Starting phenix.real_space_refine on Tue Apr 7 01:02:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a9y_15288/04_2026/8a9y_15288.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a9y_15288/04_2026/8a9y_15288.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8a9y_15288/04_2026/8a9y_15288.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a9y_15288/04_2026/8a9y_15288.map" model { file = "/net/cci-nas-00/data/ceres_data/8a9y_15288/04_2026/8a9y_15288.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a9y_15288/04_2026/8a9y_15288.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mg 2 5.21 5 S 88 5.16 5 C 14988 2.51 5 N 4004 2.21 5 O 4606 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23688 Number of models: 1 Model: "" Number of chains: 4 Chain: "E" Number of atoms: 3982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3982 Classifications: {'peptide': 497} Link IDs: {'PTRANS': 18, 'TRANS': 478} Chain: "T" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 730 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "A" Number of atoms: 7131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 903, 7131 Classifications: {'peptide': 903} Link IDs: {'PTRANS': 31, 'TRANS': 871} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: M, G, I Time building chain proxies: 9.75, per 1000 atoms: 0.41 Number of scatterers: 23688 At special positions: 0 Unit cell: (205.545, 112.89, 136.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 88 16.00 Mg 2 11.99 O 4606 8.00 N 4004 7.00 C 14988 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.95 Conformation dependent library (CDL) restraints added in 932.5 milliseconds 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5424 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 44 sheets defined 10.3% alpha, 45.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'E' and resid 159 through 162 Processing helix chain 'E' and resid 254 through 261 Processing helix chain 'E' and resid 303 through 307 removed outlier: 3.507A pdb=" N ASP E 307 " --> pdb=" O ALA E 304 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 347 removed outlier: 4.010A pdb=" N TYR E 347 " --> pdb=" O ILE E 343 " (cutoff:3.500A) Processing helix chain 'M' and resid 159 through 162 Processing helix chain 'M' and resid 254 through 261 Processing helix chain 'M' and resid 303 through 307 removed outlier: 3.507A pdb=" N ASP M 307 " --> pdb=" O ALA M 304 " (cutoff:3.500A) Processing helix chain 'M' and resid 340 through 347 removed outlier: 4.010A pdb=" N TYR M 347 " --> pdb=" O ILE M 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 113 removed outlier: 3.705A pdb=" N LYS A 111 " --> pdb=" O ASP A 107 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLN A 112 " --> pdb=" O GLU A 108 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLY A 113 " --> pdb=" O ILE A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 121 Processing helix chain 'A' and resid 167 through 171 removed outlier: 3.814A pdb=" N GLU A 170 " --> pdb=" O GLY A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 189 Processing helix chain 'A' and resid 233 through 249 Processing helix chain 'A' and resid 251 through 256 removed outlier: 4.293A pdb=" N ALA A 256 " --> pdb=" O ASN A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 300 Processing helix chain 'A' and resid 376 through 384 Processing helix chain 'A' and resid 409 through 418 Processing helix chain 'A' and resid 602 through 608 removed outlier: 5.559A pdb=" N ASN A 605 " --> pdb=" O THR A 602 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N PHE A 606 " --> pdb=" O GLN A 603 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N MET A 607 " --> pdb=" O GLU A 604 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LYS A 608 " --> pdb=" O ASN A 605 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 602 through 608' Processing helix chain 'A' and resid 779 through 786 Processing helix chain 'A' and resid 789 through 793 removed outlier: 4.504A pdb=" N GLY A 792 " --> pdb=" O GLY A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 822 Processing helix chain 'A' and resid 888 through 895 removed outlier: 3.717A pdb=" N LYS A 892 " --> pdb=" O SER A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 913 Processing helix chain 'A' and resid 939 through 941 No H-bonds generated for 'chain 'A' and resid 939 through 941' Processing helix chain 'A' and resid 961 through 969 Processing helix chain 'I' and resid 105 through 113 removed outlier: 3.704A pdb=" N LYS I 111 " --> pdb=" O ASP I 107 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLN I 112 " --> pdb=" O GLU I 108 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLY I 113 " --> pdb=" O ILE I 109 " (cutoff:3.500A) Processing helix chain 'I' and resid 116 through 121 Processing helix chain 'I' and resid 167 through 171 removed outlier: 3.814A pdb=" N GLU I 170 " --> pdb=" O GLY I 167 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 189 Processing helix chain 'I' and resid 233 through 249 Processing helix chain 'I' and resid 251 through 256 removed outlier: 4.291A pdb=" N ALA I 256 " --> pdb=" O ASN I 253 " (cutoff:3.500A) Processing helix chain 'I' and resid 294 through 300 Processing helix chain 'I' and resid 376 through 384 Processing helix chain 'I' and resid 409 through 418 Processing helix chain 'I' and resid 602 through 608 removed outlier: 5.557A pdb=" N ASN I 605 " --> pdb=" O THR I 602 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N PHE I 606 " --> pdb=" O GLN I 603 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N MET I 607 " --> pdb=" O GLU I 604 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS I 608 " --> pdb=" O ASN I 605 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 602 through 608' Processing helix chain 'I' and resid 779 through 786 Processing helix chain 'I' and resid 789 through 793 removed outlier: 4.504A pdb=" N GLY I 792 " --> pdb=" O GLY I 789 " (cutoff:3.500A) Processing helix chain 'I' and resid 815 through 822 Processing helix chain 'I' and resid 888 through 895 removed outlier: 3.716A pdb=" N LYS I 892 " --> pdb=" O SER I 888 " (cutoff:3.500A) Processing helix chain 'I' and resid 908 through 913 Processing helix chain 'I' and resid 939 through 941 No H-bonds generated for 'chain 'I' and resid 939 through 941' Processing helix chain 'I' and resid 961 through 969 Processing sheet with id=AA1, first strand: chain 'E' and resid 39 through 40 removed outlier: 3.691A pdb=" N ASP E 53 " --> pdb=" O ASP E 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 39 through 40 removed outlier: 7.320A pdb=" N ILE E 73 " --> pdb=" O GLU E 89 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N GLU E 89 " --> pdb=" O ILE E 73 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N GLY E 75 " --> pdb=" O LEU E 87 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 102 through 111 removed outlier: 3.944A pdb=" N THR E 122 " --> pdb=" O GLY E 104 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY E 106 " --> pdb=" O PHE E 120 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N PHE E 120 " --> pdb=" O GLY E 106 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N THR E 108 " --> pdb=" O TYR E 118 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N TYR E 118 " --> pdb=" O THR E 108 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N TYR E 110 " --> pdb=" O LEU E 116 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LEU E 116 " --> pdb=" O TYR E 110 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 102 through 111 removed outlier: 3.944A pdb=" N THR E 122 " --> pdb=" O GLY E 104 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY E 106 " --> pdb=" O PHE E 120 