Starting phenix.real_space_refine on Mon Oct 13 10:54:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rxc_19573/10_2025/8rxc_19573.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rxc_19573/10_2025/8rxc_19573.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8rxc_19573/10_2025/8rxc_19573.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rxc_19573/10_2025/8rxc_19573.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8rxc_19573/10_2025/8rxc_19573.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rxc_19573/10_2025/8rxc_19573.map" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 16082 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 57 5.49 5 Mg 5 5.21 5 S 76 5.16 5 C 11946 2.51 5 N 3301 2.21 5 O 3821 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19206 Number of models: 1 Model: "" Number of chains: 13 Chain: "D" Number of atoms: 3049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3049 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 384} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 3055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3055 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 14, 'TRANS': 384} Chain: "B" Number of atoms: 3039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3039 Classifications: {'peptide': 397} Link IDs: {'PTRANS': 13, 'TRANS': 383} Chain: "A" Number of atoms: 3039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3039 Classifications: {'peptide': 397} Link IDs: {'PTRANS': 13, 'TRANS': 383} Chain: "F" Number of atoms: 2965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2965 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 13, 'TRANS': 373} Chain: "E" Number of atoms: 3039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3039 Classifications: {'peptide': 397} Link IDs: {'PTRANS': 13, 'TRANS': 383} Chain: "G" Number of atoms: 440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 440 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "H" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 420 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.79, per 1000 atoms: 0.25 Number of scatterers: 19206 At special positions: 0 Unit cell: (119.915, 113.299, 120.742, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 76 16.00 P 57 15.00 Mg 5 11.99 O 3821 8.00 N 3301 7.00 C 11946 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.50 Conformation dependent library (CDL) restraints added in 943.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4332 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 20 sheets defined 36.2% alpha, 19.9% beta 7 base pairs and 32 stacking pairs defined. Time for finding SS restraints: 2.55 Creating SS restraints... Processing helix chain 'D' and resid 74 through 81 removed outlier: 3.994A pdb=" N VAL D 80 " --> pdb=" O GLU D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 114 Processing helix chain 'D' and resid 126 through 138 Processing helix chain 'D' and resid 151 through 163 Processing helix chain 'D' and resid 173 through 175 No H-bonds generated for 'chain 'D' and resid 173 through 175' Processing helix chain 'D' and resid 186 through 205 removed outlier: 3.693A pdb=" N GLU D 192 " --> pdb=" O SER D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 230 removed outlier: 4.007A pdb=" N GLU D 227 " --> pdb=" O PRO D 223 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL D 230 " --> pdb=" O LEU D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 342 Processing helix chain 'D' and resid 357 through 359 No H-bonds generated for 'chain 'D' and resid 357 through 359' Processing helix chain 'D' and resid 363 through 365 No H-bonds generated for 'chain 'D' and resid 363 through 365' Processing helix chain 'D' and resid 366 through 380 Processing helix chain 'D' and resid 404 through 415 Processing helix chain 'D' and resid 425 through 428 removed outlier: 4.143A pdb=" N THR D 428 " --> pdb=" O ASN D 425 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 425 through 428' Processing helix chain 'D' and resid 443 through 452 Processing helix chain 'C' and resid 74 through 82 removed outlier: 3.519A pdb=" N VAL C 80 " --> pdb=" O GLU C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 114 removed outlier: 3.614A pdb=" N GLN C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 138 Processing helix chain 'C' and resid 151 through 163 removed outlier: 3.560A pdb=" N GLU C 158 " --> pdb=" O SER C 154 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG C 161 " --> pdb=" O ALA C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 175 Processing helix chain 'C' and resid 186 through 205 Processing helix chain 'C' and resid 223 through 230 removed outlier: 4.129A pdb=" N GLU C 227 " --> pdb=" O PRO C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 281 removed outlier: 3.914A pdb=" N PHE C 280 " --> pdb=" O SER C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 342 Processing helix chain 'C' and resid 357 through 359 No H-bonds generated for 'chain 'C' and resid 357 through 359' Processing helix chain 'C' and resid 363 through 365 No H-bonds generated for 'chain 'C' and resid 363 through 365' Processing helix chain 'C' and resid 366 through 380 Processing helix chain 'C' and resid 404 through 415 Processing helix chain 'C' and resid 425 through 428 removed outlier: 3.779A pdb=" N THR C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 425 through 428' Processing helix chain 'C' and resid 443 through 452 Processing helix chain 'B' and resid 59 through 63 removed outlier: 4.556A pdb=" N THR B 63 " --> pdb=" O ALA B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 81 removed outlier: 3.592A pdb=" N VAL B 80 " --> pdb=" O GLU B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 116 removed outlier: 3.759A pdb=" N VAL B 115 " --> pdb=" O GLN B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 138 Processing helix chain 'B' and resid 151 through 163 Processing helix chain 'B' and resid 190 through 205 Processing helix chain 'B' and resid 224 through 230 Processing helix chain 'B' and resid 327 through 343 Processing helix chain 'B' and resid 357 through 359 No H-bonds generated for 'chain 'B' and resid 357 through 359' Processing helix chain 'B' and resid 363 through 365 No H-bonds generated for 'chain 'B' and resid 363 through 365' Processing helix chain 'B' and resid 366 through 380 Processing helix chain 'B' and resid 404 through 415 Processing helix chain 'B' and resid 425 through 428 Processing helix chain 'B' and resid 443 through 452 Processing helix chain 'A' and resid 74 through 79 Processing helix chain 'A' and resid 100 through 113 removed outlier: 3.579A pdb=" N LEU A 105 " --> pdb=" O LYS A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 135 Processing helix chain 'A' and resid 136 through 138 No H-bonds generated for 'chain 'A' and resid 136 through 138' Processing helix chain 'A' and resid 151 through 163 removed outlier: 3.647A pdb=" N GLU A 158 " --> pdb=" O SER A 154 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ARG A 161 " --> pdb=" O ALA A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 205 Processing helix chain 'A' and resid 224 through 230 removed outlier: 3.516A pdb=" N HIS A 228 " --> pdb=" O ARG A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 343 Processing helix chain 'A' and resid 345 through 347 No H-bonds generated for 'chain 'A' and resid 345 through 347' Processing helix chain 'A' and resid 357 through 359 No H-bonds generated for 'chain 'A' and resid 357 through 359' Processing helix chain 'A' and resid 363 through 365 No H-bonds generated for 'chain 'A' and resid 363 through 365' Processing helix chain 'A' and resid 366 through 380 Processing helix chain 'A' and resid 404 through 415 removed outlier: 3.510A pdb=" N ARG A 408 " --> pdb=" O ARG A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 427 No H-bonds generated for 'chain 'A' and resid 425 through 427' Processing helix chain 'A' and resid 443 through 451 Processing helix chain 'F' and resid 74 through 81 Processing helix chain 'F' and resid 100 through 114 removed outlier: 3.721A pdb=" N GLN F 114 " --> pdb=" O THR F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 138 Processing helix chain 'F' and resid 151 through 161 removed outlier: 3.523A pdb=" N GLU F 160 " --> pdb=" O ARG