Starting phenix.real_space_refine on Fri May 30 04:37:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rxc_19573/05_2025/8rxc_19573.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rxc_19573/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8rxc_19573/05_2025/8rxc_19573.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rxc_19573/05_2025/8rxc_19573.map" model { file = "/net/cci-nas-00/data/ceres_data/8rxc_19573/05_2025/8rxc_19573.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rxc_19573/05_2025/8rxc_19573.cif" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 11.70, per 1000 atoms: 0.61 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: 4.66 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 6.44 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: 6.40 Time building geometry restraints manager: 5.41 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: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.200 Construct map_model_manager: 0.020 Extract box with map and model: 0.710 Check model and map are aligned: 0.140 Set scattering table: 0.150 Process input model: 47.100 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.080 ------------------------------------------------------------------------------- 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 : 8.52 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (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 HIS 0.003 0.001 HIS A 228 PHE 0.025 0.002 PHE B 244 TYR 0.024 0.002 TYR C 147 ARG 0.008 0.001 ARG B 161 Details of bonding type rmsd hydrogen bonds : bond 0.15680 ( 758) hydrogen bonds : angle 7.39318 ( 2173) covalent geometry : bond 0.00807 (19540) covalent geometry : angle 0.86240 (26636) *********************** 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 : 2.118 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: 0.4431 (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: 0.3057 time to fit residues: 169.4281 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 : 2.177 ------------------------------------------------------------------------------- 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 200 optimal weight: 10.0000 chunk 179 optimal weight: 7.9990 chunk 99 optimal weight: 2.9990 chunk 61 optimal weight: 8.9990 chunk 121 optimal weight: 0.0010 chunk 95 optimal weight: 1.9990 chunk 185 optimal weight: 6.9990 chunk 71 optimal weight: 10.0000 chunk 112 optimal weight: 4.9990 chunk 138 optimal weight: 7.9990 chunk 215 optimal weight: 5.9990 overall best weight: 3.1994 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.085935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.063246 restraints weight = 47385.046| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 4.00 r_work: 0.2808 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 19540 Z= 0.193 Angle : 0.672 8.785 26636 Z= 0.357 Chirality : 0.045 0.229 3195 Planarity : 0.005 0.047 3264 Dihedral : 17.097 170.052 3137 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.96 % Favored : 96.87 % Rotamer: Outliers : 3.33 % Allowed : 18.62 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.17), residues: 2364 helix: 0.97 (0.19), residues: 734 sheet: 0.24 (0.21), residues: 618 loop : -0.37 (0.20), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS F 228 PHE 0.016 0.001 PHE A 166 TYR 0.016 0.001 TYR A 120 ARG 0.006 0.001 ARG B 156 Details of bonding type rmsd hydrogen bonds : bond 0.04521 ( 758) hydrogen bonds : angle 5.48918 ( 2173) covalent geometry : bond 0.00436 (19540) covalent geometry : angle 0.67205 (26636) *********************** 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 333 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 266 time to evaluate : 2.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 232 THR cc_start: 0.9425 (OUTLIER) cc_final: 0.8840 (p) REVERT: C 143 GLU cc_start: 0.7863 (tp30) cc_final: 0.7061 (tm-30) REVERT: C 192 GLU cc_start: 0.8934 (tp30) cc_final: 0.8704 (tp30) REVERT: C 217 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8377 (mm-30) REVERT: C 298 GLU cc_start: 0.8887 (tt0) cc_final: 0.8634 (tm-30) REVERT: B 217 GLU cc_start: 0.8610 (tp30) cc_final: 0.8281 (tp30) REVERT: B 398 GLU cc_start: 0.8781 (pt0) cc_final: 0.8421 (pm20) REVERT: B 432 LEU cc_start: 0.9001 (mp) cc_final: 0.8668 (tt) REVERT: A 231 ASP cc_start: 0.8305 (m-30) cc_final: 0.8024 (m-30) REVERT: F 176 MET cc_start: 0.9332 (ptt) cc_final: 0.8739 (ppp) REVERT: F 192 GLU cc_start: 0.9215 (mp0) cc_final: 0.8919 (tm-30) REVERT: F 265 MET cc_start: 0.8982 (tpp) cc_final: 0.8560 (tpp) REVERT: F 281 LEU cc_start: 0.8478 (tp) cc_final: 0.8235 (mp) REVERT: F 304 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.8657 (tt) REVERT: E 225 MET cc_start: 0.8363 (tpp) cc_final: 0.8067 (tpp) REVERT: E 236 PHE cc_start: 0.9499 (OUTLIER) cc_final: 0.8506 (t80) REVERT: E 272 GLU cc_start: 0.9113 (pt0) cc_final: 0.8627 (mt-10) outliers start: 67 outliers final: 29 residues processed: 321 average time/residue: 0.2706 time to fit residues: 138.2078 Evaluate side-chains 257 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 225 time to evaluate : 2.146 ------------------------------------------------------------------------------- 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 316 PHE Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 362 