Starting phenix.real_space_refine on Sun Jun 15 04:56:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7whr_32509/06_2025/7whr_32509.cif Found real_map, /net/cci-nas-00/data/ceres_data/7whr_32509/06_2025/7whr_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_32509/06_2025/7whr_32509.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7whr_32509/06_2025/7whr_32509.map" model { file = "/net/cci-nas-00/data/ceres_data/7whr_32509/06_2025/7whr_32509.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7whr_32509/06_2025/7whr_32509.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.06, per 1000 atoms: 0.59 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: 4.02 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 3.35 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: 6.88 Time building geometry restraints manager: 4.78 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: 0.03 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: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.610 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 42.780 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.090 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:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.800 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (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 TRP 0.015 0.001 TRP E 224 HIS 0.002 0.001 HIS B 371 PHE 0.017 0.001 PHE E 218 TYR 0.008 0.001 TYR E 233 ARG 0.002 0.000 ARG B 77 Details of bonding type rmsd hydrogen bonds : bond 0.23432 ( 312) hydrogen bonds : angle 7.93700 ( 756) covalent geometry : bond 0.00269 (17274) covalent geometry : angle 0.59932 (23376) *********************** 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 : 2.058 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: 0.7373 (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: 0.3254 time to fit residues: 140.3708 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 : 3.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 0.5980 chunk 163 optimal weight: 5.9990 chunk 90 optimal weight: 0.0030 chunk 55 optimal weight: 7.9990 chunk 110 optimal weight: 0.0170 chunk 87 optimal weight: 3.9990 chunk 169 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 102 optimal weight: 0.5980 chunk 126 optimal weight: 0.9980 chunk 196 optimal weight: 0.3980 overall best weight: 0.3228 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN ** 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 = 0.4235 r_free = 0.4235 target = 0.187594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.112935 restraints weight = 21177.399| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 3.71 r_work: 0.3257 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 moved from start: 0.0966 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 : 0.615 10.647 23376 Z= 0.302 Chirality : 0.050 0.224 2610 Planarity : 0.005 0.044 3024 Dihedral : 4.480 18.681 2316 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 0.98 % Allowed : 6.83 % Favored : 92.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.17), residues: 2148 helix: -1.10 (0.30), residues: 270 sheet: -1.22 (0.24), residues: 486 loop : -1.99 (0.15), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 224 HIS 0.003 0.001 HIS B 246 PHE 0.009 0.001 PHE E 206 TYR 0.010 0.001 TYR B 233 ARG 0.008 0.000 ARG A 10 Details of bonding type rmsd hydrogen bonds : bond 0.04558 ( 312) hydrogen bonds : angle 6.59048 ( 756) covalent geometry : bond 0.00223 (17274) covalent geometry : angle 0.61509 (23376) *********************** 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 271 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 253 time to evaluate : 1.893 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: 0.7217 (m90) cc_final: 0.6677 (m90) REVERT: A 64 ARG cc_start: 0.8896 (ptt-90) cc_final: 0.7991 (pmt-80) REVERT: A 102 ARG cc_start: 0.8112 (tmt170) cc_final: 0.7756 (tpt90) REVERT: A 135 HIS cc_start: 0.7143 (m90) cc_final: 0.6658 (m90) REVERT: A 370 GLU cc_start: 0.8281 (pm20) cc_final: 0.7720 (pm20) REVERT: C 118 ASP cc_start: 0.8311 (m-30) cc_final: 0.7910 (m-30) REVERT: C 225 MET cc_start: 0.7303 (ptp) cc_final: 0.7028 (ptp) REVERT: D 135 HIS cc_start: 0.7183 (m90) cc_final: 0.6806 (m90) REVERT: E 102 ARG cc_start: 0.8084 (tmt170) cc_final: 0.7788 (tpt90) REVERT: E 