F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 171 through 175 Processing helix chain 'F' and resid 186 through 205 Processing helix chain 'F' and resid 222 through 231 removed outlier: 4.016A pdb=" N LEU F 226 " --> pdb=" O GLY F 222 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N MET F 229 " --> pdb=" O MET F 225 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASP F 231 " --> pdb=" O GLU F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 341 Processing helix chain 'F' and resid 345 through 347 No H-bonds generated for 'chain 'F' and resid 345 through 347' Processing helix chain 'F' and resid 357 through 359 No H-bonds generated for 'chain 'F' and resid 357 through 359' Processing helix chain 'F' and resid 363 through 365 No H-bonds generated for 'chain 'F' and resid 363 through 365' Processing helix chain 'F' and resid 366 through 380 Processing helix chain 'F' and resid 404 through 415 Processing helix chain 'F' and resid 443 through 452 Processing helix chain 'E' and resid 74 through 79 Processing helix chain 'E' and resid 100 through 113 Processing helix chain 'E' and resid 126 through 138 Processing helix chain 'E' and resid 139 through 143 removed outlier: 4.427A pdb=" N SER E 142 " --> pdb=" O ASP E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 151 through 163 Processing helix chain 'E' and resid 186 through 205 Processing helix chain 'E' and resid 224 through 230 removed outlier: 3.731A pdb=" N HIS E 228 " --> pdb=" O ARG E 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 342 Processing helix chain 'E' and resid 357 through 359 No H-bonds generated for 'chain 'E' and resid 357 through 359' Processing helix chain 'E' and resid 363 through 365 No H-bonds generated for 'chain 'E' and resid 363 through 365' Processing helix chain 'E' and resid 366 through 380 Processing helix chain 'E' and resid 404 through 415 Processing helix chain 'E' and resid 425 through 428 Processing helix chain 'E' and resid 443 through 452 Processing sheet with id=AA1, first strand: chain 'D' and resid 58 through 59 removed outlier: 6.576A pdb=" N LEU E 119 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL E 91 " --> pdb=" O ILE E 210 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU E 90 " --> pdb=" O THR E 232 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N LEU E 234 " --> pdb=" O LEU E 90 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LEU E 92 " --> pdb=" O LEU E 234 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N PHE E 236 " --> pdb=" O LEU E 92 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLY E 94 " --> pdb=" O PHE E 236 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N GLY E 238 " --> pdb=" O GLY E 94 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL E 233 " --> pdb=" O VAL E 250 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 269 through 272 removed outlier: 6.760A pdb=" N VAL D 233 " --> pdb=" O VAL D 250 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LEU D 90 " --> pdb=" O THR D 232 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N LEU D 234 " --> pdb=" O LEU D 90 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N LEU D 92 " --> pdb=" O LEU D 234 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N PHE D 236 " --> pdb=" O LEU D 92 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLY D 94 " --> pdb=" O PHE D 236 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLY D 95 " --> pdb=" O GLY D 212 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU D 167 " --> pdb=" O PHE D 209 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N VAL D 211 " --> pdb=" O LEU D 167 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ILE D 169 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP D 170 " --> pdb=" O VAL D 121 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 349 through 355 removed outlier: 9.969A pdb=" N SER D 291 " --> pdb=" O GLU D 387 " (cutoff:3.500A) removed outlier: 9.191A pdb=" N PHE D 389 " --> pdb=" O SER D 291 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ILE D 293 " --> pdb=" O PHE D 389 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ILE D 420 " --> pdb=" O ILE D 439 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N VAL D 441 " --> pdb=" O ILE D 420 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N VAL D 422 " --> pdb=" O VAL D 441 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 392 through 393 removed outlier: 3.579A pdb=" N GLU D 392 " --> pdb=" O ARG D 400 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 144 through 148 removed outlier: 6.194A pdb=" N VAL C 118 " --> pdb=" O TYR C 145 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N TYR C 147 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N TYR C 120 " --> pdb=" O TYR C 147 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU C 119 " --> pdb=" O ILE C 168 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL C 91 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N GLY C 212 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE C 93 " --> pdb=" O GLY C 212 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU C 90 " --> pdb=" O THR C 232 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N LEU C 234 " --> pdb=" O LEU C 90 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LEU C 92 " --> pdb=" O LEU C 234 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N PHE C 236 " --> pdb=" O LEU C 92 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLY C 94 " --> pdb=" O PHE C 236 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL C 233 " --> pdb=" O VAL C 250 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 291 through 298 removed outlier: 6.666A pdb=" N THR C 322 " --> pdb=" O LEU C 353 " (cutoff:3.500A) removed outlier: 8.734A pdb=" N SER C 355 " --> pdb=" O THR C 322 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N THR C 324 " --> pdb=" O SER C 355 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 387 through 389 removed outlier: 6.743A pdb=" N CYS C 388 " --> pdb=" O TYR C 421 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE C 420 " --> pdb=" O ILE C 439 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N VAL C 441 " --> pdb=" O ILE C 420 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N VAL C 422 " --> pdb=" O VAL C 441 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 392 through 393 Processing sheet with id=AA9, first strand: chain 'B' and resid 144 through 147 removed outlier: 6.359A pdb=" N VAL B 118 " --> pdb=" O TYR B 145 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N TYR B 147 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N TYR B 120 " --> pdb=" O TYR B 147 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU B 167 " --> pdb=" O PHE B 209 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N VAL B 211 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU B 90 " --> pdb=" O THR B 232 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N LEU B 234 " --> pdb=" O LEU B 90 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU B 92 " --> pdb=" O LEU B 234 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N PHE B 236 " --> pdb=" O LEU B 92 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLY B 94 " --> pdb=" O PHE B 236 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N GLY B 238 " --> pdb=" O GLY B 94 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL B 233 " --> pdb=" O VAL B 250 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 323 through 324 removed outlier: 9.595A pdb=" N SER B 291 " --> pdb=" O GLU B 387 " (cutoff:3.500A) removed outlier: 9.077A pdb=" N PHE B 389 " --> pdb=" O SER B 291 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE B 293 " --> pdb=" O PHE B 389 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE B 420 " --> pdb=" O ILE B 439 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N VAL B 441 " --> pdb=" O ILE B 420 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N VAL B 422 " --> pdb=" O VAL B 441 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 392 through 393 Processing sheet with id=AB3, first strand: chain 'A' and resid 144 through 147 removed outlier: 6.610A pdb=" N LEU A 167 " --> pdb=" O PHE A 209 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N VAL A 211 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ILE A 169 " --> pdb=" O VAL A 211 