ASP 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 122 SER Chi-restraints excluded: chain A residue 233 VAL 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 110 THR Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 280 PHE Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 304 LEU 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 236 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 198 optimal weight: 10.0000 chunk 136 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 150 optimal weight: 2.9990 chunk 127 optimal weight: 7.9990 chunk 128 optimal weight: 0.9990 chunk 57 optimal weight: 8.9990 chunk 178 optimal weight: 0.5980 chunk 175 optimal weight: 20.0000 chunk 84 optimal weight: 7.9990 chunk 79 optimal weight: 20.0000 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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** ** C 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.086432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.063850 restraints weight = 47052.720| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 3.99 r_work: 0.2825 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.2332 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= 0.142 Angle : 0.605 8.911 26636 Z= 0.320 Chirality : 0.043 0.207 3195 Planarity : 0.004 0.041 3264 Dihedral : 16.759 176.039 3134 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.51 % Favored : 96.32 % Rotamer: Outliers : 2.59 % Allowed : 18.62 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.18), residues: 2364 helix: 1.33 (0.20), residues: 734 sheet: 0.35 (0.21), residues: 613 loop : -0.16 (0.21), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS C 242 PHE 0.017 0.001 PHE C 280 TYR 0.019 0.001 TYR A 120 ARG 0.006 0.000 ARG C 284 Details of bonding type rmsd hydrogen bonds : bond 0.03943 ( 758) hydrogen bonds : angle 5.07382 ( 2173) covalent geometry : bond 0.00317 (19540) covalent geometry : angle 0.60454 (26636) *********************** 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 313 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 261 time to evaluate : 2.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 279 VAL cc_start: 0.8961 (t) cc_final: 0.8740 (p) REVERT: C 143 GLU cc_start: 0.7883 (tp30) cc_final: 0.6991 (tm-30) REVERT: C 152 MET cc_start: 0.9274 (mmm) cc_final: 0.8823 (tpp) REVERT: C 192 GLU cc_start: 0.8859 (tp30) cc_final: 0.8643 (tp30) REVERT: C 298 GLU cc_start: 0.8988 (tt0) cc_final: 0.8696 (tm-30) REVERT: B 124 GLU cc_start: 0.8089 (tp30) cc_final: 0.7653 (tp30) REVERT: B 217 GLU cc_start: 0.8672 (tp30) cc_final: 0.8459 (tp30) REVERT: B 304 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9165 (tt) REVERT: B 398 GLU cc_start: 0.8864 (pt0) cc_final: 0.8579 (pm20) REVERT: A 129 GLN cc_start: 0.8833 (tp-100) cc_final: 0.8586 (tp-100) REVERT: A 219 THR cc_start: 0.8033 (m) cc_final: 0.7783 (p) REVERT: A 235 TYR cc_start: 0.8760 (t80) cc_final: 0.8491 (t80) REVERT: A 367 ASP cc_start: 0.9232 (m-30) cc_final: 0.8903 (m-30) REVERT: F 170 ASP cc_start: 0.8369 (p0) cc_final: 0.7665 (p0) REVERT: F 176 MET cc_start: 0.9198 (OUTLIER) cc_final: 0.8637 (ppp) REVERT: F 192 GLU cc_start: 0.9194 (mp0) cc_final: 0.8973 (tm-30) REVERT: F 242 HIS cc_start: 0.7817 (m90) cc_final: 0.7252 (m170) REVERT: F 297 MET cc_start: 0.9086 (mmt) cc_final: 0.8623 (mmt) REVERT: F 304 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.8674 (tt) REVERT: F 327 ASP cc_start: 0.9163 (t0) cc_final: 0.8892 (t0) REVERT: E 236 PHE cc_start: 0.9449 (OUTLIER) cc_final: 0.8460 (t80) REVERT: E 272 GLU cc_start: 0.9112 (pt0) cc_final: 0.8695 (mt-10) outliers start: 52 outliers final: 31 residues processed: 299 average time/residue: 0.2637 time to fit residues: 127.6440 Evaluate side-chains 261 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 226 time to evaluate : 2.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 184 GLN Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain C residue 132 LEU 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 304 LEU 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 180 ILE Chi-restraints excluded: chain A residue 196 GLU 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 229 MET Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 236 PHE Chi-restraints excluded: chain F residue 280 PHE Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 304 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 236 PHE Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 350 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 86 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 106 optimal weight: 0.9990 chunk 138 optimal weight: 8.9990 chunk 31 optimal weight: 8.9990 chunk 71 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 116 optimal weight: 3.9990 chunk 184 optimal weight: 9.9990 chunk 11 optimal weight: 7.9990 chunk 74 optimal weight: 0.7980 overall best weight: 3.1588 ------------------------------------------------------------------------------- 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 C 403 ASN A 189 GLN ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 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 = 0.3450 r_free = 0.3450 target = 0.085368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.062683 restraints weight = 47506.345| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 