Starting phenix.real_space_refine on Thu Sep 26 11:44:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vx5_21430/09_2024/6vx5_21430.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vx5_21430/09_2024/6vx5_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vx5_21430/09_2024/6vx5_21430.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vx5_21430/09_2024/6vx5_21430.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vx5_21430/09_2024/6vx5_21430.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vx5_21430/09_2024/6vx5_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 6.20, per 1000 atoms: 0.47 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: 3.00 Conformation dependent library (CDL) restraints added in 1.4 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: 1.14 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: 3.54 Time building geometry restraints manager: 3.50 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: 3.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.690 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 27.540 Find NCS groups from input model: 0.550 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.420 ------------------------------------------------------------------------------- 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= 0.407 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 275 time to evaluate : 1.448 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: 0.2718 time to fit residues: 105.6184 Evaluate side-chains 229 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 1.450 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 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= 0.209 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 *********************** 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 fitting. rotamer outliers: 20 poor density : 270 time to evaluate : 1.241 Fit side-chains revert: symmetry clash REVERT: E 238 GLN cc_start: 0.8558 (mt0) cc_final: 0.8340 (mt0) REVERT: E 276 PHE cc_start: 0.7397 (t80) cc_final: 0.7181 (t80) REVERT: C 149 LYS cc_start: 0.8852 (mttt) cc_final: 0.8567 (mttt) REVERT: C 203 ASP cc_start: 0.7241 (m-30) cc_final: 0.6998 (m-30) REVERT: C 282 PHE cc_start: 0.7877 (m-80) cc_final: 0.7485 (m-80) REVERT: B 100 MET cc_start: 0.9098 (mmm) cc_final: 0.8872 (mmm) REVERT: B 282 PHE cc_start: 0.7809 (m-10) cc_final: 0.7422 (m-80) REVERT: B 316 GLN cc_start: 0.8480 (tt0) cc_final: 0.7692 (tt0) REVERT: A 149 LYS cc_start: 0.8880 (mttt) cc_final: 0.8579 (mttt) REVERT: A 170 LYS cc_start: 0.8581 (mttt) cc_final: 0.8147 (mtmt) REVERT: A 230 ILE cc_start: 0.8963 (mm) cc_final: 0.8677 (mm) REVERT: A 245 TYR cc_start: 0.8273 (m-80) cc_final: 0.7860 (m-80) REVERT: A 279 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7356 (mt) REVERT: A 282 PHE cc_start: 0.7799 (m-10) cc_final: 0.7286 (m-80) REVERT: D 203 ASP cc_start: 0.7288 (m-30) cc_final: 0.7032 (m-30) REVERT: D 276 PHE cc_start: 0.7326 (t80) cc_final: 0.7116 (t80) REVERT: D 282 PHE cc_start: 0.7766 (m-10) cc_final: 0.7339 (m-80) outliers start: 20 outliers final: 7 residues processed: 279 average time/residue: 0.2249 time to fit residues: 92.0559 Evaluate side-chains 253 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 245 time to evaluate : 1.478 ------------------------------------------------------------------------------- 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 A residue 279 LEU 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 78 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 117 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 141 optimal weight: 2.9990 chunk 152 optimal weight: 0.5980 chunk 125 optimal weight: 1.9990 chunk 139 optimal weight: 0.3980 chunk 48 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 91 HIS E 262 GLN E 296 ASN C 194 GLN C 262 GLN ** C 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 GLN B 238 GLN A 262 GLN A 296 ASN ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 HIS D 262 GLN D 296 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2160 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= 0.206 Angle : 0.531 7.521 18190 Z= 0.274 Chirality : 0.040 0.166 1965 Planarity : 0.003 0.030 2275 Dihedral : 4.385 16.913 1770 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.72 % Allowed : 14.41 % Favored : 83.87 % 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: -2.34 (0.19), residues: 1565 helix: -1.12 (0.14), residues: 1120 sheet: None (None), residues: 0 loop : -2.34 (0.26), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 229 HIS 0.003 0.001 HIS E 115 PHE 0.023 0.001 PHE E 282 TYR 0.011 0.001 TYR E 85 ARG 0.003 0.000 ARG A 202 *********************** 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 287 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 263 time to evaluate : 1.446 Fit side-chains revert: symmetry clash REVERT: E 203 ASP cc_start: 0.7346 (m-30) cc_final: 0.7104 (m-30) REVERT: E 223 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8446 (mmm) REVERT: E 238 GLN cc_start: 0.8608 (mt0) cc_final: 0.8400 (mt0) REVERT: E 282 PHE cc_start: 0.7859 (m-80) cc_final: 0.7646 (m-80) REVERT: C 203 ASP cc_start: 0.7372 (m-30) cc_final: 0.7058 (m-30) REVERT: C 230 ILE cc_start: 0.8935 (mm) cc_final: 0.8733 (mm) REVERT: C 282 PHE cc_start: 0.7847 (m-80) cc_final: 0.7532 (m-80) REVERT: B 149 LYS cc_start: 0.8920 (mttt) cc_final: 0.8616 (mttt) REVERT: B 230 ILE cc_start: 0.8876 (mm) cc_final: 0.8639 (mm) REVERT: B 282 PHE cc_start: 0.7718 (m-10) cc_final: 0.7375 (m-80) REVERT: B 316 GLN cc_start: 0.8523 (tt0) cc_final: 0.7735 (tt0) REVERT: A 149 LYS cc_start: 0.8867 (mttt) cc_final: 0.8594 (mttt) REVERT: A 170 LYS cc_start: 0.8542 (mttt) cc_final: 0.8178 (mtpt) REVERT: A 230 ILE cc_start: 0.8823 (mm) cc_final: 0.8552 (mm) REVERT: A 282 PHE cc_start: 0.7811 (m-10) cc_final: 0.7276 (m-80) REVERT: D 203 ASP cc_start: 0.7283 (m-30) cc_final: 0.6990 (m-30) REVERT: D 276 PHE cc_start: 0.7232 (t80) cc_final: 0.6980 (t80) REVERT: D 282 PHE cc_start: 0.7548 (m-10) cc_final: 0.7251 (m-80) outliers start: 24 outliers final: 13 residues processed: 274 average time/residue: 0.2283 time to fit residues: 92.1690 Evaluate side-chains 266 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 252 time to evaluate : 1.486 ------------------------------------------------------------------------------- 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 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 A residue 78 VAL Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 223 MET Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 242 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 139 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 15 optimal weight: 0.0980 chunk 67 optimal weight: 0.0770 chunk 94 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 overall best weight: 0.6340 ------------------------------------------------------------------------------- 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 B 96 GLN B 262 GLN B 296 ASN A 238 GLN A 296 ASN ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13415 Z= 0.190 Angle : 0.505 7.155 18190 Z= 0.262 Chirality : 0.039 0.157 1965 Planarity : 0.003 0.032 2275 Dihedral : 4.203 15.911 1770 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.01 % Allowed : 15.70 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.65 (0.20), residues: 1565 helix: -0.57 (0.15), residues: 1130 sheet: None (None), residues: 0 loop : -2.21 (0.26), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 229 HIS 0.003 0.000 HIS E 91 PHE 0.022 0.001 PHE E 282 TYR 0.017 0.001 TYR E 97 ARG 0.001 0.000 ARG B 202 *********************** 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 294 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 266 time to evaluate : 1.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 82 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7516 (tt) REVERT: E 223 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.8480 (mmm) REVERT: E 282 PHE cc_start: 0.7848 (m-80) cc_final: 0.7599 (m-80) REVERT: C 198 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7981 (mt-10) REVERT: C 203 ASP cc_start: 0.7365 (m-30) cc_final: 0.7057 (m-30) REVERT: C 230 ILE cc_start: 0.8846 (mm) cc_final: 0.8638 (mm) REVERT: C 282 PHE cc_start: 0.7885 (m-80) cc_final: 0.7590 (m-80) REVERT: B 203 ASP cc_start: 0.7341 (m-30) cc_final: 0.6992 (m-30) REVERT: B 230 ILE cc_start: 0.8774 (mm) cc_final: 0.8565 (mm) REVERT: B 247 TYR cc_start: 0.7537 (t80) cc_final: 0.7293 (t80) REVERT: B 282 PHE cc_start: 0.7697 (m-10) cc_final: 0.7390 (m-80) REVERT: B 316 GLN cc_start: 0.8510 (tt0) cc_final: 0.7677 (tt0) REVERT: A 80 PHE cc_start: 0.7183 (m-80) cc_final: 0.6951 (m-80) REVERT: A 149 LYS cc_start: 0.8856 (mttt) cc_final: 0.8587 (mttt) REVERT: A 282 PHE cc_start: 0.7685 (m-10) cc_final: 0.7263 (m-80) REVERT: D 238 