Starting phenix.real_space_refine on Wed Mar 4 22:38:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7whr_32509/03_2026/7whr_32509.cif Found real_map, /net/cci-nas-00/data/ceres_data/7whr_32509/03_2026/7whr_32509.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7whr_32509/03_2026/7whr_32509.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7whr_32509/03_2026/7whr_32509.map" model { file = "/net/cci-nas-00/data/ceres_data/7whr_32509/03_2026/7whr_32509.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7whr_32509/03_2026/7whr_32509.cif" } resolution = 3.4 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= 0.027 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: 4 Type Number sf(0) Gaussians S 102 5.16 5 C 10842 2.51 5 N 2874 2.21 5 O 3096 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16914 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2819 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 21, 'TRANS': 342} Chain breaks: 2 Chain: "A" Number of atoms: 2819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2819 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 21, 'TRANS': 342} Chain breaks: 2 Chain: "C" Number of atoms: 2819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2819 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 21, 'TRANS': 342} Chain breaks: 2 Chain: "D" Number of atoms: 2819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2819 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 21, 'TRANS': 342} Chain breaks: 2 Chain: "E" Number of atoms: 2819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2819 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 21, 'TRANS': 342} Chain breaks: 2 Chain: "F" Number of atoms: 2819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2819 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 21, 'TRANS': 342} Chain breaks: 2 Time building chain proxies: 3.63, per 1000 atoms: 0.21 Number of scatterers: 16914 At special positions: 0 Unit cell: (128.27, 126.25, 118.17, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 102 16.00 O 3096 8.00 N 2874 7.00 C 10842 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.50 Conformation dependent library (CDL) restraints added in 828.0 milliseconds 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3936 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 51 sheets defined 21.6% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'B' and resid 22 through 26 removed outlier: 4.032A pdb=" N LEU B 25 " --> pdb=" O LEU B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 33 Processing helix chain 'B' and resid 41 through 53 removed outlier: 4.327A pdb=" N GLN B 45 " --> pdb=" O MET B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 73 Processing helix chain 'B' and resid 74 through 81 removed outlier: 5.079A pdb=" N LEU B 79 " --> pdb=" O SER B 76 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLY B 80 " --> pdb=" O ARG B 77 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL B 81 " --> pdb=" O LYS B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 100 Processing helix chain 'B' and resid 148 through 153 removed outlier: 3.927A pdb=" N TYR B 152 " --> pdb=" O GLN B 148 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY B 153 " --> pdb=" O TRP B 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 148 through 153' Processing helix chain 'B' and resid 187 through 191 Processing helix chain 'B' and resid 205 through 212 Processing helix chain 'B' and resid 229 through 241 Processing helix chain 'B' and resid 242 through 245 removed outlier: 3.723A pdb=" N VAL B 245 " --> pdb=" O PRO B 242 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 242 through 245' Processing helix chain 'A' and resid 22 through 26 removed outlier: 3.950A pdb=" N LEU A 25 " --> pdb=" O LEU A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 33 Processing helix chain 'A' and resid 42 through 53 Processing helix chain 'A' and resid 68 through 73 Processing helix chain 'A' and resid 74 through 81 removed outlier: 5.083A pdb=" N LEU A 79 " --> pdb=" O SER A 76 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLY A 80 " --> pdb=" O ARG A 77 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL A 81 " --> pdb=" O LYS A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 100 Processing helix chain 'A' and resid 148 through 153 removed outlier: 3.908A pdb=" N TYR A 152 " --> pdb=" O GLN A 148 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLY A 153 " --> pdb=" O TRP A 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 148 through 153' Processing helix chain 'A' and resid 187 through 191 Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 205 through 212 Processing helix chain 'A' and resid 229 through 241 Processing helix chain 'A' and resid 242 through 245 removed outlier: 3.713A pdb=" N VAL A 245 " --> pdb=" O PRO A 242 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 242 through 245' Processing helix chain 'C' and resid 22 through 26 removed outlier: 3.957A pdb=" N LEU C 25 " --> pdb=" O LEU C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 33 Processing helix chain 'C' and resid 41 through 53 removed outlier: 4.315A pdb=" N GLN C 45 " --> pdb=" O MET C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 73 Processing helix chain 'C' and resid 74 through 81 removed outlier: 5.112A pdb=" N LEU C 79 " --> pdb=" O SER C 76 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLY C 80 " --> pdb=" O ARG C 77 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL C 81 " --> pdb=" O LYS C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 100 Processing helix chain 'C' and resid 148 through 153 removed outlier: 3.920A pdb=" N TYR C 152 " --> pdb=" O GLN C 148 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLY C 153 " --> pdb=" O TRP C 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 148 through 153' Processing helix chain 'C' and resid 187 through 191 Processing helix chain 'C' and resid 201 through 204 removed outlier: 3.990A pdb=" N GLU C 204 " --> pdb=" O ILE C 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 201 through 204' Processing helix chain 'C' and resid 205 through 212 Processing helix chain 'C' and resid 229 through 241 Processing helix chain 'C' and resid 242 through 245 removed outlier: 3.707A pdb=" N VAL C 245 " --> pdb=" O PRO C 242 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 242 through 245' Processing helix chain 'D' and resid 22 through 26 removed outlier: 4.034A pdb=" N LEU D 25 " --> pdb=" O LEU D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 33 Processing helix chain 'D' and resid 42 through 53 Processing helix chain 'D' and resid 68 through 73 Processing helix chain 'D' and resid 74 through 81 removed outlier: 5.101A pdb=" N LEU D 79 " --> pdb=" O SER D 76 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLY D 80 " --> pdb=" O ARG D 77 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL D 81 " --> pdb=" O LYS D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 100 Processing helix chain 'D' and