Starting phenix.real_space_refine on Thu Jul 31 02:49:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vx5_21430/07_2025/6vx5_21430.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vx5_21430/07_2025/6vx5_21430.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vx5_21430/07_2025/6vx5_21430.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vx5_21430/07_2025/6vx5_21430.map" model { file = "/net/cci-nas-00/data/ceres_data/6vx5_21430/07_2025/6vx5_21430.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vx5_21430/07_2025/6vx5_21430.cif" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13056 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2611 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 8, 'TRANS': 306} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D, E Time building chain proxies: 6.52, per 1000 atoms: 0.50 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: 3.31 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.18 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: 3.45 Time building geometry restraints manager: 3.87 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: 5.530 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: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 28.820 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.350 ------------------------------------------------------------------------------- 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 : 4.97 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.012 0.002 TRP D 338 HIS 0.004 0.001 HIS E 117 PHE 0.020 0.002 PHE A 80 TYR 0.011 0.002 TYR C 97 ARG 0.002 0.000 ARG D 126 Details of bonding type rmsd hydrogen bonds : bond 0.32231 ( 680) hydrogen bonds : angle 11.03962 ( 2040) covalent geometry : bond 0.00642 (13415) covalent geometry : angle 0.79590 (18190) *********************** 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 : 1.356 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: 0.2620 time to fit residues: 102.1959 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 : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 0.7980 chunk 117 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 40 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 121 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 73 optimal weight: 0.8980 chunk 90 optimal weight: 0.5980 chunk 140 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 296 ASN E 316 GLN C 58 GLN B 58 GLN B 91 HIS B 238 GLN A 58 GLN A 91 HIS 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 = 0.4117 r_free = 0.4117 target = 0.159661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.101437 restraints weight = 17383.037| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.63 r_work: 0.3199 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13415 Z= 0.157 Angle : 0.595 8.459 18190 Z= 0.315 Chirality : 0.041 0.149 1965 Planarity : 0.004 0.030 2275 Dihedral : 4.790 18.134 1770 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.43 % Allowed : 10.97 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.70 (0.17), residues: 1565 helix: -2.27 (0.12), residues: 1095 sheet: None (None), residues: 0 loop : -2.43 (0.25), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 229 HIS 0.005 0.001 HIS D 91 PHE 0.017 0.001 PHE D 276 TYR 0.011 0.001 TYR A 326 ARG 0.003 0.000 ARG A 197 Details of bonding type rmsd hydrogen bonds : bond 0.06489 ( 680) hydrogen bonds : angle 4.85681 ( 2040) covalent geometry : bond 0.00331 (13415) covalent geometry : angle 0.59495 (18190) *********************** 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 290 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 270 time to evaluate : 2.683 Fit side-chains revert: symmetry clash REVERT: E 166 GLU cc_start: 0.8413 (mm-30) cc_final: 0.8068 (mp0) REVERT: E 230 ILE cc_start: 0.8959 (mm) cc_final: 0.8750 (mm) REVERT: E 238 GLN cc_start: 0.8721 (mt0) cc_final: 0.8511 (mt0) REVERT: E 276 PHE cc_start: 0.7253 (t80) cc_final: 0.7034 (t80) REVERT: C 149 LYS cc_start: 0.9047 (mttt) cc_final: 0.8823 (mttt) REVERT: C 203 ASP cc_start: 0.7475 (m-30) cc_final: 0.7192 (m-30) REVERT: C 282 PHE cc_start: 0.7988 (m-80) cc_final: 0.7596 (m-80) REVERT: B 100 MET cc_start: 0.9112 (mmm) cc_final: 0.8910 (mmm) REVERT: B 282 PHE cc_start: 0.7934 (m-10) cc_final: 0.7557 (m-80) REVERT: B 316 GLN cc_start: 0.8624 (tt0) cc_final: 0.7888 (tt0) REVERT: A 149 LYS cc_start: 0.9063 (mttt) cc_final: 0.8819 (mttt) REVERT: A 170 LYS cc_start: 0.8743 (mttt) cc_final: 0.8307 (mtmt) REVERT: A 230 ILE cc_start: 0.8942 (mm) cc_final: 0.8642 (mm) REVERT: A 245 TYR cc_start: 0.8284 (m-80) cc_final: 0.7876 (m-80) REVERT: A 282 PHE cc_start: 0.7904 (m-10) cc_final: 0.7394 (m-80) REVERT: D 203 ASP cc_start: 0.7563 (m-30) cc_final: 0.7268 (m-30) REVERT: D 276 PHE cc_start: 0.7211 (t80) cc_final: 0.7003 (t80) REVERT: D 282 PHE cc_start: 0.7865 (m-10) cc_final: 0.7436 (m-80) outliers start: 20 outliers final: 7 residues processed: 279 average time/residue: 0.2388 time to fit residues: 98.1157 Evaluate side-chains 254 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 247 time to evaluate : 1.407 ------------------------------------------------------------------------------- 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 232 VAL Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 232 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 67 optimal weight: 0.1980 chunk 133 optimal weight: 0.4980 chunk 29 optimal weight: 0.9980 chunk 86 optimal weight: 20.0000 chunk 87 optimal weight: 0.6980 chunk 99 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 89 optimal weight: 0.0870 chunk 73 optimal weight: 0.7980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 91 HIS E 262 GLN E 296 ASN C 194 GLN C 262 GLN ** C 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 238 GLN A 262 GLN A 296 ASN ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 HIS D 262 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.163843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.103301 restraints weight = 17637.823| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.76 r_work: 0.3211 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2241 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= 0.116 Angle : 0.509 7.536 18190 Z= 0.263 Chirality : 0.039 0.202 1965 Planarity : 0.003 0.029 2275 Dihedral : 4.277 16.998 1770 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.29 % Allowed : 14.41 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.19), residues: 1565 helix: -0.98 (0.14), residues: 1105 sheet: None (None), residues: 0 loop : -2.44 (0.25), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 229 HIS 0.005 0.001 HIS E 115 PHE 0.023 0.001 PHE E 282 TYR 0.010 0.001 TYR E 85 ARG 0.003 0.000 ARG B 202 Details of bonding type rmsd hydrogen bonds : bond 0.04482 ( 680) hydrogen bonds : angle 4.13657 ( 2040) covalent geometry : bond 0.00252 (13415) covalent geometry : angle 0.50864 (18190) *********************** 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 290 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 272 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 203 ASP cc_start: 0.7541 (m-30) cc_final: 0.7282 (m-30) REVERT: E 223 MET cc_start: 0.8887 (OUTLIER) cc_final: 0.8553 (mmm) REVERT: E 230 ILE cc_start: 0.8764 (mm) cc_final: 0.8489 (mm) REVERT: E 238 GLN cc_start: 0.8658 (mt0) cc_final: 0.8450 (mt0) REVERT: E 282 PHE cc_start: 0.7984 (m-80) cc_final: 0.7745 (m-80) REVERT: E 310 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8365 (tt) REVERT: C 103 THR cc_start: 0.8839 (p) cc_final: 0.8609 (p) REVERT: C 203 ASP cc_start: 0.7508 (m-30) cc_final: 0.7148 (m-30) REVERT: C 230 ILE cc_start: 0.8849 (mm) cc_final: 0.8604 (mm) REVERT: C 242 ILE cc_start: 0.7975 (mm) cc_final: 0.7752 (mm) REVERT: C 282 PHE cc_start: 0.7932 (m-80) cc_final: 0.7633 (m-80) REVERT: B 103 THR cc_start: 0.8931 (p) cc_final: 0.8721 (p) REVERT: B 230 ILE cc_start: 0.8779 (mm) cc_final: 0.8505 (mm) REVERT: B 282 PHE cc_start: 0.7803 (m-10) cc_final: 0.7436 (m-80) REVERT: B 316 GLN cc_start: 0.8582 (tt0) cc_final: 0.7846 (tt0) REVERT: A 149 LYS cc_start: 0.9038 (mttt) cc_final: 0.8822 (mttt) REVERT: A 170 LYS cc_start: 0.8615 (mttt) cc_final: 0.8224 (mtpt) REVERT: A 230 ILE cc_start: 0.8721 (mm) cc_final: 0.8471 (mm) REVERT: A 282 PHE cc_start: 0.7812 (m-10) cc_final: 0.7346 (m-80) REVERT: D 203 ASP cc_start: 0.7513 (m-30) cc_final: 0.7173 (m-30) REVERT: D 276 PHE cc_start: 0.7091 (t80) cc_final: 0.6814 (t80) REVERT: D 