135 HIS cc_start: 0.7099 (m90) cc_final: 0.6634 (m90) REVERT: E 370 GLU cc_start: 0.8291 (pm20) cc_final: 0.7671 (pm20) REVERT: F 118 ASP cc_start: 0.8363 (m-30) cc_final: 0.7875 (m-30) REVERT: F 135 HIS cc_start: 0.7252 (m90) cc_final: 0.6722 (m90) REVERT: F 190 ILE cc_start: 0.8656 (tp) cc_final: 0.8346 (tt) REVERT: F 225 MET cc_start: 0.7251 (ptp) cc_final: 0.6983 (ptp) outliers start: 18 outliers final: 14 residues processed: 258 average time/residue: 0.2939 time to fit residues: 114.9446 Evaluate side-chains 240 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 226 time to evaluate : 1.745 ------------------------------------------------------------------------------- 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 96 optimal weight: 0.8980 chunk 120 optimal weight: 9.9990 chunk 129 optimal weight: 6.9990 chunk 197 optimal weight: 8.9990 chunk 134 optimal weight: 0.0000 chunk 22 optimal weight: 2.9990 chunk 77 optimal weight: 0.0050 chunk 93 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 202 optimal weight: 2.9990 chunk 171 optimal weight: 0.4980 overall best weight: 0.4598 ------------------------------------------------------------------------------- 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 = 0.4241 r_free = 0.4241 target = 0.187988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.112993 restraints weight = 21174.854| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 3.49 r_work: 0.3265 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 17274 Z= 0.097 Angle : 0.590 11.740 23376 Z= 0.286 Chirality : 0.050 0.284 2610 Planarity : 0.004 0.044 3024 Dihedral : 4.373 18.556 2316 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 1.26 % Allowed : 11.15 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.17), residues: 2148 helix: -1.02 (0.31), residues: 270 sheet: -1.25 (0.24), residues: 486 loop : -1.97 (0.15), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 75 HIS 0.002 0.001 HIS D 338 PHE 0.011 0.001 PHE E 218 TYR 0.012 0.001 TYR B 233 ARG 0.009 0.000 ARG A 77 Details of bonding type rmsd hydrogen bonds : bond 0.03897 ( 312) hydrogen bonds : angle 6.12385 ( 756) covalent geometry : bond 0.00213 (17274) covalent geometry : angle 0.59035 (23376) *********************** 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 284 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 261 time to evaluate : 1.750 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: 0.7161 (m90) cc_final: 0.6617 (m90) REVERT: B 190 ILE cc_start: 0.8603 (tp) cc_final: 0.8255 (tt) REVERT: A 102 ARG cc_start: 0.8135 (tmt170) cc_final: 0.7793 (tpt90) REVERT: A 135 HIS cc_start: 0.7058 (m90) cc_final: 0.6589 (m90) REVERT: A 370 GLU cc_start: 0.8266 (pm20) cc_final: 0.7736 (pm20) REVERT: C 118 ASP cc_start: 0.8400 (m-30) cc_final: 0.7998 (m-30) REVERT: C 135 HIS cc_start: 0.7187 (m90) cc_final: 0.6684 (m90) REVERT: D 135 HIS cc_start: 0.7258 (m90) cc_final: 0.6886 (m90) REVERT: D 209 MET cc_start: 0.7895 (tpt) cc_final: 0.7323 (tpt) REVERT: E 102 ARG cc_start: 0.8085 (tmt170) cc_final: 0.7793 (tpt90) REVERT: E 135 HIS cc_start: 0.7013 (m90) cc_final: 0.6473 (m90) REVERT: E 370 GLU cc_start: 0.8302 (pm20) cc_final: 0.7737 (pm20) REVERT: F 118 ASP cc_start: 0.8387 (m-30) cc_final: 0.7982 (m-30) REVERT: F 135 HIS cc_start: 0.7220 (m90) cc_final: 0.6719 (m90) REVERT: F 190 ILE cc_start: 0.8745 (tp) cc_final: 0.8371 (tt) outliers start: 23 outliers final: 16 residues processed: 272 average time/residue: 0.2804 time to fit residues: 115.2632 Evaluate side-chains 259 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 243 time to evaluate : 1.904 ------------------------------------------------------------------------------- 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 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 25 optimal weight: 0.0270 chunk 145 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 132 optimal weight: 0.0270 chunk 17 optimal weight: 9.9990 chunk 158 optimal weight: 20.0000 chunk 162 optimal weight: 5.9990 chunk 161 optimal weight: 10.0000 chunk 65 optimal weight: 3.9990 chunk 186 optimal weight: 0.0060 chunk 70 optimal weight: 1.9990 overall best weight: 1.0116 ------------------------------------------------------------------------------- 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 = 0.4225 r_free = 0.4225 