Starting phenix.real_space_refine on Fri May 23 04:48:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a9y_15288/05_2025/8a9y_15288.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a9y_15288/05_2025/8a9y_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_15288/05_2025/8a9y_15288.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a9y_15288/05_2025/8a9y_15288.map" model { file = "/net/cci-nas-00/data/ceres_data/8a9y_15288/05_2025/8a9y_15288.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a9y_15288/05_2025/8a9y_15288.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: "G" 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: T, I, M Time building chain proxies: 22.17, per 1000 atoms: 0.94 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: 5.18 Conformation dependent library (CDL) restraints added in 2.7 seconds 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: 3.43 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: 9.70 Time building geometry restraints manager: 6.10 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: 0.11 Found NCS groups: ncs_group { reference = chain 'G' selection = chain 'T' } ncs_group { reference = chain 'A' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'M' } 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: 1.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.850 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 60.210 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.930 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (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 TRP 0.008 0.001 TRP A 878 HIS 0.004 0.001 HIS E 71 PHE 0.010 0.001 PHE I 558 TYR 0.010 0.001 TYR I 422 ARG 0.001 0.000 ARG A 408 Details of bonding type rmsd hydrogen bonds : bond 0.10930 ( 1044) hydrogen bonds : angle 5.73353 ( 2922) covalent geometry : bond 0.00210 (24260) covalent geometry : angle 0.47919 (32890) *********************** 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 : 2.513 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: 0.3213 time to fit residues: 47.8198 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 : 2.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 249 optimal weight: 10.0000 chunk 224 optimal weight: 9.9990 chunk 124 optimal weight: 9.9990 chunk 76 optimal weight: 9.9990 chunk 151 optimal weight: 9.9990 chunk 119 optimal weight: 10.0000 chunk 232 optimal weight: 9.9990 chunk 89 optimal weight: 10.0000 chunk 141 optimal weight: 9.9990 chunk 172 optimal weight: 10.0000 chunk 268 optimal weight: 10.0000 overall best weight: 9.9990 ------------------------------------------------------------------------------- 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 151 ASN A 197 ASN A 243 GLN A 247 ASN A 309 ASN A 453 ASN A 480 GLN A 627 ASN I 151 ASN I 197 ASN I 243 GLN I 247 ASN I 453 ASN I 480 GLN I 627 ASN I 754 ASN I 997 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.039806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.031897 restraints weight = 152002.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.032679 restraints weight = 65289.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.033128 restraints weight = 38523.870| |-----------------------------------------------------------------------------| r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.053 24260 Z= 0.400 Angle : 0.685 10.695 32890 Z= 0.366 Chirality : 0.047 0.189 3448 Planarity : 0.004 0.044 4300 Dihedral : 4.789 22.135 3290 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.35 % Favored : 94.58 % Rotamer: Outliers : 0.75 % Allowed : 7.06 % Favored : 92.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.15), residues: 2972 helix: 0.51 (0.35), residues: 218 sheet: 0.68 (0.15), residues: 1206 loop : -0.80 (0.15), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP M 318 HIS 0.005 0.001 HIS M 418 PHE 0.019 0.002 PHE T 72 TYR 0.023 0.002 TYR I 639 ARG 0.005 0.001 ARG A 910 Details of bonding type rmsd hydrogen bonds : bond 0.03701 ( 1044) hydrogen bonds : angle 5.46375 ( 2922) covalent geometry : bond 0.00885 (24260) covalent geometry : angle 0.68459 (32890) *********************** 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 96 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 2.732 Fit side-chains REVERT: E 213 MET cc_start: 0.8372 (mtp) cc_final: 0.8017 (mtp) REVERT: E 215 MET cc_start: 0.7454 (mmm) cc_final: 0.7211 (mmm) REVERT: E 229 MET cc_start: 0.9057 (mmm) cc_final: 0.8636 (ttm) REVERT: M 215 MET cc_start: 0.7587 (mmm) cc_final: 0.7348 (mmm) REVERT: G 14 ASP cc_start: 0.8375 (OUTLIER) cc_final: 0.7899 (t0) REVERT: A 241 MET cc_start: 0.9139 (ttt) cc_final: 0.8861 (ttt) REVERT: A 534 MET cc_start: 0.9277 (mtp) cc_final: 0.8982 (mtt) REVERT: A 561 MET cc_start: 0.8138 (tmm) cc_final: 0.7810 (tmm) REVERT: A 968 MET cc_start: 0.7768 (tpp) cc_final: 0.7366 (tpp) REVERT: I 241 MET cc_start: 0.9132 (ttt) cc_final: 0.8850 (ttt) REVERT: I 534 