Starting phenix.real_space_refine on Tue Nov 18 14:59:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vx6_21431/11_2025/6vx6_21431.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vx6_21431/11_2025/6vx6_21431.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vx6_21431/11_2025/6vx6_21431.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vx6_21431/11_2025/6vx6_21431.map" model { file = "/net/cci-nas-00/data/ceres_data/6vx6_21431/11_2025/6vx6_21431.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vx6_21431/11_2025/6vx6_21431.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians Ca 5 9.91 5 S 95 5.16 5 Cl 1 4.86 5 C 9870 2.51 5 N 2485 2.21 5 O 2605 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 105 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15061 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 3011 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 10, 'TRANS': 355} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' CL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D, E Time building chain proxies: 3.14, per 1000 atoms: 0.21 Number of scatterers: 15061 At special positions: 0 Unit cell: (97.94, 96.28, 109.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 5 19.99 Cl 1 17.00 S 95 16.00 O 2605 8.00 N 2485 7.00 C 9870 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.97 Conformation dependent library (CDL) restraints added in 733.3 milliseconds 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3470 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 0 sheets defined 69.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'E' and resid 5 through 10 removed outlier: 3.968A pdb=" N ALA E 10 " --> pdb=" O ALA E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 23 removed outlier: 3.725A pdb=" N LEU E 22 " --> pdb=" O LYS E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 52 removed outlier: 5.927A pdb=" N ARG E 34 " --> pdb=" O LYS E 30 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N GLU E 35 " --> pdb=" O LEU E 31 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU E 37 " --> pdb=" O TRP E 33 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA E 45 " --> pdb=" O GLY E 41 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU E 46 " --> pdb=" O LEU E 42 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA E 49 " --> pdb=" O ALA E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 72 removed outlier: 3.533A pdb=" N ARG E 60 " --> pdb=" O GLU E 56 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR E 61 " --> pdb=" O GLU E 57 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU E 67 " --> pdb=" O GLU E 63 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR E 68 " --> pdb=" O LYS E 64 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG E 71 " --> pdb=" O LEU E 67 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR E 72 " --> pdb=" O TYR E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 99 removed outlier: 3.959A pdb=" N VAL E 78 " --> pdb=" O SER E 74 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N SER E 79 " --> pdb=" O LEU E 75 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE E 80 " --> pdb=" O ILE E 76 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL E 81 " --> pdb=" O PRO E 77 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TYR E 85 " --> pdb=" O VAL E 81 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR E 87 " --> pdb=" O GLY E 83 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR E 97 " --> pdb=" O TRP E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 114 removed outlier: 3.790A pdb=" N CYS E 108 " --> pdb=" O ASP E 104 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL E 109 " --> pdb=" O ALA E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 144 removed outlier: 3.726A pdb=" N ARG E 125 " --> pdb=" O GLY E 121 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE E 139 " --> pdb=" O SER E 135 " (cutoff:3.500A) removed outlier: 3.846A 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 154 through 160 Processing helix chain 'E' and resid 164 through 173 removed outlier: 3.940A pdb=" N LYS E 169 " --> pdb=" O ARG E 165 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS E 170 " --> pdb=" O GLU E 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 198 removed outlier: 3.568A pdb=" N CYS E 189 " --> pdb=" O CYS E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 230 removed outlier: 3.653A pdb=" N LEU E 210 " --> pdb=" O ALA E 206 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN E 215 " --> pdb=" O LEU E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 255 removed outlier: 3.862A pdb=" N VAL E 240 " --> pdb=" O TYR E 236 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE E 253 " --> pdb=" O LEU E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 263 removed outlier: 3.565A pdb=" N GLY E 263 " --> pdb=" O PRO E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 294 removed outlier: 3.839A pdb=" N GLN E 280 " --> pdb=" O PHE E 276 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA E 291 " --> pdb=" O TRP E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 323 removed outlier: 4.347A pdb=" N SER E 318 " --> pdb=" O CYS E 314 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N MET E 319 " --> pdb=" O PHE E 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 5 through 10 removed outlier: 3.969A pdb=" N ALA A 10 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 23 removed outlier: 3.725A pdb=" N LEU A 22 " --> pdb=" O LYS A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 52 removed outlier: 5.927A pdb=" N ARG A 34 " --> pdb=" O LYS A 30 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N GLU A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A 37 " --> pdb=" O TRP A 33 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA A 45 " --> pdb=" O GLY A 41 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A 46 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA A 49 " --> pdb=" O ALA A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 72 removed outlier: 3.532A pdb=" N ARG A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A 67 " --> pdb=" O GLU A 63 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TYR A 68 " --> pdb=" O LYS A 64 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR A 72 " --> pdb=" O TYR A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 99 removed outlier: 3.960A pdb=" N VAL A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N PHE A 80 " --> pdb=" O ILE A 76 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL A 81 " --> pdb=" O PRO A 77 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TYR A 85 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR A 87 " --> pdb=" O GLY A 83 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR A 97 " --> pdb=" O TRP A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 