4.03 r_work: 0.2805 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 19540 Z= 0.179 Angle : 0.603 9.218 26636 Z= 0.317 Chirality : 0.043 0.211 3195 Planarity : 0.004 0.038 3264 Dihedral : 16.643 176.241 3134 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.43 % Favored : 96.40 % Rotamer: Outliers : 3.29 % Allowed : 18.57 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.18), residues: 2364 helix: 1.44 (0.20), residues: 740 sheet: 0.40 (0.21), residues: 612 loop : -0.17 (0.21), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS A 213 PHE 0.009 0.001 PHE B 144 TYR 0.017 0.001 TYR A 120 ARG 0.005 0.000 ARG E 224 Details of bonding type rmsd hydrogen bonds : bond 0.03838 ( 758) hydrogen bonds : angle 4.90126 ( 2173) covalent geometry : bond 0.00404 (19540) covalent geometry : angle 0.60264 (26636) *********************** 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 292 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 226 time to evaluate : 2.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 232 THR cc_start: 0.9454 (OUTLIER) cc_final: 0.8980 (p) REVERT: D 348 ASN cc_start: 0.8992 (t0) cc_final: 0.8760 (t0) REVERT: C 143 GLU cc_start: 0.7874 (tp30) cc_final: 0.7086 (tm-30) REVERT: C 152 MET cc_start: 0.9294 (mmm) cc_final: 0.8986 (tpt) REVERT: C 192 GLU cc_start: 0.8910 (tp30) cc_final: 0.8673 (tp30) REVERT: C 298 GLU cc_start: 0.9022 (tt0) cc_final: 0.8743 (tm-30) REVERT: C 403 ASN cc_start: 0.9218 (OUTLIER) cc_final: 0.8654 (p0) REVERT: B 398 GLU cc_start: 0.8902 (pt0) cc_final: 0.8645 (pm20) REVERT: A 129 GLN cc_start: 0.8854 (tp-100) cc_final: 0.8602 (tp-100) REVERT: A 219 THR cc_start: 0.8067 (m) cc_final: 0.7807 (p) REVERT: A 235 TYR cc_start: 0.8725 (t80) cc_final: 0.8432 (t80) REVERT: A 367 ASP cc_start: 0.9212 (m-30) cc_final: 0.8876 (m-30) REVERT: F 165 ASP cc_start: 0.8963 (m-30) cc_final: 0.8643 (t0) REVERT: F 176 MET cc_start: 0.9170 (ptt) cc_final: 0.8658 (ppp) REVERT: F 192 GLU cc_start: 0.9173 (mp0) cc_final: 0.8965 (tm-30) REVERT: F 217 GLU cc_start: 0.9007 (tp30) cc_final: 0.8758 (pp20) REVERT: F 242 HIS cc_start: 0.7788 (m90) cc_final: 0.7134 (m170) REVERT: F 281 LEU cc_start: 0.8368 (mp) cc_final: 0.7877 (mt) REVERT: F 297 MET cc_start: 0.9101 (mmt) cc_final: 0.8653 (mmt) REVERT: F 304 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.9061 (tt) REVERT: E 152 MET cc_start: 0.9089 (tpt) cc_final: 0.8701 (tpp) REVERT: E 229 MET cc_start: 0.9117 (OUTLIER) cc_final: 0.8813 (mpp) REVERT: E 236 PHE cc_start: 0.9439 (OUTLIER) cc_final: 0.8454 (t80) REVERT: E 272 GLU cc_start: 0.9123 (pt0) cc_final: 0.8703 (mt-10) outliers start: 66 outliers final: 42 residues processed: 279 average time/residue: 0.2567 time to fit residues: 116.6413 Evaluate side-chains 262 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 215 time to evaluate : 2.033 ------------------------------------------------------------------------------- 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 232 THR Chi-restraints excluded: chain D residue 243 THR 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 294 VAL Chi-restraints excluded: chain C residue 359 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 99 ILE 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 B residue 432 LEU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 180 ILE 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 85 VAL 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 197 LEU 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 295 VAL Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 304 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 96 ASP Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 229 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 113 optimal weight: 4.9990 chunk 178 optimal weight: 5.9990 chunk 187 optimal weight: 7.9990 chunk 125 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 chunk 145 optimal weight: 8.9990 chunk 63 optimal weight: 1.9990 chunk 38 optimal weight: 20.0000 chunk 198 optimal weight: 5.9990 chunk 151 optimal weight: 10.0000 chunk 61 optimal weight: 20.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 C 403 ASN B 403 ASN ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 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 = 0.3417 r_free = 0.3417 target = 0.083244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.060629 restraints weight = 48315.432| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 4.01 r_work: 0.2763 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 19540 Z= 0.256 Angle : 0.643 9.288 26636 Z= 0.337 Chirality : 0.044 0.189 3195 Planarity : 0.004 0.036 3264 Dihedral : 16.612 176.523 3134 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.06 % Favored : 95.77 % Rotamer: Outliers : 3.68 % Allowed : 19.11 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.18), residues: 2364 helix: 1.41 (0.20), residues: 740 sheet: 0.30 (0.21), residues: 622 loop : -0.19 (0.21), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS A 213 PHE 0.014 0.002 PHE B 144 TYR 0.017 0.001 TYR A 120 ARG 0.005 0.001 ARG C 284 Details of bonding type rmsd hydrogen bonds : bond 0.04035 ( 758) hydrogen bonds : angle 4.90552 ( 2173) covalent geometry : bond 0.00582 (19540) covalent geometry : angle 0.64312 (26636) *********************** 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 296 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 222 time to evaluate : 2.