resid 148 through 153 removed outlier: 3.940A pdb=" N TYR D 152 " --> pdb=" O GLN D 148 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY D 153 " --> pdb=" O TRP D 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 148 through 153' Processing helix chain 'D' and resid 187 through 191 Processing helix chain 'D' and resid 205 through 212 Processing helix chain 'D' and resid 229 through 241 Processing helix chain 'D' and resid 242 through 245 removed outlier: 3.721A pdb=" N VAL D 245 " --> pdb=" O PRO D 242 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 242 through 245' Processing helix chain 'E' and resid 22 through 26 removed outlier: 3.961A pdb=" N LEU E 25 " --> pdb=" O LEU E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 33 Processing helix chain 'E' and resid 42 through 53 Processing helix chain 'E' and resid 68 through 73 Processing helix chain 'E' and resid 74 through 81 removed outlier: 5.068A pdb=" N LEU E 79 " --> pdb=" O SER E 76 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLY E 80 " --> pdb=" O ARG E 77 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL E 81 " --> pdb=" O LYS E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 100 Processing helix chain 'E' and resid 148 through 153 removed outlier: 3.907A pdb=" N TYR E 152 " --> pdb=" O GLN E 148 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY E 153 " --> pdb=" O TRP E 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 148 through 153' Processing helix chain 'E' and resid 187 through 191 Processing helix chain 'E' and resid 205 through 212 Processing helix chain 'E' and resid 229 through 241 Processing helix chain 'E' and resid 242 through 245 removed outlier: 3.685A pdb=" N VAL E 245 " --> pdb=" O PRO E 242 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 242 through 245' Processing helix chain 'F' and resid 22 through 26 removed outlier: 4.020A pdb=" N LEU F 25 " --> pdb=" O LEU F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 33 Processing helix chain 'F' and resid 41 through 53 removed outlier: 4.323A pdb=" N GLN F 45 " --> pdb=" O MET F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 73 Processing helix chain 'F' and resid 74 through 81 removed outlier: 5.072A pdb=" N LEU F 79 " --> pdb=" O SER F 76 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLY F 80 " --> pdb=" O ARG F 77 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL F 81 " --> pdb=" O LYS F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 100 Processing helix chain 'F' and resid 148 through 153 removed outlier: 3.922A pdb=" N TYR F 152 " --> pdb=" O GLN F 148 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLY F 153 " --> pdb=" O TRP F 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 148 through 153' Processing helix chain 'F' and resid 187 through 191 Processing helix chain 'F' and resid 205 through 212 Processing helix chain 'F' and resid 229 through 241 Processing helix chain 'F' and resid 242 through 245 removed outlier: 3.707A pdb=" N VAL F 245 " --> pdb=" O PRO F 242 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 242 through 245' Processing sheet with id=AA1, first strand: chain 'B' and resid 82 through 83 removed outlier: 3.649A pdb=" N VAL B 57 " --> pdb=" O SER B 82 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE B 113 " --> pdb=" O ARG B 10 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 35 through 36 Processing sheet with id=AA3, first strand: chain 'B' and resid 178 through 180 removed outlier: 4.330A pdb=" N GLN B 145 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 155 through 156 removed outlier: 3.672A pdb=" N VAL B 168 " --> pdb=" O VAL B 155 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 268 through 269 removed outlier: 6.902A pdb=" N THR B 268 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N VAL B 286 " --> pdb=" O ILE B 305 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ARG B 304 " --> pdb=" O VAL B 322 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 274 through 275 removed outlier: 6.833A pdb=" N LEU B 274 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N SER B 292 " --> pdb=" O ILE B 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 350 through 351 removed outlier: 6.385A pdb=" N GLU B 350 " --> pdb=" O VAL B 368 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 360 through 362 removed outlier: 6.767A pdb=" N LYS B 361 " --> pdb=" O ILE B 378 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 82 through 83 removed outlier: 3.675A pdb=" N VAL A 57 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL A 87 " --> pdb=" O LEU A 59 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL A 61 " --> pdb=" O VAL A 87 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 82 through 83 removed outlier: 3.675A pdb=" N VAL A 57 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N PHE A 113 " --> pdb=" O ARG A 10 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 35 through 36 Processing sheet with id=AB3, first strand: chain 'A' and resid 178 through 180 removed outlier: 4.319A pdb=" N GLN A 145 " --> pdb=" O LEU A 220 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 155 through 156 removed outlier: 3.662A pdb=" N VAL A 168 " --> pdb=" O VAL A 155 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 268 through 269 removed outlier: 6.968A pdb=" N THR A 268 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N VAL A 286 " --> pdb=" O ILE A 305 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ARG A 304 " --> pdb=" O VAL A 322 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N MET A 321 " --> pdb=" O ILE A 339 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 274 through 275 removed outlier: 6.862A pdb=" N LEU A 274 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N SER A 292 " --> pdb=" O ILE A 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 350 through 351 removed outlier: 6.494A pdb=" N GLU A 350 " --> pdb=" O VAL A 368 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 360 through 362 removed outlier: 6.671A pdb=" N LYS A 361 " --> pdb=" O ILE A 378 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 82 through 83 removed outlier: 3.771A pdb=" N VAL C 57 " --> pdb=" O SER C 82 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N PHE C 113 " --> pdb=" O ARG C 10 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 35 through 36 Processing sheet with id=AC2, first strand: chain 'C' and resid 178 through 180 removed outlier: 4.280A pdb=" N GLN C 145 " --> pdb=" O LEU C 220 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 155 through 156 removed outlier: 3.704A pdb=" N VAL C 168 " --> pdb=" O VAL C 155 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 268 through 269 removed outlier: 6.920A pdb=" N THR C 268 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N VAL C 286 " --> pdb=" O ILE C 305 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ARG C 304 " --> pdb=" O VAL C 322 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N MET C 321 " --> pdb=" O ILE C 339 