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N PHE E 120 " --> pdb=" O GLY E 106 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N THR E 108 " --> pdb=" O TYR E 118 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N TYR E 118 " --> pdb=" O THR E 108 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N TYR E 110 " --> pdb=" O LEU E 116 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LEU E 116 " --> pdb=" O TYR E 110 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 168 through 175 removed outlier: 7.064A pdb=" N PHE E 168 " --> pdb=" O ARG E 188 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N ARG E 188 " --> pdb=" O PHE E 168 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ASP E 170 " --> pdb=" O ALA E 186 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALA E 186 " --> pdb=" O ASP E 170 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N GLY E 193 " --> pdb=" O MET E 213 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N MET E 213 " --> pdb=" O GLY E 193 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ILE E 195 " --> pdb=" O THR E 211 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N THR E 211 " --> pdb=" O ILE E 195 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N GLU E 197 " --> pdb=" O ALA E 209 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 221 through 229 removed outlier: 6.573A pdb=" N ILE E 236 " --> pdb=" O PRO E 224 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N VAL E 226 " --> pdb=" O TYR E 234 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N TYR E 234 " --> pdb=" O VAL E 226 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LYS E 228 " --> pdb=" O TRP E 232 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N TRP E 232 " --> pdb=" O LYS E 228 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 283 through 289 removed outlier: 5.831A pdb=" N ALA E 284 " --> pdb=" O TRP E 299 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N TRP E 299 " --> pdb=" O ALA E 284 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ARG E 294 " --> pdb=" O LEU E 327 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 349 through 351 removed outlier: 4.098A pdb=" N VAL E 500 " --> pdb=" O GLN E 351 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 349 through 351 removed outlier: 4.098A pdb=" N VAL E 500 " --> pdb=" O GLN E 351 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VAL E 498 " --> pdb=" O SER E 389 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N SER E 389 " --> pdb=" O VAL E 498 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N VAL E 500 " --> pdb=" O LYS E 387 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LYS E 387 " --> pdb=" O VAL E 500 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N THR E 502 " --> pdb=" O HIS E 385 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N HIS E 385 " --> pdb=" O THR E 502 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 357 through 358 removed outlier: 3.846A pdb=" N ALA E 357 " --> pdb=" O ILE E 378 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE E 378 " --> pdb=" O ALA E 357 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N TRP E 484 " --> pdb=" O PHE E 379 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE E 401 " --> pdb=" O VAL E 419 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ALA E 426 " --> pdb=" O ASP E 440 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ASP E 440 " --> pdb=" O ALA E 426 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N PHE E 428 " --> pdb=" O LEU E 438 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'T' and resid 25 through 26 removed outlier: 3.646A pdb=" N SER T 19 " --> pdb=" O ASN T 55 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU T 53 " --> pdb=" O ARG T 21 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'T' and resid 28 through 30 removed outlier: 6.047A pdb=" N ILE T 36 " --> pdb=" O THR T 92 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N LYS T 94 " --> pdb=" O ILE T 36 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL T 38 " --> pdb=" O LYS T 94 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'T' and resid 28 through 30 removed outlier: 6.047A pdb=" N ILE T 36 " --> pdb=" O THR T 92 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N LYS T 94 " --> pdb=" O ILE T 36 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL T 38 " --> pdb=" O LYS T 94 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ASN A 262 " --> pdb=" O TYR A 274 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N MET A 276 " --> pdb=" O ALA A 260 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ALA A 260 " --> pdb=" O MET A 276 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 39 through 40 removed outlier: 3.691A pdb=" N ASP M 53 " --> pdb=" O ASP M 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 39 through 40 removed outlier: 7.320A pdb=" N ILE M 73 " --> pdb=" O GLU M 89 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLU M 89 " --> pdb=" O ILE M 73 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N GLY M 75 " --> pdb=" O LEU M 87 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 102 through 111 removed outlier: 3.943A pdb=" N THR M 122 " --> pdb=" O GLY M 104 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY M 106 " --> pdb=" O PHE M 120 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N PHE M 120 " --> pdb=" O GLY M 106 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N THR M 108 " --> pdb=" O TYR M 118 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N TYR M 118 " --> pdb=" O THR M 108 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N TYR M 110 " --> pdb=" O LEU M 116 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LEU M 116 " --> pdb=" O TYR M 110 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 102 through 111 removed outlier: 3.943A pdb=" N THR M 122 " --> pdb=" O GLY M 104 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY M 106 " --> pdb=" O PHE M 120 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N PHE M 120 " --> pdb=" O GLY M 106 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N THR M 108 " --> pdb=" O TYR M 118 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N TYR M 118 " --> pdb=" O THR M 108 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N TYR M 110 " --> pdb=" O LEU M 116 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LEU M 116 " --> pdb=" O TYR M 110 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 168 through 175 removed outlier: 7.065A pdb=" N PHE M 168 " --> pdb=" O ARG M 188 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N ARG M 188 " --> pdb=" O PHE M 168 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ASP M 170 " --> pdb=" O ALA M 186 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALA M 186 " --> pdb=" O ASP M 170 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N GLY M 193 " --> pdb=" O MET M 213 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N MET M 213 " --> pdb=" O GLY M 193 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ILE M 195 " --> pdb=" O THR M 211 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N THR M 211 " --> pdb=" O ILE M 195 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N GLU M 197 " --> pdb=" O ALA M 209 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'M' and resid 221 through 229 removed outlier: 6.572A pdb=" N ILE M 236 " --> pdb=" O PRO M 224 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N VAL M 226 " --> pdb=" O TYR M 234 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N TYR M 234 " --> pdb=" O VAL M 226 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LYS M 228 " --> pdb=" O TRP M 232 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N