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 232 THR cc_start: 0.9492 (OUTLIER) cc_final: 0.9029 (p) REVERT: D 348 ASN cc_start: 0.9016 (t0) cc_final: 0.8792 (t0) REVERT: C 143 GLU cc_start: 0.8013 (tp30) cc_final: 0.7375 (tm-30) REVERT: C 152 MET cc_start: 0.9315 (mmm) cc_final: 0.9028 (tpt) REVERT: C 192 GLU cc_start: 0.8915 (tp30) cc_final: 0.8573 (tp30) REVERT: C 298 GLU cc_start: 0.9044 (tt0) cc_final: 0.8803 (tm-30) REVERT: B 147 TYR cc_start: 0.8433 (t80) cc_final: 0.8133 (t80) REVERT: B 217 GLU cc_start: 0.8479 (tp30) cc_final: 0.8209 (tp30) REVERT: B 398 GLU cc_start: 0.8947 (pt0) cc_final: 0.8707 (pm20) REVERT: A 124 GLU cc_start: 0.8597 (tt0) cc_final: 0.8110 (pt0) REVERT: A 129 GLN cc_start: 0.8867 (tp-100) cc_final: 0.8624 (tp-100) REVERT: A 198 MET cc_start: 0.9207 (ttm) cc_final: 0.8873 (mtp) REVERT: A 219 THR cc_start: 0.8146 (m) cc_final: 0.7902 (p) REVERT: A 235 TYR cc_start: 0.8677 (t80) cc_final: 0.8357 (t80) REVERT: A 367 ASP cc_start: 0.9236 (m-30) cc_final: 0.8907 (m-30) REVERT: F 96 ASP cc_start: 0.9113 (m-30) cc_final: 0.8834 (p0) REVERT: F 165 ASP cc_start: 0.8976 (m-30) cc_final: 0.8664 (t0) REVERT: F 176 MET cc_start: 0.9183 (OUTLIER) cc_final: 0.8800 (ppp) REVERT: F 177 SER cc_start: 0.6845 (OUTLIER) cc_final: 0.6056 (t) REVERT: F 189 GLN cc_start: 0.7015 (OUTLIER) cc_final: 0.6116 (tp-100) REVERT: F 192 GLU cc_start: 0.9175 (mp0) cc_final: 0.8929 (tm-30) REVERT: F 242 HIS cc_start: 0.7769 (m90) cc_final: 0.7174 (m170) REVERT: F 281 LEU cc_start: 0.8485 (mp) cc_final: 0.8217 (mt) REVERT: F 297 MET cc_start: 0.9106 (mmt) cc_final: 0.8675 (mmt) REVERT: E 236 PHE cc_start: 0.9460 (OUTLIER) cc_final: 0.8423 (t80) outliers start: 74 outliers final: 46 residues processed: 282 average time/residue: 0.2487 time to fit residues: 114.5896 Evaluate side-chains 261 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 210 time to evaluate : 2.033 ------------------------------------------------------------------------------- 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 169 ILE Chi-restraints excluded: chain D residue 190 VAL 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 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 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 180 ILE 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 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 176 MET Chi-restraints excluded: chain F residue 177 SER Chi-restraints excluded: chain F residue 189 GLN 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 295 VAL 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 E residue 67 VAL 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 229 MET Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 236 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 31 optimal weight: 0.6980 chunk 74 optimal weight: 8.9990 chunk 3 optimal weight: 7.9990 chunk 96 optimal weight: 9.9990 chunk 112 optimal weight: 5.9990 chunk 232 optimal weight: 0.6980 chunk 186 optimal weight: 0.5980 chunk 139 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 163 optimal weight: 9.9990 overall best weight: 2.9984 ------------------------------------------------------------------------------- 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 241 HIS ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3429 r_free = 0.3429 target = 0.083782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.061183 restraints weight = 48502.411| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 4.04 r_work: 0.2781 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 19540 Z= 0.168 Angle : 0.609 10.428 26636 Z= 0.316 Chirality : 0.043 0.233 3195 Planarity : 0.004 0.038 3264 Dihedral : 16.456 178.043 3134 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.89 % Favored : 95.98 % Rotamer: Outliers : 3.24 % Allowed : 20.11 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.18), residues: 2364 helix: 1.51 (0.20), residues: 739 sheet: 0.26 (0.21), residues: 623 loop : -0.13 (0.22), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.002 HIS C 241 PHE 0.016 0.001 PHE E 316 TYR 0.016 0.001 TYR A 120 ARG 0.006 0.000 ARG C 404 Details of bonding type rmsd hydrogen bonds : bond 0.03670 ( 758) hydrogen bonds : angle 4.72974 ( 2173) covalent geometry : bond 0.00382 (19540) covalent geometry : angle 0.60873 (26636) *********************** 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: 65 poor density : 219 time to evaluate : 2.163 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 232 THR cc_start: 0.9472 (OUTLIER) cc_final: 0.9009 (p) REVERT: D 348 ASN cc_start: 0.9054 (t0) cc_final: 0.8837 (t0) REVERT: C 143 GLU cc_start: 0.7994 (tp30) cc_final: 0.7420 (tm-30) REVERT: C 152 MET cc_start: 0.9289 (mmm) cc_final: 0.9000 (tpt) REVERT: C 192 GLU cc_start: 0.8899 (tp30) cc_final: 0.8535 (tp30) REVERT: C 298 GLU cc_start: 0.9014 (tt0) cc_final: 0.8794 (tm-30) REVERT: B 147 TYR cc_start: 0.8380 (t80) cc_final: 0.8151 (t80) REVERT: B 217 GLU cc_start: 0.8515 (tp30) cc_final: 0.8296 (tp30) REVERT: A 124 GLU cc_start: 0.8542 (tt0) cc_final: 0.8133 (pt0) REVERT: A 129 GLN cc_start: 0.8874 (tp-100) cc_final: 0.8630 (tp-100) REVERT: A 198 MET cc_start: 0.9159 (ttm) cc_final: 0.8848 (mtp) REVERT: A 219 THR cc_start: 0.8142 (m) cc_final: 0.7878 (p) REVERT: A 235 TYR cc_start: 0.8624 (t80) cc_final: 0.8359 (t80) REVERT: A 367 ASP cc_start: 0.9184 (m-30) cc_final: 0.8854 (m-30) REVERT: F 96 ASP cc_start: 0.9083 (m-30) cc_final: 0.8832 (p0) REVERT: F 165 ASP cc_start: 0.9035 (m-30) cc_final: 0.8714 (t0) REVERT: F 176 MET cc_start: 0.9143 (OUTLIER) cc_final: 0.8756 (ppp) REVERT: F 177 SER cc_start: 0.6781 (OUTLIER) cc_final: 0.5767 (t) REVERT: F 189 GLN cc_start: 0.7035 (OUTLIER) cc_final: 0.6195 (tp-100) REVERT: F 192 GLU cc_start: 0.9174 (mp0) cc_final: 0.8942 (tm-30) REVERT: F 297 MET cc_start: 0.9057 (mmt) cc_final: 0.8668 (mmt) REVERT: E 152 MET cc_start: 0.9112 (tpt) cc_final: 0.8755 (tpp) REVERT: E 165 ASP cc_start: 0.8539 (m-30) cc_final: 0.7692 (t0) REVERT: E 229 MET cc_start: 0.9206 (OUTLIER) cc_final: 0.8996 (mtm) REVERT: E 236 PHE cc_start: 0.9430 (OUTLIER) cc_final: 0.8389 (t80) outliers start: 65 outliers final: 42 residues processed: 269 average time/residue: 0.2568 time to fit residues: 112.2362 Evaluate side-chains 258 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 210 time to evaluate : 2.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 108 VAL 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 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 186 SER 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 118 VAL Chi-restraints excluded: chain A residue 180 ILE 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 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 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 303 ILE Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 350 ASP Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 96 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 229 MET Chi-restraints excluded: chain E residue 236 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 89 optimal weight: 5.9990 chunk 182 optimal weight: 10.0000 chunk 129 optimal weight: 20.0000 chunk 100 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 141 optimal weight: 2.9990 chunk 125 optimal weight: 20.0000 chunk 44 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 179 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.084148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.061522 restraints weight = 47724.713| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 4.01 r_work: 0.2791 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.3190 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= 0.151 Angle : 0.612 11.763 26636 Z= 0.313 Chirality : 0.043 0.236 3195 Planarity : 0.004 0.037 3264 Dihedral : 16.357 178.939 3134 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.81 % Favored : 96.07 % Rotamer: Outliers : 2.94 % Allowed : 20.41 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.18), residues: 2364 helix: 1.57 (0.20), residues: 739 sheet: 0.26 (0.21), residues: 624 loop : -0.16 (0.22), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.017 0.001 HIS F 228 PHE 0.020 0.001 PHE C 280 TYR 0.015 0.001 TYR A 120 ARG 0.004 0.000 ARG E 224 Details of bonding type rmsd hydrogen bonds : bond 0.03543 ( 758) hydrogen bonds : angle 4.63990 ( 2173) covalent geometry : bond 0.00342 (19540) covalent geometry : angle 0.61245 (26636) *********************** 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 292 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 233 time to evaluate : 2.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 232 THR cc_start: 0.9457 (OUTLIER) cc_final: 0.8987 (p) REVERT: D 348 ASN cc_start: 0.9071 (t0) cc_final: 0.8774 (t0) REVERT: C 143 GLU cc_start: 0.8081 (tp30) cc_final: 0.7553 (tm-30) REVERT: C 152 MET cc_start: 0.9294 (mmm) cc_final: 0.9019 (tpt) REVERT: C 192 GLU cc_start: 0.8921 (tp30) cc_final: 0.8551 (tp30) REVERT: C 298 GLU cc_start: 0.9012 (tt0) cc_final: 0.8792 (tm-30) REVERT: B 147 TYR cc_start: 0.8397 (t80) cc_final: 0.8183 (t80) REVERT: B 156 ARG cc_start: 0.9293 (ttm-80) cc_final: 0.9024 (ttm170) REVERT: B 217 GLU cc_start: 0.8637 (tp30) cc_final: 0.8399 (tp30) REVERT: A 198 MET cc_start: 0.9112 (ttm) cc_final: 0.8814 (mtp) REVERT: A 219 THR cc_start: 0.8144 (m) cc_final: 0.7876 (p) REVERT: A 235 TYR cc_start: 0.8621 (t80) cc_final: 0.8363 (t80) REVERT: A 350 ASP cc_start: 0.8620 (m-30) cc_final: 0.8281 (m-30) REVERT: A 367 ASP cc_start: 0.9173 (m-30) cc_final: 0.8853 (m-30) REVERT: F 96 ASP cc_start: 0.9085 (m-30) cc_final: 0.8847 (p0) REVERT: F 165 ASP cc_start: 0.9086 (m-30) cc_final: 0.8754 (t0) REVERT: F 176 MET cc_start: 0.9152 (OUTLIER) cc_final: 0.8772 (ppp) REVERT: F 177 SER cc_start: 0.6764 (OUTLIER) cc_final: 0.5694 (t) REVERT: F 189 GLN cc_start: 0.7005 (OUTLIER) cc_final: 0.6143 (tp-100) REVERT: F 192 GLU cc_start: 0.9172 (mp0) cc_final: 0.8951 (tm-30) REVERT: F 242 HIS cc_start: 0.7952 (m90) cc_final: 0.7222 (m170) REVERT: F 297 MET cc_start: 0.9027 (mmt) cc_final: 0.8670 (mmt) REVERT: F 298 GLU cc_start: 0.7999 (tm-30) cc_final: 0.7742 (tm-30) REVERT: E 152 MET cc_start: 0.9131 (tpt) cc_final: 0.8765 (tpp) REVERT: E 165 ASP cc_start: 0.8543 (m-30) cc_final: 0.7720 (t0) REVERT: E 236 PHE cc_start: 0.9421 (OUTLIER) cc_final: 0.8346 (t80) REVERT: E 272 GLU cc_start: 0.9114 (pt0) cc_final: 0.8673 (mt-10) REVERT: E 297 MET cc_start: 0.9266 (tpp) cc_final: 0.8726 (mmm) REVERT: E 327 ASP cc_start: 0.8739 (t0) cc_final: 0.8474 (t0) outliers start: 59 outliers final: 45 residues processed: 276 average time/residue: 0.2655 time to fit residues: 118.6341 Evaluate side-chains 265 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 215 time to evaluate : 2.