MET cc_start: 0.9259 (mtp) cc_final: 0.8922 (mtt) REVERT: I 561 MET cc_start: 0.8185 (tmm) cc_final: 0.7899 (tmm) REVERT: I 968 MET cc_start: 0.7713 (tpp) cc_final: 0.7253 (tpp) outliers start: 19 outliers final: 12 residues processed: 87 average time/residue: 0.3091 time to fit residues: 47.7540 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 : 2.826 ------------------------------------------------------------------------------- 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 G residue 14 ASP Chi-restraints excluded: chain A residue 453 ASN Chi-restraints excluded: chain I residue 427 MET Chi-restraints excluded: chain I residue 453 ASN Chi-restraints excluded: chain I residue 487 MET Chi-restraints excluded: chain I residue 607 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 265 optimal weight: 5.9990 chunk 119 optimal weight: 0.9990 chunk 248 optimal weight: 5.9990 chunk 21 optimal weight: 20.0000 chunk 243 optimal weight: 0.9990 chunk 200 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 202 optimal weight: 5.9990 chunk 118 optimal weight: 10.0000 chunk 284 optimal weight: 0.9990 chunk 74 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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** A 754 ASN A 955 GLN I 997 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.040473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.032595 restraints weight = 151448.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.033385 restraints weight = 64272.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.033774 restraints weight = 37573.454| |-----------------------------------------------------------------------------| r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 24260 Z= 0.144 Angle : 0.494 7.716 32890 Z= 0.268 Chirality : 0.043 0.154 3448 Planarity : 0.003 0.038 4300 Dihedral : 4.217 20.709 3290 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.24 % Favored : 95.69 % Rotamer: Outliers : 0.91 % Allowed : 7.02 % Favored : 92.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.15), residues: 2972 helix: 0.78 (0.36), residues: 220 sheet: 0.82 (0.15), residues: 1172 loop : -0.74 (0.15), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 878 HIS 0.004 0.001 HIS I 482 PHE 0.015 0.001 PHE I 758 TYR 0.014 0.001 TYR I 422 ARG 0.003 0.000 ARG I 345 Details of bonding type rmsd hydrogen bonds : bond 0.02765 ( 1044) hydrogen bonds : angle 4.97194 ( 2922) covalent geometry : bond 0.00308 (24260) covalent geometry : angle 0.49447 (32890) *********************** 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 101 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 78 time to evaluate : 2.661 Fit side-chains REVERT: E 215 MET cc_start: 0.7351 (mmm) cc_final: 0.7046 (mmm) REVERT: E 216 MET cc_start: 0.7962 (mmm) cc_final: 0.7539 (tpp) REVERT: E 229 MET cc_start: 0.9069 (mmm) cc_final: 0.8674 (ttm) REVERT: M 213 MET cc_start: 0.8388 (mtp) cc_final: 0.7957 (mtp) REVERT: M 216 MET cc_start: 0.8101 (mmm) cc_final: 0.7808 (tpp) REVERT: A 241 MET cc_start: 0.9015 (ttt) cc_final: 0.8737 (ttt) REVERT: A 534 MET cc_start: 0.9177 (mtp) cc_final: 0.8930 (mtt) REVERT: A 561 MET cc_start: 0.8089 (tmm) cc_final: 0.7699 (tmm) REVERT: A 968 MET cc_start: 0.7767 (tpp) cc_final: 0.7406 (tpp) REVERT: A 970 MET cc_start: 0.8273 (ptp) cc_final: 0.7914 (ptp) REVERT: I 241 MET cc_start: 0.9011 (ttt) cc_final: 0.8734 (ttt) REVERT: I 534 MET cc_start: 0.9204 (mtp) cc_final: 0.8916 (mtt) REVERT: I 561 MET cc_start: 0.8114 (tmm) cc_final: 0.7788 (tmm) REVERT: I 968 MET cc_start: 0.7686 (tpp) cc_final: 0.7258 (tpt) outliers start: 23 outliers final: 14 residues processed: 92 average time/residue: 0.2937 time to fit residues: 47.8005 Evaluate side-chains 91 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 2.720 ------------------------------------------------------------------------------- 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 487 MET Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain I residue 427 MET 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 196 optimal weight: 2.9990 chunk 235 optimal weight: 0.9980 chunk 59 optimal weight: 7.9990 chunk 287 optimal weight: 7.9990 chunk 177 optimal weight: 0.0770 chunk 164 optimal weight: 10.0000 chunk 277 optimal weight: 20.0000 chunk 211 optimal weight: 9.9990 chunk 128 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 chunk 251 optimal weight: 6.9990 overall best weight: 3.4144 ------------------------------------------------------------------------------- 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 = 0.040290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.032415 restraints weight = 150382.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.033211 restraints weight = 64551.