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 274 through 275 removed outlier: 6.911A pdb=" N LEU C 274 " --> pdb=" O ILE C 293 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N SER C 292 " --> pdb=" O ILE C 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'C' and resid 350 through 351 removed outlier: 6.515A pdb=" N GLU C 350 " --> pdb=" O VAL C 368 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'C' and resid 360 through 362 removed outlier: 6.775A pdb=" N LYS C 361 " --> pdb=" O ILE C 378 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'D' and resid 82 through 83 removed outlier: 3.652A pdb=" N VAL D 57 " --> pdb=" O SER D 82 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N VAL D 87 " --> pdb=" O VAL D 57 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N LEU D 59 " --> pdb=" O VAL D 87 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'D' and resid 82 through 83 removed outlier: 3.652A pdb=" N VAL D 57 " --> pdb=" O SER D 82 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N PHE D 113 " --> pdb=" O ARG D 10 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 35 through 36 Processing sheet with id=AD2, first strand: chain 'D' and resid 178 through 180 removed outlier: 4.267A pdb=" N GLN D 145 " --> pdb=" O LEU D 220 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 155 through 156 removed outlier: 3.672A pdb=" N VAL D 168 " --> pdb=" O VAL D 155 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 268 through 269 removed outlier: 6.900A pdb=" N THR D 268 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N VAL D 286 " --> pdb=" O ILE D 305 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ARG D 304 " --> pdb=" O VAL D 322 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 274 through 275 removed outlier: 6.835A pdb=" N LEU D 274 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N SER D 292 " --> pdb=" O ILE D 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'D' and resid 350 through 351 removed outlier: 6.384A pdb=" N GLU D 350 " --> pdb=" O VAL D 368 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'D' and resid 360 through 362 removed outlier: 6.766A pdb=" N LYS D 361 " --> pdb=" O ILE D 378 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'E' and resid 82 through 83 removed outlier: 3.723A pdb=" N VAL E 57 " --> pdb=" O SER E 82 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL E 87 " --> pdb=" O LEU E 59 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL E 61 " --> pdb=" O VAL E 87 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'E' and resid 82 through 83 removed outlier: 3.723A pdb=" N VAL E 57 " --> pdb=" O SER E 82 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE E 113 " --> pdb=" O ARG E 10 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 35 through 36 Processing sheet with id=AE2, first strand: chain 'E' and resid 178 through 180 removed outlier: 4.309A pdb=" N GLN E 145 " --> pdb=" O LEU E 220 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 155 through 156 removed outlier: 3.663A pdb=" N VAL E 168 " --> pdb=" O VAL E 155 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 268 through 269 removed outlier: 6.963A pdb=" N THR E 268 " --> pdb=" O ILE E 287 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N VAL E 286 " --> pdb=" O ILE E 305 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ARG E 304 " --> pdb=" O VAL E 322 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N MET E 321 " --> pdb=" O ILE E 339 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 274 through 275 removed outlier: 6.868A pdb=" N LEU E 274 " --> pdb=" O ILE E 293 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N SER E 292 " --> pdb=" O ILE E 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'E' and resid 350 through 351 removed outlier: 6.494A pdb=" N GLU E 350 " --> pdb=" O VAL E 368 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'E' and resid 360 through 362 removed outlier: 6.673A pdb=" N LYS E 361 " --> pdb=" O ILE E 378 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'F' and resid 82 through 83 removed outlier: 3.867A pdb=" N VAL F 57 " --> pdb=" O SER F 82 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ALA F 11 " --> pdb=" O ILE F 58 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ALA F 60 " --> pdb=" O ALA F 11 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ILE F 13 " --> pdb=" O ALA F 60 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N PHE F 113 " --> pdb=" O ARG F 10 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 35 through 36 Processing sheet with id=AF1, first strand: chain 'F' and resid 178 through 180 removed outlier: 4.283A pdb=" N GLN F 145 " --> pdb=" O LEU F 220 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 155 through 156 removed outlier: 3.705A pdb=" N VAL F 168 " --> pdb=" O VAL F 155 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 268 through 269 removed outlier: 6.920A pdb=" N THR F 268 " --> pdb=" O ILE F 287 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N VAL F 286 " --> pdb=" O ILE F 305 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ARG F 304 " --> pdb=" O VAL F 322 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N MET F 321 " --> pdb=" O ILE F 339 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 274 through 275 removed outlier: 6.912A pdb=" N LEU F 274 " --> pdb=" O ILE F 293 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N SER F 292 " --> pdb=" O ILE F 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'F' and resid 350 through 351 removed outlier: 6.503A pdb=" N GLU F 350 " --> pdb=" O VAL F 368 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'F' and resid 360 through 362 removed outlier: 6.794A pdb=" N LYS F 361 " --> pdb=" O ILE F 378 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 312 hydrogen bonds defined for protein. 756 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: 2.84 Time building geometry restraints manager: 1.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5541 1.34 - 1.46: 2992 1.46 - 1.58: 8567 1.58 - 1.69: 0 1.69 - 1.81: 174 Bond restraints: 17274 Sorted by residual: bond pdb=" CG1 ILE A 46 " pdb=" CD1 ILE A 46 " ideal model delta sigma weight residual 1.513 1.460 0.053 3.90e-02 6.57e+02 1.87e+00 bond pdb=" CG1 ILE D 46 " pdb=" CD1 ILE D 46 " ideal model delta sigma weight residual 1.513 1.460 0.053 3.90e-02 6.57e+02 1.86e+00 bond pdb=" CG1 ILE E 46 " pdb=" CD1 ILE E 46 " ideal model delta sigma weight residual 1.513 1.461 0.052 3.90e-02 6.57e+02 1.79e+00 bond pdb=" CA LYS D 170 " pdb=" CB LYS D 170 " ideal model delta sigma weight residual 1.522 1.531 -0.008 7.00e-03 2.04e+04 1.45e+00 bond pdb=" CA LYS E 170 " pdb=" CB LYS E 170 " ideal model delta sigma weight residual 1.522 1.531 -0.008 7.00e-03 2.04e+04 1.40e+00 ... (remaining 17269 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 23070 2.18 - 4.35: 267 4.35 - 6.53: 33 6.53 - 8.71: 3 8.71 - 10.88: 3 Bond angle restraints: 23376 Sorted by residual: angle pdb=" CA LEU E 92 " pdb=" CB LEU E 92 " pdb=" CG LEU E 92 " ideal