TRP M 232 " --> pdb=" O LYS M 228 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'M' and resid 283 through 289 removed outlier: 5.831A pdb=" N ALA M 284 " --> pdb=" O TRP M 299 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N TRP M 299 " --> pdb=" O ALA M 284 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ARG M 294 " --> pdb=" O LEU M 327 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'M' and resid 349 through 351 removed outlier: 4.098A pdb=" N VAL M 500 " --> pdb=" O GLN M 351 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'M' and resid 349 through 351 removed outlier: 4.098A pdb=" N VAL M 500 " --> pdb=" O GLN M 351 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VAL M 498 " --> pdb=" O SER M 389 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N SER M 389 " --> pdb=" O VAL M 498 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N VAL M 500 " --> pdb=" O LYS M 387 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LYS M 387 " --> pdb=" O VAL M 500 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N THR M 502 " --> pdb=" O HIS M 385 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N HIS M 385 " --> pdb=" O THR M 502 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'M' and resid 357 through 358 removed outlier: 3.846A pdb=" N ALA M 357 " --> pdb=" O ILE M 378 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE M 378 " --> pdb=" O ALA M 357 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N TRP M 484 " --> pdb=" O PHE M 379 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE M 401 " --> pdb=" O VAL M 419 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ALA M 426 " --> pdb=" O ASP M 440 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ASP M 440 " --> pdb=" O ALA M 426 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N PHE M 428 " --> pdb=" O LEU M 438 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 25 through 26 removed outlier: 3.646A pdb=" N SER G 19 " --> pdb=" O ASN G 55 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU G 53 " --> pdb=" O ARG G 21 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 28 through 30 removed outlier: 6.047A pdb=" N ILE G 36 " --> pdb=" O THR G 92 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N LYS G 94 " --> pdb=" O ILE G 36 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL G 38 " --> pdb=" O LYS G 94 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 28 through 30 removed outlier: 6.047A pdb=" N ILE G 36 " --> pdb=" O THR G 92 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N LYS G 94 " --> pdb=" O ILE G 36 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL G 38 " --> pdb=" O LYS G 94 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ASN I 262 " --> pdb=" O TYR I 274 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N MET I 276 " --> pdb=" O ALA I 260 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ALA I 260 " --> pdb=" O MET I 276 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 101 through 104 removed outlier: 4.097A pdb=" N ILE A 179 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N THR A 203 " --> pdb=" O GLU A 177 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ILE A 179 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE A 201 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N VAL A 181 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL A 199 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU A 156 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N ILE A 202 " --> pdb=" O LEU A 156 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ILE A 158 " --> pdb=" O ILE A 202 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N THR A 204 " --> pdb=" O ILE A 158 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 128 through 131 Processing sheet with id=AD2, first strand: chain 'A' and resid 984 through 986 removed outlier: 3.724A pdb=" N VAL A 304 " --> pdb=" O LEU A 331 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ARG A 421 " --> pdb=" O ARG A 457 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ARG A 457 " --> pdb=" O ARG A 421 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N MET A 487 " --> pdb=" O GLY A 448 " (cutoff:3.500A) removed outlier: 10.467A pdb=" N THR A 591 " --> pdb=" O GLY A 626 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N GLY A 626 " --> pdb=" O THR A 591 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLN A 879 " --> pdb=" O LEU A 951 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N LEU A 951 " --> pdb=" O GLN A 879 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N VAL A 881 " --> pdb=" O LEU A 949 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N LEU A 949 " --> pdb=" O VAL A 881 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 464 through 465 Processing sheet with id=AD4, first strand: chain 'A' and resid 638 through 640 removed outlier: 6.480A pdb=" N ILE A 638 " --> pdb=" O ASN A 676 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 719 through 723 Processing sheet with id=AD6, first strand: chain 'A' and resid 804 through 806 removed outlier: 6.788A pdb=" N GLN A 804 " --> pdb=" O ILE A 852 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 809 through 812 removed outlier: 4.448A pdb=" N GLY A 811 " --> pdb=" O ARG A 834 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 885 through 887 Processing sheet with id=AD9, first strand: chain 'I' and resid 101 through 104 removed outlier: 4.096A pdb=" N ILE I 179 " --> pdb=" O VAL I 104 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N THR I 203 " --> pdb=" O GLU I 177 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ILE I 179 " --> pdb=" O ILE I 201 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE I 201 " --> pdb=" O ILE I 179 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N VAL I 181 " --> pdb=" O VAL I 199 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL I 199 " --> pdb=" O VAL I 181 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LEU I 156 " --> pdb=" O ILE I 200 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N ILE I 202 " --> pdb=" O LEU I 156 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ILE I 158 " --> pdb=" O ILE I 202 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N THR I 204 " --> pdb=" O ILE I 158 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 128 through 131 Processing sheet with id=AE2, first strand: chain 'I' and resid 984 through 986 removed outlier: 3.724A pdb=" N VAL I 304 " --> pdb=" O LEU I 331 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ARG I 421 " --> pdb=" O ARG I 457 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ARG I 457 " --> pdb=" O ARG I 421 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N MET I 487 " --> pdb=" O GLY I 448 " (cutoff:3.500A) removed outlier: 10.467A pdb=" N THR I 591 " --> pdb=" O GLY I 626 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N GLY I 626 " --> pdb=" O THR I 591 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N GLN I 879 " --> pdb=" O LEU I 951 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N LEU I 951 " --> pdb=" O GLN I 879 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N VAL I 881 " --> pdb=" O LEU I 949 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N LEU I 949 " --> pdb=" O VAL I 881 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 464 through 465 Processing sheet with id=AE4, first strand: chain 'I' and resid 638 through 640 removed outlier: 6.480A pdb=" N ILE I 638 " --> pdb=" O ASN I 676 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 719 through 723 Processing sheet with id=AE6, first strand: chain 'I' and resid 804 through 806 removed outlier: 6.788A pdb=" N GLN I 804 " --> pdb=" O ILE I 852 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 809 through 812 removed outlier: 4.447A pdb=" N GLY I 811 " --> pdb=" O ARG I 834 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 885 through 887 1084 hydrogen bonds defined for protein. 