282 PHE cc_start: 0.7620 (m-10) cc_final: 0.7322 (m-80) outliers start: 18 outliers final: 10 residues processed: 277 average time/residue: 0.2268 time to fit residues: 93.1159 Evaluate side-chains 261 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 249 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 223 MET Chi-restraints excluded: chain E residue 242 ILE Chi-restraints excluded: chain E residue 296 ASN Chi-restraints excluded: chain E residue 310 LEU 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 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 242 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 41 optimal weight: 0.6980 chunk 124 optimal weight: 8.9990 chunk 128 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 67 optimal weight: 0.2980 chunk 92 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 69 optimal weight: 0.0040 chunk 23 optimal weight: 10.0000 overall best weight: 0.5594 ------------------------------------------------------------------------------- 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 96 GLN C 238 GLN B 96 GLN B 262 GLN B 296 ASN A 238 GLN A 296 ASN ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.162458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.103034 restraints weight = 17544.684| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.94 r_work: 0.3154 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2411 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 : 0.491 6.768 18190 Z= 0.255 Chirality : 0.039 0.142 1965 Planarity : 0.003 0.031 2275 Dihedral : 4.139 16.032 1770 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.15 % Allowed : 16.06 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.20), residues: 1565 helix: -0.49 (0.15), residues: 1125 sheet: None (None), residues: 0 loop : -2.18 (0.26), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 229 HIS 0.003 0.000 HIS E 91 PHE 0.021 0.001 PHE E 282 TYR 0.017 0.001 TYR B 247 ARG 0.001 0.000 ARG D 92 Details of bonding type rmsd hydrogen bonds : bond 0.04278 ( 680) hydrogen bonds : angle 3.97614 ( 2040) covalent geometry : bond 0.00281 (13415) covalent geometry : angle 0.49095 (18190) *********************** 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 298 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 268 time to evaluate : 1.497 Fit side-chains revert: symmetry clash REVERT: E 82 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7268 (tt) REVERT: E 166 GLU cc_start: 0.8359 (mm-30) cc_final: 0.7910 (mp0) REVERT: E 230 ILE cc_start: 0.8526 (mm) cc_final: 0.8240 (mm) REVERT: E 238 GLN cc_start: 0.8529 (mt0) cc_final: 0.8260 (mt0) REVERT: E 282 PHE cc_start: 0.7784 (m-80) cc_final: 0.7536 (m-80) REVERT: C 44 MET cc_start: 0.8681 (mtp) cc_final: 0.8278 (mmm) REVERT: C 198 GLU cc_start: 0.8329 (mt-10) cc_final: 0.8072 (mt-10) REVERT: C 203 ASP cc_start: 0.7556 (m-30) cc_final: 0.7157 (m-30) REVERT: C 230 ILE cc_start: 0.8551 (mm) cc_final: 0.8291 (mm) REVERT: C 282 PHE cc_start: 0.7891 (m-80) cc_final: 0.7639 (m-80) REVERT: B 203 ASP cc_start: 0.7516 (m-30) cc_final: 0.7232 (m-30) REVERT: B 223 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.8390 (mmm) REVERT: B 230 ILE cc_start: 0.8518 (mm) cc_final: 0.8284 (mm) REVERT: B 282 PHE cc_start: 0.7610 (m-10) cc_final: 0.7342 (m-80) REVERT: B 316 GLN cc_start: 0.8327 (tt0) cc_final: 0.7527 (tt0) REVERT: A 80 PHE cc_start: 0.7118 (m-80) cc_final: 0.6894 (m-80) REVERT: A 149 LYS cc_start: 0.8929 (mttt) cc_final: 0.8714 (mttt) REVERT: A 282 PHE cc_start: 0.7636 (m-10) cc_final: 0.7218 (m-80) REVERT: D 203 ASP cc_start: 0.7397 (m-30) cc_final: 0.7020 (m-30) REVERT: D 238 GLN cc_start: 0.8692 (mt0) cc_final: 0.8402 (mt0) REVERT: D 276 PHE cc_start: 0.6904 (t80) cc_final: 0.6610 (t80) REVERT: D 282 PHE cc_start: 0.7513 (m-10) cc_final: 0.7252 (m-80) outliers start: 30 outliers final: 19 residues processed: 277 average time/residue: 0.2170 time to fit residues: 90.5705 Evaluate side-chains 277 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 256 time to evaluate : 1.379 ------------------------------------------------------------------------------- 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 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 B residue 145 