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU A 90 " --> pdb=" O THR A 232 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N LEU A 234 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU A 92 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N PHE A 236 " --> pdb=" O LEU A 92 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N GLY A 94 " --> pdb=" O PHE A 236 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL A 233 " --> pdb=" O VAL A 250 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 291 through 298 Processing sheet with id=AB5, first strand: chain 'A' and resid 387 through 389 removed outlier: 6.758A pdb=" N CYS A 388 " --> pdb=" O TYR A 421 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE A 420 " --> pdb=" O ILE A 439 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N VAL A 441 " --> pdb=" O ILE A 420 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N VAL A 422 " --> pdb=" O VAL A 441 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 392 through 393 removed outlier: 3.711A pdb=" N GLU A 392 " --> pdb=" O ARG A 400 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 144 through 148 removed outlier: 6.525A pdb=" N VAL F 118 " --> pdb=" O TYR F 145 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N TYR F 147 " --> pdb=" O VAL F 118 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N TYR F 120 " --> pdb=" O TYR F 147 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU F 167 " --> pdb=" O PHE F 209 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N VAL F 211 " --> pdb=" O LEU F 167 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ILE F 169 " --> pdb=" O VAL F 211 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N VAL F 91 " --> pdb=" O ILE F 210 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N GLY F 212 " --> pdb=" O VAL F 91 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ILE F 93 " --> pdb=" O GLY F 212 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LEU F 90 " --> pdb=" O THR F 232 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N LEU F 234 " --> pdb=" O LEU F 90 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEU F 92 " --> pdb=" O LEU F 234 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N PHE F 236 " --> pdb=" O LEU F 92 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLY F 94 " --> pdb=" O PHE F 236 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL F 233 " --> pdb=" O VAL F 250 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU F 259 " --> pdb=" O ALA F 249 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 323 through 324 removed outlier: 3.710A pdb=" N ARG F 301 " --> pdb=" O GLU F 298 " (cutoff:3.500A) removed outlier: 9.549A pdb=" N SER F 291 " --> pdb=" O GLU F 387 " (cutoff:3.500A) removed outlier: 9.037A pdb=" N PHE F 389 " --> pdb=" O SER F 291 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE F 293 " --> pdb=" O PHE F 389 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N CYS F 388 " --> pdb=" O TYR F 421 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 392 through 393 removed outlier: 3.877A pdb=" N GLU F 392 " --> pdb=" O ARG F 400 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 323 through 324 removed outlier: 9.641A pdb=" N SER E 291 " --> pdb=" O GLU E 387 " (cutoff:3.500A) removed outlier: 9.064A pdb=" N PHE E 389 " --> pdb=" O SER E 291 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ILE E 293 " --> pdb=" O PHE E 389 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N CYS E 388 " --> pdb=" O TYR E 421 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 392 through 393 removed outlier: 3.577A pdb=" N GLU E 392 " --> pdb=" O ARG E 400 " (cutoff:3.500A) 744 hydrogen bonds defined for protein. 2145 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 14 hydrogen bonds 28 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 32 stacking parallelities Total time for adding SS restraints: 3.61 Time building geometry restraints manager: 2.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 6416 1.36 - 1.50: 4681 1.50 - 1.64: 8268 1.64 - 1.78: 52 1.78 - 1.93: 123 Bond restraints: 19540 Sorted by residual: bond pdb=" C3' AGS E 501 " pdb=" C4' AGS E 501 " ideal model delta sigma weight residual 1.526 1.312 0.214 1.10e-02 8.26e+03 3.78e+02 bond pdb=" C3' AGS D 501 " pdb=" C4' AGS D 501 " ideal model delta sigma weight residual 1.526 1.314 0.212 1.10e-02 8.26e+03 3.72e+02 bond pdb=" C3' AGS F 501 " pdb=" C4' AGS F 501 " ideal model delta sigma weight residual 1.526 1.319 0.207 1.10e-02 8.26e+03 3.55e+02 bond pdb=" C3' AGS B 502 " pdb=" C4' AGS B 502 " ideal model delta sigma weight residual 1.526 1.319 0.207 1.10e-02 8.26e+03 3.55e+02 bond pdb=" C3' AGS C 501 " pdb=" C4' AGS C 501 " ideal model delta sigma weight residual 1.526 1.321 0.205 1.10e-02 8.26e+03 3.46e+02 ... (remaining 19535 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.41: 26431 3.41 - 6.83: 157 6.83 - 10.24: 28 10.24 - 13.66: 10 13.66 - 17.07: 10 Bond angle restraints: 26636 Sorted by residual: angle pdb=" C5 AGS E 501 " pdb=" C6 AGS E 501 " pdb=" N6 AGS E 501 " ideal model delta sigma weight residual 123.61 138.45 -14.84 1.03e+00 9.46e-01 2.09e+02 angle pdb=" C5 AGS D 501 " pdb=" C6 AGS D 501 " pdb=" N6 AGS D 501 " ideal model delta sigma weight residual 123.61 138.35 -14.74 1.03e+00 9.46e-01 2.05e+02 angle pdb=" N1 AGS E 501 " pdb=" C6 AGS E 501 " pdb=" N6 AGS E 501 " ideal model delta sigma weight residual 118.30 101.23 17.07 1.19e+00 7.01e-01 2.04e+02 angle pdb=" C5 AGS C 501 " pdb=" C6 AGS C 501 " pdb=" N6 AGS C 501 " ideal model delta sigma weight residual 123.61 138.27 -14.66 1.03e+00 9.46e-01 2.03e+02 angle pdb=" C5 AGS B 502 " pdb=" C6 AGS B 502 " pdb=" N6 AGS B 502 " ideal model delta sigma weight residual 123.61 138.19 -14.58 1.03e+00 9.46e-01 2.01e+02 ... (remaining 26631 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.47: 11296 35.47 - 70.93: 518 70.93 - 106.40: 52 106.40 - 141.87: 2 141.87 - 177.33: 3 Dihedral angle restraints: 11871 sinusoidal: 5127 harmonic: 6744 Sorted by residual: dihedral pdb=" CA ILE D 180 " pdb=" C ILE D 180 " pdb=" N SER D 181 " pdb=" CA SER D 181 " ideal model delta harmonic sigma weight residual 180.00 152.65 27.35 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA PHE F 280 " pdb=" C PHE F 280 " pdb=" N LEU F 281 " pdb=" CA LEU F 281 " ideal model delta harmonic sigma weight residual -180.00 -152.84 -27.16 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA PHE A 280 " pdb=" C PHE A 280 " pdb=" N LEU A 281 " pdb=" CA LEU A 281 " ideal model delta harmonic sigma weight residual 180.00 152.86 27.14 0 5.00e+00 4.00e-02 2.95e+01 ... (remaining 11868 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2359 0.048 - 0.097: 632 0.097 - 0.145: 185 0.145 - 0.194: 14 0.194 - 0.242: 5 Chirality restraints: 3195 Sorted by residual: chirality pdb=" CB ILE B 168 " pdb=" CA ILE B 168 " pdb=" CG1 ILE B 168 " pdb=" CG2 ILE B 168 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA LEU D 415 " pdb=" N LEU D 415 " pdb=" C LEU D 415 " pdb=" CB LEU D 415 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CB ILE B 180 " pdb=" CA ILE B 180 " pdb=" CG1 ILE B 180 " pdb=" CG2 ILE B 180 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 3192 not shown) Planarity restraints: 3264 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 191 " -0.020 2.00e-02 2.50e+03 3.92e-02 1.54e+01 pdb=" C ARG B 191 " 0.068 2.00e-02 2.50e+03 pdb=" O ARG B 191 " -0.025 2.00e-02 2.50e+03 pdb=" N GLU B 192 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 96 " -0.047 5.00e-02 4.00e+02 7.17e-02 8.23e+00 pdb=" N PRO A 97 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 97 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 97 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 380 " 0.012 2.00e-02 2.50e+03 2.45e-02 6.01e+00 pdb=" C ASP C 380 " -0.042 2.00e-02 2.50e+03 pdb=" O ASP C 380 " 0.016 2.00e-02 2.50e+03 pdb=" N LYS C 381 " 0.014 2.00e-02 2.50e+03 ... (remaining 3261 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 121 2.50 - 3.10: 14050 3.10 - 3.70: 28688 3.70 - 4.30: 42995 4.30 - 4.90: 70689 Nonbonded interactions: 156543 Sorted by model distance: nonbonded pdb=" OG SER E 102 " pdb="MG MG E 502 " model vdw 1.903 2.170 nonbonded pdb=" OG SER D 102 " pdb="MG MG D 502 " model vdw 1.917 2.170 nonbonded pdb=" O2G AGS D 