target = 0.186361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.110381 restraints weight = 21308.919| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 3.50 r_work: 0.3231 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6797 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17274 Z= 0.115 Angle : 0.593 11.976 23376 Z= 0.288 Chirality : 0.050 0.282 2610 Planarity : 0.004 0.044 3024 Dihedral : 4.392 18.602 2316 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 1.15 % Allowed : 14.54 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.17), residues: 2148 helix: -0.82 (0.31), residues: 270 sheet: -1.31 (0.23), residues: 486 loop : -1.92 (0.15), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 224 HIS 0.003 0.001 HIS D 338 PHE 0.012 0.001 PHE E 218 TYR 0.013 0.001 TYR B 233 ARG 0.003 0.000 ARG C 64 Details of bonding type rmsd hydrogen bonds : bond 0.03616 ( 312) hydrogen bonds : angle 5.68017 ( 756) covalent geometry : bond 0.00268 (17274) covalent geometry : angle 0.59259 (23376) *********************** 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 267 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 246 time to evaluate : 1.919 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: 0.8341 (mpp) cc_final: 0.7915 (mpp) REVERT: B 135 HIS cc_start: 0.7226 (m90) cc_final: 0.6725 (m90) REVERT: B 190 ILE cc_start: 0.8622 (tp) cc_final: 0.8264 (tt) REVERT: A 102 ARG cc_start: 0.8165 (tmt170) cc_final: 0.7802 (tpt90) REVERT: A 135 HIS cc_start: 0.7054 (m90) cc_final: 0.6568 (m90) REVERT: A 370 GLU cc_start: 0.8266 (pm20) cc_final: 0.7733 (pm20) REVERT: C 31 LYS cc_start: 0.7964 (tttt) cc_final: 0.7664 (tptm) REVERT: C 118 ASP cc_start: 0.8457 (m-30) cc_final: 0.7770 (m-30) REVERT: C 135 HIS cc_start: 0.7228 (m90) cc_final: 0.6749 (m90) REVERT: D 106 MET cc_start: 0.8343 (mpp) cc_final: 0.7914 (mpp) REVERT: D 135 HIS cc_start: 0.7191 (m90) cc_final: 0.6826 (m90) REVERT: D 190 ILE cc_start: 0.8593 (tp) cc_final: 0.8259 (tt) REVERT: E 102 ARG cc_start: 0.8144 (tmt170) cc_final: 0.7842 (tpt90) REVERT: E 135 HIS cc_start: 0.7170 (m90) cc_final: 0.6674 (m90) REVERT: E 370 GLU cc_start: 0.8289 (pm20) cc_final: 0.7757 (pm20) REVERT: F 31 LYS cc_start: 0.7965 (tttt) cc_final: 0.7662 (tptm) REVERT: F 118 ASP cc_start: 0.8430 (m-30) cc_final: 0.7725 (m-30) REVERT: F 135 HIS cc_start: 0.7222 (m90) cc_final: 0.6766 (m90) outliers start: 21 outliers final: 20 residues processed: 252 average time/residue: 0.3281 time to fit residues: 124.8843 Evaluate side-chains 257 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 237 time to evaluate : 2.174 ------------------------------------------------------------------------------- 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 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 143 VAL 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 143 VAL 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 61 optimal weight: 1.9990 chunk 162 optimal weight: 0.2980 chunk 141 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 187 optimal weight: 6.9990 chunk 74 optimal weight: 0.0670 chunk 200 optimal weight: 20.0000 chunk 201 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 164 optimal weight: 10.0000 chunk 101 optimal weight: 3.9990 overall best weight: 1.0322 ------------------------------------------------------------------------------- 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 = 0.4223 r_free = 0.4223 target = 0.186177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.110018 restraints weight = 21408.963| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 3.53 r_work: 0.3224 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17274 Z= 0.115 Angle : 0.587 12.083 23376 Z= 0.283 Chirality : 0.049 0.268 2610 Planarity : 0.004 0.043 3024 Dihedral : 4.383 18.640 2316 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 1.48 % Allowed : 16.94 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.17), residues: 2148 helix: -0.61 (0.32), residues: 270 sheet: -1.30 (0.23), residues: 546 loop : -1.89 (0.16), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 224 HIS 0.003 0.001 HIS B 338 PHE 0.013 0.001 PHE E 206 TYR 0.012 0.001 TYR B 233 ARG 0.006 0.000 ARG B 77 Details of bonding type rmsd hydrogen bonds : bond 0.03495 ( 312) hydrogen bonds : angle 5.41519 ( 756) covalent geometry : bond 