THR Chi-restraints excluded: chain B residue 223 MET Chi-restraints excluded: chain B residue 319 MET Chi-restraints excluded: chain A residue 78 VAL 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 223 MET Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 242 ILE 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 14 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 chunk 105 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 100 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 chunk 130 optimal weight: 0.6980 chunk 113 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 296 ASN B 238 GLN B 296 ASN A 96 GLN A 296 ASN ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.162297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.102575 restraints weight = 17760.621| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.94 r_work: 0.3146 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13415 Z= 0.134 Angle : 0.495 7.474 18190 Z= 0.255 Chirality : 0.039 0.140 1965 Planarity : 0.003 0.031 2275 Dihedral : 4.057 15.587 1770 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.22 % Allowed : 16.63 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.20), residues: 1565 helix: -0.15 (0.15), residues: 1125 sheet: None (None), residues: 0 loop : -2.07 (0.26), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 229 HIS 0.003 0.000 HIS E 91 PHE 0.020 0.001 PHE E 282 TYR 0.020 0.001 TYR E 97 ARG 0.002 0.000 ARG B 202 Details of bonding type rmsd hydrogen bonds : bond 0.04190 ( 680) hydrogen bonds : angle 3.88277 ( 2040) covalent geometry : bond 0.00307 (13415) covalent geometry : angle 0.49525 (18190) *********************** 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 290 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 259 time to evaluate : 1.559 Fit side-chains revert: symmetry clash REVERT: E 82 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7309 (tt) REVERT: E 166 GLU cc_start: 0.8467 (mm-30) cc_final: 0.7899 (mp0) REVERT: E 230 ILE cc_start: 0.8491 (mm) cc_final: 0.8180 (mm) REVERT: E 238 GLN cc_start: 0.8503 (mt0) cc_final: 0.8284 (mt0) REVERT: E 282 PHE cc_start: 0.7743 (m-80) cc_final: 0.7524 (m-80) REVERT: C 44 MET cc_start: 0.8659 (mtp) cc_final: 0.8352 (mmm) REVERT: C 198 GLU cc_start: 0.8339 (mt-10) cc_final: 0.8046 (mt-10) REVERT: C 203 ASP cc_start: 0.7586 (m-30) cc_final: 0.7170 (m-30) REVERT: C 230 ILE cc_start: 0.8574 (mm) cc_final: 0.8311 (mm) REVERT: C 282 PHE cc_start: 0.7864 (m-80) cc_final: 0.7606 (m-80) REVERT: B 282 PHE cc_start: 0.7577 (m-10) cc_final: 0.7294 (m-80) REVERT: B 316 GLN cc_start: 0.8298 (tt0) cc_final: 0.7521 (tt0) REVERT: A 282 PHE cc_start: 0.7605 (m-10) cc_final: 0.7184 (m-80) REVERT: D 166 GLU cc_start: 0.8440 (mm-30) cc_final: 0.8228 (tm-30) REVERT: D 238 GLN cc_start: 0.8688 (mt0) cc_final: 0.8422 (mt0) REVERT: D 276 PHE cc_start: 0.6856 (t80) cc_final: 0.6550 (t80) REVERT: D 282 PHE cc_start: 0.7527 (m-10) cc_final: 0.7285 (m-80) outliers start: 31 outliers final: 22 residues processed: 269 average time/residue: 0.2508 time to fit residues: 102.3484 Evaluate side-chains 271 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 248 time to evaluate : 1.493 ------------------------------------------------------------------------------- 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 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 B residue 145 THR Chi-restraints excluded: chain B residue 238 GLN Chi-restraints excluded: chain B residue 319 MET Chi-restraints excluded: chain A residue 78 VAL 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 223 MET Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 242 ILE 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 63 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 chunk 55 optimal weight: 9.9990 chunk 120 optimal weight: 0.9990 chunk 70 optimal weight: 0.1980 chunk 3 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 88 optimal weight: 0.0570 chunk 138 optimal weight: 0.0270 chunk 117 optimal weight: 8.9990 chunk 147 optimal weight: 9.9990 overall best weight: 0.3958 ------------------------------------------------------------------------------- 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 238 GLN C 296 ASN ** B 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 ASN A 296 ASN ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.163349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.103849 restraints weight = 17731.649| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.94 r_work: 0.3166 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13415 Z= 0.109 Angle : 0.479 7.736 18190 Z= 0.246 Chirality : 0.038 0.144 1965 Planarity : 0.002 0.032 2275 Dihedral : 3.961 14.780 1770 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.86 % Allowed : 17.