501 " pdb="MG MG D 502 " model vdw 1.972 2.170 nonbonded pdb=" OG SER F 102 " pdb="MG MG F 502 " model vdw 1.978 2.170 nonbonded pdb=" O3G AGS D 501 " pdb="MG MG D 502 " model vdw 1.987 2.170 ... (remaining 156538 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 66 through 452) selection = (chain 'B' and resid 66 through 452) selection = (chain 'C' and resid 66 through 452) selection = (chain 'D' and resid 66 through 452) selection = (chain 'E' and resid 66 through 452) selection = (chain 'F' and resid 66 through 452) } 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: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.580 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2407 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 : 0.008 0.214 19540 Z= 0.582 Angle : 0.862 17.073 26636 Z= 0.601 Chirality : 0.047 0.242 3195 Planarity : 0.005 0.072 3264 Dihedral : 19.205 177.331 7539 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.51 % Allowed : 4.74 % Favored : 94.75 % Rotamer: Outliers : 0.30 % Allowed : 17.07 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.13 (0.16), residues: 2364 helix: -1.03 (0.16), residues: 721 sheet: 0.19 (0.21), residues: 599 loop : -0.98 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 161 TYR 0.024 0.002 TYR C 147 PHE 0.025 0.002 PHE B 244 HIS 0.003 0.001 HIS A 228 Details of bonding type rmsd covalent geometry : bond 0.00807 (19540) covalent geometry : angle 0.86240 (26636) hydrogen bonds : bond 0.15680 ( 758) hydrogen bonds : angle 7.39318 ( 2173) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 358 time to evaluate : 0.754 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: A 239 GLU cc_start: 0.5649 (tt0) cc_final: 0.5431 (tt0) REVERT: F 96 ASP cc_start: 0.4655 (m-30) cc_final: 0.4432 (m-30) REVERT: F 225 MET cc_start: 0.5346 (pmm) cc_final: 0.5130 (pmm) REVERT: F 315 MET cc_start: 0.3607 (mtm) cc_final: 0.3088 (mmm) outliers start: 6 outliers final: 3 residues processed: 363 average time/residue: 0.1499 time to fit residues: 83.8997 Evaluate side-chains 245 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 242 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ASN Chi-restraints excluded: chain F residue 300 THR Chi-restraints excluded: chain F residue 350 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 235 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 403 ASN ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** 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 = 0.3404 r_free = 0.3404 target = 0.082811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.060553 restraints weight = 48057.253| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 3.94 r_work: 0.2752 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 19540 Z= 0.317 Angle : 0.738 10.174 26636 Z= 0.390 Chirality : 0.047 0.238 3195 Planarity : 0.005 0.050 3264 Dihedral : 17.235 169.425 3137 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.34 % Favored : 96.49 % Rotamer: Outliers : 4.08 % Allowed : 18.82 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.17), residues: 2364 helix: 0.75 (0.19), residues: 734 sheet: 0.20 (0.20), residues: 621 loop : -0.55 (0.20), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 156 TYR 0.018 0.002 TYR A 120 PHE 0.020 0.002 PHE D 236 HIS 0.012 0.002 HIS F 228 Details of bonding type rmsd covalent geometry : bond 0.00720 (19540) covalent geometry : angle 0.73787 (26636) hydrogen bonds : bond 0.05102 ( 758) hydrogen bonds : angle 5.62895 ( 2173) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 247 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 57 MET cc_start: 0.7990 (tpt) cc_final: 0.7740 (tpt) REVERT: D 232 THR cc_start: 0.9487 (OUTLIER) cc_final: 0.8926 (p) REVERT: D 279 VAL cc_start: 0.8987 (t) cc_final: 0.8759 (p) REVERT: C 143 GLU cc_start: 0.7945 (tp30) cc_final: 0.7191 (tm-30) REVERT: C 192 GLU cc_start: 0.8976 (tp30) cc_final: 0.8769 (tp30) REVERT: C 217 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8411 (mm-30) REVERT: C 298 GLU cc_start: 0.8902 (tt0) cc_final: 0.8682 (tm-30) REVERT: C 403 ASN cc_start: 0.9119 (OUTLIER) cc_final: 0.8585 (p0) REVERT: B 398 GLU cc_start: 0.8812 (pt0) cc_final: 0.8453 (pm20) REVERT: B 432 LEU cc_start: 0.9007 (mp) cc_final: 0.8634 (tt) REVERT: F 176 MET cc_start: 0.9351 (ptt) cc_final: 0.8763 (ppp) REVERT: F 192 GLU cc_start: 0.9223 (mp0) cc_final: 0.8876 (tm-30) REVERT: F 297 MET cc_start: 0.9116 (mmt) cc_final: 0.8737 (mmt) REVERT: E 106 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.9131 (tp) REVERT: E 225 MET cc_start: 0.8481 (tpp) cc_final: 0.8203 (tpp) REVERT: E 231 ASP cc_start: 0.8405 (t0) cc_final: 0.8147 (t0) REVERT: E 272 GLU cc_start: 0.9134 (pt0) cc_final: 0.8507 (mt-10) REVERT: E 398 GLU cc_start: 0.8392 (pt0) cc_final: 0.8099 (pm20) outliers start: 82 outliers final: 43 residues processed: 312 average time/residue: 0.1311 time to fit residues: 66.3675 Evaluate side-chains 269 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 223 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 316 PHE Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 242 HIS Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 403 ASN Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 280 PHE Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 350 ASP Chi-restraints excluded: chain F residue 384 ASN Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 322 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 93 optimal weight: 5.9990 chunk 71 optimal weight: 8.9990 chunk 74 optimal weight: 6.9990 chunk 177 optimal weight: 20.0000 chunk 215 optimal weight: 4.9990 chunk 220 optimal weight: 4.9990 chunk 229 optimal weight: 1.9990 chunk 225 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 119 optimal weight: 9.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 153 GLN C 241 HIS C 403 ASN ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.084055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.061516 restraints weight = 48016.199| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 4.00 r_work: 0.2779 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 19540 Z= 0.183 Angle : 0.630 9.683 26636 Z= 0.334 Chirality : 0.044 0.203 3195 Planarity : 0.004 0.041 3264 Dihedral : 16.954 174.830 3134 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.85 % Favored : 95.98 % Rotamer: Outliers : 2.94 % Allowed : 19.36 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.18), residues: 2364 helix: 1.27 (0.20), residues: 732 sheet: 0.25 (0.21), residues: 623 loop : -0.23 (0.21), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 404 TYR 0.019 0.001 TYR A 120 PHE 0.013 0.001 PHE A 166 HIS 0.009 0.001 HIS F 228 Details of bonding type rmsd covalent geometry : bond 0.00412 (19540) covalent geometry : angle 0.63029 (26636) hydrogen bonds : bond 0.04212 ( 758) hydrogen bonds : angle 5.14332 ( 2173) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 248 time to evaluate : 0.701 Fit side-chains revert: symmetry clash REVERT: D 176 MET cc_start: 0.8952 (mtp) cc_final: 0.8620 (mtp) REVERT: D 232 THR cc_start: 0.9472 (OUTLIER) cc_final: 0.8972 (p) REVERT: D 242 HIS cc_start: 0.7490 (OUTLIER) cc_final: 0.7158 (m-70) REVERT: C 143 GLU cc_start: 0.7994 (tp30) cc_final: 0.7189 (tm-30) REVERT: C 152 MET cc_start: 0.9360 (mmm) cc_final: 0.8897 (tpp) REVERT: C 153 GLN cc_start: 0.9171 (mm110) cc_final: 0.8829 (mm-40) REVERT: C 192 GLU cc_start: 0.8940 (tp30) cc_final: 0.8666 (tp30) REVERT: C 298 GLU cc_start: 0.8928 (tt0) cc_final: 0.8697 (tm-30) REVERT: B 124 GLU cc_start: 0.8144 (tp30) cc_final: 0.7919 (tp30) REVERT: B 398 GLU cc_start: 0.8873 (pt0) cc_final: 0.8568 (pm20) REVERT: B 432 LEU cc_start: 0.9075 (mp) cc_final: 0.8839 (tt) REVERT: A 129 GLN cc_start: 0.8841 (tp-100) cc_final: 0.8612 (tp-100) REVERT: A 219 THR cc_start: 0.8052 (m) cc_final: 0.7780 (p) REVERT: F 170 ASP cc_start: 0.8397 (p0) cc_final: 0.8195 (p0) REVERT: F 176 MET cc_start: 0.9257 (OUTLIER) cc_final: 0.8671 (ppp) REVERT: F 192 GLU cc_start: 0.9194 (mp0) cc_final: 0.8941 (tm-30) REVERT: F 242 HIS cc_start: 0.7724 (m90) cc_final: 0.7169 (m170) REVERT: F 297 MET cc_start: 0.9073 (mmt) cc_final: 0.8640 (mmt) REVERT: F 327 ASP cc_start: 0.9158 (t0) cc_final: 0.8912 (t0) REVERT: E 231 ASP cc_start: 0.8427 (t0) cc_final: 0.8182 (t0) REVERT: E 398 GLU cc_start: 0.8363 (pt0) cc_final: 0.8154 (pm20) outliers start: 59 outliers final: 33 residues processed: 288 average time/residue: 0.1259 time to fit residues: 59.8269 Evaluate side-chains 251 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 215 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 242 HIS Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 176 MET Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 229 MET Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 280 PHE Chi-restraints excluded: chain F residue 300 THR Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 350 ASP Chi-restraints excluded: chain F residue 384 ASN Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 277 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 199 optimal weight: 9.9990 chunk 43 optimal weight: 0.9980 chunk 222 optimal weight: 9.9990 chunk 32 optimal weight: 6.9990 chunk 39 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 chunk 180 optimal weight: 3.9990 chunk 178 optimal weight: 5.9990 chunk 224 optimal weight: 5.9990 chunk 101 optimal weight: 9.9990 chunk 195 optimal weight: 10.