114 removed outlier: 3.789A pdb=" N CYS A 108 " --> pdb=" O ASP A 104 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 144 removed outlier: 3.726A pdb=" N ARG A 125 " --> pdb=" O GLY A 121 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE A 139 " --> pdb=" O SER A 135 " (cutoff:3.500A) removed outlier: 3.845A 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 154 through 160 Processing helix chain 'A' and resid 164 through 173 removed outlier: 3.940A pdb=" N LYS A 169 " --> pdb=" O ARG A 165 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS A 170 " --> pdb=" O GLU A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 198 removed outlier: 3.568A pdb=" N CYS A 189 " --> pdb=" O CYS A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 230 removed outlier: 3.653A pdb=" N LEU A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 255 removed outlier: 3.862A pdb=" N VAL A 240 " --> pdb=" O TYR A 236 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 263 removed outlier: 3.565A pdb=" N GLY A 263 " --> pdb=" O PRO A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 294 removed outlier: 3.839A pdb=" N GLN A 280 " --> pdb=" O PHE A 276 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA A 291 " --> pdb=" O TRP A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 323 removed outlier: 4.346A pdb=" N SER A 318 " --> pdb=" O CYS A 314 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N MET A 319 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 10 removed outlier: 3.969A pdb=" N ALA B 10 " --> pdb=" O ALA B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 23 removed outlier: 3.726A pdb=" N LEU B 22 " --> pdb=" O LYS B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 52 removed outlier: 5.928A pdb=" N ARG B 34 " --> pdb=" O LYS B 30 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N GLU B 35 " --> pdb=" O LEU B 31 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU B 37 " --> pdb=" O TRP B 33 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA B 45 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA B 49 " --> pdb=" O ALA B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 72 removed outlier: 3.532A pdb=" N ARG B 60 " --> pdb=" O GLU B 56 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TYR B 68 " --> pdb=" O LYS B 64 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR B 72 " --> pdb=" O TYR B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 99 removed outlier: 3.959A pdb=" N VAL B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER B 79 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N PHE B 80 " --> pdb=" O ILE B 76 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL B 81 " --> pdb=" O PRO B 77 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR B 85 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR B 87 " --> pdb=" O GLY B 83 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR B 97 " --> pdb=" O TRP B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 114 removed outlier: 3.791A pdb=" N CYS B 108 " --> pdb=" O ASP B 104 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL B 109 " --> pdb=" O ALA B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 144 removed outlier: 3.726A pdb=" N ARG B 125 " --> pdb=" O GLY B 121 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE B 139 " --> pdb=" O SER B 135 " (cutoff:3.500A) removed outlier: 3.846A 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 154 through 160 Processing helix chain 'B' and resid 164 through 173 removed outlier: 3.940A pdb=" N LYS B 169 " --> pdb=" O ARG B 165 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS B 170 " --> pdb=" O GLU B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 198 removed outlier: 3.569A pdb=" N CYS B 189 " --> pdb=" O CYS B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 230 removed outlier: 3.654A pdb=" N LEU B 210 " --> pdb=" O ALA B 206 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN B 215 " --> pdb=" O LEU B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 255 removed outlier: 3.862A pdb=" N VAL B 240 " --> pdb=" O TYR B 236 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 263 removed outlier: 3.565A pdb=" N GLY B 263 " --> pdb=" O PRO B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 294 removed outlier: 3.838A pdb=" N GLN B 280 " --> pdb=" O PHE B 276 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA B 291 " --> pdb=" O TRP B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 323 removed outlier: 4.347A pdb=" N SER B 318 " --> pdb=" O CYS B 314 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N MET B 319 " --> pdb=" O PHE B 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 10 removed outlier: 3.968A pdb=" N ALA C 10 " --> pdb=" O ALA C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 23 removed outlier: 3.725A pdb=" N LEU C 22 " --> pdb=" O LYS C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 52 removed outlier: 5.928A pdb=" N ARG C 34 " --> pdb=" O LYS C 30 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N GLU C 35 " --> pdb=" O LEU C 31 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU C 37 " --> pdb=" O TRP C 33 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA C 45 " --> pdb=" O GLY C 41 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU C 46 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 72 removed outlier: 3.532A pdb=" N ARG C 60 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR C 61 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU C 67 " --> pdb=" O GLU C 63 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR C 68 " --> pdb=" O LYS C 64 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG C 71 " --> pdb=" O LEU C 67 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR C 72 " --> pdb=" O TYR C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 99 removed outlier: 3.960A pdb=" N VAL C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER C 79 " --> pdb=" O LEU C 75 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE C 80 " --> pdb=" O ILE C 76 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL C 81 " --> pdb=" O PRO C 77 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TYR C 85 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR C 87 " --> pdb=" O GLY C 83 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR C 97 " --> pdb=" O TRP C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 114 removed outlier: 3.791A pdb=" N CYS C 108 " --> pdb=" O ASP C 104 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL C 109 " --> pdb=" O ALA C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 144 removed outlier: 3.725A pdb=" N ARG C 125 " --> pdb=" O GLY C 121 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE C 139 " --> pdb=" O SER C 135 " (cutoff:3.500A) removed outlier: 3.846A 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 