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.20), residues: 1565 helix: 0.07 (0.15), residues: 1120 sheet: None (None), residues: 0 loop : -2.07 (0.26), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 229 HIS 0.003 0.000 HIS E 91 PHE 0.020 0.001 PHE E 282 TYR 0.019 0.001 TYR E 97 ARG 0.001 0.000 ARG B 202 Details of bonding type rmsd hydrogen bonds : bond 0.03979 ( 680) hydrogen bonds : angle 3.79379 ( 2040) covalent geometry : bond 0.00242 (13415) covalent geometry : angle 0.47939 (18190) *********************** 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 271 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 245 time to evaluate : 1.492 Fit side-chains REVERT: E 82 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7336 (tt) REVERT: E 166 GLU cc_start: 0.8453 (mm-30) cc_final: 0.7817 (mp0) REVERT: E 230 ILE cc_start: 0.8485 (mm) cc_final: 0.8179 (mm) REVERT: E 282 PHE cc_start: 0.7734 (m-80) cc_final: 0.7506 (m-80) REVERT: C 166 GLU cc_start: 0.8333 (mm-30) cc_final: 0.7872 (mp0) REVERT: C 198 GLU cc_start: 0.8356 (mt-10) cc_final: 0.8027 (mt-10) REVERT: C 230 ILE cc_start: 0.8567 (mm) cc_final: 0.8360 (mm) REVERT: C 282 PHE cc_start: 0.7882 (m-80) cc_final: 0.7663 (m-80) REVERT: B 44 MET cc_start: 0.8649 (mtp) cc_final: 0.8322 (mmm) REVERT: B 282 PHE cc_start: 0.7593 (m-10) cc_final: 0.7292 (m-80) REVERT: B 316 GLN cc_start: 0.8272 (tt0) cc_final: 0.7459 (tt0) REVERT: A 44 MET cc_start: 0.8699 (mtp) cc_final: 0.8372 (mmm) REVERT: A 80 PHE cc_start: 0.6884 (m-80) cc_final: 0.6506 (m-80) REVERT: A 282 PHE cc_start: 0.7558 (m-10) cc_final: 0.7161 (m-80) REVERT: D 44 MET cc_start: 0.8522 (mtp) cc_final: 0.8287 (mmm) REVERT: D 238 GLN cc_start: 0.8669 (mt0) cc_final: 0.8444 (mt0) REVERT: D 282 PHE cc_start: 0.7528 (m-10) cc_final: 0.7282 (m-80) outliers start: 26 outliers final: 22 residues processed: 254 average time/residue: 0.2134 time to fit residues: 82.2610 Evaluate side-chains 267 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 244 time to evaluate : 1.516 ------------------------------------------------------------------------------- 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 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 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 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 33 optimal weight: 7.9990 chunk 78 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 149 optimal weight: 0.4980 chunk 153 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 64 optimal weight: 9.9990 chunk 56 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 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.162806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.102890 restraints weight = 17648.241| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.97 r_work: 0.3151 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13415 Z= 0.133 Angle : 0.503 9.741 18190 Z= 0.255 Chirality : 0.039 0.142 1965 Planarity : 0.003 0.031 2275 Dihedral : 3.941 14.602 1770 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.94 % Allowed : 17.56 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.20), residues: 1565 helix: 0.16 (0.15), residues: 1125 sheet: None (None), residues: 0 loop : -1.95 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 229 HIS 0.004 0.000 HIS E 91 PHE 0.019 0.001 PHE E 282 TYR 0.022 0.001 TYR E 97 ARG 0.001 0.000 ARG A 92 Details of bonding type rmsd hydrogen bonds : bond 0.04042 ( 680) hydrogen bonds : angle 3.79647 ( 2040) covalent geometry : bond 0.00309 (13415) covalent geometry : angle 0.50257 (18190) *********************** 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 267 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 