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 GLN ** A 213 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 = 0.3409 r_free = 0.3409 target = 0.082907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.060519 restraints weight = 47909.525| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 3.98 r_work: 0.2752 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 19540 Z= 0.240 Angle : 0.639 10.550 26636 Z= 0.335 Chirality : 0.044 0.205 3195 Planarity : 0.004 0.040 3264 Dihedral : 16.857 175.426 3134 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.19 % Favored : 95.64 % Rotamer: Outliers : 4.03 % Allowed : 19.71 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.18), residues: 2364 helix: 1.38 (0.20), residues: 733 sheet: 0.19 (0.21), residues: 626 loop : -0.27 (0.21), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 224 TYR 0.017 0.001 TYR A 120 PHE 0.013 0.001 PHE C 280 HIS 0.021 0.002 HIS C 242 Details of bonding type rmsd covalent geometry : bond 0.00546 (19540) covalent geometry : angle 0.63882 (26636) hydrogen bonds : bond 0.04192 ( 758) hydrogen bonds : angle 5.00670 ( 2173) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 220 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 176 MET cc_start: 0.8927 (mtp) cc_final: 0.8712 (mtp) REVERT: D 232 THR cc_start: 0.9502 (OUTLIER) cc_final: 0.9029 (p) REVERT: D 348 ASN cc_start: 0.9068 (t0) cc_final: 0.8857 (t0) REVERT: C 143 GLU cc_start: 0.7940 (tp30) cc_final: 0.7353 (tm-30) REVERT: C 152 MET cc_start: 0.9346 (mmm) cc_final: 0.9027 (tpt) REVERT: C 153 GLN cc_start: 0.9224 (mm110) cc_final: 0.8884 (mm-40) REVERT: C 192 GLU cc_start: 0.8953 (tp30) cc_final: 0.8645 (tp30) REVERT: C 298 GLU cc_start: 0.9020 (tt0) cc_final: 0.8789 (tm-30) REVERT: B 398 GLU cc_start: 0.8933 (pt0) cc_final: 0.8651 (pm20) REVERT: B 432 LEU cc_start: 0.9100 (mp) cc_final: 0.8832 (tt) REVERT: A 124 GLU cc_start: 0.8606 (tt0) cc_final: 0.8177 (pt0) REVERT: A 129 GLN cc_start: 0.8867 (tp-100) cc_final: 0.8636 (tp-100) REVERT: A 198 MET cc_start: 0.9162 (ttm) cc_final: 0.8772 (mtp) REVERT: A 219 THR cc_start: 0.8109 (m) cc_final: 0.7840 (p) REVERT: A 367 ASP cc_start: 0.9234 (m-30) cc_final: 0.8891 (m-30) REVERT: F 165 ASP cc_start: 0.8950 (m-30) cc_final: 0.8666 (t0) REVERT: F 176 MET cc_start: 0.9236 (ptt) cc_final: 0.8781 (ppp) REVERT: F 177 SER cc_start: 0.7054 (OUTLIER) cc_final: 0.6092 (t) REVERT: F 189 GLN cc_start: 0.7069 (OUTLIER) cc_final: 0.6162 (tp-100) REVERT: F 192 GLU cc_start: 0.9192 (mp0) cc_final: 0.8916 (tm-30) REVERT: F 225 MET cc_start: 0.6992 (pmm) cc_final: 0.6222 (pmm) REVERT: F 297 MET cc_start: 0.9057 (mmt) cc_final: 0.8641 (mmt) REVERT: F 415 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.9016 (mm) REVERT: E 106 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9155 (tp) REVERT: E 231 ASP cc_start: 0.8439 (t0) cc_final: 0.8179 (t0) REVERT: E 236 PHE cc_start: 0.9464 (OUTLIER) cc_final: 0.8302 (t80) outliers start: 81 outliers final: 45 residues processed: 286 average time/residue: 0.1227 time to fit residues: 58.4430 Evaluate side-chains 263 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 212 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 177 SER Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 229 MET Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 280 PHE Chi-restraints excluded: chain F residue 300 THR Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain F residue 350 ASP Chi-restraints excluded: chain F residue 384 ASN Chi-restraints excluded: chain F residue 415 LEU Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 236 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 69 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 174 optimal weight: 7.9990 chunk 146 optimal weight: 3.9990 chunk 99 optimal weight: 0.0570 chunk 7 optimal weight: 6.9990 chunk 215 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 235 optimal weight: 8.9990 chunk 210 optimal weight: 7.9990 overall best weight: 0.9300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 241 HIS C 242 HIS B 403 ASN A 213 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.085335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.063140 restraints weight = 47194.882| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 3.98 r_work: 0.2818 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19540 Z= 0.117 Angle : 0.593 10.325 26636 Z= 0.309 Chirality : 0.043 0.199 3195 Planarity : 0.004 0.042 3264 Dihedral : 16.514 178.136 3134 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.51 % Favored : 96.32 % Rotamer: Outliers : 2.89 % Allowed : 20.51 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.18), residues: 2364 helix: 1.52 (0.20), residues: 739 sheet: 0.29 (0.21), residues: 620 loop : -0.20 (0.21), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 284 TYR 0.017 0.001 TYR A 120 PHE 0.009 0.001 PHE D 316 HIS 0.007 0.001 HIS F 228 Details of bonding type rmsd covalent geometry : bond 0.00254 (19540) covalent geometry : angle 0.59283 (26636) hydrogen bonds : bond 0.03469 ( 758) hydrogen bonds : angle 4.70235 ( 2173) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 251 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 348 ASN cc_start: 0.9037 (t0) cc_final: 0.8814 (t0) REVERT: C 139 ASP cc_start: 0.3834 (t0) cc_final: 0.3297 (t70) REVERT: C 143 GLU cc_start: 0.8019 (tp30) cc_final: 0.7462 (tm-30) REVERT: C 152 MET cc_start: 0.9413 (mmm) cc_final: 0.9078 (tpt) REVERT: C 153 GLN cc_start: 0.9236 (mm110) cc_final: 0.8938 (mm-40) REVERT: C 176 MET cc_start: 0.8925 (mtp) cc_final: 0.8333 (mmm) REVERT: C 192 GLU cc_start: 0.8946 (tp30) cc_final: 0.8599 (tp30) REVERT: C 298 GLU cc_start: 0.9003 (tt0) cc_final: 0.8764 (tm-30) REVERT: C 327 ASP cc_start: 0.8313 (t0) cc_final: 0.8088 (t0) REVERT: B 432 LEU cc_start: 0.9106 (mp) cc_final: 0.8839 (tt) REVERT: A 124 GLU cc_start: 0.8572 (tt0) cc_final: 0.8130 (pt0) REVERT: A 129 GLN cc_start: 0.8882 (tp-100) cc_final: 0.8634 (tp-100) REVERT: A 198 MET cc_start: 0.9070 (ttm) cc_final: 0.8697 (mtp) REVERT: A 219 THR cc_start: 0.8073 (m) cc_final: 0.7829 (p) REVERT: A 231 ASP cc_start: 0.8342 (m-30) cc_final: 0.7999 (m-30) REVERT: A 350 ASP cc_start: 0.8702 (m-30) cc_final: 0.8412 (m-30) REVERT: A 367 ASP cc_start: 0.9183 (m-30) cc_final: 0.8978 (m-30) REVERT: F 96 ASP cc_start: 0.9085 (m-30) cc_final: 0.8820 (p0) REVERT: F 165 ASP cc_start: 0.8996 (m-30) cc_final: 0.8686 (t0) REVERT: F 176 MET cc_start: 0.9177 (OUTLIER) cc_final: 0.8760 (ppp) REVERT: F 177 SER cc_start: 0.6836 (OUTLIER) cc_final: 0.5693 (t) REVERT: F 189 GLN cc_start: 0.6920 (OUTLIER) cc_final: 0.6090 (tp-100) REVERT: F 192 GLU cc_start: 0.9192 (mp0) cc_final: 0.8929 (tm-30) REVERT: F 297 MET cc_start: 0.9012 (mmt) cc_final: 0.8681 (mmt) REVERT: F 415 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8972 (mm) REVERT: E 165 ASP cc_start: 0.8479 (m-30) cc_final: 0.7634 (t0) REVERT: E 231 ASP cc_start: 0.8403 (t0) cc_final: 0.8131 (t0) REVERT: E 236 PHE cc_start: 0.9368 (OUTLIER) cc_final: 0.8362 (t80) REVERT: E 272 GLU cc_start: 0.9099 (pt0) cc_final: 0.8628 (mt-10) REVERT: E 297 MET cc_start: 0.9219 (tpp) cc_final: 0.8760 (mmm) outliers start: 58 outliers final: 30 residues processed: 295 