GLN cc_start: 0.8762 (mt0) cc_final: 0.8546 (mt0) REVERT: D 276 PHE cc_start: 0.7282 (t80) cc_final: 0.6989 (t80) REVERT: D 282 PHE cc_start: 0.7545 (m-10) cc_final: 0.7282 (m-80) outliers start: 28 outliers final: 19 residues processed: 275 average time/residue: 0.2165 time to fit residues: 89.4040 Evaluate side-chains 274 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 253 time to evaluate : 1.539 ------------------------------------------------------------------------------- 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 242 ILE Chi-restraints excluded: chain E residue 296 ASN Chi-restraints excluded: chain E residue 319 MET Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain B residue 145 THR 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 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 85 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 111 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 B 238 GLN B 296 ASN A 296 ASN ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 13415 Z= 0.240 Angle : 0.514 7.437 18190 Z= 0.266 Chirality : 0.040 0.145 1965 Planarity : 0.003 0.033 2275 Dihedral : 4.170 15.724 1770 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.29 % Allowed : 16.42 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.33 (0.20), residues: 1565 helix: -0.33 (0.15), residues: 1130 sheet: None (None), residues: 0 loop : -2.09 (0.27), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 229 HIS 0.003 0.001 HIS E 91 PHE 0.020 0.001 PHE E 282 TYR 0.022 0.001 TYR E 97 ARG 0.001 0.000 ARG A 92 *********************** 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 287 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 255 time to evaluate : 1.341 Fit side-chains revert: symmetry clash REVERT: E 82 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7566 (tt) REVERT: E 166 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7417 (pm20) REVERT: E 223 MET cc_start: 0.8756 (OUTLIER) cc_final: 0.8482 (mmm) REVERT: E 238 GLN cc_start: 0.8916 (mt0) cc_final: 0.8637 (mt0) REVERT: E 282 PHE cc_start: 0.7812 (m-80) cc_final: 0.7599 (m-80) REVERT: C 282 PHE cc_start: 0.7855 (m-80) cc_final: 0.7573 (m-80) REVERT: B 149 LYS cc_start: 0.8884 (mttt) cc_final: 0.8471 (mttt) REVERT: B 282 PHE cc_start: 0.7693 (m-10) cc_final: 0.7414 (m-80) REVERT: B 316 GLN cc_start: 0.8484 (tt0) cc_final: 0.7657 (tt0) REVERT: A 282 PHE cc_start: 0.7643 (m-10) cc_final: 0.7244 (m-80) REVERT: D 238 GLN cc_start: 0.8793 (mt0) cc_final: 0.8395 (mt0) REVERT: D 276 PHE cc_start: 0.7242 (t80) cc_final: 0.6925 (t80) REVERT: D 282 PHE cc_start: 0.7555 (m-10) cc_final: 0.7303 (m-80) outliers start: 32 outliers final: 21 residues processed: 268 average time/residue: 0.2190 time to fit residues: 87.8990 Evaluate side-chains 269 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 245 time to evaluate : 1.361 ------------------------------------------------------------------------------- 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 166 GLU 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 238 GLN Chi-restraints excluded: chain B residue 319 MET Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 223 MET Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 134 optimal weight: 0.3980 chunk 29 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 149 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 12 optimal weight: 0.0270 chunk 49 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 chunk 144 optimal weight: 0.8980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 91 HIS E 238 GLN E 296 ASN C 296 ASN 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13415 Z= 0.167 Angle : 0.496 8.121 18190 Z= 0.254 Chirality : 0.039 0.146 1965 Planarity : 0.002 0.034 2275 Dihedral : 4.039 15.143 1770 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.22 % Allowed : 16.70 % Favored : 81.08 % 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: -1.03 (0.20), residues: 1565 helix: -0.09 (0.15), residues: 1130 sheet: None (None), residues: 0 loop : -2.04 (0.27), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP E 229 HIS 0.003 0.000 HIS E 91 PHE 0.021 0.001 PHE E 282 TYR 0.017 0.001 TYR E 97 ARG 0.001 0.000 ARG B 202 *********************** 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 284 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 253 time to evaluate : 1.