model delta sigma weight residual 116.30 127.18 -10.88 3.50e+00 8.16e-02 9.67e+00 angle pdb=" CA LEU D 92 " pdb=" CB LEU D 92 " pdb=" CG LEU D 92 " ideal model delta sigma weight residual 116.30 127.02 -10.72 3.50e+00 8.16e-02 9.39e+00 angle pdb=" CA LEU B 92 " pdb=" CB LEU B 92 " pdb=" CG LEU B 92 " ideal model delta sigma weight residual 116.30 126.32 -10.02 3.50e+00 8.16e-02 8.20e+00 angle pdb=" C LYS B 203 " pdb=" CA LYS B 203 " pdb=" CB LYS B 203 " ideal model delta sigma weight residual 110.42 115.96 -5.54 1.99e+00 2.53e-01 7.75e+00 angle pdb=" CA GLN D 214 " pdb=" CB GLN D 214 " pdb=" CG GLN D 214 " ideal model delta sigma weight residual 114.10 118.88 -4.78 2.00e+00 2.50e-01 5.71e+00 ... (remaining 23371 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 9413 17.68 - 35.35: 783 35.35 - 53.03: 134 53.03 - 70.71: 7 70.71 - 88.39: 13 Dihedral angle restraints: 10350 sinusoidal: 4200 harmonic: 6150 Sorted by residual: dihedral pdb=" CA GLU F 89 " pdb=" C GLU F 89 " pdb=" N GLU F 90 " pdb=" CA GLU F 90 " ideal model delta harmonic sigma weight residual 180.00 160.87 19.13 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA GLU C 89 " pdb=" C GLU C 89 " pdb=" N GLU C 90 " pdb=" CA GLU C 90 " ideal model delta harmonic sigma weight residual 180.00 161.04 18.96 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA ARG E 23 " pdb=" C ARG E 23 " pdb=" N PRO E 24 " pdb=" CA PRO E 24 " ideal model delta harmonic sigma weight residual 180.00 -161.05 -18.95 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 10347 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1868 0.045 - 0.090: 446 0.090 - 0.135: 282 0.135 - 0.180: 8 0.180 - 0.225: 6 Chirality restraints: 2610 Sorted by residual: chirality pdb=" CB ILE D 185 " pdb=" CA ILE D 185 " pdb=" CG1 ILE D 185 " pdb=" CG2 ILE D 185 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CB ILE A 185 " pdb=" CA ILE A 185 " pdb=" CG1 ILE A 185 " pdb=" CG2 ILE A 185 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.78e-01 chirality pdb=" CB ILE B 185 " pdb=" CA ILE B 185 " pdb=" CG1 ILE B 185 " pdb=" CG2 ILE B 185 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.71e-01 ... (remaining 2607 not shown) Planarity restraints: 3024 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP F 276 " -0.029 5.00e-02 4.00e+02 4.40e-02 3.09e+00 pdb=" N PRO F 277 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO F 277 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 277 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 276 " 0.029 5.00e-02 4.00e+02 4.38e-02 3.07e+00 pdb=" N PRO E 277 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO E 277 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 277 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 276 " -0.029 5.00e-02 4.00e+02 4.38e-02 3.07e+00 pdb=" N PRO C 277 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO C 277 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 277 " -0.024 5.00e-02 4.00e+02 ... (remaining 3021 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1050 2.73 - 3.27: 17097 3.27 - 3.82: 25599 3.82 - 4.36: 30721 4.36 - 4.90: 52817 Nonbonded interactions: 127284 Sorted by model distance: nonbonded pdb=" OG SER A 325 " pdb=" O SER A 343 " model vdw 2.190 3.040 nonbonded pdb=" OG SER E 325 " pdb=" O SER E 343 " model vdw 2.191 3.040 nonbonded pdb=" OG SER C 325 " pdb=" O SER C 343 " model vdw 2.202 3.040 nonbonded pdb=" OG SER F 325 " pdb=" O SER F 343 " model vdw 2.207 3.040 nonbonded pdb=" OG SER B 325 " pdb=" O SER B 343 " model vdw 2.217 3.040 ... (remaining 127279 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.180 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.490 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 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 : 0.003 0.053 17274 Z= 0.127 Angle : 0.599 10.882 23376 Z= 0.305 Chirality : 0.050 0.225 2610 Planarity : 0.005 0.053 3024 Dihedral : 13.107 88.387 6414 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.33 (0.17), residues: 2148 helix: -0.70 (0.33), residues: 276 sheet: -0.97 (0.24), residues: 480 loop : -2.04 (0.15), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 77 TYR 0.008 0.001 TYR E 233 PHE 0.017 0.001 PHE E 218 TRP 0.015 0.001 TRP E 224 HIS 0.002 0.001 HIS B 371 Details of bonding type rmsd covalent geometry : bond 0.00269 (17274) covalent geometry : angle 0.59932 (23376) hydrogen bonds : bond 0.23432 ( 312) hydrogen bonds : angle 7.93700 ( 756) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 282 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 72 MET cc_start: 0.8059 (ttp) cc_final: 0.7801 (ttm) REVERT: B 237 MET cc_start: 0.7643 (ttp) cc_final: 0.7378 (ttp) REVERT: A 102 ARG cc_start: 0.8188 (tmt170) cc_final: 0.7866 (tpt90) REVERT: A 370 GLU cc_start: 0.8120 (pm20) cc_final: 0.7380 (pm20) REVERT: C 72 MET cc_start: 0.8242 (ttp) cc_final: 0.8025 (ttm) REVERT: C 118 ASP cc_start: 0.8363 (m-30) cc_final: 0.7982 (m-30) REVERT: C 225 MET cc_start: 0.7702 (ptp) cc_final: 0.7475 (ptp) REVERT: D 72 MET cc_start: 0.8061 (ttp) cc_final: 0.7795 (ttm) REVERT: D 135 HIS cc_start: 0.7218 (m90) cc_final: 0.6766 (m90) REVERT: D 237 MET cc_start: 0.7636 (ttp) cc_final: 0.7374 (ttp) REVERT: E 102 ARG cc_start: 0.8136 (tmt170) cc_final: 0.7913 (tpt90) REVERT: E 370 GLU cc_start: 0.8125 (pm20) cc_final: 0.7381 (pm20) REVERT: F 72 MET cc_start: 0.8228 (ttp) cc_final: 0.8002 (ttm) REVERT: F 118 ASP cc_start: 0.8347 (m-30) cc_final: 0.7933 (m-30) REVERT: F 225 MET cc_start: 0.7675 (ptp) cc_final: 0.7420 (ptp) outliers start: 0 outliers final: 0 residues processed: 282 average time/residue: 0.1186 time to fit residues: 51.1120 Evaluate side-chains 223 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 0.0030 chunk 194 optimal weight: 20.0000 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.0570 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 20.0000 chunk 212 optimal weight: 2.9990 chunk 77 optimal weight: 0.0770 overall best weight: 0.3666 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 116 ASN ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.186923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.112433 restraints weight = 21113.134| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 3.73 r_work: 0.3250 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6786 moved from start: 0.0923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 17274 Z= 0.106 Angle : 0.613 10.535 23376 Z= 0.302 Chirality : 0.050 0.237 2610 Planarity : 0.005 0.043 3024 Dihedral : 4.489 18.743 2316 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 0.93 % Allowed : 6.72 % Favored : 92.