average time/residue: 0.1256 time to fit residues: 61.0481 Evaluate side-chains 253 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 218 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 225 MET Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 315 MET Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 176 MET Chi-restraints excluded: chain F residue 177 SER Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 229 MET Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 280 PHE Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 350 ASP Chi-restraints excluded: chain F residue 415 LEU Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 236 PHE Chi-restraints excluded: chain E residue 350 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 65 optimal weight: 0.8980 chunk 181 optimal weight: 20.0000 chunk 13 optimal weight: 10.0000 chunk 202 optimal weight: 9.9990 chunk 168 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 231 optimal weight: 8.9990 chunk 161 optimal weight: 20.0000 chunk 220 optimal weight: 5.9990 chunk 116 optimal weight: 4.9990 chunk 34 optimal weight: 10.0000 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 213 HIS ** D 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 HIS A 213 HIS ** E 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.082453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.059999 restraints weight = 48250.553| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 4.01 r_work: 0.2750 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 19540 Z= 0.254 Angle : 0.637 10.423 26636 Z= 0.332 Chirality : 0.044 0.258 3195 Planarity : 0.004 0.038 3264 Dihedral : 16.580 177.202 3134 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.48 % Favored : 95.39 % Rotamer: Outliers : 3.68 % Allowed : 20.31 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.18), residues: 2364 helix: 1.47 (0.20), residues: 740 sheet: 0.15 (0.21), residues: 630 loop : -0.26 (0.22), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 404 TYR 0.019 0.002 TYR B 147 PHE 0.024 0.002 PHE C 263 HIS 0.005 0.001 HIS F 228 Details of bonding type rmsd covalent geometry : bond 0.00578 (19540) covalent geometry : angle 0.63697 (26636) hydrogen bonds : bond 0.03974 ( 758) hydrogen bonds : angle 4.81592 ( 2173) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 210 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 232 THR cc_start: 0.9498 (OUTLIER) cc_final: 0.9028 (p) REVERT: D 348 ASN cc_start: 0.9087 (t0) cc_final: 0.8767 (t0) REVERT: C 152 MET cc_start: 0.9399 (mmm) cc_final: 0.9068 (tpt) REVERT: C 153 GLN cc_start: 0.9265 (mm110) cc_final: 0.8935 (mm-40) REVERT: C 192 GLU cc_start: 0.9005 (tp30) cc_final: 0.8669 (tp30) REVERT: C 198 MET cc_start: 0.9471 (ttp) cc_final: 0.9266 (ttp) REVERT: C 298 GLU cc_start: 0.9020 (tt0) cc_final: 0.8801 (tm-30) REVERT: B 147 TYR cc_start: 0.8472 (t80) cc_final: 0.8139 (t80) REVERT: B 432 LEU cc_start: 0.9117 (mp) cc_final: 0.8821 (tt) REVERT: A 191 ARG cc_start: 0.8125 (mtm-85) cc_final: 0.7806 (mtm-85) REVERT: A 198 MET cc_start: 0.9141 (ttm) cc_final: 0.8751 (mtp) REVERT: A 219 THR cc_start: 0.8119 (m) cc_final: 0.7891 (p) REVERT: A 225 MET cc_start: 0.8810 (ppp) cc_final: 0.8463 (ppp) REVERT: A 367 ASP cc_start: 0.9251 (m-30) cc_final: 0.8950 (m-30) REVERT: F 96 ASP cc_start: 0.9112 (m-30) cc_final: 0.8839 (p0) REVERT: F 165 ASP cc_start: 0.9046 (m-30) cc_final: 0.8691 (t0) REVERT: F 176 MET cc_start: 0.9217 (OUTLIER) cc_final: 0.8819 (ppp) REVERT: F 177 SER cc_start: 0.6839 (OUTLIER) cc_final: 0.5835 (t) REVERT: F 189 GLN cc_start: 0.7000 (OUTLIER) cc_final: 0.6070 (tp-100) REVERT: F 192 GLU cc_start: 0.9201 (mp0) cc_final: 0.8924 (tm-30) REVERT: F 297 MET cc_start: 0.8991 (mmt) cc_final: 0.8615 (mmt) REVERT: E 165 ASP cc_start: 0.8524 (m-30) cc_final: 0.7696 (t0) REVERT: E 229 MET cc_start: 0.9130 (mtm) cc_final: 0.8891 (mtm) REVERT: E 231 ASP cc_start: 0.8457 (t0) cc_final: 0.8156 (t0) REVERT: E 236 PHE cc_start: 0.9437 (OUTLIER) cc_final: 0.8281 (t80) REVERT: E 272 GLU cc_start: 0.9122 (pt0) cc_final: 0.8596 (mt-10) outliers start: 74 outliers final: 52 residues processed: 268 average time/residue: 0.1278 time to fit residues: 55.8797 Evaluate side-chains 265 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 208 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 316 PHE Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 315 MET Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 176 MET Chi-restraints excluded: chain F residue 177 SER Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 280 PHE Chi-restraints excluded: chain F residue 300 THR Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 350 ASP Chi-restraints excluded: chain F residue 384 ASN Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 236 PHE Chi-restraints excluded: chain E residue 322 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 139 optimal weight: 7.9990 chunk 184 optimal weight: 7.9990 chunk 105 optimal weight: 1.9990 chunk 84 optimal weight: 8.9990 chunk 20 optimal weight: 0.0370 chunk 36 optimal weight: 2.9990 chunk 144 optimal weight: 0.9980 chunk 61 optimal weight: 10.0000 chunk 178 optimal weight: 8.9990 chunk 235 optimal weight: 8.9990 chunk 119 optimal weight: 10.0000 overall best weight: 2.8064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 242 HIS ** F 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 228 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 = 0.3422 r_free = 0.3422 target = 0.083196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.060664 restraints weight = 48263.327| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 4.02 r_work: 0.2769 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19540 Z= 0.161 Angle : 0.599 11.457 26636 Z= 0.310 Chirality : 0.043 0.274 3195 Planarity : 0.003 0.038 3264 Dihedral : 16.405 178.571 3134 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.02 % Favored : 95.90 % Rotamer: Outliers : 2.69 % Allowed : 21.11 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.18), residues: 2364 helix: 1.48 (0.20), residues: 740 sheet: 0.18 (0.21), residues: 629 loop : -0.26 (0.22), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 404 TYR 0.016 0.001 TYR A 120 PHE 0.019 0.001 PHE C 263 HIS 0.016 0.001 HIS F 228 Details of bonding type rmsd covalent geometry : bond 0.00364 (19540) covalent geometry : angle 0.59861 (26636) hydrogen bonds : bond 0.03600 ( 758) hydrogen bonds : angle 4.67700 ( 2173) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 228 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 232 THR cc_start: 0.9474 (OUTLIER) cc_final: 0.9003 (p) REVERT: D 348 ASN cc_start: 0.9107 (t0) cc_final: 0.8820 (t0) REVERT: C 75 GLU cc_start: 0.9206 (OUTLIER) cc_final: 0.8956 (tm-30) REVERT: C 143 GLU cc_start: 0.8119 (tp30) cc_final: 0.7645 (tm-30) REVERT: C 152 MET cc_start: 0.9400 (mmm) cc_final: 0.9042 (tpt) REVERT: C 153 GLN cc_start: 0.9265 (mm110) cc_final: 0.8918 (mm-40) REVERT: C 176 MET cc_start: 0.8945 (mtp) cc_final: 0.8326 (mmm) REVERT: C 192 GLU cc_start: 0.8987 (tp30) cc_final: 0.8629 (tp30) REVERT: C 298 GLU cc_start: 0.8977 (tt0) cc_final: 0.8775 (tm-30) REVERT: C 327 ASP cc_start: 0.8428 (t0) cc_final: 0.8150 (t0) REVERT: B 147 TYR cc_start: 0.8383 (t80) cc_final: 0.8103 (t80) REVERT: B 156 ARG cc_start: 0.9310 (ttm-80) cc_final: 0.9034 (ttm170) REVERT: B 432 LEU cc_start: 0.9116 (mp) cc_final: 0.8803 (tt) REVERT: A 124 GLU cc_start: 0.8654 (tt0) cc_final: 0.8082 (pt0) REVERT: A 170 ASP cc_start: 0.8195 (t0) cc_final: 0.6760 (t0) REVERT: A 191 ARG cc_start: 0.8045 (mtm-85) cc_final: 0.7750 (mtm-85) REVERT: A 198 MET cc_start: 0.9113 (ttm) cc_final: 0.8736 (mtp) REVERT: A 219 THR cc_start: 0.8114 (m) cc_final: 0.7869 (p) REVERT: A 225 MET cc_start: 0.8828 (ppp) cc_final: 0.8439 (ppp) REVERT: A 367 ASP cc_start: 0.9230 (m-30) cc_final: 0.8929 (m-30) REVERT: F 96 ASP cc_start: 0.9086 (m-30) cc_final: 0.8826 (p0) REVERT: F 165 ASP cc_start: 0.9058 (m-30) cc_final: 0.8666 (t0) REVERT: F 174 THR cc_start: 0.9476 (OUTLIER) cc_final: 0.9226 (p) REVERT: F 176 MET cc_start: 0.9211 (OUTLIER) cc_final: 0.8807 (ppp) REVERT: F 177 SER cc_start: 0.6756 (OUTLIER) cc_final: 0.5674 (t) REVERT: F 189 GLN cc_start: 0.6987 (OUTLIER) cc_final: 0.6115 (tp-100) REVERT: F 192 GLU cc_start: 0.9214 (mp0) cc_final: 0.8939 (tm-30) REVERT: F 242 