240 time to evaluate : 2.125 Fit side-chains REVERT: E 44 MET cc_start: 0.8538 (mtp) cc_final: 0.8295 (mmm) REVERT: E 82 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7356 (tt) REVERT: E 97 TYR cc_start: 0.7964 (t80) cc_final: 0.7591 (t80) REVERT: E 166 GLU cc_start: 0.8457 (mm-30) cc_final: 0.7766 (mp0) REVERT: E 230 ILE cc_start: 0.8480 (mm) cc_final: 0.8186 (mm) REVERT: E 238 GLN cc_start: 0.8686 (mt0) cc_final: 0.8418 (mt0) REVERT: E 282 PHE cc_start: 0.7722 (m-80) cc_final: 0.7498 (m-80) REVERT: C 107 MET cc_start: 0.8734 (ptt) cc_final: 0.8525 (ptt) REVERT: C 198 GLU cc_start: 0.8380 (mt-10) cc_final: 0.8041 (mt-10) REVERT: C 230 ILE cc_start: 0.8499 (mm) cc_final: 0.8240 (mm) REVERT: C 282 PHE cc_start: 0.7869 (m-80) cc_final: 0.7635 (m-80) REVERT: B 44 MET cc_start: 0.8613 (mtp) cc_final: 0.8319 (mmm) REVERT: B 282 PHE cc_start: 0.7564 (m-10) cc_final: 0.7306 (m-80) REVERT: B 316 GLN cc_start: 0.8265 (tt0) cc_final: 0.7444 (tt0) REVERT: A 44 MET cc_start: 0.8665 (mtp) cc_final: 0.8362 (mmm) REVERT: A 80 PHE cc_start: 0.6930 (m-80) cc_final: 0.6572 (m-80) REVERT: A 282 PHE cc_start: 0.7547 (m-10) cc_final: 0.7160 (m-80) REVERT: D 238 GLN cc_start: 0.8635 (mt0) cc_final: 0.8306 (mt0) REVERT: D 282 PHE cc_start: 0.7507 (m-10) cc_final: 0.7257 (m-80) outliers start: 27 outliers final: 23 residues processed: 251 average time/residue: 0.2231 time to fit residues: 85.9904 Evaluate side-chains 260 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 236 time to evaluate : 1.382 ------------------------------------------------------------------------------- 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 B residue 145 THR Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 319 MET Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 79 optimal weight: 0.5980 chunk 133 optimal weight: 0.7980 chunk 132 optimal weight: 0.9980 chunk 43 optimal weight: 0.3980 chunk 1 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 127 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 238 GLN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.162792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.102959 restraints weight = 17696.989| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.91 r_work: 0.3183 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13415 Z= 0.144 Angle : 0.510 8.421 18190 Z= 0.260 Chirality : 0.040 0.140 1965 Planarity : 0.003 0.032 2275 Dihedral : 3.941 14.669 1770 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.08 % Allowed : 18.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.21), residues: 1565 helix: 0.22 (0.15), residues: 1125 sheet: None (None), residues: 0 loop : -1.90 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 229 HIS 0.003 0.000 HIS E 91 PHE 0.023 0.001 PHE E 276 TYR 0.047 0.001 TYR E 97 ARG 0.001 0.000 ARG B 92 Details of bonding type rmsd hydrogen bonds : bond 0.04102 ( 680) hydrogen bonds : angle 3.82699 ( 2040) covalent geometry : bond 0.00339 (13415) covalent geometry : angle 0.50980 (18190) *********************** 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 269 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 240 time to evaluate : 1.967 Fit side-chains REVERT: E 44 MET cc_start: 0.8527 (mtp) cc_final: 0.8312 (mmm) REVERT: E 82 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7354 (tt) REVERT: E 230 ILE cc_start: 0.8471 (mm) cc_final: 0.8144 (mm) REVERT: E 238 GLN cc_start: 0.8674 (mt0) cc_final: 0.8421 (mt0) REVERT: E 282 PHE cc_start: 0.7725 (m-80) cc_final: 0.7498 (m-80) REVERT: C 230 ILE cc_start: 0.8517 (mm) cc_final: 0.8287 (mm) REVERT: C 282 PHE cc_start: 0.7869 (m-80) cc_final: 0.7630 (m-80) REVERT: B 44 MET cc_start: 0.8598 (mtp) cc_final: 0.8386 (mmm) REVERT: B 80 PHE cc_start: 0.7548 (t80) cc_final: 0.6898 (m-80) REVERT: B 198 GLU cc_start: 0.8330 (mt-10) cc_final: 0.7998 (mt-10) REVERT: B 230 ILE cc_start: 0.8459 (mm) cc_final: 0.8210 (mm) REVERT: B 282 PHE cc_start: 0.7583 (m-10) cc_final: 0.7338 (m-80) REVERT: B 316 GLN cc_start: 0.8298 (tt0) cc_final: 0.7464 (tt0) REVERT: A 44 MET cc_start: 0.8653 (mtp) cc_final: 0.8370 (mmm) REVERT: A 80 PHE cc_start: 0.7029 (m-80) cc_final: 0.6479 (m-80) REVERT: A 282 PHE cc_start: 0.7566 (m-10) cc_final: 0.7211 (m-80) REVERT: A 