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.47 (0.17), residues: 2148 helix: -1.09 (0.30), residues: 270 sheet: -1.23 (0.24), residues: 486 loop : -1.99 (0.15), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 10 TYR 0.011 0.001 TYR B 233 PHE 0.009 0.001 PHE E 206 TRP 0.007 0.001 TRP E 224 HIS 0.003 0.001 HIS D 338 Details of bonding type rmsd covalent geometry : bond 0.00226 (17274) covalent geometry : angle 0.61313 (23376) hydrogen bonds : bond 0.04611 ( 312) hydrogen bonds : angle 6.63317 ( 756) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 255 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 135 HIS cc_start: 0.7219 (m90) cc_final: 0.6676 (m90) REVERT: A 102 ARG cc_start: 0.8117 (tmt170) cc_final: 0.7760 (tpt90) REVERT: A 135 HIS cc_start: 0.7145 (m90) cc_final: 0.6659 (m90) REVERT: A 370 GLU cc_start: 0.8278 (pm20) cc_final: 0.7660 (pm20) REVERT: C 118 ASP cc_start: 0.8319 (m-30) cc_final: 0.7921 (m-30) REVERT: C 225 MET cc_start: 0.7330 (ptp) cc_final: 0.7055 (ptp) REVERT: D 135 HIS cc_start: 0.7181 (m90) cc_final: 0.6733 (m90) REVERT: E 102 ARG cc_start: 0.8078 (tmt170) cc_final: 0.7795 (tpt90) REVERT: E 135 HIS cc_start: 0.7238 (m90) cc_final: 0.6756 (m90) REVERT: E 370 GLU cc_start: 0.8290 (pm20) cc_final: 0.7670 (pm20) REVERT: F 118 ASP cc_start: 0.8365 (m-30) cc_final: 0.7870 (m-30) REVERT: F 190 ILE cc_start: 0.8605 (tp) cc_final: 0.8294 (tt) REVERT: F 225 MET cc_start: 0.7286 (ptp) cc_final: 0.7022 (ptp) outliers start: 17 outliers final: 14 residues processed: 260 average time/residue: 0.1217 time to fit residues: 47.4239 Evaluate side-chains 243 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 229 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 246 HIS Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 246 HIS Chi-restraints excluded: chain D residue 321 MET Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 185 ILE Chi-restraints excluded: chain F residue 246 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 188 optimal weight: 0.6980 chunk 157 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 chunk 45 optimal weight: 0.0270 chunk 165 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 200 optimal weight: 20.0000 chunk 144 optimal weight: 10.0000 chunk 105 optimal weight: 0.9980 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.186858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.111375 restraints weight = 21386.492| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 3.51 r_work: 0.3243 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6777 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 17274 Z= 0.106 Angle : 0.598 11.525 23376 Z= 0.290 Chirality : 0.050 0.284 2610 Planarity : 0.004 0.043 3024 Dihedral : 4.433 18.688 2316 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 1.31 % Allowed : 10.71 % Favored : 87.98 % 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: -2.46 (0.17), residues: 2148 helix: -1.02 (0.30), residues: 270 sheet: -1.28 (0.24), residues: 486 loop : -1.98 (0.15), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 77 TYR 0.012 0.001 TYR B 233 PHE 0.010 0.001 PHE E 218 TRP 0.006 0.001 TRP E 75 HIS 0.002 0.001 HIS D 338 Details of bonding type rmsd covalent geometry : bond 0.00240 (17274) covalent geometry : angle 0.59816 (23376) hydrogen bonds : bond 0.03953 ( 312) hydrogen bonds : angle 6.14067 ( 756) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 249 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 135 HIS cc_start: 0.7179 (m90) cc_final: 0.6679 (m90) REVERT: B 190 ILE cc_start: 0.8613 (tp) cc_final: 0.8269 (tt) REVERT: A 102 ARG cc_start: 0.8141 (tmt170) cc_final: 0.7793 (tpt90) REVERT: A 135 HIS cc_start: 0.7074 (m90) cc_final: 0.6594 (m90) REVERT: A 370 GLU cc_start: 0.8267 (pm20) cc_final: 0.7740 (pm20) REVERT: C 118 ASP cc_start: 0.8420 (m-30) cc_final: 0.8024 (m-30) REVERT: C 135 HIS cc_start: 0.7219 (m90) cc_final: 0.6697 (m90) REVERT: C 225 MET cc_start: 0.7336 (ptp) cc_final: 0.7112 (ptp) REVERT: E 102 ARG cc_start: 0.8136 (tmt170) cc_final: 0.7832 (tpt90) REVERT: E 135 HIS cc_start: 0.7147 (m90) cc_final: 0.6631 (m90) REVERT: E 370 GLU cc_start: 0.8290 (pm20) cc_final: 0.7762 (pm20) REVERT: F 118 ASP cc_start: 0.8416 (m-30) cc_final: 0.7988 (m-30) REVERT: F 135 HIS cc_start: 0.7220 (m90) cc_final: 0.6697 (m90) REVERT: F 190 ILE cc_start: 0.8723 (tp) cc_final: 0.8340 (tt) outliers start: 24 outliers final: 17 residues processed: 261 average time/residue: 0.1290 time to fit residues: 50.9270 Evaluate side-chains 250 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 233 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 246 HIS Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 246 HIS Chi-restraints excluded: chain D residue 321 MET Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 185 ILE Chi-restraints excluded: chain F residue 246 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 92 optimal weight: 10.0000 chunk 62 optimal weight: 0.5980 chunk 27 optimal weight: 5.9990 chunk 112 optimal weight: 8.9990 chunk 90 optimal weight: 10.0000 chunk 134 optimal weight: 0.0370 chunk 140 optimal weight: 1.9990 chunk 150 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 193 optimal weight: 0.6980 chunk 163 optimal weight: 6.9990 overall best weight: 1.4662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 HIS ** E 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.184233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.108454 restraints weight = 21367.835| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 3.47 r_work: 0.3201 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17274 Z= 0.140 Angle : 0.611 11.639 23376 Z= 0.299 Chirality : 0.050 0.286 2610 Planarity : 0.004 0.045 3024 Dihedral : 4.547 18.874 2316 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 1.04 % Allowed : 14.37 % Favored : 84.59 % 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: -2.43 (0.17), residues: 2148 helix: -0.81 (0.31), residues: 270 sheet: -1.36 (0.22), residues: 546 loop : -1.96 (0.15), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 77 TYR 0.013 0.001 TYR B 233 PHE 0.013 0.001 PHE E 218 TRP 0.005 0.001 TRP D 75 HIS 0.003 0.001 HIS D 338 Details of bonding type rmsd covalent geometry : bond 0.00336 (17274) covalent geometry : angle 0.61119 (23376) hydrogen bonds : bond 0.03843 ( 312) hydrogen bonds : angle 5.70550 ( 756) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 244 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 106 MET cc_start: 0.8343 (mpp) cc_final: 0.7916 (mpp) REVERT: B 135 HIS cc_start: 0.7174 (m90) cc_final: 0.6734 (m90) REVERT: B 190 ILE cc_start: 0.8630 (tp) cc_final: 0.8272 (tt) REVERT: A 102 ARG cc_start: 0.8164 (tmt170) cc_final: 0.7805 (tpt90) REVERT: A 135 HIS cc_start: 0.7113 (m90) cc_final: 0.6646 (m90) REVERT: A 190 ILE cc_start: 0.8578 (tp) cc_final: 0.8291 (tt) REVERT: A 370 GLU cc_start: 0.8264 (pm20) cc_final: 0.7692 (pm20) REVERT: C 118 ASP cc_start: 0.8517 (m-30) cc_final: 0.8132 (m-30) REVERT: D 106 MET cc_start: 0.8355 (mpp) cc_final: 0.7936 (mpp) REVERT: D 190 ILE cc_start: 0.8587 (tp) cc_final: 0.8266 (tt) REVERT: E 102 ARG cc_start: 0.8147 (tmt170) cc_final: 0.7814 (tpt90) REVERT: E 135 HIS cc_start: 0.7189 (m90) cc_final: 0.6755 (m90) REVERT: E 190 ILE cc_start: 0.8608 (tp) cc_final: 0.8313 (tt) REVERT: E 370 GLU cc_start: 0.8273 (pm20) cc_final: 0.7699 (pm20) REVERT: F 118 ASP cc_start: 0.8464 (m-30) cc_final: 0.8076 (m-30) outliers start: 19 outliers final: 17 residues processed: 251 average time/residue: 0.1199 time to fit residues: 46.0566 Evaluate side-chains 251 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 234 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain A residue 75 TRP Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 246 HIS Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 246 HIS Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 246 HIS Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 185 ILE Chi-restraints excluded: chain F residue 246 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 211 optimal weight: 0.9980 chunk 14 optimal weight: 20.0000 chunk 31 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 121 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 chunk 55 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.182726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.106514 restraints weight = 21399.128| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 3.49 r_work: 0.3175 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6845 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17274 Z= 0.157 Angle : 0.619 11.778 23376 Z= 0.302 Chirality : 0.050 0.273 2610 Planarity : 0.004 0.044 3024 Dihedral : 4.643 19.201 2316 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 1.75 % Allowed : 16.72 % Favored : 81.53 % 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: -2.41 (0.17), residues: 2148 helix: -0.63 (0.32), residues: 270 sheet: -1.35 (0.22), residues: 582 loop : -2.00 (0.16), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 77 TYR 0.014 0.001 TYR B 233 PHE 0.010 0.001 PHE E 218 TRP 0.004 0.001 TRP E 224 HIS 0.004 0.001 HIS D 338 Details of bonding type rmsd covalent geometry : bond 0.00380 (17274) covalent geometry : angle 0.61873 (23376) hydrogen bonds : bond 0.03825 ( 312) hydrogen bonds : angle 5.48107 ( 756) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 230 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 106 MET cc_start: 0.8343 (mpp) cc_final: 0.7901 (mpp) REVERT: A 102 ARG cc_start: 0.8157 (tmt170) cc_final: 0.7780 (tpt90) REVERT: A 190 ILE cc_start: 0.8626 (tp) cc_final: 0.8295 (tt) REVERT: A 370 GLU cc_start: 0.8275 (pm20) cc_final: 0.7710 (pm20) REVERT: C 31 LYS cc_start: 0.8010 (tttt) cc_final: 0.7708 (tptm) REVERT: C 72 MET cc_start: 0.7386 (ttp) cc_final: 0.7136 (ttp) REVERT: C 118 ASP cc_start: 0.8518 (m-30) cc_final: 0.7835 (m-30) REVERT: D 106 MET cc_start: 0.8356 (mpp) cc_final: 0.7924 (mpp) REVERT: D 190 ILE cc_start: 0.8598 (tp) cc_final: 0.8225 (tt) REVERT: E 102 ARG cc_start: 0.8142 (tmt170) cc_final: 0.7794 (tpt90) REVERT: E 190 ILE cc_start: 0.8644 (tp) cc_final: 0.8304 (tt) REVERT: E 370 GLU cc_start: 0.8280 (pm20) cc_final: 0.7708 (pm20) REVERT: F 72 MET cc_start: 0.7416 (ttp) cc_final: 0.7151 (ttp) REVERT: F 118 ASP cc_start: 0.8525 (m-30) cc_final: 0.8176 (m-30) outliers start: 32 outliers final: 28 residues processed: 243 average time/residue: 0.1255 time to fit residues: 46.6651 Evaluate side-chains 249 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 221 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain A residue 75 TRP Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 246 HIS Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 85 PHE Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 246 HIS Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 246 HIS Chi-restraints excluded: chain E residue 75 TRP Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 246 HIS Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 185 ILE Chi-restraints excluded: chain F residue 246 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 185 optimal weight: 6.9990 chunk 86 optimal weight: 20.0000 chunk 191 optimal weight: 3.9990 chunk 213 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 206 optimal weight: 0.3980 chunk 107 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 152 optimal weight: 0.8980 chunk 36 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.183983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.107575 restraints weight = 21271.711| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 3.52 r_work: 0.3192 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17274 Z= 0.126 Angle : 0.602 12.323 23376 Z= 0.291 Chirality : 0.050 0.264 2610 Planarity : 0.004 0.044 3024 Dihedral : 4.567 19.054 2316 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 1.69 % Allowed : 18.25 % Favored : 80.05 % 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: -2.33 (0.17), residues: 2148 helix: -0.82 (0.30), residues: 306 sheet: -1.31 (0.22), residues: 582 loop : -1.89 (0.16), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 77 TYR 0.013 0.001 TYR B 233 PHE 0.010 0.001 PHE A 206 TRP 0.004 0.001 TRP A 224 HIS 0.003 0.001 HIS B 338 Details of bonding type rmsd covalent geometry : bond 0.00302 (17274) covalent geometry : angle 0.60179 (23376) hydrogen bonds : bond 0.03581 ( 312) hydrogen bonds : angle 5.33193 ( 756) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 242 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 106 MET cc_start: 0.8339 (mpp) cc_final: 0.7894 (mpp) REVERT: A 102 ARG cc_start: 0.8160 (tmt170) cc_final: 0.7784 (tpt90) REVERT: A 190 ILE cc_start: 0.8672 (tp) cc_final: 0.8329 (tt) REVERT: A 370 GLU cc_start: 0.8299 (pm20) cc_final: 0.7726 (pm20) REVERT: C 31 LYS cc_start: 0.7983 (tttt) cc_final: 0.7691 (tptm) REVERT: C 118 ASP cc_start: 0.8500 (m-30) cc_final: 0.7782 (m-30) REVERT: D 106 MET cc_start: 0.8339 (mpp) cc_final: 0.7895 (mpp) REVERT: D 190 ILE cc_start: 0.8627 (tp) cc_final: 0.8233 (tt) REVERT: E 102 ARG cc_start: 0.8119 (tmt170) cc_final: 0.7765 (tpt90) REVERT: E 190 ILE cc_start: 0.8665 (tp) cc_final: 0.8310 (tt) REVERT: E 370 GLU cc_start: 0.8302 (pm20) cc_final: 0.7728 (pm20) REVERT: F 31 LYS cc_start: 0.8086 (tttt) cc_final: 0.7776 (tptm) REVERT: F 72 MET cc_start: 0.7432 (ttp) cc_final: 0.7176 (ttp) REVERT: F 118 ASP cc_start: 0.8491 (m-30) cc_final: 0.7851 (m-30) REVERT: F 190 ILE cc_start: 0.8756 (tp) cc_final: 0.8508 (tp) outliers start: 31 outliers final: 29 residues processed: 252 average time/residue: 0.1118 time to fit residues: 43.9258 Evaluate side-chains 257 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 228 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 75 TRP Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 246 HIS Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 246 HIS Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 246 HIS Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 75 TRP Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 246 HIS Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 185 ILE Chi-restraints excluded: chain F residue 246 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 206 optimal weight: 0.0070 chunk 56 optimal weight: 0.0040 chunk 57 optimal weight: 5.9990 chunk 146 optimal weight: 0.7980 chunk 139 optimal weight: 0.9990 chunk 205 optimal weight: 1.9990 chunk 170 optimal weight: 0.0370 