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 243 THR 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 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 A residue 81 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 180 ILE 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 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 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 312 THR Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 350 ASP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 156 optimal weight: 9.9990 chunk 50 optimal weight: 10.0000 chunk 192 optimal weight: 10.0000 chunk 205 optimal weight: 0.6980 chunk 196 optimal weight: 10.0000 chunk 148 optimal weight: 6.9990 chunk 172 optimal weight: 7.9990 chunk 157 optimal weight: 5.9990 chunk 133 optimal weight: 0.9980 chunk 183 optimal weight: 3.9990 chunk 76 optimal weight: 10.0000 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 242 HIS ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3420 r_free = 0.3420 target = 0.082940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.060399 restraints weight = 48356.460| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 4.02 r_work: 0.2767 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 19540 Z= 0.199 Angle : 0.628 11.948 26636 Z= 0.324 Chirality : 0.043 0.232 3195 Planarity : 0.004 0.038 3264 Dihedral : 16.388 179.034 3134 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.89 % Favored : 96.02 % Rotamer: Outliers : 3.19 % Allowed : 20.66 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.18), residues: 2364 helix: 1.49 (0.20), residues: 740 sheet: 0.29 (0.21), residues: 620 loop : -0.24 (0.22), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS A 213 PHE 0.012 0.001 PHE C 263 TYR 0.015 0.001 TYR A 120 ARG 0.006 0.000 ARG F 161 Details of bonding type rmsd hydrogen bonds : bond 0.03735 ( 758) hydrogen bonds : angle 4.71494 ( 2173) covalent geometry : bond 0.00452 (19540) covalent geometry : angle 0.62816 (26636) *********************** 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 280 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 216 time to evaluate : 2.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 217 GLU cc_start: 0.9377 (tt0) cc_final: 0.9043 (tp30) REVERT: D 232 THR cc_start: 0.9484 (OUTLIER) cc_final: 0.9015 (p) REVERT: D 348 ASN cc_start: 0.9109 (t0) cc_final: 0.8821 (t0) REVERT: C 143 GLU cc_start: 0.8129 (tp30) cc_final: 0.7589 (tm-30) REVERT: C 152 MET cc_start: 0.9313 (mmm) cc_final: 0.9055 (tpt) REVERT: C 192 GLU cc_start: 0.8935 (tp30) cc_final: 0.8553 (tp30) REVERT: C 242 HIS cc_start: 0.7620 (OUTLIER) cc_final: 0.7156 (m90) REVERT: B 217 GLU cc_start: 0.8720 (tp30) cc_final: 0.8483 (tp30) REVERT: A 124 GLU cc_start: 0.8605 (tt0) cc_final: 0.8181 (pt0) REVERT: A 198 MET cc_start: 0.9109 (ttm) cc_final: 0.8801 (mtp) REVERT: A 219 THR cc_start: 0.8164 (m) cc_final: 0.7900 (p) REVERT: A 225 MET cc_start: 0.8840 (ppp) cc_final: 0.8534 (ppp) REVERT: A 235 TYR cc_start: 0.8625 (t80) cc_final: 0.8377 (t80) REVERT: A 297 MET cc_start: 0.8476 (mmm) cc_final: 0.8245 (mmm) REVERT: A 350 ASP cc_start: 0.8657 (m-30) cc_final: 0.8376 (m-30) REVERT: A 367 ASP cc_start: 0.9184 (m-30) cc_final: 0.8823 (m-30) REVERT: F 96 ASP cc_start: 0.9091 (m-30) cc_final: 0.8845 (p0) REVERT: F 165 ASP cc_start: 0.9106 (m-30) cc_final: 0.8710 (t0) REVERT: F 176 MET cc_start: 0.9179 (OUTLIER) cc_final: 0.8811 (ppp) REVERT: F 177 SER cc_start: 0.6784 (OUTLIER) cc_final: 0.5924 (t) REVERT: F 189 GLN cc_start: 0.7035 (OUTLIER) cc_final: 0.6157 (tp-100) REVERT: F 192 GLU cc_start: 0.9184 (mp0) cc_final: 0.8968 (tm-30) REVERT: F 242 HIS cc_start: 0.7890 (m90) cc_final: 0.7138 (m170) REVERT: F 297 MET cc_start: 0.9031 (mmt) cc_final: 0.8661 (mmt) REVERT: F 298 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7660 (tm-30) REVERT: E 152 MET cc_start: 0.9151 (tpt) cc_final: 0.8794 (tpp) REVERT: E 165 ASP cc_start: 0.8568 (m-30) cc_final: 0.7736 (t0) REVERT: E 236 PHE cc_start: 0.9451 (OUTLIER) cc_final: 0.8421 (t80) REVERT: E 272 GLU cc_start: 0.9124 (pt0) cc_final: 0.8657 (mt-10) outliers start: 64 outliers final: 50 residues processed: 266 average time/residue: 0.2583 time to fit residues: 110.8561 Evaluate side-chains 258 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 202 time to evaluate : 2.048 ------------------------------------------------------------------------------- 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 169 ILE 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 294 VAL 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 241 HIS Chi-restraints excluded: chain C residue 242 HIS 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 180 ILE 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 A residue 359 VAL Chi-restraints excluded: chain F residue 85 VAL 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 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 312 THR Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 350 ASP Chi-restraints excluded: chain E residue 67 VAL 