2922 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.71 Time building geometry restraints manager: 2.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7765 1.34 - 1.46: 5876 1.46 - 1.58: 10457 1.58 - 1.69: 0 1.69 - 1.81: 162 Bond restraints: 24260 Sorted by residual: bond pdb=" C ALA I 757 " pdb=" N PHE I 758 " ideal model delta sigma weight residual 1.334 1.365 -0.032 1.24e-02 6.50e+03 6.52e+00 bond pdb=" C ALA A 757 " pdb=" N PHE A 758 " ideal model delta sigma weight residual 1.334 1.365 -0.032 1.24e-02 6.50e+03 6.51e+00 bond pdb=" C ALA A 757 " pdb=" O ALA A 757 " ideal model delta sigma weight residual 1.237 1.264 -0.027 1.17e-02 7.31e+03 5.49e+00 bond pdb=" C ALA I 757 " pdb=" O ALA I 757 " ideal model delta sigma weight residual 1.237 1.264 -0.027 1.17e-02 7.31e+03 5.41e+00 bond pdb=" CA ILE M 268 " pdb=" CB ILE M 268 " ideal model delta sigma weight residual 1.540 1.525 0.015 1.36e-02 5.41e+03 1.15e+00 ... (remaining 24255 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.88: 32777 2.88 - 5.76: 105 5.76 - 8.65: 2 8.65 - 11.53: 4 11.53 - 14.41: 2 Bond angle restraints: 32890 Sorted by residual: angle pdb=" N VAL A 86 " pdb=" CA VAL A 86 " pdb=" C VAL A 86 " ideal model delta sigma weight residual 111.77 106.89 4.88 1.04e+00 9.25e-01 2.20e+01 angle pdb=" N VAL I 86 " pdb=" CA VAL I 86 " pdb=" C VAL I 86 " ideal model delta sigma weight residual 111.77 106.93 4.84 1.04e+00 9.25e-01 2.17e+01 angle pdb=" CA MET A 968 " pdb=" CB MET A 968 " pdb=" CG MET A 968 " ideal model delta sigma weight residual 114.10 123.22 -9.12 2.00e+00 2.50e-01 2.08e+01 angle pdb=" CA MET I 968 " pdb=" CB MET I 968 " pdb=" CG MET I 968 " ideal model delta sigma weight residual 114.10 123.20 -9.10 2.00e+00 2.50e-01 2.07e+01 angle pdb=" CA LEU I 121 " pdb=" CB LEU I 121 " pdb=" CG LEU I 121 " ideal model delta sigma weight residual 116.30 130.71 -14.41 3.50e+00 8.16e-02 1.70e+01 ... (remaining 32885 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.06: 13293 15.06 - 30.13: 683 30.13 - 45.19: 170 45.19 - 60.26: 22 60.26 - 75.32: 6 Dihedral angle restraints: 14174 sinusoidal: 5590 harmonic: 8584 Sorted by residual: dihedral pdb=" CA MET M 215 " pdb=" C MET M 215 " pdb=" N MET M 216 " pdb=" CA MET M 216 " ideal model delta harmonic sigma weight residual 180.00 -162.23 -17.77 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA MET E 215 " pdb=" C MET E 215 " pdb=" N MET E 216 " pdb=" CA MET E 216 " ideal model delta harmonic sigma weight residual 180.00 -162.27 -17.73 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA ASP A 96 " pdb=" CB ASP A 96 " pdb=" CG ASP A 96 " pdb=" OD1 ASP A 96 " ideal model delta sinusoidal sigma weight residual -30.00 -89.17 59.17 1 2.00e+01 2.50e-03 1.17e+01 ... (remaining 14171 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 2233 0.033 - 0.065: 822 0.065 - 0.098: 203 0.098 - 0.130: 179 0.130 - 0.163: 11 Chirality restraints: 3448 Sorted by residual: chirality pdb=" CA ASP A 717 " pdb=" N ASP A 717 " pdb=" C ASP A 717 " pdb=" CB ASP A 717 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.62e-01 chirality pdb=" CA ASP I 717 " pdb=" N ASP I 717 " pdb=" C ASP I 717 " pdb=" CB ASP I 717 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.27e-01 chirality pdb=" CA ILE E 195 " pdb=" N ILE E 195 " pdb=" C ILE E 195 " pdb=" CB ILE E 195 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.09e-01 ... (remaining 3445 not shown) Planarity restraints: 4300 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET I 968 " -0.007 2.00e-02 2.50e+03 1.38e-02 1.90e+00 pdb=" C MET I 968 " 0.024 2.00e-02 2.50e+03 pdb=" O MET I 968 " -0.009 2.00e-02 2.50e+03 pdb=" N ARG I 969 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 968 " 0.007 2.00e-02 2.50e+03 1.37e-02 1.89e+00 pdb=" C MET A 968 " -0.024 2.00e-02 2.50e+03 pdb=" O MET A 968 " 0.009 2.00e-02 2.50e+03 pdb=" N ARG A 969 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE I 592 " -0.021 5.00e-02 4.00e+02 3.24e-02 1.68e+00 pdb=" N PRO I 593 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO I 593 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO I 593 " -0.018 5.00e-02 4.00e+02 ... (remaining 4297 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 412 2.66 - 3.22: 21431 3.22 - 3.78: 36801 3.78 - 4.34: 51772 4.34 - 4.90: 86982 Nonbonded interactions: 197398 Sorted by model distance: nonbonded pdb=" OD2 ASP A 848 " pdb="MG MG A1101 " model vdw 2.100 2.170 nonbonded pdb=" OD2 ASP I 848 " pdb="MG MG I1101 " model vdw 2.100 2.170 nonbonded pdb=" OD1 ASN I 841 " pdb="MG MG I1101 " model vdw 2.103 2.170 nonbonded pdb=" OD1 ASN A 841 " pdb="MG MG A1101 " model vdw 2.103 2.170 nonbonded pdb=" OD1 ASP A 837 " pdb="MG MG A1101 " model vdw 2.115 2.170 ... (remaining 197393 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: 0.04 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'M' } ncs_group { reference = chain 'T' selection = chain 'G' } ncs_group { reference = chain 'A' selection = chain 'I' } 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 group one per residue 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: 1.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 27.500 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 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 : 0.002 0.032 24260 Z= 0.108 Angle : 0.479 14.411 32890 Z= 0.257 Chirality : 0.043 0.163 3448 Planarity : 0.003 0.032 4300 Dihedral : 9.988 75.322 8750 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.21 % Favored : 95.73 % Rotamer: Outliers : 0.04 % Allowed : 4.96 % Favored : 95.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.16), residues: 2972 helix: 1.57 (0.37), residues: 218 sheet: 0.96 (0.15), residues: 1168 loop : -0.59 (0.15), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 408 TYR 0.010 0.001 TYR I 422 PHE 0.010 0.001 PHE I 558 TRP 0.008 0.001 TRP A 878 HIS 0.004 0.001 HIS E 71 Details of bonding type rmsd covalent geometry : bond 0.00210 (24260) covalent geometry : angle 0.47919 (32890) hydrogen bonds : bond 0.10930 ( 1044) hydrogen bonds : angle 5.73353 ( 2922) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 87 time to evaluate : 0.841 Fit side-chains REVERT: M 356 MET cc_start: 0.8538 (mmm) cc_final: 0.8085 (mmp) REVERT: A 241 MET cc_start: 0.8922 (ttt) cc_final: 0.8721 (ttt) REVERT: I 241 MET cc_start: 0.9017 (ttt) cc_final: 0.8697 (ttt) REVERT: I 561 MET cc_start: 0.8232 (tmm) cc_final: 0.7967 (tmm) outliers start: 1 outliers final: 0 residues processed: 87 average time/residue: 0.1339 time to fit residues: 19.9719 Evaluate side-chains 77 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 9.9990 chunk 111 optimal weight: 8.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 22 GLN E 248 GLN E 427 ASN ** E 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 22 GLN M 248 GLN M 427 ASN ** M 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 243 GLN A 247 ASN A 309 ASN A 627 ASN A1013 ASN I 151 ASN I 243 GLN I 247 ASN I 453 ASN I 480 GLN I 627 ASN I 754 ASN I1013 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.040464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.032577 restraints weight = 150938.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.033383 restraints weight = 64920.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.033908 restraints weight = 38213.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.034143 restraints weight = 26120.