154 through 160 Processing helix chain 'C' and resid 164 through 173 removed outlier: 3.941A pdb=" N LYS C 169 " --> pdb=" O ARG C 165 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS C 170 " --> pdb=" O GLU C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 198 removed outlier: 3.568A pdb=" N CYS C 189 " --> pdb=" O CYS C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 230 removed outlier: 3.653A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN C 215 " --> pdb=" O LEU C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 255 removed outlier: 3.862A pdb=" N VAL C 240 " --> pdb=" O TYR C 236 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE C 253 " --> pdb=" O LEU C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 263 removed outlier: 3.566A pdb=" N GLY C 263 " --> pdb=" O PRO C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 294 removed outlier: 3.839A pdb=" N GLN C 280 " --> pdb=" O PHE C 276 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA C 291 " --> pdb=" O TRP C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 323 removed outlier: 4.347A pdb=" N SER C 318 " --> pdb=" O CYS C 314 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N MET C 319 " --> pdb=" O PHE C 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 10 removed outlier: 3.969A pdb=" N ALA D 10 " --> pdb=" O ALA D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 23 removed outlier: 3.725A pdb=" N LEU D 22 " --> pdb=" O LYS D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 52 removed outlier: 5.927A pdb=" N ARG D 34 " --> pdb=" O LYS D 30 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N GLU D 35 " --> pdb=" O LEU D 31 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU D 37 " --> pdb=" O TRP D 33 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA D 45 " --> pdb=" O GLY D 41 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU D 46 " --> pdb=" O LEU D 42 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA D 49 " --> pdb=" O ALA D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 72 removed outlier: 3.532A pdb=" N ARG D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR D 61 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU D 67 " --> pdb=" O GLU D 63 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR D 68 " --> pdb=" O LYS D 64 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG D 71 " --> pdb=" O LEU D 67 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR D 72 " --> pdb=" O TYR D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 99 removed outlier: 3.959A pdb=" N VAL D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER D 79 " --> pdb=" O LEU D 75 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE D 80 " --> pdb=" O ILE D 76 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL D 81 " --> pdb=" O PRO D 77 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR D 85 " --> pdb=" O VAL D 81 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR D 87 " --> pdb=" O GLY D 83 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR D 97 " --> pdb=" O TRP D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 114 removed outlier: 3.791A pdb=" N CYS D 108 " --> pdb=" O ASP D 104 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N VAL D 109 " --> pdb=" O ALA D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 144 removed outlier: 3.726A pdb=" N ARG D 125 " --> pdb=" O GLY D 121 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE D 139 " --> pdb=" O SER D 135 " (cutoff:3.500A) removed outlier: 3.845A 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 154 through 160 Processing helix chain 'D' and resid 164 through 173 removed outlier: 3.941A pdb=" N LYS D 169 " --> pdb=" O ARG D 165 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS D 170 " --> pdb=" O GLU D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 198 removed outlier: 3.569A pdb=" N CYS D 189 " --> pdb=" O CYS D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 230 removed outlier: 3.653A pdb=" N LEU D 210 " --> pdb=" O ALA D 206 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN D 215 " --> pdb=" O LEU D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 255 removed outlier: 3.862A pdb=" N VAL D 240 " --> pdb=" O TYR D 236 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE D 253 " --> pdb=" O LEU D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 263 removed outlier: 3.566A pdb=" N GLY D 263 " --> pdb=" O PRO D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 294 removed outlier: 3.838A pdb=" N GLN D 280 " --> pdb=" O PHE D 276 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA D 291 " --> pdb=" O TRP D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 323 removed outlier: 4.347A pdb=" N SER D 318 " --> pdb=" O CYS D 314 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N MET D 319 " --> pdb=" O PHE D 315 " (cutoff:3.500A) 770 hydrogen bonds defined for protein. 2250 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.05 Time building geometry restraints manager: 1.44 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: 4103 1.33 - 1.45: 3153 1.45 - 1.57: 8069 1.57 - 1.69: 0 1.69 - 1.81: 145 Bond restraints: 15470 Sorted by residual: bond pdb=" N VAL A 183 " pdb=" CA VAL A 183 " ideal model delta sigma weight residual 1.461 1.498 -0.037 1.23e-02 6.61e+03 8.90e+00 bond pdb=" N VAL D 183 " pdb=" CA VAL D 183 " ideal model delta sigma weight residual 1.461 1.498 -0.036 1.23e-02 6.61e+03 8.75e+00 bond pdb=" N VAL E 183 " pdb=" CA VAL E 183 " ideal model delta sigma weight residual 1.461 1.497 -0.036 1.23e-02 6.61e+03 8.58e+00 bond pdb=" N VAL C 183 " pdb=" CA VAL C 183 " ideal model delta sigma weight residual 1.461 1.497 -0.036 1.23e-02 6.61e+03 8.51e+00 bond pdb=" N VAL B 183 " pdb=" CA VAL B 183 " ideal model delta sigma weight residual 1.461 1.497 -0.036 1.23e-02 6.61e+03 8.47e+00 ... (remaining 15465 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 20235 1.91 - 3.83: 599 3.83 - 5.74: 117 5.74 - 7.65: 24 7.65 - 9.56: 5 Bond angle restraints: 20980 Sorted by residual: angle pdb=" N LEU B 88 " pdb=" CA LEU B 88 " pdb=" C LEU B 88 " ideal model delta sigma weight residual 111.82 106.39 5.43 1.16e+00 7.43e-01 2.19e+01 angle pdb=" N LEU D 88 " pdb=" CA LEU D 88 " pdb=" C LEU D 88 " ideal model delta sigma weight residual 111.82 106.39 5.43 1.16e+00 7.43e-01 2.19e+01 angle pdb=" N LEU E 88 " pdb=" CA LEU E 88 " pdb=" C LEU E 88 " ideal model delta sigma weight residual 111.82 106.42 5.40 1.16e+00 7.43e-01 2.17e+01 angle pdb=" N LEU A 88 " pdb=" CA LEU A 88 " pdb=" C LEU A 88 " ideal model delta sigma weight residual 111.82 106.43 5.39 1.16e+00 7.43e-01 2.16e+01 angle pdb=" N LEU C 88 " pdb=" CA LEU C 88 " pdb=" C LEU C 88 " ideal model delta sigma weight residual 111.82 106.44 5.38 1.16e+00 7.43e-01 2.15e+01 ... (remaining 20975 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.45: 