HIS cc_start: 0.7850 (m90) cc_final: 0.7025 (m170) REVERT: F 297 MET cc_start: 0.8959 (mmt) cc_final: 0.8621 (mmt) REVERT: F 298 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7805 (tm-30) REVERT: F 415 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8977 (mm) REVERT: E 165 ASP cc_start: 0.8552 (m-30) cc_final: 0.7712 (t0) REVERT: E 176 MET cc_start: 0.8380 (ptp) cc_final: 0.7732 (mtt) REVERT: E 229 MET cc_start: 0.9123 (mtm) cc_final: 0.8891 (mtm) REVERT: E 231 ASP cc_start: 0.8440 (t0) cc_final: 0.8125 (t0) REVERT: E 236 PHE cc_start: 0.9406 (OUTLIER) cc_final: 0.8285 (t80) REVERT: E 272 GLU cc_start: 0.9097 (pt0) cc_final: 0.8596 (mt-10) REVERT: E 297 MET cc_start: 0.9272 (tpp) cc_final: 0.8864 (mmm) outliers start: 54 outliers final: 40 residues processed: 271 average time/residue: 0.1339 time to fit residues: 58.5721 Evaluate side-chains 264 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 216 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 315 MET Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 176 MET Chi-restraints excluded: chain F residue 177 SER Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 229 MET Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 280 PHE Chi-restraints excluded: chain F residue 300 THR Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 350 ASP Chi-restraints excluded: chain F residue 415 LEU Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 236 PHE Chi-restraints excluded: chain E residue 350 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 98 optimal weight: 8.9990 chunk 22 optimal weight: 8.9990 chunk 45 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 182 optimal weight: 5.9990 chunk 188 optimal weight: 9.9990 chunk 96 optimal weight: 9.9990 chunk 169 optimal weight: 20.0000 chunk 30 optimal weight: 0.0170 chunk 119 optimal weight: 10.0000 chunk 11 optimal weight: 0.0170 overall best weight: 3.6062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 242 HIS ** F 213 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 = 0.3410 r_free = 0.3410 target = 0.082357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.059937 restraints weight = 48347.792| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 4.00 r_work: 0.2755 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 19540 Z= 0.193 Angle : 0.609 11.962 26636 Z= 0.316 Chirality : 0.043 0.269 3195 Planarity : 0.004 0.038 3264 Dihedral : 16.360 178.764 3134 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.23 % Favored : 95.69 % Rotamer: Outliers : 2.94 % Allowed : 20.81 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.18), residues: 2364 helix: 1.48 (0.20), residues: 740 sheet: 0.20 (0.21), residues: 629 loop : -0.32 (0.22), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 224 TYR 0.015 0.001 TYR A 120 PHE 0.021 0.001 PHE C 263 HIS 0.007 0.001 HIS F 228 Details of bonding type rmsd covalent geometry : bond 0.00439 (19540) covalent geometry : angle 0.60933 (26636) hydrogen bonds : bond 0.03699 ( 758) hydrogen bonds : angle 4.69589 ( 2173) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 223 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 232 THR cc_start: 0.9488 (OUTLIER) cc_final: 0.9015 (p) REVERT: D 348 ASN cc_start: 0.9113 (t0) cc_final: 0.8846 (t0) REVERT: C 75 GLU cc_start: 0.9209 (OUTLIER) cc_final: 0.8942 (tm-30) REVERT: C 143 GLU cc_start: 0.8204 (tp30) cc_final: 0.7695 (tm-30) REVERT: C 152 MET cc_start: 0.9398 (mmm) cc_final: 0.9043 (tpt) REVERT: C 153 GLN cc_start: 0.9284 (mm110) cc_final: 0.8929 (mm-40) REVERT: C 176 MET cc_start: 0.8918 (mtp) cc_final: 0.8393 (mmm) REVERT: C 192 GLU cc_start: 0.9001 (tp30) cc_final: 0.8645 (tp30) REVERT: C 327 ASP cc_start: 0.8453 (t0) cc_final: 0.8215 (t0) REVERT: B 147 TYR cc_start: 0.8443 (t80) cc_final: 0.8182 (t80) REVERT: B 432 LEU cc_start: 0.9107 (mp) cc_final: 0.8787 (tt) REVERT: A 124 GLU cc_start: 0.8677 (tt0) cc_final: 0.8076 (pt0) REVERT: A 170 ASP cc_start: 0.8230 (t0) cc_final: 0.6821 (t0) REVERT: A 191 ARG cc_start: 0.8046 (mtm-85) cc_final: 0.7754 (mtm-85) REVERT: A 219 THR cc_start: 0.8123 (m) cc_final: 0.7872 (p) REVERT: A 225 MET cc_start: 0.8825 (ppp) cc_final: 0.8440 (ppp) REVERT: A 367 ASP cc_start: 0.9231 (m-30) cc_final: 0.8927 (m-30) REVERT: F 96 ASP cc_start: 0.9096 (m-30) cc_final: 0.8842 (p0) REVERT: F 165 ASP cc_start: 0.9101 (m-30) cc_final: 0.8699 (t0) REVERT: F 176 MET cc_start: 0.9216 (OUTLIER) cc_final: 0.8818 (ppp) REVERT: F 177 SER cc_start: 0.6803 (OUTLIER) cc_final: 0.5811 (t) REVERT: F 189 GLN cc_start: 0.7015 (OUTLIER) cc_final: 0.6119 (tp-100) REVERT: F 192 GLU cc_start: 0.9202 (mp0) cc_final: 0.8931 (tm-30) REVERT: F 242 HIS cc_start: 0.7865 (m90) cc_final: 0.7069 (m170) REVERT: F 298 GLU cc_start: 0.8040 (tm-30) cc_final: 0.7688 (tm-30) REVERT: F 415 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8952 (mm) REVERT: E 152 MET cc_start: 0.9139 (tpt) cc_final: 0.8781 (tpp) REVERT: E 165 ASP cc_start: 0.8528 (m-30) cc_final: 0.7698 (t0) REVERT: E 176 MET cc_start: 0.8488 (ptp) cc_final: 0.7882 (mtt) REVERT: E 229 MET cc_start: 0.9114 (mtm) cc_final: 0.8884 (mtm) REVERT: E 231 ASP cc_start: 0.8434 (t0) cc_final: 0.8098 (t0) REVERT: E 236 PHE cc_start: 0.9422 (OUTLIER) cc_final: 0.8303 (t80) REVERT: E 272 GLU cc_start: 0.9119 (pt0) cc_final: 0.8634 (mt-10) REVERT: E 297 MET cc_start: 0.9288 (tpp) cc_final: 0.8907 (mmm) outliers start: 59 outliers final: 46 residues processed: 269 average time/residue: 0.1280 time to fit residues: 56.4064 Evaluate side-chains 260 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 207 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 316 PHE Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 315 MET Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 176 MET Chi-restraints excluded: chain F residue 177 SER Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 280 PHE Chi-restraints excluded: chain F residue 300 THR Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 350 ASP Chi-restraints excluded: chain F residue 415 LEU Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 236 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 93 optimal weight: 6.9990 chunk 134 optimal weight: 8.9990 chunk 178 optimal weight: 7.9990 chunk 133 optimal weight: 8.9990 chunk 149 optimal weight: 10.0000 chunk 207 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 192 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 114 optimal weight: 0.7980 overall best weight: 1.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 329 ASN C 242 HIS ** F 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.083987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.061647 restraints weight = 47620.354| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 4.02 r_work: 0.2787 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19540 Z= 0.136 Angle : 0.607 12.575 26636 Z= 0.311 Chirality : 0.043 0.266 3195 Planarity : 0.003 0.038 3264 Dihedral : 16.209 179.937 3134 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.06 % Favored : 95.85 % Rotamer: Outliers : 2.69 % Allowed : 21.40 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.18), residues: 2364 helix: 1.55 (0.20), residues: 740 sheet: 0.27 (0.21), residues: 620 loop : -0.35 (0.22), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 156 TYR 0.022 0.001 TYR E 147 PHE 0.018 0.001 PHE C 263 HIS 0.008 0.001 HIS D 242 Details of bonding type rmsd covalent geometry : bond 0.00309 (19540) covalent geometry : angle 0.60684 (26636) hydrogen bonds : bond 0.03422 ( 758) hydrogen bonds : angle 4.58331 ( 2173) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 229 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 232 THR cc_start: 0.9473 (OUTLIER) cc_final: 0.8995 (p) REVERT: D 348 ASN cc_start: 0.9095 (t0) cc_final: 0.8847 (t0) REVERT: C 75 GLU cc_start: 0.9174 (OUTLIER) cc_final: 0.8955 (tm-30) REVERT: C 143 GLU cc_start: 0.8171 (tp30) cc_final: 0.7723 (tm-30) REVERT: C 152 MET cc_start: 0.9395 (mmm) cc_final: 0.9031 (tpt) REVERT: C 153 GLN cc_start: 0.9282 (mm110) cc_final: 0.8934 (mm-40) REVERT: C 192 GLU cc_start: 0.9024 (tp30) cc_final: 0.8654 (tp30) REVERT: C 298 GLU cc_start: 0.8726 (tm-30) cc_final: 0.8155 (tm-30) REVERT: C 327 ASP cc_start: 0.8400 (t0) cc_final: 0.8147 (t0) REVERT: B 147 TYR cc_start: 0.8449 (t80) cc_final: 0.8221 (t80) REVERT: B 