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.034249 restraints weight = 23209.466| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 24260 Z= 0.212 Angle : 0.543 9.672 32890 Z= 0.292 Chirality : 0.044 0.170 3448 Planarity : 0.003 0.040 4300 Dihedral : 4.117 17.394 3290 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.91 % Favored : 95.02 % Rotamer: Outliers : 0.52 % Allowed : 6.75 % Favored : 92.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.15), residues: 2972 helix: 0.84 (0.36), residues: 230 sheet: 0.87 (0.15), residues: 1200 loop : -0.73 (0.16), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 576 TYR 0.017 0.002 TYR M 415 PHE 0.013 0.001 PHE T 72 TRP 0.009 0.001 TRP A 685 HIS 0.006 0.001 HIS I 482 Details of bonding type rmsd covalent geometry : bond 0.00463 (24260) covalent geometry : angle 0.54270 (32890) hydrogen bonds : bond 0.02979 ( 1044) hydrogen bonds : angle 4.91977 ( 2922) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.887 Fit side-chains REVERT: E 215 MET cc_start: 0.7217 (mmm) cc_final: 0.6898 (mmm) REVERT: E 216 MET cc_start: 0.7844 (mmm) cc_final: 0.7400 (tpp) REVERT: E 229 MET cc_start: 0.8982 (mmm) cc_final: 0.8506 (ttm) REVERT: M 213 MET cc_start: 0.8413 (mtp) cc_final: 0.7892 (mtp) REVERT: M 215 MET cc_start: 0.7289 (mmm) cc_final: 0.7080 (mmm) REVERT: G 14 ASP cc_start: 0.8212 (OUTLIER) cc_final: 0.7887 (t0) REVERT: A 241 MET cc_start: 0.9077 (ttt) cc_final: 0.8824 (ttt) REVERT: A 561 MET cc_start: 0.8107 (tmm) cc_final: 0.7781 (tmm) REVERT: A 722 MET cc_start: 0.8214 (tpp) cc_final: 0.7769 (tpp) REVERT: A 968 MET cc_start: 0.7559 (tpp) cc_final: 0.7168 (tpp) REVERT: I 241 MET cc_start: 0.9137 (ttt) cc_final: 0.8854 (ttt) REVERT: I 427 MET cc_start: 0.7595 (OUTLIER) cc_final: 0.7336 (mmm) REVERT: I 561 MET cc_start: 0.8167 (tmm) cc_final: 0.7876 (tmm) REVERT: I 968 MET cc_start: 0.7619 (tpp) cc_final: 0.7287 (tpt) outliers start: 13 outliers final: 6 residues processed: 83 average time/residue: 0.1323 time to fit residues: 19.3911 Evaluate side-chains 85 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain T residue 22 LEU Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain G residue 14 ASP Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain I residue 427 MET Chi-restraints excluded: chain I residue 487 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 7 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 151 optimal weight: 8.9990 chunk 85 optimal weight: 0.0070 chunk 248 optimal weight: 6.9990 chunk 150 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 178 optimal weight: 9.9990 chunk 154 optimal weight: 10.0000 chunk 244 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 overall best weight: 4.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 ASN A 453 ASN A 480 GLN I 197 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.040554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.032640 restraints weight = 150390.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.033495 restraints weight = 64423.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.033911 restraints weight = 36104.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.034252 restraints weight = 26947.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.034303 restraints weight = 22685.837| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 24260 Z= 0.178 Angle : 0.492 7.976 32890 Z= 0.266 Chirality : 0.043 0.157 3448 Planarity : 0.003 0.038 4300 Dihedral : 4.031 18.565 3290 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.58 % Favored : 95.36 % Rotamer: Outliers : 0.87 % Allowed : 7.42 % Favored : 91.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.15), residues: 2972 helix: 1.00 (0.37), residues: 220 sheet: 0.81 (0.15), residues: 1204 loop : -0.67 (0.16), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 294 TYR 0.015 0.001 TYR I 422 PHE 0.014 0.001 PHE I 758 TRP 0.011 0.001 TRP M 318 HIS 0.004 0.001 HIS M 71 Details of bonding type rmsd covalent geometry : bond 0.00388 (24260) covalent geometry : angle 0.49193 (32890) hydrogen bonds : bond 0.02813 ( 1044) hydrogen bonds : angle 4.81414 ( 2922) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 77 time to evaluate : 1.039 Fit side-chains REVERT: E 215 MET cc_start: 0.7500 (mmm) cc_final: 0.7080 (mmm) REVERT: E 216 MET cc_start: 0.7941 (mmm) cc_final: 0.7546 (tpp) REVERT: E 229 MET cc_start: 0.8991 (mmm) cc_final: 0.8570 (ttm) REVERT: M 216 MET cc_start: 0.8044 (mmm) cc_final: 0.7823 (tpp) REVERT: A 241 MET cc_start: 0.9085 (ttt) cc_final: 0.8807 (ttt) REVERT: A 561 MET cc_start: 0.8108 (tmm) cc_final: 0.7744 (tmm) REVERT: A 968 MET cc_start: 0.7437 (tpp) cc_final: 0.6902 (tpp) REVERT: I 241 MET cc_start: 0.9101 (ttt) cc_final: 0.8782 (ttt) REVERT: I 561 MET cc_start: 0.8121 (tmm) cc_final: 0.7815 (tmm) REVERT: I 968 MET cc_start: 0.7728 (tpp) cc_final: 0.7209 (tpp) outliers start: 22 outliers final: 12 residues processed: 91 average time/residue: 0.1331 time to fit residues: 21.5388 Evaluate side-chains 89 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain T residue 22 LEU Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 183 MET Chi-restraints excluded: chain A residue 453 ASN Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain I residue 433 VAL Chi-restraints excluded: chain I residue 487 MET Chi-restraints excluded: chain I residue 509 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 30 optimal weight: 0.0020 chunk 28 optimal weight: 20.0000 chunk 151 optimal weight: 9.9990 chunk 153 optimal weight: 0.9990 chunk 144 optimal weight: 0.9990 chunk 131 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 208 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 179 optimal weight: 8.9990 chunk 194 optimal weight: 9.9990 overall best weight: 2.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 453 ASN ** 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 = 0.3246 r_free = 0.3246 target = 0.040876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.032993 restraints weight = 152799.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.033837 restraints weight = 64635.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.034282 restraints weight = 35680.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.034648 restraints weight = 25962.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.034692 restraints weight = 21523.945| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 24260 Z= 0.113 Angle : 0.460 7.898 32890 Z= 0.250 Chirality : 0.043 0.144 3448 Planarity : 0.003 0.036 4300 Dihedral : 3.887 17.329 3290 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.34 % Favored : 95.59 % Rotamer: Outliers : 0.87 % Allowed : 7.70 % Favored : 91.