7840 15.45 - 30.91: 910 30.91 - 46.36: 155 46.36 - 61.82: 45 61.82 - 77.27: 25 Dihedral angle restraints: 8975 sinusoidal: 3575 harmonic: 5400 Sorted by residual: dihedral pdb=" C VAL A 183 " pdb=" N VAL A 183 " pdb=" CA VAL A 183 " pdb=" CB VAL A 183 " ideal model delta harmonic sigma weight residual -122.00 -131.87 9.87 0 2.50e+00 1.60e-01 1.56e+01 dihedral pdb=" C VAL D 183 " pdb=" N VAL D 183 " pdb=" CA VAL D 183 " pdb=" CB VAL D 183 " ideal model delta harmonic sigma weight residual -122.00 -131.87 9.87 0 2.50e+00 1.60e-01 1.56e+01 dihedral pdb=" C VAL C 183 " pdb=" N VAL C 183 " pdb=" CA VAL C 183 " pdb=" CB VAL C 183 " ideal model delta harmonic sigma weight residual -122.00 -131.83 9.83 0 2.50e+00 1.60e-01 1.55e+01 ... (remaining 8972 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1739 0.053 - 0.105: 419 0.105 - 0.158: 76 0.158 - 0.210: 26 0.210 - 0.263: 15 Chirality restraints: 2275 Sorted by residual: chirality pdb=" CA PRO C 77 " pdb=" N PRO C 77 " pdb=" C PRO C 77 " pdb=" CB PRO C 77 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA PRO D 77 " pdb=" N PRO D 77 " pdb=" C PRO D 77 " pdb=" CB PRO D 77 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA PRO E 77 " pdb=" N PRO E 77 " pdb=" C PRO E 77 " pdb=" CB PRO E 77 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.69e+00 ... (remaining 2272 not shown) Planarity restraints: 2625 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 351 " 0.015 2.00e-02 2.50e+03 2.94e-02 8.66e+00 pdb=" C THR A 351 " -0.051 2.00e-02 2.50e+03 pdb=" O THR A 351 " 0.020 2.00e-02 2.50e+03 pdb=" N ALA A 352 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 351 " -0.015 2.00e-02 2.50e+03 2.93e-02 8.61e+00 pdb=" C THR B 351 " 0.051 2.00e-02 2.50e+03 pdb=" O THR B 351 " -0.020 2.00e-02 2.50e+03 pdb=" N ALA B 352 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 351 " -0.015 2.00e-02 2.50e+03 2.92e-02 8.54e+00 pdb=" C THR C 351 " 0.051 2.00e-02 2.50e+03 pdb=" O THR C 351 " -0.019 2.00e-02 2.50e+03 pdb=" N ALA C 352 " -0.016 2.00e-02 2.50e+03 ... (remaining 2622 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4107 2.79 - 3.32: 12796 3.32 - 3.84: 25125 3.84 - 4.37: 32863 4.37 - 4.90: 53533 Nonbonded interactions: 128424 Sorted by model distance: nonbonded pdb=" O ASN C 296 " pdb="CA CA C 501 " model vdw 2.260 2.510 nonbonded pdb=" O ASN E 296 " pdb="CA CA E 501 " model vdw 2.273 2.510 nonbonded pdb=" O ALA C 10 " pdb="CA CA D 501 " model vdw 2.277 2.510 nonbonded pdb=" O LEU A 75 " pdb=" OH TYR A 284 " model vdw 2.289 3.040 nonbonded pdb=" O LEU B 75 " pdb=" OH TYR B 284 " model vdw 2.289 3.040 ... (remaining 128419 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 2 through 367) selection = (chain 'B' and resid 2 through 367) selection = (chain 'C' and resid 2 through 367) selection = (chain 'D' and resid 2 through 367) selection = (chain 'E' and resid 2 through 367) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.700 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: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.430 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 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 : 0.005 0.045 15470 Z= 0.268 Angle : 0.819 9.563 20980 Z= 0.492 Chirality : 0.053 0.263 2275 Planarity : 0.004 0.040 2625 Dihedral : 14.085 77.272 5505 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.94 % Allowed : 8.49 % Favored : 90.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.69 (0.12), residues: 1820 helix: -4.58 (0.05), residues: 1055 sheet: None (None), residues: 0 loop : -2.27 (0.18), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 344 TYR 0.031 0.002 TYR D 236 PHE 0.020 0.002 PHE D 282 TRP 0.010 0.001 TRP C 93 HIS 0.002 0.000 HIS D 115 Details of bonding type rmsd covalent geometry : bond 0.00483 (15470) covalent geometry : angle 0.81938 (20980) hydrogen bonds : bond 0.30767 ( 770) hydrogen bonds : angle 11.88766 ( 2250) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 263 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 165 ARG cc_start: 0.7717 (tpp80) cc_final: 0.7512 (mpt180) REVERT: A 175 ASN cc_start: 0.7994 (t0) cc_final: 0.7779 (m-40) REVERT: A 203 ASP cc_start: 0.7708 (m-30) cc_final: 0.7472 (m-30) REVERT: D 64 LYS cc_start: 0.7760 (mttm) cc_final: 0.7468 (mtpt) REVERT: D 68 TYR cc_start: 0.7975 (t80) cc_final: 0.7758 (t80) outliers start: 15 outliers final: 0 residues processed: 278 average time/residue: 0.7492 time to fit residues: 225.4610 Evaluate side-chains 163 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 58 GLN E 293 GLN ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 GLN A 296 ASN A 361 GLN B 58 GLN ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 GLN D 115 HIS D 293 GLN D 361 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.143550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.110356 restraints weight = 18757.964| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.91 r_work: 0.2968 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 15470 Z= 0.173 Angle : 0.585 11.013 20980 Z= 0.301 Chirality : 0.039 0.134 2275 Planarity : 0.004 0.023 2625 Dihedral : 4.355 15.223 2055 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.08 % Allowed : 14.28 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.96 (0.16), residues: 1820 helix: -2.02 (0.12), residues: 1090 sheet: None (None), residues: 0 loop : -1.63 (0.19), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 218 TYR 0.021 0.002 TYR D 236 PHE 0.022 0.002 PHE E 283 TRP 0.014 0.001 TRP D 182 HIS 0.002 0.000 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00394 (15470) covalent geometry : angle 0.58487 (20980) hydrogen bonds : bond 0.04930 ( 770) hydrogen bonds : angle 4.78543 ( 2250) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 199 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 61 TYR cc_start: 0.7575 (t80) cc_final: 0.7263 (t80) REVERT: E 165 ARG cc_start: 0.8410 (tpp80) cc_final: 0.8083 (mpt180) REVERT: A 68 TYR cc_start: 0.8038 (t80) cc_final: 0.7761 (t80) REVERT: A 72 TYR cc_start: 0.7275 (m-10) cc_final: 0.7012 (m-80) REVERT: A 203 ASP cc_start: 0.8245 (m-30) cc_final: 0.7901 (m-30) REVERT: A 334 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.7692 (mmtp) REVERT: A 337 TYR cc_start: 0.8045 (m-80) cc_final: 0.7771 (m-80) REVERT: B 34 ARG cc_start: 0.8295 (ttm110) cc_final: 0.8081 (mtt90) REVERT: B 64 LYS cc_start: 0.7499 (mttm) cc_final: 0.7148 (mtpt) REVERT: D 68 TYR cc_start: 0.8125 (t80) cc_final: 0.7760 (t80) outliers start: 33 outliers final: 11 residues processed: 220 average time/residue: 0.6773 time to fit residues: 163.0275 Evaluate side-chains 177 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 165 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 251 CYS Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 251 