432 LEU cc_start: 0.9104 (mp) cc_final: 0.8775 (tt) REVERT: A 191 ARG cc_start: 0.8005 (mtm-85) cc_final: 0.7586 (mtm-85) REVERT: A 198 MET cc_start: 0.9138 (ttm) cc_final: 0.8703 (mtp) REVERT: A 219 THR cc_start: 0.8161 (m) cc_final: 0.7929 (p) REVERT: A 225 MET cc_start: 0.8806 (ppp) cc_final: 0.8395 (ppp) REVERT: A 231 ASP cc_start: 0.8410 (m-30) cc_final: 0.8060 (m-30) REVERT: A 367 ASP cc_start: 0.9202 (m-30) cc_final: 0.8910 (m-30) REVERT: F 165 ASP cc_start: 0.9129 (m-30) cc_final: 0.8742 (t0) REVERT: F 176 MET cc_start: 0.9204 (OUTLIER) cc_final: 0.8826 (ppp) REVERT: F 177 SER cc_start: 0.6765 (OUTLIER) cc_final: 0.5700 (t) REVERT: F 189 GLN cc_start: 0.7000 (OUTLIER) cc_final: 0.6162 (tp-100) REVERT: F 192 GLU cc_start: 0.9183 (mp0) cc_final: 0.8938 (tm-30) REVERT: F 297 MET cc_start: 0.8992 (mmt) cc_final: 0.8572 (mmt) REVERT: F 298 GLU cc_start: 0.8055 (tm-30) cc_final: 0.7699 (tm-30) REVERT: F 327 ASP cc_start: 0.9176 (t0) cc_final: 0.8904 (t0) REVERT: F 415 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8971 (mm) REVERT: E 152 MET cc_start: 0.9118 (tpt) cc_final: 0.8749 (tpp) REVERT: E 165 ASP cc_start: 0.8512 (m-30) cc_final: 0.7691 (t0) REVERT: E 176 MET cc_start: 0.8463 (ptp) cc_final: 0.7956 (mtt) REVERT: E 229 MET cc_start: 0.9132 (mtm) cc_final: 0.8905 (mtm) REVERT: E 231 ASP cc_start: 0.8427 (t0) cc_final: 0.8094 (t0) REVERT: E 236 PHE cc_start: 0.9375 (OUTLIER) cc_final: 0.8264 (t80) REVERT: E 272 GLU cc_start: 0.9114 (pt0) cc_final: 0.8641 (mt-10) outliers start: 54 outliers final: 42 residues processed: 271 average time/residue: 0.1203 time to fit residues: 53.7289 Evaluate side-chains 255 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 206 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 315 MET Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 176 MET Chi-restraints excluded: chain F residue 177 SER Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 280 PHE Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 350 ASP Chi-restraints excluded: chain F residue 415 LEU Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 236 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 118 optimal weight: 2.9990 chunk 115 optimal weight: 9.9990 chunk 192 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 chunk 132 optimal weight: 10.0000 chunk 225 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 15 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 HIS ** F 213 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 = 0.3441 r_free = 0.3441 target = 0.084233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.061793 restraints weight = 47789.285| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 4.04 r_work: 0.2796 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19540 Z= 0.134 Angle : 0.620 13.076 26636 Z= 0.316 Chirality : 0.043 0.262 3195 Planarity : 0.003 0.040 3264 Dihedral : 16.140 179.563 3134 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.10 % Favored : 95.81 % Rotamer: Outliers : 2.64 % Allowed : 21.85 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.18), residues: 2364 helix: 1.59 (0.20), residues: 740 sheet: 0.31 (0.22), residues: 611 loop : -0.41 (0.21), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 404 TYR 0.018 0.001 TYR E 147 PHE 0.022 0.001 PHE C 280 HIS 0.006 0.001 HIS F 228 Details of bonding type rmsd covalent geometry : bond 0.00306 (19540) covalent geometry : angle 0.61970 (26636) hydrogen bonds : bond 0.03385 ( 758) hydrogen bonds : angle 4.55917 ( 2173) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 228 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 217 GLU cc_start: 0.9384 (tt0) cc_final: 0.9052 (tp30) REVERT: D 348 ASN cc_start: 0.9087 (t0) cc_final: 0.8838 (t0) REVERT: C 74 MET cc_start: 0.9304 (mtp) cc_final: 0.9030 (mtp) REVERT: C 75 GLU cc_start: 0.9156 (OUTLIER) cc_final: 0.8953 (tm-30) REVERT: C 143 GLU cc_start: 0.8122 (tp30) cc_final: 0.7751 (tm-30) REVERT: C 152 MET cc_start: 0.9359 (mmm) cc_final: 0.8991 (tpt) REVERT: C 153 GLN cc_start: 0.9273 (mm110) cc_final: 0.8929 (mm-40) REVERT: C 192 GLU cc_start: 0.9013 (tp30) cc_final: 0.8655 (tp30) REVERT: C 298 GLU cc_start: 0.8722 (tm-30) cc_final: 0.8117 (tm-30) REVERT: C 327 ASP cc_start: 0.8412 (t0) cc_final: 0.8156 (t0) REVERT: B 147 TYR cc_start: 0.8450 (t80) cc_final: 0.8186 (t80) REVERT: B 196 GLU cc_start: 0.8904 (mt-10) cc_final: 0.8471 (tt0) REVERT: B 432 LEU cc_start: 0.9091 (mp) cc_final: 0.8774 (tt) REVERT: A 124 GLU cc_start: 0.8699 (tt0) cc_final: 0.8167 (pt0) REVERT: A 170 ASP cc_start: 0.8313 (t0) cc_final: 0.6994 (t0) REVERT: A 191 ARG cc_start: 0.8029 (mtm-85) cc_final: 0.7599 (mtm-85) REVERT: A 198 MET cc_start: 0.9062 (ttm) cc_final: 0.8688 (mtp) REVERT: A 219 THR cc_start: 0.8245 (m) cc_final: 0.8003 (p) REVERT: A 225 MET cc_start: 0.8806 (ppp) cc_final: 0.8400 (ppp) REVERT: A 231 ASP cc_start: 0.8404 (m-30) cc_final: 0.8047 (m-30) REVERT: A 350 ASP cc_start: 0.8619 (m-30) cc_final: 0.8246 (m-30) REVERT: A 367 ASP cc_start: 0.9172 (m-30) cc_final: 0.8899 (m-30) REVERT: F 165 ASP cc_start: 0.9127 (m-30) cc_final: 0.8742 (t0) REVERT: F 176 MET cc_start: 0.9170 (OUTLIER) cc_final: 0.8823 (ppp) REVERT: F 177 SER cc_start: 0.6732 (OUTLIER) cc_final: 0.5636 (t) REVERT: F 189 GLN cc_start: 0.6983 (OUTLIER) cc_final: 0.6123 (tp-100) REVERT: F 192 GLU cc_start: 0.9186 (mp0) cc_final: 0.8959 (tm-30) REVERT: F 298 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7579 (tm-30) REVERT: F 327 ASP cc_start: 0.9166 (t0) cc_final: 0.8907 (t0) REVERT: E 152 MET cc_start: 0.9097 (tpt) cc_final: 0.8722 (tpp) REVERT: E 165 ASP cc_start: 0.8499 (m-30) cc_final: 0.7697 (t0) REVERT: E 176 MET cc_start: 0.8496 (ptp) cc_final: 0.8074 (mtt) REVERT: E 224 ARG cc_start: 0.8434 (tpp80) cc_final: 0.8226 (tpp80) REVERT: E 229 MET cc_start: 0.9123 (mtm) cc_final: 0.8903 (mtm) REVERT: E 231 ASP cc_start: 0.8440 (t0) cc_final: 0.8134 (t0) REVERT: E 236 PHE cc_start: 0.9392 (OUTLIER) cc_final: 0.8270 (t80) REVERT: E 272 GLU cc_start: 0.9098 (pt0) cc_final: 0.8625 (mt-10) outliers start: 53 outliers final: 43 residues processed: 266 average time/residue: 0.1264 time to fit residues: 55.5899 Evaluate side-chains 269 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 221 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 316 PHE Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 315 MET Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 176 MET Chi-restraints excluded: chain F residue 177 SER Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 280 PHE Chi-restraints excluded: chain F residue 300 THR Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 350 ASP Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 236 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 9 optimal weight: 9.9990 chunk 124 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 135 optimal weight: 20.0000 chunk 155 optimal weight: 6.9990 chunk 56 optimal weight: 0.7980 chunk 38 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 12 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 86 optimal weight: 7.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 HIS ** F 213 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 = 0.3434 r_free = 0.3434 target = 0.083657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.061256 restraints weight = 47924.571| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 4.02 r_work: 0.2788 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19540 Z= 0.150 Angle : 0.632 12.952 26636 Z= 0.321 Chirality : 0.043 0.263 3195 Planarity : 0.003 0.046 3264 Dihedral : 16.105 179.269 3134 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.44 % Favored : 95.47 % Rotamer: Outliers : 2.74 % Allowed : 21.75 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.18), residues: 2364 helix: 1.59 (0.20), residues: 741 sheet: 0.31 (0.22), residues: 609 loop : -0.43 (0.21), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 321 TYR 0.014 0.001 TYR A 120 PHE 0.019 0.001 PHE C 263 HIS 0.005 0.001 HIS F 228 Details of bonding type rmsd covalent geometry : bond 0.00344 (19540) covalent geometry : angle 0.63153 (26636) hydrogen bonds : bond 0.03429 ( 758) hydrogen bonds : angle 4.55161 ( 2173) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4721.90 seconds wall clock time: 81 minutes 46.20 seconds (4906.20 seconds total)