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.15), residues: 2972 helix: 0.76 (0.36), residues: 232 sheet: 0.87 (0.15), residues: 1200 loop : -0.66 (0.16), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 294 TYR 0.013 0.001 TYR I 424 PHE 0.015 0.001 PHE I 758 TRP 0.012 0.001 TRP I 878 HIS 0.005 0.001 HIS M 71 Details of bonding type rmsd covalent geometry : bond 0.00243 (24260) covalent geometry : angle 0.45960 (32890) hydrogen bonds : bond 0.02509 ( 1044) hydrogen bonds : angle 4.68897 ( 2922) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 78 time to evaluate : 0.883 Fit side-chains REVERT: E 229 MET cc_start: 0.9077 (mmm) cc_final: 0.8662 (ttm) REVERT: M 213 MET cc_start: 0.8382 (mtp) cc_final: 0.7966 (mtp) REVERT: M 216 MET cc_start: 0.8079 (mmm) cc_final: 0.7730 (tpp) REVERT: A 241 MET cc_start: 0.9046 (ttt) cc_final: 0.8754 (ttt) REVERT: A 534 MET cc_start: 0.9091 (mtp) cc_final: 0.8812 (mtt) REVERT: A 561 MET cc_start: 0.8080 (tmm) cc_final: 0.7718 (tmm) REVERT: A 968 MET cc_start: 0.7425 (tpp) cc_final: 0.7106 (tpt) REVERT: I 561 MET cc_start: 0.8117 (tmm) cc_final: 0.7825 (tmm) REVERT: I 968 MET cc_start: 0.7772 (tpp) cc_final: 0.7286 (tpt) outliers start: 22 outliers final: 15 residues processed: 93 average time/residue: 0.1302 time to fit residues: 21.3946 Evaluate side-chains 92 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain T residue 22 LEU Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain I residue 433 VAL Chi-restraints excluded: chain I residue 487 MET Chi-restraints excluded: chain I residue 509 MET Chi-restraints excluded: chain I residue 574 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 293 optimal weight: 0.3980 chunk 55 optimal weight: 20.0000 chunk 165 optimal weight: 20.0000 chunk 63 optimal weight: 5.9990 chunk 151 optimal weight: 10.0000 chunk 122 optimal weight: 9.9990 chunk 268 optimal weight: 8.9990 chunk 163 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 127 optimal weight: 7.9990 chunk 220 optimal weight: 9.9990 overall best weight: 5.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 754 ASN A 955 GLN I 480 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.040119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.032205 restraints weight = 149412.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.032986 restraints weight = 64573.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.033390 restraints weight = 36420.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.033579 restraints weight = 29005.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.033723 restraints weight = 24135.173| |-----------------------------------------------------------------------------| r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 24260 Z= 0.213 Angle : 0.521 12.402 32890 Z= 0.279 Chirality : 0.044 0.150 3448 Planarity : 0.003 0.035 4300 Dihedral : 4.180 19.324 3290 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.18 % Favored : 94.75 % Rotamer: Outliers : 1.15 % Allowed : 8.02 % Favored : 90.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.15), residues: 2972 helix: 0.83 (0.37), residues: 218 sheet: 0.74 (0.15), residues: 1224 loop : -0.72 (0.16), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 576 TYR 0.016 0.001 TYR I 422 PHE 0.015 0.001 PHE I 758 TRP 0.010 0.001 TRP M 318 HIS 0.004 0.001 HIS E 71 Details of bonding type rmsd covalent geometry : bond 0.00468 (24260) covalent geometry : angle 0.52137 (32890) hydrogen bonds : bond 0.02855 ( 1044) hydrogen bonds : angle 4.86085 ( 2922) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 77 time to evaluate : 0.667 Fit side-chains REVERT: E 229 MET cc_start: 0.9090 (mmm) cc_final: 0.8560 (ttm) REVERT: E 384 VAL cc_start: 0.9327 (OUTLIER) cc_final: 0.9057 (p) REVERT: M 384 VAL cc_start: 0.9319 (OUTLIER) cc_final: 0.9063 (p) REVERT: A 241 MET cc_start: 0.9087 (ttt) cc_final: 0.8885 (ttm) REVERT: A 561 MET cc_start: 0.8075 (tmm) cc_final: 0.7764 (tmm) REVERT: I 241 MET cc_start: 0.9111 (ttt) cc_final: 0.8803 (ttt) REVERT: I 534 MET cc_start: 0.9232 (mtp) cc_final: 0.8945 (mtt) REVERT: I 561 MET cc_start: 0.8142 (tmm) cc_final: 0.7783 (tmm) REVERT: I 968 MET cc_start: 0.7767 (tpp) cc_final: 0.7216 (tpp) outliers start: 29 outliers final: 18 residues processed: 98 average time/residue: 0.1349 time to fit residues: 23.2085 Evaluate side-chains 97 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 77 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain T residue 22 LEU Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 183 MET Chi-restraints excluded: chain M residue 384 VAL Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain I residue 433 VAL Chi-restraints excluded: chain I residue 487 MET Chi-restraints excluded: chain I residue 509 MET Chi-restraints excluded: chain I residue 574 THR Chi-restraints excluded: chain I residue 796 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 111 optimal weight: 6.9990 chunk 36 optimal weight: 30.0000 chunk 65 optimal weight: 6.9990 chunk 282 optimal weight: 6.9990 chunk 158 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 39 optimal weight: 20.0000 chunk 147 optimal weight: 20.0000 chunk 1 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 69 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.039971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.032176 restraints weight = 151227.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.032895 restraints weight = 64549.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.033328 restraints weight = 36744.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.033599 restraints weight = 28537.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.033705 restraints weight = 23351.015| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 24260 Z= 0.276 Angle : 0.565 10.251 32890 Z= 0.302 Chirality : 0.045 0.158 3448 Planarity : 0.003 0.035 4300 Dihedral : 4.470 21.305 3290 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.25 % Favored : 94.68 % Rotamer: Outliers : 1.31 % Allowed : 8.41 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.15), residues: 2972 helix: 0.57 (0.36), residues: 218 sheet: 0.59 (0.15), residues: 1230 loop : -0.79 (0.16), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 910 TYR 0.017 0.002 TYR I 422 PHE 0.014 0.001 PHE I 758 TRP 0.013 0.001 TRP M 318 HIS 0.004 0.001 HIS E 71 Details of bonding type rmsd covalent geometry : bond 0.00607 (24260) covalent geometry : angle 0.56467 (32890) hydrogen bonds : bond 0.02997 ( 1044) hydrogen bonds : angle 5.05055 ( 2922) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 77 time to evaluate : 0.937 Fit side-chains REVERT: E 216 MET cc_start: 0.8268 (mmm) cc_final: 0.7864 (tpp) REVERT: E 229 MET cc_start: 0.9155 (mmm) cc_final: 0.8613 (ttm) REVERT: E 307 ASP cc_start: 0.8668 (OUTLIER) cc_final: 0.7900 (p0) REVERT: E 384 VAL cc_start: 0.9307 (OUTLIER) cc_final: 0.9046 (p) REVERT: M 216 MET cc_start: 0.8348 (mmm) cc_final: 0.8127 (mmm) REVERT: M 384 VAL cc_start: 0.9315 (OUTLIER) cc_final: 0.9064 (p) REVERT: A 241 MET cc_start: 0.9082 (ttt) cc_final: 0.8842 (ttt) REVERT: A 561 MET cc_start: 0.8064 (tmm) cc_final: 0.7745 (tmm) REVERT: A 968 MET cc_start: 0.7489 (tpt) cc_final: 0.6873 (tpp) REVERT: I 241 MET cc_start: 0.9146 (ttt) cc_final: 0.8824 (ttt) REVERT: I 561 MET cc_start: 0.8115 (tmm) cc_final: 0.7740 (tmm) REVERT: I 968 MET cc_start: 0.7635 (tpp) cc_final: 0.7274 (tpp) outliers start: 33 outliers final: 22 residues processed: 103 average time/residue: 0.1338 time to fit residues: 24.2264 Evaluate side-chains 102 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 77 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 307 ASP Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain T residue 22 LEU Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 176 THR Chi-restraints excluded: chain M residue 183 MET Chi-restraints excluded: chain M residue 384 VAL Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 219 SER Chi-restraints excluded: chain I residue 433 VAL Chi-restraints excluded: chain I residue 487 MET Chi-restraints excluded: chain I residue 509 MET Chi-restraints excluded: chain I residue 574 THR Chi-restraints excluded: chain I residue 796 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 225 optimal weight: 6.9990 chunk 137 optimal weight: 1.9990 chunk 26 optimal weight: 0.2980 chunk 19 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 10 optimal weight: 9.9990 chunk 243 optimal weight: 0.9990 chunk 245 optimal weight: 5.9990 chunk 262 optimal weight: 10.0000 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 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 = 0.3236 r_free = 0.3236 target = 0.040657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.032831 restraints weight = 150869.