310 LEU cc_start: 0.8428 (tt) cc_final: 0.8188 (tt) REVERT: D 166 GLU cc_start: 0.8400 (tt0) cc_final: 0.8190 (tm-30) REVERT: D 238 GLN cc_start: 0.8575 (mt0) cc_final: 0.8261 (mt0) REVERT: D 282 PHE cc_start: 0.7501 (m-10) cc_final: 0.7271 (m-80) outliers start: 29 outliers final: 21 residues processed: 252 average time/residue: 0.2416 time to fit residues: 92.9044 Evaluate side-chains 260 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 238 time to evaluate : 1.419 ------------------------------------------------------------------------------- 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 B residue 78 VAL Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 319 MET Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 223 MET Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 319 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 59 optimal weight: 0.9990 chunk 153 optimal weight: 1.9990 chunk 127 optimal weight: 7.9990 chunk 134 optimal weight: 0.9990 chunk 133 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 91 HIS 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 = 0.4123 r_free = 0.4123 target = 0.162342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.102789 restraints weight = 17601.550| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.85 r_work: 0.3149 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13415 Z= 0.154 Angle : 0.523 7.981 18190 Z= 0.266 Chirality : 0.040 0.155 1965 Planarity : 0.003 0.032 2275 Dihedral : 3.954 14.561 1770 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.15 % Allowed : 18.28 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.21), residues: 1565 helix: 0.27 (0.15), residues: 1125 sheet: None (None), residues: 0 loop : -1.83 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 229 HIS 0.004 0.001 HIS E 91 PHE 0.020 0.001 PHE E 282 TYR 0.035 0.001 TYR E 97 ARG 0.001 0.000 ARG A 92 Details of bonding type rmsd hydrogen bonds : bond 0.04186 ( 680) hydrogen bonds : angle 3.85135 ( 2040) covalent geometry : bond 0.00362 (13415) covalent geometry : angle 0.52277 (18190) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 239 time to evaluate : 1.391 Fit side-chains REVERT: E 82 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7363 (tt) REVERT: E 230 ILE cc_start: 0.8527 (mm) cc_final: 0.8261 (mm) REVERT: E 238 GLN cc_start: 0.8697 (mt0) cc_final: 0.8456 (mt0) REVERT: E 282 PHE cc_start: 0.7736 (m-80) cc_final: 0.7510 (m-80) REVERT: C 44 MET cc_start: 0.8736 (mmm) cc_final: 0.8307 (mmm) REVERT: C 229 TRP cc_start: 0.8038 (t60) cc_final: 0.7743 (t60) REVERT: C 230 ILE cc_start: 0.8547 (mm) cc_final: 0.8215 (mm) REVERT: C 282 PHE cc_start: 0.7856 (m-80) cc_final: 0.7624 (m-80) REVERT: B 80 PHE cc_start: 0.7646 (t80) cc_final: 0.7077 (m-80) REVERT: B 198 GLU cc_start: 0.8346 (mt-10) cc_final: 0.8021 (mt-10) REVERT: B 203 ASP cc_start: 0.7517 (m-30) cc_final: 0.7266 (m-30) REVERT: B 282 PHE cc_start: 0.7589 (m-10) cc_final: 0.7359 (m-80) REVERT: B 316 GLN cc_start: 0.8298 (tt0) cc_final: 0.7463 (tt0) REVERT: A 282 PHE cc_start: 0.7578 (m-10) cc_final: 0.7233 (m-80) REVERT: D 166 GLU cc_start: 0.8419 (tt0) cc_final: 0.8195 (tm-30) REVERT: D 238 GLN cc_start: 0.8574 (mt0) cc_final: 0.8280 (mt0) REVERT: D 282 PHE cc_start: 0.7497 (m-10) cc_final: 0.7279 (m-80) outliers start: 30 outliers final: 23 residues processed: 254 average time/residue: 0.2105 time to fit residues: 81.2037 Evaluate side-chains 260 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 236 time to evaluate : 1.384 ------------------------------------------------------------------------------- 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 117 HIS 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 29 optimal weight: 0.9980 chunk 142 optimal weight: 0.6980 chunk 151 optimal weight: 0.3980 chunk 33 optimal weight: 5.9990 chunk 7 optimal weight: 0.0670 chunk 117 optimal weight: 0.0070 chunk 85 optimal weight: 0.0040 chunk 52 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 6.9990 chunk 104 optimal weight: 0.9990 overall best weight: 0.2348 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 91 HIS C 238 GLN C 296 ASN B 95 ASN B 296 ASN A 238 GLN A 296 ASN ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.166027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.105596 