0.00270 (17274) covalent geometry : angle 0.58669 (23376) *********************** 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 274 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 247 time to evaluate : 1.743 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: 0.8340 (mpp) cc_final: 0.7886 (mpp) REVERT: B 135 HIS cc_start: 0.7183 (m90) cc_final: 0.6748 (m90) REVERT: A 102 ARG cc_start: 0.8165 (tmt170) cc_final: 0.7805 (tpt90) REVERT: A 135 HIS cc_start: 0.7174 (m90) cc_final: 0.6704 (m90) REVERT: A 370 GLU cc_start: 0.8286 (pm20) cc_final: 0.7705 (pm20) REVERT: C 31 LYS cc_start: 0.7963 (tttt) cc_final: 0.7678 (tptm) REVERT: C 92 LEU cc_start: 0.6513 (mp) cc_final: 0.6290 (mp) REVERT: C 118 ASP cc_start: 0.8435 (m-30) cc_final: 0.7722 (m-30) REVERT: D 106 MET cc_start: 0.8357 (mpp) cc_final: 0.7910 (mpp) REVERT: D 135 HIS cc_start: 0.7101 (m90) cc_final: 0.6646 (m90) REVERT: D 190 ILE cc_start: 0.8600 (tp) cc_final: 0.8235 (tt) REVERT: E 102 ARG cc_start: 0.8115 (tmt170) cc_final: 0.7789 (tpt90) REVERT: E 135 HIS cc_start: 0.7228 (m90) cc_final: 0.6741 (m90) REVERT: E 370 GLU cc_start: 0.8289 (pm20) cc_final: 0.7708 (pm20) REVERT: F 31 LYS cc_start: 0.7966 (tttt) cc_final: 0.7677 (tptm) REVERT: F 118 ASP cc_start: 0.8439 (m-30) cc_final: 0.7742 (m-30) REVERT: F 135 HIS cc_start: 0.7159 (m90) cc_final: 0.6727 (m90) outliers start: 27 outliers final: 22 residues processed: 257 average time/residue: 0.2795 time to fit residues: 109.4062 Evaluate side-chains 260 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 238 time to evaluate : 1.804 ------------------------------------------------------------------------------- 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 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 143 VAL 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 56 GLU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 124 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 chunk 115 optimal weight: 0.8980 chunk 190 optimal weight: 2.9990 chunk 145 optimal weight: 5.9990 chunk 128 optimal weight: 8.9990 chunk 64 optimal weight: 6.9990 chunk 84 optimal weight: 10.0000 chunk 192 optimal weight: 8.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 = 0.4203 r_free = 0.4203 target = 0.183847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.107420 restraints weight = 21461.894| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 3.51 r_work: 0.3191 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6821 moved from start: 0.1570 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= 0.141 Angle : 0.601 12.157 23376 Z= 0.293 Chirality : 0.050 0.254 2610 Planarity : 0.004 0.042 3024 Dihedral : 4.497 18.889 2316 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 1.80 % Allowed : 18.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.17), residues: 2148 helix: -0.74 (0.30), residues: 306 sheet: -1.36 (0.22), residues: 546 loop : -1.81 (0.16), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 224 HIS 0.004 0.001 HIS B 338 PHE 0.012 0.001 PHE E 206 TYR 0.013 0.001 TYR D 233 ARG 0.003 0.000 ARG A 77 Details of bonding type rmsd hydrogen bonds : bond 0.03637 ( 312) hydrogen bonds : angle 5.26402 ( 756) covalent geometry : bond 0.00340 (17274) covalent geometry : angle 0.60142 (23376) *********************** 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 272 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 239 time to evaluate : 1.933 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: 0.8333 (mpp) cc_final: 0.7870 (mpp) REVERT: B 135 HIS cc_start: 0.7215 (m90) cc_final: 0.6777 (m90) REVERT: A 102 ARG cc_start: 0.8175 (tmt170) cc_final: 0.7801 (tpt90) REVERT: A 135 HIS cc_start: 0.7370 (m90) cc_final: 0.7003 (m90) REVERT: A 370 GLU cc_start: 0.8273 (pm20) cc_final: 0.7739 (pm20) REVERT: C 31 LYS cc_start: 0.7990 (tttt) cc_final: 0.7700 (tptm) REVERT: C 92 LEU cc_start: 0.6476 (mp) cc_final: 0.6249 (mp) REVERT: C 118 ASP cc_start: 0.8510 (m-30) cc_final: 0.7838 (m-30) REVERT: D 106 MET cc_start: 0.8342 (mpp) cc_final: 0.7890 (mpp) REVERT: D 135 HIS cc_start: 0.7005 (m90) cc_final: 0.6503 (m90) REVERT: D 150 GLU cc_start: 0.9273 (pp20) cc_final: 0.9064 (pm20) REVERT: D 190 ILE cc_start: 0.8660 (tp) cc_final: 0.8259 (tt) REVERT: E 74 GLU cc_start: 0.8069 (tt0) cc_final: 0.7443 (tm-30) REVERT: E 102 ARG cc_start: 0.8129 (tmt170) cc_final: 0.7794 (tpt90) REVERT: E 370 GLU cc_start: 0.8293 (pm20) cc_final: 0.7717 (pm20) REVERT: F 31 LYS cc_start: 0.8062 (tttt) cc_final: 0.7773 (tptm) REVERT: F 72 MET cc_start: 0.7432 (ttp) cc_final: 0.7175 (ttp) REVERT: F 118 ASP cc_start: 0.8468 (m-30) cc_final: 0.7799 (m-30) outliers start: 33 outliers final: 28 residues processed: 254 average time/residue: 0.2778 time to fit residues: 107.9092 Evaluate side-chains 257 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 229 time to evaluate : 1.938 ------------------------------------------------------------------------------- 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 341 ASP 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 52 VAL Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 143 VAL 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 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 117 SER Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 185 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 160 optimal weight: 20.0000 chunk 15 optimal weight: 0.8980 chunk 146 optimal weight: 0.7980 chunk 187 optimal weight: 0.9990 chunk 138 optimal weight: 0.7980 chunk 134 optimal weight: 6.9990 chunk 11 optimal weight: 0.6980 chunk 210 optimal weight: 3.9990 chunk 117 optimal weight: 8.9990 chunk 153 optimal weight: 2.9990 chunk 203 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.4223 r_free = 0.4223 target = 0.186087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.109682 restraints weight = 21271.499| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 3.53 r_work: 0.3226 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6802 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 17274 Z= 0.106 Angle : 0.592 12.930 23376 Z= 0.285 Chirality : 0.050 0.356 2610 Planarity : 0.004 0.038 3024 Dihedral : 4.388 18.606 2316 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 2.02 % Allowed : 18.20 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.17), residues: 2148 helix: -0.39 (0.32), residues: 270 sheet: -1.30 (0.23), residues: 546 loop : -1.86 (0.16), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 224 HIS 0.003 0.001 HIS B 338 PHE 0.010 0.001 PHE E 206 TYR 0.013 0.001 TYR D 233 ARG 0.002 0.000 ARG D 77 Details of bonding type rmsd hydrogen bonds : bond 0.03285 ( 312) hydrogen bonds : angle 5.20517 ( 756) covalent geometry : bond 0.00249 (17274) covalent geometry : angle 0.59153 (23376) *********************** 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 277 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 240 time to evaluate : 1.772 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: 0.8327 (mpp) cc_final: 0.7869 (mpp) REVERT: B 135 HIS cc_start: 0.7180 (m90) cc_final: 0.6754 (m90) REVERT: A 102 ARG cc_start: 0.8157 (tmt170) cc_final: 0.7787 (tpt90) REVERT: A 135 HIS cc_start: 0.7334 (m90) cc_final: 0.6890 (m90) REVERT: A 370 GLU cc_start: 0.8297 (pm20) cc_final: 0.7715 (pm20) REVERT: C 31 LYS cc_start: 0.7949 (tttt) cc_final: 0.7650 (tptm) REVERT: C 92 LEU cc_start: 0.6468 (OUTLIER) cc_final: 0.6237 (mp) REVERT: C 118 ASP cc_start: 0.8461 (m-30) cc_final: 0.7756 (m-30) REVERT: D 106 MET cc_start: 0.8346 (mpp) cc_final: 0.7803 (mpp) REVERT: D 135 HIS cc_start: 0.7000 (m90) cc_final: 0.6528 (m90) REVERT: D 150 GLU cc_start: 0.9273 (pp20) cc_final: 0.9065 (pm20) REVERT: D 190 ILE cc_start: 0.8706 (tp) cc_final: 0.8313 (tt) REVERT: E 102 ARG cc_start: 0.8129 (tmt170) cc_final: 0.7761 (tpt90) REVERT: E 370 GLU cc_start: 0.8296 (pm20) cc_final: 0.7711 (pm20) REVERT: F 31 LYS cc_start: 0.7953 (tttt) cc_final: 0.7670 (tptm) REVERT: F 118 ASP cc_start: 0.8434 (m-30) cc_final: 0.7764 (m-30) REVERT: F 190 ILE cc_start: 0.8779 (tp) cc_final: 0.8542 (tp) outliers start: 37 outliers final: 30 residues processed: 257 average time/residue: 0.2580 time to fit residues: 102.1474 Evaluate side-chains 257 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 226 time to evaluate : 1.730 ------------------------------------------------------------------------------- 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 B residue 341 ASP 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 117 SER 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 92 LEU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 246 HIS Chi-restraints excluded: chain D residue 