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.033607 restraints weight = 63806.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.034069 restraints weight = 36053.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.034233 restraints weight = 27667.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.034551 restraints weight = 23239.194| |-----------------------------------------------------------------------------| r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 24260 Z= 0.095 Angle : 0.474 9.574 32890 Z= 0.257 Chirality : 0.043 0.148 3448 Planarity : 0.003 0.034 4300 Dihedral : 4.031 19.424 3290 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.17 % Favored : 95.76 % Rotamer: Outliers : 0.79 % Allowed : 9.64 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.15), residues: 2972 helix: 0.83 (0.36), residues: 218 sheet: 0.76 (0.15), residues: 1204 loop : -0.73 (0.16), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 345 TYR 0.010 0.001 TYR I 422 PHE 0.013 0.001 PHE I 758 TRP 0.015 0.001 TRP I 878 HIS 0.004 0.001 HIS E 71 Details of bonding type rmsd covalent geometry : bond 0.00198 (24260) covalent geometry : angle 0.47416 (32890) hydrogen bonds : bond 0.02417 ( 1044) hydrogen bonds : angle 4.68701 ( 2922) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 77 time to evaluate : 0.741 Fit side-chains REVERT: E 216 MET cc_start: 0.8314 (mmm) cc_final: 0.7949 (tpp) REVERT: E 229 MET cc_start: 0.9107 (mmm) cc_final: 0.8578 (ttm) REVERT: E 384 VAL cc_start: 0.9309 (OUTLIER) cc_final: 0.9051 (p) REVERT: T 22 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8451 (mt) REVERT: M 216 MET cc_start: 0.8422 (mmm) cc_final: 0.8159 (mmm) REVERT: M 229 MET cc_start: 0.9105 (mmm) cc_final: 0.8551 (ttm) REVERT: M 384 VAL cc_start: 0.9306 (OUTLIER) cc_final: 0.9048 (p) REVERT: A 229 MET cc_start: 0.8451 (mtt) cc_final: 0.8239 (mtt) REVERT: A 241 MET cc_start: 0.9003 (ttt) cc_final: 0.8757 (ttt) REVERT: A 427 MET cc_start: 0.7644 (tpp) cc_final: 0.6984 (mmm) REVERT: A 561 MET cc_start: 0.8071 (tmm) cc_final: 0.7663 (tmm) REVERT: A 968 MET cc_start: 0.7548 (tpt) cc_final: 0.7203 (tpp) REVERT: I 229 MET cc_start: 0.8430 (mtt) cc_final: 0.8228 (mtt) REVERT: I 241 MET cc_start: 0.9075 (ttt) cc_final: 0.8731 (ttt) REVERT: I 561 MET cc_start: 0.8088 (tmm) cc_final: 0.7707 (tmm) REVERT: I 968 MET cc_start: 0.7546 (tpp) cc_final: 0.7217 (tpp) outliers start: 20 outliers final: 12 residues processed: 92 average time/residue: 0.1368 time to fit residues: 22.0609 Evaluate side-chains 92 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain T residue 22 LEU Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 384 VAL Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain I residue 219 SER Chi-restraints excluded: chain I residue 487 MET Chi-restraints excluded: chain I residue 574 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 180 optimal weight: 10.0000 chunk 28 optimal weight: 20.0000 chunk 274 optimal weight: 6.9990 chunk 71 optimal weight: 0.6980 chunk 186 optimal weight: 8.9990 chunk 133 optimal weight: 10.0000 chunk 235 optimal weight: 9.9990 chunk 222 optimal weight: 9.9990 chunk 290 optimal weight: 9.9990 chunk 203 optimal weight: 0.0010 chunk 84 optimal weight: 0.2980 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 467 ASN ** 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 = 0.3222 r_free = 0.3222 target = 0.040346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.032457 restraints weight = 151921.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.033267 restraints weight = 63745.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.033695 restraints weight = 35939.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.033879 restraints weight = 27955.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.034083 restraints weight = 23509.776| |-----------------------------------------------------------------------------| r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24260 Z= 0.152 Angle : 0.492 9.670 32890 Z= 0.264 Chirality : 0.043 0.138 3448 Planarity : 0.003 0.034 4300 Dihedral : 4.046 18.286 3290 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.61 % Favored : 95.32 % Rotamer: Outliers : 1.07 % Allowed : 9.40 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.15), residues: 2972 helix: 0.82 (0.36), residues: 218 sheet: 0.76 (0.15), residues: 1204 loop : -0.75 (0.16), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 576 TYR 0.013 0.001 TYR I 422 PHE 0.014 0.001 PHE I 758 TRP 0.011 0.001 TRP A 685 HIS 0.005 0.001 HIS E 71 Details of bonding type rmsd covalent geometry : bond 0.00332 (24260) covalent geometry : angle 0.49195 (32890) hydrogen bonds : bond 0.02585 ( 1044) hydrogen bonds : angle 4.69527 ( 2922) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 77 time to evaluate : 0.788 Fit side-chains REVERT: E 216 MET cc_start: 0.8451 (mmm) cc_final: 0.8111 (tpp) REVERT: E 229 MET cc_start: 0.9126 (mmm) cc_final: 0.8578 (ttm) REVERT: E 384 VAL cc_start: 0.9331 (OUTLIER) cc_final: 0.9075 (p) REVERT: T 22 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8453 (mt) REVERT: M 213 MET cc_start: 0.8580 (mtp) cc_final: 0.8143 (mtp) REVERT: M 215 MET cc_start: 0.7431 (mmm) cc_final: 0.7122 (mmm) REVERT: M 216 MET cc_start: 0.8528 (mmm) cc_final: 0.8259 (mmm) REVERT: M 229 MET cc_start: 0.9110 (mmm) cc_final: 0.8544 (ttm) REVERT: M 384 VAL cc_start: 0.9337 (OUTLIER) cc_final: 0.9083 (p) REVERT: A 561 MET cc_start: 0.8087 (tmm) cc_final: 0.7696 (tmm) REVERT: A 968 MET cc_start: 0.7565 (tpt) cc_final: 0.7213 (tpp) REVERT: I 241 MET cc_start: 0.9108 (ttt) cc_final: 0.8778 (ttt) REVERT: I 561 MET cc_start: 0.8106 (tmm) cc_final: 0.7716 (tmm) REVERT: I 968 MET cc_start: 0.7693 (tpp) cc_final: 0.7295 (tpp) outliers start: 27 outliers final: 16 residues processed: 97 average time/residue: 0.1295 time to fit residues: 22.2818 Evaluate side-chains 96 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain T residue 22 LEU Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 384 VAL Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain I residue 219 SER Chi-restraints excluded: chain I residue 364 THR Chi-restraints excluded: chain I residue 487 MET Chi-restraints excluded: chain I residue 574 THR Chi-restraints excluded: chain I residue 796 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 191 optimal weight: 7.9990 chunk 216 optimal weight: 10.0000 chunk 127 optimal weight: 7.9990 chunk 170 optimal weight: 7.9990 chunk 112 optimal weight: 5.9990 chunk 206 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 chunk 223 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 5 optimal weight: 9.9990 chunk 230 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 467 ASN ** 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 = 0.3223 r_free = 0.3223 target = 0.040313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.032495 restraints weight = 149462.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.033239 restraints weight = 63436.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.033722 restraints weight = 36046.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.033927 restraints weight = 27608.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.034093 restraints weight = 22925.514| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 24260 Z= 0.172 Angle : 0.503 10.129 32890 Z= 0.269 Chirality : 0.043 0.139 3448 Planarity : 0.003 0.034 4300 Dihedral : 4.135 19.049 3290 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.71 % Favored : 95.22 % Rotamer: Outliers : 0.91 % Allowed : 9.60 % Favored : 89.