CYS Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 251 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 149 optimal weight: 0.1980 chunk 38 optimal weight: 0.0050 chunk 51 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 156 optimal weight: 0.9990 chunk 172 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 GLN ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 GLN D 361 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.145103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.111951 restraints weight = 18991.319| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 1.92 r_work: 0.3001 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 15470 Z= 0.122 Angle : 0.497 10.714 20980 Z= 0.252 Chirality : 0.038 0.120 2275 Planarity : 0.003 0.022 2625 Dihedral : 3.986 15.347 2055 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.14 % Allowed : 15.60 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.17), residues: 1820 helix: -0.46 (0.14), residues: 1080 sheet: None (None), residues: 0 loop : -1.40 (0.20), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 168 TYR 0.011 0.001 TYR D 236 PHE 0.023 0.001 PHE E 80 TRP 0.010 0.001 TRP D 182 HIS 0.002 0.000 HIS D 91 Details of bonding type rmsd covalent geometry : bond 0.00274 (15470) covalent geometry : angle 0.49697 (20980) hydrogen bonds : bond 0.04256 ( 770) hydrogen bonds : angle 4.17398 ( 2250) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 207 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 165 ARG cc_start: 0.8393 (tpp80) cc_final: 0.8077 (mpt180) REVERT: E 168 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.8213 (ttm170) REVERT: A 68 TYR cc_start: 0.7993 (t80) cc_final: 0.7779 (t80) REVERT: A 72 TYR cc_start: 0.7347 (m-10) cc_final: 0.7058 (m-10) REVERT: A 203 ASP cc_start: 0.8249 (m-30) cc_final: 0.7912 (m-30) REVERT: A 262 GLN cc_start: 0.7740 (OUTLIER) cc_final: 0.7384 (mm110) REVERT: B 64 LYS cc_start: 0.7487 (mttm) cc_final: 0.7226 (mtpt) REVERT: B 163 MET cc_start: 0.9403 (ttm) cc_final: 0.9198 (ttp) REVERT: B 212 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8527 (mt-10) REVERT: C 165 ARG cc_start: 0.8090 (tpp-160) cc_final: 0.7664 (mpt180) REVERT: C 328 ASP cc_start: 0.8907 (t70) cc_final: 0.8673 (t70) REVERT: D 11 LYS cc_start: 0.8177 (ttmt) cc_final: 0.7958 (ttpt) REVERT: D 68 TYR cc_start: 0.7882 (t80) cc_final: 0.7603 (t80) outliers start: 34 outliers final: 13 residues processed: 230 average time/residue: 0.6942 time to fit residues: 174.2618 Evaluate side-chains 194 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 179 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 168 ARG Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 251 CYS Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 251 CYS Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 251 CYS Chi-restraints excluded: chain C residue 282 PHE Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 251 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 159 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 142 optimal weight: 0.0970 chunk 121 optimal weight: 0.7980 chunk 101 optimal weight: 0.0980 chunk 71 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 chunk 149 optimal weight: 1.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 95 ASN A 296 ASN A 361 GLN ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 GLN ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 ASN D 280 GLN D 361 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.145638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.112876 restraints weight = 18872.102| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.91 r_work: 0.3115 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15470 Z= 0.110 Angle : 0.493 11.691 20980 Z= 0.244 Chirality : 0.037 0.118 2275 Planarity : 0.003 0.023 2625 Dihedral : 3.793 15.237 2055 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.08 % Allowed : 16.98 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.18), residues: 1820 helix: 0.28 (0.15), residues: 1140 sheet: None (None), residues: 0 loop : -1.26 (0.21), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 168 TYR 0.009 0.001 TYR D 236 PHE 0.018 0.001 PHE A 80 TRP 0.010 0.001 TRP D 182 HIS 0.003 0.000 HIS A 91 Details of bonding type rmsd covalent geometry : bond 0.00243 (15470) covalent geometry : angle 0.49251 (20980) hydrogen bonds : bond 0.03998 ( 770) hydrogen bonds : angle 3.88584 ( 2250) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 207 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 71 ARG cc_start: 0.8067 (ptm160) cc_final: 0.7727 (ptm-80) REVERT: E 95 ASN cc_start: 0.9062 (m-40) cc_final: 0.8862 (m-40) REVERT: E 165 ARG cc_start: 0.8344 (tpp80) cc_final: 0.8015 (mpt180) REVERT: E 168 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.8186 (ttm170) REVERT: A 72 TYR cc_start: 0.7408 (m-10) cc_final: 0.7207 (m-10) REVERT: A 175 ASN cc_start: 0.8491 (t0) cc_final: 0.7905 (m-40) REVERT: A 203 ASP cc_start: 0.8215 (m-30) cc_final: 0.7804 (m-30) REVERT: A 334 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.7790 (mmtp) REVERT: B 64 LYS cc_start: 0.7571 (mttm) cc_final: 0.7328 (mtpt) REVERT: B 71 ARG cc_start: 0.8198 (ptm160) cc_final: 0.7928 (ppp-140) REVERT: B 163 MET cc_start: 0.9389 (ttm) cc_final: 0.9171 (ttp) REVERT: B 212 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8539 (mt-10) REVERT: C 64 LYS cc_start: 0.7733 (mttm) cc_final: 0.7496 (mtpt) REVERT: C 165 ARG cc_start: 0.8054 (tpp-160) cc_final: 0.7632 (mpt180) REVERT: C 173 ASN cc_start: 0.8516 (m-40) cc_final: 0.8308 (m110) REVERT: C 328 ASP cc_start: 0.8893 (t70) cc_final: 0.8405 (t70) REVERT: D 68 TYR cc_start: 0.7949 (t80) cc_final: 0.7709 (t80) REVERT: D 71 ARG cc_start: 0.8065 (ptm160) cc_final: 0.7784 (ptm-80) outliers start: 33 outliers final: 16 residues processed: 231 average time/residue: 0.7103 time to fit residues: 178.9898 Evaluate side-chains 198 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 180 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 168 ARG Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 251 CYS Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 251 CYS Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain B residue 25 ARG Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 251 CYS Chi-restraints excluded: chain C residue 282 PHE Chi-restraints excluded: chain D residue 25 ARG Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 177 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 109 optimal weight: 0.0970 chunk 6 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 143 optimal weight: 0.4980 chunk 65 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 174 optimal weight: 0.2980 chunk 15 optimal weight: 0.7980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 GLN ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 ASN ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 GLN D 361 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.145422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.112629 restraints weight = 18827.826| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 1.91 r_work: 0.2992 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 15470 Z= 0.107 Angle : 0.478 11.323 20980 Z= 0.240 Chirality : 0.037 0.148 2275 Planarity : 0.002 0.023 2625 Dihedral : 3.694 15.303 2055 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.57 % Allowed : 17.86 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.19), residues: 1820 helix: 0.66 (0.15), residues: 1175 sheet: None (None), residues: 0 loop : -1.10 (0.22), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 168 TYR 0.018 0.001 TYR A 68 PHE 0.019 0.001 PHE B 80 TRP 0.010 0.001 TRP D 182 HIS 0.003 0.000 HIS A 91 Details of bonding type rmsd covalent geometry : bond 0.00238 (15470) covalent geometry : angle 0.47848 (20980) hydrogen bonds : bond 0.03923 ( 770) hydrogen bonds : angle 3.77095 ( 2250) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 201 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 165 ARG cc_start: 0.8459 (tpp80) cc_final: 0.8073 (mpt180) REVERT: E 168 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.8263 (ttm170) REVERT: E 361 GLN cc_start: 0.7574 (mt0) cc_final: 0.7083 (mm-40) REVERT: A 175 ASN cc_start: 0.8557 (t0) cc_final: 0.7935 (m-40) REVERT: A 203 ASP cc_start: 0.8248 (m-30) cc_final: 0.7793 (m-30) REVERT: B 64 LYS cc_start: 0.7486 (mttm) cc_final: 0.7283 (mtpt) REVERT: B 71 ARG cc_start: 0.8211 (ptm160) cc_final: 0.7892 (ppp-140) REVERT: B 163 MET cc_start: 0.9377 (ttm) cc_final: 0.9153 (ttp) REVERT: C 64 LYS cc_start: 0.7476 (mttm) cc_final: 0.7253 (mtpt) REVERT: C 165 ARG cc_start: 0.8144 (tpp-160) cc_final: 0.7735 (mpt180) REVERT: C 262 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.7696 (mm110) REVERT: D 68 TYR cc_start: 0.7867 (t80) cc_final: 0.7602 (t80) REVERT: D 71 ARG cc_start: 0.8022 (ptm160) cc_final: 0.7739 (ptm-80) outliers start: 25 outliers final: 14 residues processed: 218 average time/residue: 0.6970 time to fit residues: 165.9169 Evaluate side-chains 200 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 184 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 168 ARG Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 251 CYS Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 251 CYS Chi-restraints excluded: chain B residue 25 ARG Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 223 MET Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 282 PHE Chi-restraints excluded: chain D residue 25 ARG Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 251 CYS Chi-restraints excluded: chain D residue 282 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 177 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 162 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 143 optimal weight: 0.0070 chunk 172 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 ASN ** E 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 ASN A 361 GLN ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.144939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.112117 restraints weight = 18807.928| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 1.92 r_work: 0.2999 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15470 Z= 0.122 Angle : 0.511 11.547 20980 Z= 0.250 Chirality : 0.038 0.141 2275 Planarity : 0.003 0.023 2625 Dihedral : 3.689 15.088 2055 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.38 % Allowed : 18.81 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.19), residues: 1820 helix: 0.99 (0.16), residues: 1140 sheet: None (None), residues: 0 loop : -0.83 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 168 TYR 0.011 0.001 TYR D 236 PHE 0.017 0.001 PHE D 80 TRP 0.010 0.001 TRP D 182 HIS 0.002 0.000 HIS A 91 Details of bonding type rmsd covalent geometry : bond 0.00277 (15470) covalent geometry : angle 0.51116 (20980) hydrogen bonds : bond 0.04010 ( 770) hydrogen bonds : angle 3.77824 ( 2250) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 197 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 165 ARG cc_start: 0.8463 (tpp80) cc_final: 0.8084 (mpt180) REVERT: E 168 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8325 (ttm170) REVERT: E 204 ASN cc_start: 0.8629 (m-40) cc_final: 0.8366 (m-40) REVERT: E 361 GLN cc_start: 0.7563 (mt0) cc_final: 0.7077 (mm-40) REVERT: A 68 TYR cc_start: 0.7798 (t80) cc_final: 0.7563 (t80) REVERT: A 175 ASN cc_start: 0.8581 (t0) cc_final: 0.8240 (m110) REVERT: A 203 ASP cc_start: 0.8254 (m-30) cc_final: 0.7943 (m-30) REVERT: B 71 ARG cc_start: 0.8220 (ptm160) cc_final: 0.7896 (ppp-140) REVERT: C 64 LYS cc_start: 0.7426 (mttm) cc_final: 0.7187 (mtpt) REVERT: C 165 ARG cc_start: 0.8179 (tpp-160) cc_final: 0.7779 (mpt180) REVERT: C 262 GLN cc_start: 0.7941 (OUTLIER) cc_final: 0.7699 (mm110) REVERT: D 68 TYR cc_start: 0.7953 (t80) cc_final: 0.7637 (t80) REVERT: D 71 ARG cc_start: 0.8020 (ptm160) cc_final: 0.7749 (ptm-80) outliers start: 22 outliers final: 15 residues processed: 211 average time/residue: 0.6722 time to fit residues: 155.2374 Evaluate side-chains 206 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 189 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 168 ARG Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 251 CYS Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 251 CYS Chi-restraints excluded: chain B residue 25 ARG Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 251 CYS Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 282 PHE Chi-restraints excluded: chain C residue 331 MET Chi-restraints excluded: chain D residue 25 ARG Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 251 CYS Chi-restraints excluded: chain D residue 282 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 0.2980 chunk 170 optimal weight: 0.1980 chunk 14 optimal weight: 0.0770 chunk 55 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 41 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 GLN ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 ASN B 361 GLN ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 361 GLN ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.146482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.113875 restraints weight = 18593.105| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 1.90 r_work: 0.3011 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15470 Z= 0.101 Angle : 0.478 11.430 20980 Z= 0.237 Chirality : 0.037 0.140 2275 Planarity : 0.002 0.022 2625 Dihedral : 3.605 14.897 2055 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 1.45 % Allowed : 19.25 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.19), residues: 1820 helix: 1.13 (0.15), residues: 1175 sheet: None (None), residues: 0 loop : -0.91 (0.22), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 168 TYR 0.010 0.001 TYR E 337 PHE 0.016 0.001 PHE C 276 TRP 0.010 0.001 TRP D 182 HIS 0.002 0.000 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00221 (15470) covalent geometry : angle 0.47796 (20980) hydrogen bonds : bond 0.03813 ( 770) hydrogen bonds : angle 3.69481 ( 2250) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 203 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 165 ARG cc_start: 0.8456 (tpp80) cc_final: 0.8073 (mpt180) REVERT: E 168 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.8274 (ttm170) REVERT: E 175 ASN cc_start: 0.8468 (t0) cc_final: 0.8040 (m110) REVERT: E 204 ASN cc_start: 0.8636 (m-40) cc_final: 0.8346 (m-40) REVERT: E 361 GLN cc_start: 0.7557 (mt0) cc_final: 0.7112 (mm-40) REVERT: A 175 ASN cc_start: 0.8537 (t0) cc_final: 0.8214 (m110) REVERT: A 203 ASP cc_start: 0.8248 (m-30) cc_final: 0.7775 (m-30) REVERT: B 71 ARG cc_start: 0.8155 (ptm160) cc_final: 0.7866 (ppp-140) REVERT: B 175 ASN cc_start: 0.8502 (t0) cc_final: 0.8157 (m110) REVERT: C 68 TYR cc_start: 0.7710 (t80) cc_final: 0.7355 (t80) REVERT: C 77 PRO cc_start: 0.8867 (Cg_exo) cc_final: 0.8588 (Cg_endo) REVERT: C 165 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7823 (mpt180) REVERT: C 262 GLN cc_start: 0.7972 (OUTLIER) cc_final: 0.7683 (mm110) REVERT: D 68 TYR cc_start: 0.7854 (t80) cc_final: 0.7607 (t80) REVERT: D 71 ARG cc_start: 0.7984 (ptm160) cc_final: 0.7783 (ptm-80) outliers start: 23 outliers final: 14 residues processed: 220 average time/residue: 0.6437 time to fit residues: 155.4537 Evaluate side-chains 204 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 187 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 168 ARG Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 251 CYS Chi-restraints excluded: chain B residue 25 ARG Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain C residue 165 ARG Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 251 CYS Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 282 PHE Chi-restraints excluded: chain D residue 25 ARG Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 251 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 158 optimal weight: 0.6980 chunk 142 optimal weight: 0.0040 chunk 121 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 179 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 118 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 155 optimal weight: 3.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 ASN A 361 GLN ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 GLN ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN C 308 ASN C 361 GLN ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.145617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.112870 restraints weight = 18818.904| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 1.92 r_work: 0.2993 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15470 Z= 0.121 Angle : 0.514 12.121 20980 Z= 0.252 Chirality : 0.038 0.139 2275 Planarity : 0.002 0.022 2625 Dihedral : 3.628 14.472 2055 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 1.70 % Allowed : 19.56 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.20), residues: 1820 helix: 1.26 (0.16), residues: 1140 sheet: None (None), residues: 0 loop : -0.66 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 168 TYR 0.023 0.001 TYR A 68 PHE 0.017 0.001 PHE A 276 TRP 0.010 0.001 TRP D 182 HIS 0.002 0.001 HIS A 91 Details of bonding type rmsd covalent geometry : bond 0.00274 (15470) covalent geometry : angle 0.51441 (20980) hydrogen bonds : bond 0.04000 ( 770) hydrogen bonds : angle 3.75056 ( 2250) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 200 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 165 ARG cc_start: 0.8461 (tpp80) cc_final: 0.8083 (mpt180) REVERT: E 168 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.8302 (ttm170) REVERT: E 175 ASN cc_start: 0.8479 (t0) cc_final: 0.8023 (m110) REVERT: E 204 ASN cc_start: 0.8689 (m-40) cc_final: 0.8398 (m-40) REVERT: E 361 GLN cc_start: 0.7572 (mt0) cc_final: 0.7118 (mm-40) REVERT: A 168 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.7420 (ttm110) REVERT: A 175 ASN cc_start: 0.8574 (t0) cc_final: 0.8229 (m110) REVERT: A 203 ASP cc_start: 0.8302 (m-30) cc_final: 0.7998 (m-30) REVERT: B 71 ARG cc_start: 0.8158 (ptm160) cc_final: 0.7859 (ppp-140) REVERT: B 175 ASN cc_start: 0.8488 (t0) cc_final: 0.8130 (m110) REVERT: C 71 ARG cc_start: 0.7924 (ptm160) cc_final: 0.7468 (ptm-80) REVERT: C 77 PRO cc_start: 0.8907 (Cg_exo) cc_final: 0.8654 (Cg_endo) REVERT: C 165 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7815 (mpt180) REVERT: D 68 TYR cc_start: 0.7888 (t80) cc_final: 0.7600 (t80) outliers start: 27 outliers final: 16 residues processed: 218 average time/residue: 0.6551 time to fit residues: 156.6062 Evaluate side-chains 208 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 189 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 168 ARG Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 251 CYS Chi-restraints excluded: chain E residue 282 PHE Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 251 CYS Chi-restraints excluded: chain B residue 25 ARG Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain C residue 165 ARG Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 251 CYS Chi-restraints excluded: chain C residue 282 PHE Chi-restraints excluded: chain D residue 25 ARG Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 251 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 150 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 57 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 144 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 166 optimal weight: 0.6980 chunk 157 optimal weight: 1.9990 chunk 169 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 308 ASN ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 GLN ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 ASN ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 308 ASN C 361 GLN ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.140554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.106644 restraints weight = 18850.905| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.95 r_work: 0.3204 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15470 Z= 0.147 Angle : 0.533 11.627 20980 Z= 0.264 Chirality : 0.039 0.133 2275 Planarity : 0.003 0.023 2625 Dihedral : 3.719 14.385 2055 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.51 % Allowed : 20.19 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.20), residues: 1820 helix: 1.17 (0.15), residues: 1180 sheet: None (None), residues: 0 loop : -0.77 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 71 TYR 0.014 0.001 TYR C 236 PHE 0.020 0.001 PHE A 80 TRP 0.010 0.001 TRP D 182 HIS 0.002 0.001 HIS A 91 Details of