28 THR 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 341 ASP Chi-restraints excluded: chain E residue 52 VAL 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 E residue 246 HIS Chi-restraints excluded: chain F residue 52 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 28 optimal weight: 5.9990 chunk 197 optimal weight: 10.0000 chunk 162 optimal weight: 0.2980 chunk 155 optimal weight: 0.2980 chunk 98 optimal weight: 0.9990 chunk 50 optimal weight: 20.0000 chunk 157 optimal weight: 3.9990 chunk 178 optimal weight: 0.7980 chunk 115 optimal weight: 0.0570 chunk 6 optimal weight: 5.9990 chunk 140 optimal weight: 2.9990 overall best weight: 0.4900 ------------------------------------------------------------------------------- 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 = 0.4240 r_free = 0.4240 target = 0.187710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.111500 restraints weight = 21187.835| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 3.52 r_work: 0.3251 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6775 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17274 Z= 0.098 Angle : 0.589 13.206 23376 Z= 0.284 Chirality : 0.049 0.318 2610 Planarity : 0.004 0.038 3024 Dihedral : 4.265 18.162 2316 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 2.13 % Allowed : 18.25 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.17), residues: 2148 helix: -0.33 (0.32), residues: 270 sheet: -1.23 (0.24), residues: 486 loop : -1.84 (0.15), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 224 HIS 0.003 0.001 HIS B 338 PHE 0.010 0.001 PHE E 206 TYR 0.011 0.001 TYR D 233 ARG 0.003 0.000 ARG D 77 Details of bonding type rmsd hydrogen bonds : bond 0.03228 ( 312) hydrogen bonds : angle 5.14149 ( 756) covalent geometry : bond 0.00225 (17274) covalent geometry : angle 0.58926 (23376) *********************** 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 283 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 244 time to evaluate : 1.827 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: 0.8299 (mpp) cc_final: 0.7800 (mpp) REVERT: B 135 HIS cc_start: 0.7124 (m90) cc_final: 0.6657 (m90) REVERT: B 209 MET cc_start: 0.7113 (tpt) cc_final: 0.6904 (tpt) REVERT: A 102 ARG cc_start: 0.8137 (tmt170) cc_final: 0.7779 (tpt90) REVERT: A 135 HIS cc_start: 0.7264 (m90) cc_final: 0.6780 (m90) REVERT: A 370 GLU cc_start: 0.8293 (pm20) cc_final: 0.7752 (pm20) REVERT: C 31 LYS cc_start: 0.7958 (tttt) cc_final: 0.7656 (tptm) REVERT: C 72 MET cc_start: 0.7415 (ttp) cc_final: 0.7126 (ttm) REVERT: C 92 LEU cc_start: 0.6709 (OUTLIER) cc_final: 0.6504 (mp) REVERT: C 118 ASP cc_start: 0.8441 (m-30) cc_final: 0.7739 (m-30) REVERT: C 135 HIS cc_start: 0.7112 (m90) cc_final: 0.6664 (m90) REVERT: D 106 MET cc_start: 0.8321 (mpp) cc_final: 0.7813 (mpp) REVERT: D 135 HIS cc_start: 0.7031 (m90) cc_final: 0.6616 (m90) REVERT: E 102 ARG cc_start: 0.7987 (tmt170) cc_final: 0.7653 (tpt90) REVERT: E 135 HIS cc_start: 0.7283 (m90) cc_final: 0.6837 (m90) REVERT: E 305 ILE cc_start: 0.8145 (mm) cc_final: 0.7933 (mp) REVERT: E 370 GLU cc_start: 0.8291 (pm20) cc_final: 0.7751 (pm20) REVERT: F 31 LYS cc_start: 0.7960 (tttt) cc_final: 0.7656 (tptm) REVERT: F 118 ASP cc_start: 0.8400 (m-30) cc_final: 0.7695 (m-30) REVERT: F 135 HIS cc_start: 0.7147 (m90) cc_final: 0.6713 (m90) REVERT: F 190 ILE cc_start: 0.8720 (tp) cc_final: 0.8469 (tp) outliers start: 39 outliers final: 29 residues processed: 264 average time/residue: 0.3154 time to fit residues: 129.0900 Evaluate side-chains 273 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 243 time to evaluate : 1.918 ------------------------------------------------------------------------------- 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 B residue 341 ASP 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 117 SER 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 92 LEU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 143 VAL 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 341 ASP Chi-restraints excluded: chain E residue 52 VAL 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 F residue 52 VAL Chi-restraints excluded: chain F residue 75 TRP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 137 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 135 optimal weight: 0.9990 chunk 54 optimal