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.15), residues: 2972 helix: 0.80 (0.37), residues: 218 sheet: 0.70 (0.15), residues: 1222 loop : -0.77 (0.16), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 345 TYR 0.014 0.001 TYR I 422 PHE 0.014 0.001 PHE I 758 TRP 0.010 0.001 TRP I 685 HIS 0.005 0.001 HIS E 71 Details of bonding type rmsd covalent geometry : bond 0.00376 (24260) covalent geometry : angle 0.50299 (32890) hydrogen bonds : bond 0.02640 ( 1044) hydrogen bonds : angle 4.74463 ( 2922) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 77 time to evaluate : 0.902 Fit side-chains REVERT: E 215 MET cc_start: 0.7329 (mmm) cc_final: 0.7035 (mmm) REVERT: E 216 MET cc_start: 0.8575 (mmm) cc_final: 0.8244 (tpp) REVERT: E 229 MET cc_start: 0.9114 (mmm) cc_final: 0.8586 (ttm) REVERT: E 384 VAL cc_start: 0.9323 (OUTLIER) cc_final: 0.9056 (p) REVERT: T 22 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8470 (mt) REVERT: T 58 GLU cc_start: 0.8574 (pm20) cc_final: 0.8268 (pm20) REVERT: M 213 MET cc_start: 0.8654 (mtp) cc_final: 0.8205 (mtp) REVERT: M 216 MET cc_start: 0.8563 (mmm) cc_final: 0.8270 (mmm) REVERT: M 229 MET cc_start: 0.9100 (mmm) cc_final: 0.8538 (ttm) REVERT: M 384 VAL cc_start: 0.9343 (OUTLIER) cc_final: 0.9089 (p) REVERT: A 561 MET cc_start: 0.8069 (tmm) cc_final: 0.7703 (tmm) REVERT: A 968 MET cc_start: 0.7557 (tpt) cc_final: 0.7191 (tpp) REVERT: I 241 MET cc_start: 0.9109 (ttt) cc_final: 0.8782 (ttt) REVERT: I 561 MET cc_start: 0.8080 (tmm) cc_final: 0.7729 (tmm) REVERT: I 968 MET cc_start: 0.7628 (tpp) cc_final: 0.7253 (tpp) outliers start: 23 outliers final: 17 residues processed: 95 average time/residue: 0.1276 time to fit residues: 21.4321 Evaluate side-chains 97 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 77 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain T residue 22 LEU Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 384 VAL Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain I residue 219 SER Chi-restraints excluded: chain I residue 364 THR Chi-restraints excluded: chain I residue 433 VAL Chi-restraints excluded: chain I residue 487 MET Chi-restraints excluded: chain I residue 574 THR Chi-restraints excluded: chain I residue 796 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 63 optimal weight: 10.0000 chunk 197 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 169 optimal weight: 9.9990 chunk 253 optimal weight: 4.9990 chunk 273 optimal weight: 9.9990 chunk 150 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 199 optimal weight: 10.0000 chunk 287 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 467 ASN ** 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 = 0.3225 r_free = 0.3225 target = 0.040290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.032522 restraints weight = 149839.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.033237 restraints weight = 65445.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.033725 restraints weight = 37418.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.033968 restraints weight = 28364.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.034071 restraints weight = 23248.284| |-----------------------------------------------------------------------------| r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 24260 Z= 0.164 Angle : 0.500 10.293 32890 Z= 0.267 Chirality : 0.043 0.138 3448 Planarity : 0.003 0.034 4300 Dihedral : 4.116 18.966 3290 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.74 % Favored : 95.19 % Rotamer: Outliers : 0.99 % Allowed : 9.48 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.15), residues: 2972 helix: 0.82 (0.37), residues: 218 sheet: 0.72 (0.15), residues: 1204 loop : -0.76 (0.16), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 294 TYR 0.013 0.001 TYR I 422 PHE 0.013 0.001 PHE I 758 TRP 0.010 0.001 TRP I 878 HIS 0.005 0.001 HIS E 71 Details of bonding type rmsd covalent geometry : bond 0.00359 (24260) covalent geometry : angle 0.50041 (32890) hydrogen bonds : bond 0.02609 ( 1044) hydrogen bonds : angle 4.72691 ( 2922) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 77 time to evaluate : 0.765 Fit side-chains REVERT: E 216 MET cc_start: 0.8558 (mmm) cc_final: 0.8235 (tpp) REVERT: E 229 MET cc_start: 0.9022 (mmm) cc_final: 0.8480 (ttm) REVERT: E 384 VAL cc_start: 0.9314 (OUTLIER) cc_final: 0.9046 (p) REVERT: T 22 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8466 (mt) REVERT: T 58 GLU cc_start: 0.8575 (pm20) cc_final: 0.8267 (pm20) REVERT: M 213 MET cc_start: 0.8671 (mtp) cc_final: 0.8235 (mtp) REVERT: M 216 MET cc_start: 0.8607 (mmm) cc_final: 0.8272 (mmm) REVERT: M 229 MET cc_start: 0.9074 (mmm) cc_final: 0.8517 (ttm) REVERT: M 384 VAL cc_start: 0.9326 (OUTLIER) cc_final: 0.9069 (p) REVERT: A 561 MET cc_start: 0.8065 (tmm) cc_final: 0.7702 (tmm) REVERT: A 968 MET cc_start: 0.7563 (tpt) cc_final: 0.7202 (tpp) REVERT: I 241 MET cc_start: 0.9105 (ttt) cc_final: 0.8782 (ttt) REVERT: I 561 MET cc_start: 0.8080 (tmm) cc_final: 0.7722 (tmm) REVERT: I 968 MET cc_start: 0.7632 (tpp) cc_final: 0.7249 (tpp) outliers start: 25 outliers final: 20 residues processed: 97 average time/residue: 0.1331 time to fit residues: 22.7045 Evaluate side-chains 100 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 77 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain T residue 22 LEU Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 384 VAL Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain I residue 219 SER Chi-restraints excluded: chain I residue 364 THR Chi-restraints excluded: chain I residue 433 VAL Chi-restraints excluded: chain I residue 487 MET Chi-restraints excluded: chain I residue 574 THR Chi-restraints excluded: chain I residue 796 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 246 optimal weight: 10.0000 chunk 275 optimal weight: 9.9990 chunk 25 optimal weight: 30.0000 chunk 232 optimal weight: 9.9990 chunk 142 optimal weight: 9.9990 chunk 281 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 218 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 207 optimal weight: 10.0000 chunk 166 optimal weight: 3.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 467 ASN ** 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 = 0.3212 r_free = 0.3212 target = 0.040085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.032263 restraints weight = 148670.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.033045 restraints weight = 62673.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.033450 restraints weight = 35765.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.033681 restraints weight = 27778.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.033941 restraints weight = 22914.431| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 24260 Z= 0.214 Angle : 0.533 12.229 32890 Z= 0.283 Chirality : 0.043 0.143 3448 Planarity : 0.003 0.033 4300 Dihedral : 4.265 20.102 3290 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.15 % Favored : 94.78 % Rotamer: Outliers : 1.07 % Allowed : 9.44 % Favored : 89.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.16), residues: 2972 helix: 0.73 (0.37), residues: 218 sheet: 0.66 (0.15), residues: 1218 loop : -0.77 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 502 TYR 0.015 0.001 TYR A 422 PHE 0.014 0.001 PHE I 758 TRP 0.009 0.001 TRP I 685 HIS 0.005 0.001 HIS E 71 Details of bonding type rmsd covalent geometry : bond 0.00470 (24260) covalent geometry : angle 0.53345 (32890) hydrogen bonds : bond 0.02777 ( 1044) hydrogen bonds : angle 4.85348 ( 2922) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3183.67 seconds wall clock time: 56 minutes 44.94 seconds (3404.94 seconds total)