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 232 THR Chi-restraints excluded: chain E residue 236 PHE Chi-restraints excluded: chain E residue 350 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 61 optimal weight: 5.9990 chunk 12 optimal weight: 9.9990 chunk 213 optimal weight: 0.0570 chunk 109 optimal weight: 6.9990 chunk 116 optimal weight: 9.9990 chunk 72 optimal weight: 1.9990 chunk 193 optimal weight: 4.9990 chunk 11 optimal weight: 0.2980 chunk 163 optimal weight: 9.9990 chunk 205 optimal weight: 2.9990 chunk 78 optimal weight: 20.0000 overall best weight: 2.0704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 329 ASN ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3438 r_free = 0.3438 target = 0.083933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.061553 restraints weight = 48030.637| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 4.01 r_work: 0.2794 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.3408 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= 0.142 Angle : 0.618 12.615 26636 Z= 0.317 Chirality : 0.043 0.227 3195 Planarity : 0.003 0.037 3264 Dihedral : 16.297 179.892 3134 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.98 % Favored : 95.94 % Rotamer: Outliers : 2.54 % Allowed : 21.45 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.18), residues: 2364 helix: 1.52 (0.20), residues: 740 sheet: 0.38 (0.22), residues: 610 loop : -0.28 (0.21), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.024 0.002 HIS C 241 PHE 0.021 0.001 PHE C 280 TYR 0.014 0.001 TYR A 120 ARG 0.007 0.000 ARG C 240 Details of bonding type rmsd hydrogen bonds : bond 0.03473 ( 758) hydrogen bonds : angle 4.59370 ( 2173) covalent geometry : bond 0.00322 (19540) covalent geometry : angle 0.61787 (26636) *********************** 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 275 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 224 time to evaluate : 2.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 217 GLU cc_start: 0.9391 (tt0) cc_final: 0.9042 (tp30) REVERT: D 232 THR cc_start: 0.9467 (OUTLIER) cc_final: 0.8998 (p) REVERT: D 348 ASN cc_start: 0.9087 (t0) cc_final: 0.8818 (t0) REVERT: C 143 GLU cc_start: 0.8141 (tp30) cc_final: 0.7683 (tm-30) REVERT: C 152 MET cc_start: 0.9286 (mmm) cc_final: 0.9010 (tpt) REVERT: C 192 GLU cc_start: 0.8926 (tp30) cc_final: 0.8528 (tp30) REVERT: B 217 GLU cc_start: 0.8709 (tp30) cc_final: 0.8461 (tp30) REVERT: A 124 GLU cc_start: 0.8615 (tt0) cc_final: 0.8187 (pt0) REVERT: A 198 MET cc_start: 0.9068 (ttm) cc_final: 0.8796 (mtp) REVERT: A 219 THR cc_start: 0.8184 (m) cc_final: 0.7919 (p) REVERT: A 225 MET cc_start: 0.8829 (ppp) cc_final: 0.8505 (ppp) REVERT: A 235 TYR cc_start: 0.8606 (t80) cc_final: 0.8358 (t80) REVERT: A 350 ASP cc_start: 0.8632 (m-30) cc_final: 0.8332 (m-30) REVERT: A 367 ASP cc_start: 0.9165 (m-30) cc_final: 0.8810 (m-30) REVERT: F 96 ASP cc_start: 0.9099 (m-30) cc_final: 0.8859 (p0) REVERT: F 165 ASP cc_start: 0.9094 (m-30) cc_final: 0.8711 (t0) REVERT: F 176 MET cc_start: 0.9146 (OUTLIER) cc_final: 0.8793 (ppp) REVERT: F 177 SER cc_start: 0.6759 (OUTLIER) cc_final: 0.5762 (t) REVERT: F 189 GLN cc_start: 0.7010 (OUTLIER) cc_final: 0.6156 (tp-100) REVERT: F 192 GLU cc_start: 0.9184 (mp0) cc_final: 0.8976 (tm-30) REVERT: F 297 MET cc_start: 0.8986 (mmt) cc_final: 0.8641 (mmt) REVERT: F 298 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7639 (tm-30) REVERT: E 152 MET cc_start: 0.9132 (tpt) cc_final: 0.8762 (tpp) REVERT: E 165 ASP cc_start: 0.8543 (m-30) cc_final: 0.7733 (t0) REVERT: E 176 MET cc_start: 0.8533 (ptp) cc_final: 0.7950 (mtt) REVERT: E 236 PHE cc_start: 0.9420 (OUTLIER) cc_final: 0.8445 (t80) REVERT: E 272 GLU cc_start: 0.9106 (pt0) cc_final: 0.8648 (mt-10) REVERT: E 297 MET cc_start: 0.9259 (tpp) cc_final: 0.8681 (mmm) REVERT: E 327 ASP cc_start: 0.8784 (t0) cc_final: 0.8523 (t0) outliers start: 51 outliers final: 43 residues processed: 263 average time/residue: 0.2648 time to fit residues: 112.6398 Evaluate side-chains 252 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 204 time to evaluate : 2.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain C residue 81 LEU 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 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 242 HIS Chi-restraints excluded: chain B residue 250 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 180 ILE 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 254 PHE 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 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 232 THR Chi-restraints excluded: chain E residue 236 PHE Chi-restraints excluded: chain E residue 350 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 40 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 86 optimal weight: 9.9990 chunk 83 optimal weight: 2.9990 chunk 106 optimal weight: 10.0000 chunk 142 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 117 optimal weight: 20.0000 chunk 22 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 148 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 403 ASN ** 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 = 0.3406 r_free = 0.3406 target = 0.082029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.059424 restraints weight = 48520.992| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 4.02 r_work: 0.2746 