weight: 10.0000 chunk 176 optimal weight: 4.9990 chunk 132 optimal weight: 0.0170 chunk 122 optimal weight: 20.0000 chunk 95 optimal weight: 3.9990 chunk 202 optimal weight: 0.8980 chunk 72 optimal weight: 10.0000 chunk 208 optimal weight: 4.9990 overall best weight: 1.3222 ------------------------------------------------------------------------------- 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 = 0.4215 r_free = 0.4215 target = 0.185048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.108746 restraints weight = 21450.581| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 3.52 r_work: 0.3210 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17274 Z= 0.132 Angle : 0.611 13.170 23376 Z= 0.298 Chirality : 0.050 0.285 2610 Planarity : 0.004 0.037 3024 Dihedral : 4.389 18.537 2316 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 2.13 % Allowed : 18.52 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.17), residues: 2148 helix: -0.58 (0.30), residues: 306 sheet: -1.35 (0.23), residues: 486 loop : -1.75 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 224 HIS 0.003 0.001 HIS B 338 PHE 0.011 0.001 PHE E 206 TYR 0.013 0.001 TYR D 233 ARG 0.005 0.000 ARG D 77 Details of bonding type rmsd hydrogen bonds : bond 0.03419 ( 312) hydrogen bonds : angle 5.11666 ( 756) covalent geometry : bond 0.00322 (17274) covalent geometry : angle 0.61055 (23376) *********************** 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 264 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 225 time to evaluate : 2.345 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: 0.8307 (mpp) cc_final: 0.7814 (mpp) REVERT: B 135 HIS cc_start: 0.7107 (m90) cc_final: 0.6688 (m90) REVERT: A 102 ARG cc_start: 0.8147 (tmt170) cc_final: 0.7774 (tpt90) REVERT: A 107 GLN cc_start: 0.9041 (tm-30) cc_final: 0.8581 (tm-30) REVERT: A 135 HIS cc_start: 0.7321 (m90) cc_final: 0.6872 (m90) REVERT: A 370 GLU cc_start: 0.8325 (pm20) cc_final: 0.7776 (pm20) REVERT: C 31 LYS cc_start: 0.8005 (tttt) cc_final: 0.7692 (tptm) REVERT: C 72 MET cc_start: 0.7443 (ttp) cc_final: 0.7161 (ttm) REVERT: C 92 LEU cc_start: 0.6538 (OUTLIER) cc_final: 0.6333 (mp) REVERT: C 118 ASP cc_start: 0.8477 (m-30) cc_final: 0.7783 (m-30) REVERT: C 135 HIS cc_start: 0.7182 (m90) cc_final: 0.6729 (m90) REVERT: D 106 MET cc_start: 0.8339 (mpp) cc_final: 0.7835 (mpp) REVERT: D 135 HIS cc_start: 0.6983 (m90) cc_final: 0.6505 (m90) REVERT: E 102 ARG cc_start: 0.8015 (tmt170) cc_final: 0.7457 (tpt90) REVERT: E 370 GLU cc_start: 0.8284 (pm20) cc_final: 0.7746 (pm20) REVERT: F 31 LYS cc_start: 0.7988 (tttt) cc_final: 0.7647 (tptm) REVERT: F 118 ASP cc_start: 0.8470 (m-30) cc_final: 0.7745 (m-30) REVERT: F 135 HIS cc_start: 0.7232 (m90) cc_final: 0.6826 (m90) REVERT: F 190 ILE cc_start: 0.8722 (tp) cc_final: 0.8476 (tp) outliers start: 39 outliers final: 30 residues processed: 249 average time/residue: 0.3015 time to fit residues: 116.5201 Evaluate side-chains 255 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 224 time to evaluate : 2.033 ------------------------------------------------------------------------------- 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 143 VAL 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 75 TRP 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 92 LEU Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 143 VAL 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 117 SER Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 246 HIS 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 125 optimal weight: 10.0000 chunk 135 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 80 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 chunk 106 optimal weight: 2.9990 chunk 179 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 185 optimal weight: 0.0670 chunk 141 optimal weight: 4.9990 overall best weight: 1.6124 ------------------------------------------------------------------------------- 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 = 0.183249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.106950 restraints weight = 21405.798| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 3.50 r_work: 0.3186 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17274 Z= 0.151 Angle : 0.634 13.551 23376 Z= 0.310 Chirality : 0.050 0.292 2610 Planarity : 0.004 0.037 