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 82 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7585 (tt) REVERT: E 166 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7461 (pm20) REVERT: E 238 GLN cc_start: 0.8861 (mt0) cc_final: 0.8629 (mt0) REVERT: E 282 PHE cc_start: 0.7790 (m-80) cc_final: 0.7573 (m-80) REVERT: C 44 MET cc_start: 0.8666 (mtp) cc_final: 0.8440 (mmm) REVERT: C 198 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7900 (mt-10) REVERT: C 230 ILE cc_start: 0.8851 (mm) cc_final: 0.8599 (mm) REVERT: C 282 PHE cc_start: 0.7847 (m-80) cc_final: 0.7586 (m-80) REVERT: B 282 PHE cc_start: 0.7694 (m-10) cc_final: 0.7406 (m-80) REVERT: B 316 GLN cc_start: 0.8465 (tt0) cc_final: 0.7662 (tt0) REVERT: A 80 PHE cc_start: 0.6952 (m-80) cc_final: 0.6580 (m-80) REVERT: A 282 PHE cc_start: 0.7573 (m-10) cc_final: 0.7198 (m-80) REVERT: A 310 LEU cc_start: 0.8744 (tt) cc_final: 0.8451 (tt) REVERT: D 238 GLN cc_start: 0.8748 (mt0) cc_final: 0.8441 (mt0) REVERT: D 282 PHE cc_start: 0.7544 (m-10) cc_final: 0.7305 (m-80) outliers start: 31 outliers final: 25 residues processed: 265 average time/residue: 0.2148 time to fit residues: 85.8392 Evaluate side-chains 271 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 244 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 166 GLU 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 319 MET Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 223 MET Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 16 optimal weight: 0.6980 chunk 85 optimal weight: 9.9990 chunk 109 optimal weight: 0.5980 chunk 84 optimal weight: 7.9990 chunk 126 optimal weight: 10.0000 chunk 83 optimal weight: 0.6980 chunk 149 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 91 optimal weight: 0.2980 chunk 68 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 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 91 HIS E 296 ASN C 238 GLN C 296 ASN ** C 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 ASN A 296 ASN ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2703 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= 0.191 Angle : 0.497 7.544 18190 Z= 0.255 Chirality : 0.039 0.149 1965 Planarity : 0.003 0.035 2275 Dihedral : 4.011 14.888 1770 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.15 % Allowed : 17.28 % Favored : 80.57 % 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: -0.85 (0.20), residues: 1565 helix: 0.04 (0.15), residues: 1130 sheet: None (None), residues: 0 loop : -1.97 (0.27), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP E 229 HIS 0.003 0.000 HIS E 91 PHE 0.020 0.001 PHE E 282 TYR 0.021 0.001 TYR E 97 ARG 0.001 0.000 ARG A 92 *********************** 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 275 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 245 time to evaluate : 1.435 Fit side-chains revert: symmetry clash REVERT: E 82 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7600 (tt) REVERT: E 97 TYR cc_start: 0.7659 (t80) cc_final: 0.7276 (t80) REVERT: E 166 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7483 (pm20) REVERT: E 238 GLN cc_start: 0.8859 (mt0) cc_final: 0.8628 (mt0) REVERT: E 282 PHE cc_start: 0.7773 (m-80) cc_final: 0.7554 (m-80) REVERT: C 282 PHE cc_start: 0.7849 (m-80) cc_final: 0.7623 (m-80) REVERT: B 44 MET cc_start: 0.8663 (mtp) cc_final: 0.8450 (mmm) REVERT: B 238 GLN cc_start: 0.8709 (mt0) cc_final: 0.8456 (mt0) REVERT: B 282 PHE cc_start: 0.7670 (m-10) cc_final: 0.7401 (m-80) REVERT: B 316 GLN cc_start: 0.8472 (tt0) cc_final: 0.7653 (tt0) REVERT: A 44 MET cc_start: 0.8737 (mtp) cc_final: 0.8502 (mmm) REVERT: A 80 PHE cc_start: 0.6974 (m-80) cc_final: 0.6618 (m-80) REVERT: A 282 PHE cc_start: 0.7597 (m-10) cc_final: 0.7224 (m-80) REVERT: D 238 GLN cc_start: 0.8753 (mt0) cc_final: 0.8359 (mt0) REVERT: D 282 PHE cc_start: 0.7548 (m-10) cc_final: 0.7293 (m-80) outliers start: 30 outliers final: 25 residues processed: 259 average time/residue: 0.2223 time to fit residues: 86.9718 Evaluate side-chains 265 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 238 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 166 GLU 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 319 MET Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 223 MET Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 223 MET Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 296 ASN Chi-restraints excluded: chain D residue 319 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 59 optimal weight: 0.6980 