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 19540 Z= 0.241 Angle : 0.668 13.236 26636 Z= 0.343 Chirality : 0.044 0.226 3195 Planarity : 0.004 0.036 3264 Dihedral : 16.429 179.728 3134 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.48 % Favored : 95.43 % Rotamer: Outliers : 2.69 % Allowed : 21.50 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.18), residues: 2364 helix: 1.49 (0.20), residues: 741 sheet: 0.30 (0.22), residues: 607 loop : -0.39 (0.21), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS A 213 PHE 0.015 0.001 PHE D 244 TYR 0.023 0.001 TYR E 147 ARG 0.005 0.000 ARG F 161 Details of bonding type rmsd hydrogen bonds : bond 0.03919 ( 758) hydrogen bonds : angle 4.75276 ( 2173) covalent geometry : bond 0.00549 (19540) covalent geometry : angle 0.66843 (26636) ********************** 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 254 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 200 time to evaluate : 2.135 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 217 GLU cc_start: 0.9399 (tt0) cc_final: 0.9061 (tp30) REVERT: D 232 THR cc_start: 0.9497 (OUTLIER) cc_final: 0.9024 (p) REVERT: D 348 ASN cc_start: 0.9117 (t0) cc_final: 0.8844 (t0) REVERT: C 143 GLU cc_start: 0.8192 (tp30) cc_final: 0.7734 (tm-30) REVERT: C 152 MET cc_start: 0.9330 (mmm) cc_final: 0.9044 (tpt) REVERT: C 192 GLU cc_start: 0.8980 (tp30) cc_final: 0.8600 (tp30) REVERT: C 242 HIS cc_start: 0.7675 (OUTLIER) cc_final: 0.7421 (m90) REVERT: B 196 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8447 (tt0) REVERT: B 198 MET cc_start: 0.8760 (tpp) cc_final: 0.8502 (tpt) REVERT: A 198 MET cc_start: 0.9148 (ttm) cc_final: 0.8814 (mtp) REVERT: A 219 THR cc_start: 0.8173 (m) cc_final: 0.7910 (p) REVERT: A 225 MET cc_start: 0.8853 (ppp) cc_final: 0.8557 (ppp) REVERT: A 235 TYR cc_start: 0.8635 (t80) cc_final: 0.8373 (t80) REVERT: A 350 ASP cc_start: 0.8660 (m-30) cc_final: 0.8381 (m-30) REVERT: A 367 ASP cc_start: 0.9202 (m-30) cc_final: 0.8857 (m-30) REVERT: F 96 ASP cc_start: 0.9141 (m-30) cc_final: 0.8862 (p0) REVERT: F 165 ASP cc_start: 0.9135 (m-30) cc_final: 0.8698 (t0) REVERT: F 176 MET cc_start: 0.9186 (OUTLIER) cc_final: 0.8832 (ppp) REVERT: F 177 SER cc_start: 0.6843 (OUTLIER) cc_final: 0.5928 (t) REVERT: F 189 GLN cc_start: 0.7063 (OUTLIER) cc_final: 0.6157 (tp-100) REVERT: F 192 GLU cc_start: 0.9187 (mp0) cc_final: 0.8959 (tm-30) REVERT: F 242 HIS cc_start: 0.7812 (m90) cc_final: 0.7537 (m90) REVERT: E 152 MET cc_start: 0.9151 (tpt) cc_final: 0.8795 (tpp) REVERT: E 165 ASP cc_start: 0.8570 (m-30) cc_final: 0.7749 (t0) REVERT: E 236 PHE cc_start: 0.9479 (OUTLIER) cc_final: 0.8531 (t80) REVERT: E 272 GLU cc_start: 0.9120 (pt0) cc_final: 0.8666 (mt-10) REVERT: E 297 MET cc_start: 0.9279 (tpp) cc_final: 0.8578 (mmm) outliers start: 54 outliers final: 46 residues processed: 241 average time/residue: 0.2482 time to fit residues: 98.5896 Evaluate side-chains 257 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 205 time to evaluate : 2.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 294 VAL 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 242 HIS 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 242 HIS 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 180 ILE 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 254 PHE 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 110 THR 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 322 THR Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 350 ASP 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 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 80 optimal weight: 0.0470 chunk 27 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 chunk 180 optimal weight: 5.9990 chunk 170 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 chunk 153 optimal weight: 3.9990 chunk 110 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 chunk 165 optimal weight: 5.9990 chunk 174 optimal weight: 6.9990 overall best weight: 2.0086 ------------------------------------------------------------------------------- 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** ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.084040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.061409 restraints weight = 47380.326| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 4.03 r_work: 0.2788 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.3560 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= 0.143 Angle : 0.638 13.273 26636 Z= 0.326 Chirality : 0.043 0.216 3195 Planarity : 0.004 0.038 3264 Dihedral : 16.317 178.751 3134 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.10 % Favored : 95.81 % Rotamer: Outliers : 2.39 % Allowed : 22.25 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.18), residues: 2364 helix: 1.54 (0.20), residues: 744 sheet: 0.30 (0.22), residues: 609 loop : -0.42 (0.21), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS C 241 PHE 0.012 0.001 PHE C 244 TYR 0.019 0.001 TYR E 147 ARG 0.004 0.000 ARG F 161 Details of bonding type rmsd hydrogen bonds : bond 0.03499 ( 758) hydrogen bonds : angle 4.60714 ( 2173) covalent geometry : bond 0.00326 (19540) covalent geometry : angle 0.63776 (26636) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8867.34 seconds wall clock time: 154 minutes 15.50 seconds (9255.50 seconds total)