chunk 160 optimal weight: 0.9990 chunk 19 optimal weight: 0.0770 chunk 150 optimal weight: 6.9990 chunk 185 optimal weight: 4.9990 overall best weight: 0.1846 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.189740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.113997 restraints weight = 21222.150| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 3.53 r_work: 0.3246 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6768 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17274 Z= 0.092 Angle : 0.587 13.303 23376 Z= 0.280 Chirality : 0.050 0.358 2610 Planarity : 0.004 0.043 3024 Dihedral : 4.273 18.379 2316 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 1.53 % Allowed : 19.34 % Favored : 79.13 % 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: -2.21 (0.17), residues: 2148 helix: -0.44 (0.32), residues: 270 sheet: -1.24 (0.24), residues: 486 loop : -1.85 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 77 TYR 0.011 0.001 TYR D 233 PHE 0.009 0.001 PHE E 206 TRP 0.006 0.001 TRP C 336 HIS 0.003 0.001 HIS B 338 Details of bonding type rmsd covalent geometry : bond 0.00201 (17274) covalent geometry : angle 0.58714 (23376) hydrogen bonds : bond 0.03079 ( 312) hydrogen bonds : angle 5.23394 ( 756) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 253 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 106 MET cc_start: 0.8280 (mpp) cc_final: 0.7781 (mpp) REVERT: B 135 HIS cc_start: 0.7181 (m90) cc_final: 0.6695 (m90) REVERT: B 209 MET cc_start: 0.7077 (tpt) cc_final: 0.6877 (tpt) REVERT: A 102 ARG cc_start: 0.8130 (tmt170) cc_final: 0.7765 (tpt90) REVERT: A 135 HIS cc_start: 0.7213 (m90) cc_final: 0.6742 (m90) REVERT: A 190 ILE cc_start: 0.8690 (tp) cc_final: 0.8274 (tt) REVERT: A 305 ILE cc_start: 0.8142 (mm) cc_final: 0.7912 (mp) REVERT: A 370 GLU cc_start: 0.8314 (pm20) cc_final: 0.7720 (pm20) REVERT: C 31 LYS cc_start: 0.7949 (tttt) cc_final: 0.7655 (tptm) REVERT: C 118 ASP cc_start: 0.8379 (m-30) cc_final: 0.7691 (m-30) REVERT: C 135 HIS cc_start: 0.7204 (m90) cc_final: 0.6737 (m90) REVERT: D 31 LYS cc_start: 0.7298 (tttt) cc_final: 0.6958 (tptm) REVERT: D 106 MET cc_start: 0.8292 (mpp) cc_final: 0.7789 (mpp) REVERT: E 102 ARG cc_start: 0.8113 (tmt170) cc_final: 0.7748 (tpt90) REVERT: E 135 HIS cc_start: 0.7212 (m90) cc_final: 0.6732 (m90) REVERT: E 190 ILE cc_start: 0.8686 (tp) cc_final: 0.8335 (tt) REVERT: E 305 ILE cc_start: 0.8151 (mm) cc_final: 0.7924 (mp) REVERT: E 370 GLU cc_start: 0.8313 (pm20) cc_final: 0.7719 (pm20) REVERT: F 31 LYS cc_start: 0.7977 (tttt) cc_final: 0.7688 (tptm) REVERT: F 118 ASP cc_start: 0.8368 (m-30) cc_final: 0.7717 (m-30) REVERT: F 135 HIS cc_start: 0.7091 (m90) cc_final: 0.6643 (m90) REVERT: F 190 ILE cc_start: 0.8760 (tp) cc_final: 0.8514 (tp) outliers start: 28 outliers final: 19 residues processed: 266 average time/residue: 0.1137 time to fit residues: 46.8626 Evaluate side-chains 261 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 242 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 75 TRP Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 246 HIS Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 246 HIS Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 75 TRP Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 185 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 179 optimal weight: 6.9990 chunk 150 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 207 optimal weight: 3.9990 chunk 122 optimal weight: 20.0000 chunk 161 optimal weight: 10.0000 chunk 109 optimal weight: 0.0270 chunk 130 optimal weight: 1.9990 chunk 86 optimal weight: 20.0000 chunk 162 optimal weight: 1.9990 chunk 46 optimal weight: 0.2980 overall best weight: 1.0644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.186178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.109841 restraints weight = 21488.623| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 3.54 r_work: 0.3224 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6784 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17274 Z= 0.118 Angle : 0.602 13.066 23376 Z= 0.292 Chirality : 0.049 0.227 2610 Planarity : 0.004 0.039 3024 Dihedral : 4.323 18.425 2316 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 1.91 % Allowed : 20.27 % Favored : 77.81 % 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: -2.18 (0.17), residues: 2148 helix: -0.27 (0.32), residues: 270 sheet: -1.24 (0.24), residues: 486 loop : -1.85 (0.15), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 77 TYR 0.013 0.001 TYR D 233 PHE 0.010 0.001 PHE D 113 TRP 0.006 0.001 TRP E 224 HIS 0.003 0.001 HIS B 338 Details of bonding type rmsd covalent geometry : bond 0.00280 (17274) covalent geometry : angle 0.60161 (23376) hydrogen bonds : bond 0.03381 ( 312) hydrogen bonds : angle 5.10121 ( 756) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 229 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 ARG cc_start: 0.8479 (mtm180) cc_final: 0.8208 (ptp-170) REVERT: B 106 MET cc_start: 0.8305 (mpp) cc_final: 0.7822 (mpp) REVERT: B 135 HIS cc_start: 0.7160 (m90) cc_final: 0.6726 (m90) REVERT: A 102 ARG cc_start: 0.8152 (tmt170) cc_final: 0.7775 (tpt90) REVERT: A 135 HIS cc_start: 0.7306 (m90) cc_final: 0.6865 (m90) REVERT: A 190 ILE cc_start: 0.8672 (tp) cc_final: 0.8344 (tt) REVERT: A 370 GLU cc_start: 0.8293 (pm20) cc_final: 0.7751 (pm20) REVERT: C 31 LYS cc_start: 0.8040 (tttt) cc_final: 0.7737 (tptm) REVERT: C 118 ASP cc_start: 0.8428 (m-30) cc_final: 0.7740 (m-30) REVERT: D 64 ARG cc_start: 0.8497 (mtm180) cc_final: 0.8227 (ptp-170) REVERT: D 106 MET cc_start: 0.8313 (mpp) cc_final: 0.7825 (mpp) REVERT: D 150 GLU cc_start: 0.9268 (pp20) cc_final: 0.9057 (pm20) REVERT: E 102 ARG cc_start: 0.8011 (tmt170) cc_final: 0.7673 (tpt90) REVERT: E 190 ILE cc_start: 0.8687 (tp) cc_final: 0.8337 (tt) REVERT: E 370 GLU cc_start: 0.8292 (pm20) cc_final: 0.7749 (pm20) REVERT: F 31 LYS cc_start: 0.8123 (tttt) cc_final: 0.7829 (tptm) REVERT: F 118 ASP cc_start: 0.8422 (m-30) cc_final: 0.7779 (m-30) REVERT: F 190 ILE cc_start: 0.8717 (tp) cc_final: 0.8466 (tp) outliers start: 35 outliers final: 24 residues processed: 252 average time/residue: 0.1188 time to fit residues: 46.7794 Evaluate side-chains 249 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 225 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 75 TRP Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 246 HIS Chi-restraints excluded: chain D residue 325 SER Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 75 TRP Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 185 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 199 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 90 optimal weight: 0.0980 chunk 91 optimal weight: 10.0000 chunk 158 optimal weight: 20.0000 chunk 127 optimal weight: 10.0000 chunk 189 optimal weight: 0.9990 chunk 170 optimal weight: 4.9990 chunk 196 optimal weight: 5.9990 chunk 152 optimal weight: 10.0000 chunk 109 optimal weight: 0.8980 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 145 