chunk 89 optimal weight: 0.0770 chunk 45 optimal weight: 0.4980 chunk 29 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 101 optimal weight: 0.5980 chunk 73 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 117 optimal weight: 20.0000 chunk 135 optimal weight: 0.9980 overall best weight: 0.5138 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 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 0.044 13415 Z= 0.176 Angle : 0.515 10.650 18190 Z= 0.260 Chirality : 0.039 0.148 1965 Planarity : 0.003 0.035 2275 Dihedral : 3.975 14.729 1770 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.37 % Allowed : 17.92 % Favored : 79.71 % 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 (0.21), residues: 1565 helix: 0.14 (0.15), residues: 1130 sheet: None (None), residues: 0 loop : -1.93 (0.27), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP E 229 HIS 0.004 0.000 HIS E 91 PHE 0.023 0.001 PHE E 276 TYR 0.031 0.001 TYR E 97 ARG 0.001 0.000 ARG A 92 *********************** 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 274 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 241 time to evaluate : 1.380 Fit side-chains revert: symmetry clash REVERT: E 82 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7615 (tt) REVERT: E 166 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7465 (pm20) REVERT: E 282 PHE cc_start: 0.7781 (m-80) cc_final: 0.7561 (m-80) REVERT: C 282 PHE cc_start: 0.7878 (m-80) cc_final: 0.7668 (m-80) REVERT: B 282 PHE cc_start: 0.7647 (m-10) cc_final: 0.7389 (m-80) REVERT: B 316 GLN cc_start: 0.8456 (tt0) cc_final: 0.7629 (tt0) REVERT: A 80 PHE cc_start: 0.7050 (m-80) cc_final: 0.6686 (m-80) REVERT: A 282 PHE cc_start: 0.7590 (m-10) cc_final: 0.7224 (m-80) REVERT: D 238 GLN cc_start: 0.8732 (mt0) cc_final: 0.8368 (mt0) REVERT: D 282 PHE cc_start: 0.7551 (m-10) cc_final: 0.7323 (m-80) outliers start: 33 outliers final: 22 residues processed: 257 average time/residue: 0.2154 time to fit residues: 83.3392 Evaluate side-chains 259 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 235 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 166 GLU 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 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 296 ASN Chi-restraints excluded: chain D residue 319 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 143 optimal weight: 0.6980 chunk 130 optimal weight: 0.9990 chunk 139 optimal weight: 0.6980 chunk 83 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 109 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 125 optimal weight: 3.9990 chunk 131 optimal weight: 0.8980 chunk 138 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 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 238 GLN E 296 ASN C 238 GLN C 296 ASN B 194 GLN B 296 ASN A 296 ASN ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13415 Z= 0.216 Angle : 0.550 11.867 18190 Z= 0.273 Chirality : 0.040 0.147 1965 Planarity : 0.003 0.034 2275 Dihedral : 3.996 15.014 1770 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.15 % Allowed : 18.49 % Favored : 79.35 % 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: 0.20 (0.15), residues: 1130 sheet: None (None), residues: 0 loop : -1.86 (0.27), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP E 229 HIS 0.004 0.000 HIS E 91 PHE 0.020 0.001 PHE E 282 TYR 0.019 0.001 TYR E 85 ARG 0.001 0.000 ARG E 92 *********************** 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 275 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 245 time to evaluate : 1.421 Fit side-chains REVERT: E 82 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7643 (tt) REVERT: E 166 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7487 (pm20) REVERT: E 282 PHE cc_start: 0.7768 (m-80) cc_final: 0.7545 (m-80) REVERT: C 282 PHE cc_start: 0.7859 (m-80) cc_final: 0.7647 (m-80) REVERT: B 80 PHE cc_start: 0.7646 (t80) cc_final: 0.7018 (m-80) REVERT: B 149 LYS cc_start: 0.8874 (mttt) cc_final: 0.8607 (mttt) REVERT: B 282 PHE cc_start: 0.7609 (m-10) cc_final: 0.7374 (m-80) REVERT: B 316 GLN cc_start: 0.8449 (tt0) cc_final: 0.7613 (tt0) REVERT: A 80 PHE cc_start: 0.7146 (m-80) cc_final: 0.6593 (m-80) REVERT: A 282 PHE cc_start: 0.7579 (m-10) cc_final: 0.7229 (m-80) REVERT: D 238 GLN cc_start: 0.8703 (mt0) cc_final: 0.8365 (mt0) REVERT: D 282 PHE cc_start: 0.7539 (m-10) cc_final: 0.7312 (m-80) outliers start: 30 outliers final: 23 residues processed: 260 average