bonding type rmsd covalent geometry : bond 0.00341 (15470) covalent geometry : angle 0.53342 (20980) hydrogen bonds : bond 0.04213 ( 770) hydrogen bonds : angle 3.82850 ( 2250) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 194 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 165 ARG cc_start: 0.8447 (tpp80) cc_final: 0.8033 (mpt180) REVERT: E 168 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.8338 (ttm170) REVERT: E 175 ASN cc_start: 0.8503 (t0) cc_final: 0.8046 (m110) REVERT: E 204 ASN cc_start: 0.8778 (m-40) cc_final: 0.8499 (m-40) REVERT: E 361 GLN cc_start: 0.7669 (mt0) cc_final: 0.7211 (mm-40) REVERT: A 168 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.7979 (ttm170) REVERT: A 175 ASN cc_start: 0.8560 (t0) cc_final: 0.8214 (m110) REVERT: A 203 ASP cc_start: 0.8355 (m-30) cc_final: 0.8042 (m-30) REVERT: B 71 ARG cc_start: 0.8200 (ptm160) cc_final: 0.7933 (ppp-140) REVERT: B 175 ASN cc_start: 0.8495 (t0) cc_final: 0.8147 (m110) REVERT: C 77 PRO cc_start: 0.8967 (Cg_exo) cc_final: 0.8749 (Cg_endo) REVERT: C 165 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7845 (mpt180) REVERT: C 262 GLN cc_start: 0.7894 (OUTLIER) cc_final: 0.7598 (mm110) outliers start: 24 outliers final: 16 residues processed: 212 average time/residue: 0.6441 time to fit residues: 149.6852 Evaluate side-chains 208 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 188 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 168 ARG Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 251 CYS Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 251 CYS Chi-restraints excluded: chain B residue 25 ARG Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain C residue 165 ARG Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 251 CYS Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 282 PHE Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 251 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 179 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 153 optimal weight: 0.9990 chunk 178 optimal weight: 4.9990 chunk 125 optimal weight: 0.5980 chunk 104 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 130 optimal weight: 0.9990 chunk 101 optimal weight: 0.0770 chunk 150 optimal weight: 0.9980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 58 GLN A 361 GLN ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 ASN ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 308 ASN C 361 GLN ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.141742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.107815 restraints weight = 18890.641| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.96 r_work: 0.3221 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15470 Z= 0.124 Angle : 0.526 12.620 20980 Z= 0.258 Chirality : 0.038 0.131 2275 Planarity : 0.003 0.023 2625 Dihedral : 3.707 15.174 2055 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.57 % Allowed : 20.00 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.20), residues: 1820 helix: 1.21 (0.15), residues: 1180 sheet: None (None), residues: 0 loop : -0.74 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 71 TYR 0.030 0.001 TYR E 68 PHE 0.023 0.001 PHE A 276 TRP 0.010 0.001 TRP D 182 HIS 0.002 0.000 HIS A 91 Details of bonding type rmsd covalent geometry : bond 0.00283 (15470) covalent geometry : angle 0.52641 (20980) hydrogen bonds : bond 0.04052 ( 770) hydrogen bonds : angle 3.80065 ( 2250) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 192 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 42 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8740 (mp) REVERT: E 165 ARG cc_start: 0.8366 (tpp80) cc_final: 0.7957 (mpt180) REVERT: E 168 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8315 (ttm170) REVERT: E 175 ASN cc_start: 0.8524 (t0) cc_final: 0.8070 (m110) REVERT: E 204 ASN cc_start: 0.8790 (m-40) cc_final: 0.8496 (m-40) REVERT: E 361 GLN cc_start: 0.7722 (mt0) cc_final: 0.7259 (mm-40) REVERT: A 168 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.7924 (ttm170) REVERT: A 175 ASN cc_start: 0.8537 (t0) cc_final: 0.8199 (m110) REVERT: A 203 ASP cc_start: 0.8330 (m-30) cc_final: 0.8009 (m-30) REVERT: A 337 TYR cc_start: 0.7959 (m-80) cc_final: 0.7697 (m-80) REVERT: B 71 ARG cc_start: 0.8187 (ptm160) cc_final: 0.7923 (ppp-140) REVERT: B 175 ASN cc_start: 0.8457 (t0) cc_final: 0.8127 (m110) REVERT: C 77 PRO cc_start: 0.8969 (Cg_exo) cc_final: 0.8745 (Cg_endo) REVERT: C 165 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7854 (mpt180) REVERT: D 42 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8789 (mp) outliers start: 25 outliers final: 16 residues processed: 210 average time/residue: 0.6293 time to fit residues: 145.1287 Evaluate side-chains 206 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 185 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 168 ARG Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 251 CYS Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 251 CYS Chi-restraints excluded: chain B residue 25 ARG Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain C residue 165 ARG Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 251 CYS Chi-restraints excluded: chain C residue 282 PHE Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 251 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 16 optimal weight: 0.6980 chunk 128 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 174 optimal weight: 0.9980 chunk 114 optimal weight: 0.9980 chunk 80 optimal weight: 0.5980 chunk 167 optimal weight: 0.2980 chunk 157 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 58 GLN A 361 GLN ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 ASN ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 361 GLN ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.141052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.107049 restraints weight = 18808.410| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.95 r_work: 0.3207 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15470 Z= 0.139 Angle : 0.531 11.735 20980 Z= 0.264 Chirality : 0.039 0.127 2275 Planarity : 0.003 0.035 2625 Dihedral : 3.773 15.334 2055 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.51 % Allowed : 20.38 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.20), residues: 1820 helix: 1.18 (0.15), residues: 1180 sheet: None (None), residues: 0 loop : -0.69 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 71 TYR 0.020 0.001 TYR C 68 PHE 0.018 0.001 PHE C 276 TRP 0.010 0.001 TRP D 182 HIS 0.002 0.000 HIS A 91 Details of bonding type rmsd covalent geometry : bond 0.00321 (15470) covalent geometry : angle 0.53149 (20980) hydrogen bonds : bond 0.04188 ( 770) hydrogen bonds : angle 3.83280 ( 2250) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4969.79 seconds wall clock time: 85 minutes 34.80 seconds (5134.80 seconds total)