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.179985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.103281 restraints weight = 21407.053| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 3.52 r_work: 0.3128 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 17274 Z= 0.220 Angle : 0.682 12.850 23376 Z= 0.341 Chirality : 0.052 0.241 2610 Planarity : 0.005 0.049 3024 Dihedral : 4.837 19.530 2316 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.45 % Favored : 90.55 % Rotamer: Outliers : 1.75 % Allowed : 20.38 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.32 (0.18), residues: 2148 helix: -0.62 (0.30), residues: 306 sheet: -1.27 (0.23), residues: 570 loop : -1.96 (0.16), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 77 TYR 0.014 0.001 TYR D 233 PHE 0.014 0.001 PHE A 36 TRP 0.009 0.001 TRP A 336 HIS 0.005 0.002 HIS D 338 Details of bonding type rmsd covalent geometry : bond 0.00540 (17274) covalent geometry : angle 0.68161 (23376) hydrogen bonds : bond 0.04157 ( 312) hydrogen bonds : angle 5.24317 ( 756) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 216 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 341 ASP cc_start: 0.7962 (OUTLIER) cc_final: 0.7591 (t70) REVERT: A 102 ARG cc_start: 0.8176 (tmt170) cc_final: 0.7749 (tpt90) REVERT: A 370 GLU cc_start: 0.8341 (pm20) cc_final: 0.7823 (pm20) REVERT: C 31 LYS cc_start: 0.8149 (tttt) cc_final: 0.7805 (tptm) REVERT: C 118 ASP cc_start: 0.8515 (m-30) cc_final: 0.7858 (m-30) REVERT: D 150 GLU cc_start: 0.9274 (pp20) cc_final: 0.9046 (pm20) REVERT: D 341 ASP cc_start: 0.7939 (OUTLIER) cc_final: 0.7573 (t70) REVERT: E 102 ARG cc_start: 0.8083 (tmt170) cc_final: 0.7713 (tpt90) REVERT: E 190 ILE cc_start: 0.8709 (tp) cc_final: 0.8365 (tt) REVERT: E 370 GLU cc_start: 0.8336 (pm20) cc_final: 0.7814 (pm20) REVERT: F 31 LYS cc_start: 0.8187 (tttt) cc_final: 0.7860 (tptm) REVERT: F 118 ASP cc_start: 0.8587 (m-30) cc_final: 0.8054 (m-30) outliers start: 32 outliers final: 28 residues processed: 234 average time/residue: 0.1107 time to fit residues: 40.6056 Evaluate side-chains 242 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 212 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 246 HIS Chi-restraints excluded: chain D residue 325 SER Chi-restraints excluded: chain D residue 341 ASP Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 75 TRP Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 185 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 83 optimal weight: 1.9990 chunk 178 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 134 optimal weight: 0.0060 chunk 144 optimal weight: 10.0000 chunk 79 optimal weight: 0.1980 chunk 24 optimal weight: 0.8980 chunk 114 optimal weight: 5.9990 chunk 199 optimal weight: 8.9990 overall best weight: 1.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 145 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.183565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.107277 restraints weight = 21326.120| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 3.48 r_work: 0.3190 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6811 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17274 Z= 0.119 Angle : 0.629 13.496 23376 Z= 0.307 Chirality : 0.050 0.244 2610 Planarity : 0.004 0.042 3024 Dihedral : 4.603 19.127 2316 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 1.42 % Allowed : 20.60 % Favored : 77.98 % 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: -2.15 (0.18), residues: 2148 helix: -0.07 (0.32), residues: 270 sheet: -1.20 (0.23), residues: 570 loop : -1.90 (0.16), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 77 TYR 0.011 0.001 TYR D 233 PHE 0.011 0.001 PHE E 218 TRP 0.009 0.001 TRP C 224 HIS 0.003 0.001 HIS B 338 Details of bonding type rmsd covalent geometry : bond 0.00286 (17274) covalent geometry : angle 0.62885 (23376) hydrogen bonds : bond 0.03515 ( 312) hydrogen bonds : angle 5.15389 ( 756) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 219 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 150 GLU cc_start: 0.9267 (pp20) cc_final: 0.9052 (pm20) REVERT: B 341 ASP cc_start: 0.7976 (OUTLIER) cc_final: 0.7671 (t70) REVERT: A 102 ARG cc_start: 0.8155 (tmt170) cc_final: 0.7734 (tpt90) REVERT: A 281 ILE cc_start: 0.8541 (mm) cc_final: 0.8278 (tp) REVERT: A 370 GLU cc_start: 0.8340 (pm20) cc_final: 0.7775 (pm20) REVERT: C 31 LYS cc_start: 0.7980 (tttt) cc_final: 0.7643 (tptm) REVERT: C 118 ASP cc_start: 0.8461 (m-30) cc_final: 0.7757 (m-30) REVERT: D 150 GLU cc_start: 0.9276 (pp20) cc_final: 0.9048 (pm20) REVERT: D 341 ASP cc_start: 0.7949 (OUTLIER) cc_final: 0.7648 (t70) REVERT: E 102 ARG cc_start: 0.8021 (tmt170) cc_final: 0.7426 (tpt90) REVERT: E 281 ILE cc_start: 0.8549 (mm) cc_final: 0.8266 (tp) REVERT: E 370 GLU cc_start: 0.8344 (pm20) cc_final: 0.7777 (pm20) REVERT: F 31 LYS cc_start: 0.8074 (tttt) cc_final: 0.7787 (tptm) REVERT: F 118 ASP cc_start: 0.8526 (m-30) cc_final: 0.7965 (m-30) REVERT: F 190 ILE cc_start: 0.8751 (tp) cc_final: 0.8515 (tp) outliers start: 26 outliers final: 22 residues processed: 235 average time/residue: 0.1083 time to fit residues: 40.4591 Evaluate side-chains 238 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 214 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 246 HIS Chi-restraints excluded: chain D residue 341 ASP Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 75 TRP Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 185 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 165 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 78 optimal weight: 0.0020 chunk 67 optimal weight: 0.7980 chunk 96 optimal weight: 9.9990 chunk 192 optimal weight: 7.9990 chunk 133 optimal weight: 0.0570 chunk 186 optimal weight: 1.9990 chunk 18 optimal weight: 0.0270 chunk 59 optimal weight: 3.9990 overall best weight: 0.5766 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.186250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.110386 restraints weight = 21155.326| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 3.49 r_work: 0.3234 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6792 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 17274 Z= 0.106 Angle : 0.619 14.078 23376 Z= 0.300 Chirality : 0.049 0.246 2610 Planarity : 0.004 0.037 3024 Dihedral : 4.410 18.358 2316 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 1.48 % Allowed : 20.82 % Favored : 77.70 % 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: -2.05 (0.17), residues: 2148 helix: -0.09 (0.32), residues: 270 sheet: -1.09 (0.23), residues: 522 loop : -1.81 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 77 TYR 0.011 0.001 TYR D 233 PHE 0.011 0.001 PHE E 218 TRP 0.009 0.001 TRP C 224 HIS 0.003 0.001 HIS D 338 Details of bonding type rmsd covalent geometry : bond 0.00247 (17274) covalent geometry : angle 0.61898 (23376) hydrogen bonds : bond 0.03307 ( 312) hydrogen bonds : angle 5.05893 ( 756) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3957.20 seconds wall clock time: 68 minutes 24.37 seconds (4104.37 seconds total)