time/residue: 0.2112 time to fit residues: 82.4629 Evaluate side-chains 260 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 235 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 166 GLU 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 78 VAL Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 319 MET Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 223 MET Chi-restraints excluded: chain A residue 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 147 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 142 optimal weight: 0.7980 chunk 122 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 94 optimal weight: 3.9990 chunk 75 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 91 HIS E 238 GLN E 296 ASN C 194 GLN C 296 ASN B 296 ASN A 238 GLN A 296 ASN ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13415 Z= 0.254 Angle : 0.568 11.298 18190 Z= 0.284 Chirality : 0.041 0.142 1965 Planarity : 0.003 0.034 2275 Dihedral : 4.061 16.078 1770 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.08 % Allowed : 18.92 % 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: -0.58 (0.21), residues: 1565 helix: 0.22 (0.15), residues: 1130 sheet: None (None), residues: 0 loop : -1.81 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP B 229 HIS 0.004 0.001 HIS E 91 PHE 0.022 0.001 PHE A 276 TYR 0.020 0.001 TYR E 85 ARG 0.004 0.000 ARG D 165 ********************** 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 266 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 237 time to evaluate : 1.424 Fit side-chains REVERT: E 82 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7661 (tt) REVERT: E 166 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7491 (pm20) REVERT: E 282 PHE cc_start: 0.7765 (m-80) cc_final: 0.7542 (m-80) REVERT: C 282 PHE cc_start: 0.7827 (m-80) cc_final: 0.7603 (m-80) REVERT: B 80 PHE cc_start: 0.7659 (t80) cc_final: 0.7056 (m-80) REVERT: B 198 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7969 (mt-10) REVERT: B 316 GLN cc_start: 0.8458 (tt0) cc_final: 0.7617 (tt0) REVERT: A 282 PHE cc_start: 0.7562 (m-10) cc_final: 0.7213 (m-80) REVERT: D 44 MET cc_start: 0.8847 (mmm) cc_final: 0.8305 (mmm) REVERT: D 238 GLN cc_start: 0.8682 (mt0) cc_final: 0.8392 (mt0) REVERT: D 282 PHE cc_start: 0.7539 (m-10) cc_final: 0.7309 (m-80) outliers start: 29 outliers final: 24 residues processed: 252 average time/residue: 0.2171 time to fit residues: 82.6656 Evaluate side-chains 263 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 237 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 166 GLU 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 78 VAL Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 319 MET Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 223 MET Chi-restraints excluded: chain A residue 238 GLN Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 223 MET Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 296 ASN Chi-restraints excluded: chain D residue 319 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 113 optimal weight: 0.0040 chunk 18 optimal weight: 0.6980 chunk 34 optimal weight: 5.9990 chunk 123 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 126 optimal weight: 7.9990 chunk 15 optimal weight: 0.3980 chunk 22 optimal weight: 0.6980 chunk 108 optimal weight: 0.8980 overall best weight: 0.4992 ------------------------------------------------------------------------------- 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 95 ASN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.162758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.103730 restraints weight = 17547.665| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.83 r_work: 0.3162 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13415 Z= 0.184 Angle : 0.556 11.046 18190 Z= 0.279 Chirality : 0.040 0.149 1965 Planarity : 0.003 0.034 2275 Dihedral : 4.052 19.048 1770 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.94 % Allowed : 19.07 % 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: -0.51 (0.21), residues: 1565 helix: 0.31 (0.15), residues: 1125 sheet: None (None), residues: 0 loop : -1.88 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.002 TRP B 229 HIS 0.004 0.000 HIS E 91 PHE 0.021 0.001 PHE E 282 TYR 0.018 0.001 TYR E 85 ARG 0.004 0.000 ARG D 165 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2940.45 seconds wall clock time: 53 minutes 20.37 seconds (3200.37 seconds total)