restraints weight = 17617.683| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.95 r_work: 0.3193 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13415 Z= 0.100 Angle : 0.519 12.440 18190 Z= 0.257 Chirality : 0.038 0.146 1965 Planarity : 0.003 0.032 2275 Dihedral : 3.852 13.884 1770 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.51 % Allowed : 19.28 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.21), residues: 1565 helix: 0.46 (0.15), residues: 1125 sheet: None (None), residues: 0 loop : -1.90 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP B 229 HIS 0.004 0.000 HIS E 91 PHE 0.021 0.001 PHE E 282 TYR 0.010 0.001 TYR E 97 ARG 0.005 0.000 ARG D 165 Details of bonding type rmsd hydrogen bonds : bond 0.03767 ( 680) hydrogen bonds : angle 3.73318 ( 2040) covalent geometry : bond 0.00216 (13415) covalent geometry : angle 0.51889 (18190) ********************** 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 269 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 248 time to evaluate : 1.538 Fit side-chains REVERT: E 230 ILE cc_start: 0.8470 (mm) cc_final: 0.8183 (mm) REVERT: E 238 GLN cc_start: 0.8647 (mt0) cc_final: 0.8384 (mt0) REVERT: E 282 PHE cc_start: 0.7732 (m-80) cc_final: 0.7476 (m-80) REVERT: C 44 MET cc_start: 0.8710 (mmm) cc_final: 0.8294 (mmm) REVERT: C 80 PHE cc_start: 0.7309 (t80) cc_final: 0.7084 (m-80) REVERT: C 229 TRP cc_start: 0.7985 (t60) cc_final: 0.7736 (t60) REVERT: C 230 ILE cc_start: 0.8477 (mm) cc_final: 0.8134 (mm) REVERT: B 85 TYR cc_start: 0.8546 (t80) cc_final: 0.8245 (t80) REVERT: B 198 GLU cc_start: 0.8312 (mt-10) cc_final: 0.7959 (mt-10) REVERT: B 203 ASP cc_start: 0.7423 (m-30) cc_final: 0.7123 (m-30) REVERT: B 282 PHE cc_start: 0.7537 (m-10) cc_final: 0.7293 (m-80) REVERT: B 316 GLN cc_start: 0.8200 (tt0) cc_final: 0.7360 (tt0) REVERT: A 80 PHE cc_start: 0.6723 (m-80) cc_final: 0.6477 (m-80) REVERT: A 310 LEU cc_start: 0.8295 (tt) cc_final: 0.8058 (tt) REVERT: D 166 GLU cc_start: 0.8349 (tt0) cc_final: 0.8108 (tm-30) REVERT: D 238 GLN cc_start: 0.8562 (mt0) cc_final: 0.8322 (mt0) REVERT: D 282 PHE cc_start: 0.7490 (m-10) cc_final: 0.7274 (m-80) outliers start: 21 outliers final: 14 residues processed: 256 average time/residue: 0.2232 time to fit residues: 86.8628 Evaluate side-chains 256 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 242 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 117 HIS Chi-restraints excluded: chain E residue 223 MET Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain B residue 319 MET Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 238 GLN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 33 optimal weight: 4.9990 chunk 125 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 117 optimal weight: 0.0870 chunk 72 optimal weight: 0.5980 chunk 64 optimal weight: 9.9990 chunk 98 optimal weight: 0.8980 chunk 71 optimal weight: 0.5980 chunk 25 optimal weight: 0.1980 chunk 10 optimal weight: 0.6980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 91 HIS C 194 GLN C 296 ASN B 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 = 0.4140 r_free = 0.4140 target = 0.162515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.102717 restraints weight = 17904.184| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.90 r_work: 0.3182 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13415 Z= 0.114 Angle : 0.527 11.543 18190 Z= 0.262 Chirality : 0.039 0.152 1965 Planarity : 0.003 0.032 2275 Dihedral : 3.868 18.134 1770 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.22 % Allowed : 19.78 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.21), residues: 1565 helix: 0.59 (0.16), residues: 1110 sheet: None (None), residues: 0 loop : -1.72 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP B 229 HIS 0.004 0.000 HIS E 91 PHE 0.027 0.001 PHE C 282 TYR 0.018 0.001 TYR C 247 ARG 0.005 0.000 ARG E 165 Details of bonding type rmsd hydrogen bonds : bond 0.03822 ( 680) hydrogen bonds : angle 3.72753 ( 2040) covalent geometry : bond 0.00260 (13415) covalent geometry : angle 0.52707 (18190) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7737.61 seconds wall clock time: 138 minutes 25.02 seconds (8305.02 seconds total)