt0) cc_final: 0.8146 (tm-30) REVERT: D 282 PHE cc_start: 0.7512 (m-10) cc_final: 0.7269 (m-80) outliers start: 31 outliers final: 25 residues processed: 249 average time/residue: 0.0907 time to fit residues: 35.1965 Evaluate side-chains 258 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 232 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 78 VAL 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 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 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 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: 0.9980 chunk 101 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 116 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 120 optimal weight: 0.0570 chunk 22 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 128 optimal weight: 5.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- 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 95 ASN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.162866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.103780 restraints weight = 17696.287| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.86 r_work: 0.3164 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13415 Z= 0.130 Angle : 0.545 12.004 18190 Z= 0.267 Chirality : 0.040 0.145 1965 Planarity : 0.003 0.033 2275 Dihedral : 3.896 14.458 1770 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.37 % Allowed : 17.99 % Favored : 79.64 % 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: -0.43 (0.21), residues: 1565 helix: 0.36 (0.15), residues: 1125 sheet: None (None), residues: 0 loop : -1.85 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 165 TYR 0.019 0.001 TYR E 85 PHE 0.023 0.001 PHE A 80 TRP 0.046 0.001 TRP D 229 HIS 0.001 0.000 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00302 (13415) covalent geometry : angle 0.54467 (18190) hydrogen bonds : bond 0.04001 ( 680) hydrogen bonds : angle 3.79263 ( 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 270 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 237 time to evaluate : 0.492 Fit side-chains REVERT: E 97 TYR cc_start: 0.8004 (t80) cc_final: 0.7418 (t80) REVERT: E 166 GLU cc_start: 0.8378 (mm-30) cc_final: 0.7952 (mp0) REVERT: E 230 ILE cc_start: 0.8463 (mm) cc_final: 0.8191 (mm) REVERT: E 282 PHE cc_start: 0.7684 (m-80) cc_final: 0.7478 (m-80) REVERT: C 44 MET cc_start: 0.8711 (mmm) cc_final: 0.8277 (mmm) REVERT: C 198 GLU cc_start: 0.8352 (mt-10) cc_final: 0.8060 (mt-10) REVERT: C 229 TRP cc_start: 0.8035 (t60) cc_final: 0.7785 (t60) REVERT: C 230 ILE cc_start: 0.8554 (mm) cc_final: 0.8267 (mm) REVERT: B 80 PHE cc_start: 0.7488 (t80) cc_final: 0.6906 (m-80) REVERT: B 85 TYR cc_start: 0.8608 (t80) cc_final: 0.8289 (t80) REVERT: B 203 ASP cc_start: 0.7421 (m-30) cc_final: 0.7155 (m-30) REVERT: B 230 ILE cc_start: 0.8407 (mm) cc_final: 0.8199 (mm) REVERT: B 282 PHE cc_start: 0.7544 (m-10) cc_final: 0.7314 (m-80) REVERT: B 316 GLN cc_start: 0.8228 (tt0) cc_final: 0.7397 (tt0) REVERT: A 80 PHE cc_start: 0.6823 (m-80) cc_final: 0.6403 (m-80) REVERT: A 282 PHE cc_start: 0.7472 (m-10) cc_final: 0.7133 (m-80) REVERT: D 166 GLU cc_start: 0.8360 (tt0) cc_final: 0.8127 (tm-30) REVERT: D 238 GLN cc_start: 0.8567 (mt0) cc_final: 0.8361 (mt0) REVERT: D 282 PHE cc_start: 0.7516 (m-10) cc_final: 0.7303 (m-80) outliers start: 33 outliers final: 27 residues processed: 253 average time/residue: 0.0921 time to fit residues: 36.1517 Evaluate side-chains 261 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 234 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 78 VAL 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 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 319 MET Chi-restraints excluded: chain A residue 82 LEU 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 60 optimal weight: 0.9990 chunk 87 optimal weight: 0.5980 chunk 33 optimal weight: 9.9990 chunk 129 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 152 optimal weight: 0.4980 chunk 92 optimal weight: 0.0370 chunk 85 optimal weight: 9.9990 chunk 81 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 101 optimal weight: 0.5980 overall best weight: 0.5058 ------------------------------------------------------------------------------- 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 95 ASN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.163150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.104469 restraints weight = 17622.687| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.84 r_work: 0.3197 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2971 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= 0.120 Angle : 0.534 11.259 18190 Z= 0.263 Chirality : 0.039 0.144 1965 Planarity : 0.003 0.032 2275 Dihedral : 3.870 18.308 1770 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.15 % Allowed : 18.57 % 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: -0.30 (0.21), residues: 1565 helix: 0.47 (0.15), residues: 1125 sheet: None (None), residues: 0 loop : -1.81 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 165 TYR 0.019 0.001 TYR E 85 PHE 0.027 0.001 PHE C 282 TRP 0.063 0.002 TRP D 229 HIS 0.001 0.000 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00275 (13415) covalent geometry : angle 0.53446 (18190) hydrogen bonds : bond 0.03905 ( 680) hydrogen bonds : angle 3.76851 ( 2040) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3171.74 seconds wall clock time: 54 minutes 57.88 seconds (3297.88 seconds total)