3024 Dihedral : 4.515 18.933 2316 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 1.86 % Allowed : 19.07 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.17), residues: 2148 helix: -0.59 (0.30), residues: 306 sheet: -1.32 (0.22), residues: 534 loop : -1.87 (0.16), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 224 HIS 0.003 0.001 HIS B 338 PHE 0.011 0.001 PHE E 218 TYR 0.013 0.001 TYR D 233 ARG 0.008 0.000 ARG D 77 Details of bonding type rmsd hydrogen bonds : bond 0.03537 ( 312) hydrogen bonds : angle 5.13742 ( 756) covalent geometry : bond 0.00369 (17274) covalent geometry : angle 0.63351 (23376) ********************** 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 259 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 225 time to evaluate : 2.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 ARG cc_start: 0.8378 (mtm180) cc_final: 0.8068 (ptp-170) REVERT: B 106 MET cc_start: 0.8326 (mpp) cc_final: 0.7849 (mpp) REVERT: B 150 GLU cc_start: 0.9270 (pp20) cc_final: 0.9056 (pm20) REVERT: B 341 ASP cc_start: 0.8085 (OUTLIER) cc_final: 0.7747 (t0) REVERT: A 102 ARG cc_start: 0.8085 (tmt170) cc_final: 0.7710 (tpt90) REVERT: A 370 GLU cc_start: 0.8327 (pm20) cc_final: 0.7789 (pm20) REVERT: C 31 LYS cc_start: 0.8018 (tttt) cc_final: 0.7663 (tptm) REVERT: C 92 LEU cc_start: 0.6582 (OUTLIER) cc_final: 0.6361 (mp) REVERT: C 118 ASP cc_start: 0.8491 (m-30) cc_final: 0.7794 (m-30) REVERT: D 64 ARG cc_start: 0.8361 (mtm180) cc_final: 0.8057 (ptp-170) REVERT: D 106 MET cc_start: 0.8356 (mpp) cc_final: 0.7867 (mpp) REVERT: D 135 HIS cc_start: 0.6996 (m90) cc_final: 0.6470 (m90) REVERT: E 74 GLU cc_start: 0.8093 (tt0) cc_final: 0.7472 (tm-30) REVERT: E 102 ARG cc_start: 0.8014 (tmt170) cc_final: 0.7446 (tpt90) REVERT: E 370 GLU cc_start: 0.8341 (pm20) cc_final: 0.7758 (pm20) REVERT: F 31 LYS cc_start: 0.8048 (tttt) cc_final: 0.7721 (tptm) REVERT: F 118 ASP cc_start: 0.8474 (m-30) cc_final: 0.7796 (m-30) REVERT: F 190 ILE cc_start: 0.8744 (tp) cc_final: 0.8507 (tp) outliers start: 34 outliers final: 30 residues processed: 243 average time/residue: 0.3340 time to fit residues: 127.7159 Evaluate side-chains 252 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 220 time to evaluate : 3.116 ------------------------------------------------------------------------------- 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 143 VAL Chi-restraints excluded: chain B residue 184 TYR 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 75 TRP 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 92 LEU Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 143 VAL 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 117 SER Chi-restraints excluded: chain E residue 143 VAL 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 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 157 optimal weight: 0.6980 chunk 89 optimal weight: 9.9990 chunk 100 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 148 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 96 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 chunk 171 optimal weight: 5.9990 chunk 105 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4217 r_free = 0.4217 target = 0.185350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.109374 restraints weight = 21264.640| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 3.51 r_work: 0.3223 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 moved from start: 0.1880 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= 0.112 Angle : 0.623 13.485 23376 Z= 0.302 Chirality : 0.050 0.292 2610 Planarity : 0.004 0.049 3024 Dihedral : 4.408 18.472 2316 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 1.86 % Allowed : 19.23 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.17), residues: 2148 helix: -0.03 (0.32), residues: 270 sheet: -1.22 (0.23), residues: 534 loop : -1.78 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 224 HIS 0.003 0.001 HIS B 338 PHE 0.011 0.001 PHE E 218 TYR 0.012 0.001 TYR D 233 ARG 0.018 0.000 ARG D 77 Details of bonding type rmsd hydrogen bonds : bond 0.03328 ( 312) hydrogen bonds : angle 5.07937 ( 756) covalent geometry : bond 0.00268 (17274) covalent geometry : angle 0.62334 (23376) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9947.89 seconds wall clock time: 178 minutes 44.94 seconds (10724.94 seconds total)