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.033585 restraints weight = 37620.914| |-----------------------------------------------------------------------------| r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2246 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= 0.154 Angle : 0.486 8.787 32890 Z= 0.262 Chirality : 0.043 0.148 3448 Planarity : 0.003 0.036 4300 Dihedral : 4.083 18.330 3290 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.74 % Favored : 95.19 % Rotamer: Outliers : 1.15 % Allowed : 8.29 % Favored : 90.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.15), residues: 2972 helix: 0.89 (0.36), residues: 218 sheet: 0.73 (0.15), residues: 1204 loop : -0.73 (0.16), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 878 HIS 0.005 0.001 HIS I 482 PHE 0.015 0.001 PHE I 758 TYR 0.013 0.001 TYR I 422 ARG 0.002 0.000 ARG A 576 Details of bonding type rmsd hydrogen bonds : bond 0.02663 ( 1044) hydrogen bonds : angle 4.80536 ( 2922) covalent geometry : bond 0.00336 (24260) covalent geometry : angle 0.48605 (32890) *********************** 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 106 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 77 time to evaluate : 2.557 Fit side-chains REVERT: E 229 MET cc_start: 0.9119 (mmm) cc_final: 0.8549 (ttm) REVERT: E 307 ASP cc_start: 0.8683 (OUTLIER) cc_final: 0.8021 (p0) REVERT: M 307 ASP cc_start: 0.8705 (OUTLIER) cc_final: 0.8120 (p0) REVERT: A 241 MET cc_start: 0.9027 (ttt) cc_final: 0.8756 (ttt) REVERT: A 561 MET cc_start: 0.8098 (tmm) cc_final: 0.7686 (tmm) REVERT: A 968 MET cc_start: 0.7802 (tpp) cc_final: 0.7451 (tpp) REVERT: A 970 MET cc_start: 0.8331 (ptp) cc_final: 0.7978 (ptp) REVERT: I 241 MET cc_start: 0.9035 (ttt) cc_final: 0.8761 (ttt) REVERT: I 561 MET cc_start: 0.8105 (tmm) cc_final: 0.7765 (tmm) REVERT: I 968 MET cc_start: 0.7860 (tpp) cc_final: 0.7369 (tpt) outliers start: 29 outliers final: 16 residues processed: 98 average time/residue: 0.3022 time to fit residues: 52.8939 Evaluate side-chains 94 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 2.527 ------------------------------------------------------------------------------- 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 307 ASP 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 307 ASP Chi-restraints excluded: chain G residue 56 LEU 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 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 128 optimal weight: 0.9990 chunk 7 optimal weight: 0.1980 chunk 287 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 chunk 168 optimal weight: 6.9990 chunk 208 optimal weight: 2.9990 chunk 39 optimal weight: 20.0000 chunk 28 optimal weight: 9.9990 chunk 173 optimal weight: 9.9990 chunk 122 optimal weight: 9.9990 chunk 179 optimal weight: 10.0000 overall best weight: 3.8388 ------------------------------------------------------------------------------- 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 = 0.3217 r_free = 0.3217 target = 0.040155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.032293 restraints weight = 150157.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.033057 restraints weight = 63947.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.033370 restraints weight = 37809.200| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 24260 Z= 0.166 Angle : 0.489 8.702 32890 Z= 0.264 Chirality : 0.043 0.146 3448 Planarity : 0.003 0.034 4300 Dihedral : 4.106 19.778 3290 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.68 % Favored : 95.26 % Rotamer: Outliers : 1.19 % Allowed : 8.65 % Favored : 90.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.15), residues: 2972 helix: 0.88 (0.37), residues: 218 sheet: 0.72 (0.15), residues: 1204 loop : -0.73 (0.16), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 878 HIS 0.005 0.001 HIS M 71 PHE 0.015 0.001 PHE I 758 TYR 0.014 0.001 TYR I 422 ARG 0.002 0.000 ARG A 910 Details of bonding type rmsd hydrogen bonds : bond 0.02662 ( 1044) hydrogen bonds : angle 4.77903 ( 2922) covalent geometry : bond 0.00363 (24260) covalent geometry : angle 0.48884 (32890) *********************** 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: 30 poor density : 76 time to evaluate : 2.495 Fit side-chains REVERT: E 229 MET cc_start: 0.9128 (mmm) cc_final: 0.8577 (ttm) REVERT: E 307 ASP cc_start: 0.8678 (OUTLIER) cc_final: 0.7987 (p0) REVERT: E 384 VAL cc_start: 0.9356 (OUTLIER) cc_final: 0.9094 (p) REVERT: M 216 MET cc_start: 0.8312 (mmm) cc_final: 0.7775 (tpp) REVERT: M 307 ASP cc_start: 0.8731 (OUTLIER) cc_final: 0.8092 (p0) REVERT: M 384 VAL cc_start: 0.9351 (OUTLIER) cc_final: 0.9096 (p) REVERT: A 241 MET cc_start: 0.9025 (ttt) cc_final: 0.8776 (ttt) REVERT: A 561 MET cc_start: 0.8095 (tmm) cc_final: 0.7677 (tmm) REVERT: A 968 MET cc_start: 0.7911 (tpp) cc_final: 0.7568 (tpt) REVERT: A 970 MET cc_start: 0.8360 (ptp) cc_final: 0.7996 (ptp) REVERT: I 241 MET cc_start: 0.9022 (ttt) cc_final: 0.8753 (ttt) REVERT: I 534 MET cc_start: 0.9191 (mtp) cc_final: 0.8891 (mtt) REVERT: I 561 MET cc_start: 0.8116 (tmm) cc_final: 0.7715 (tmm) REVERT: I 968 MET cc_start: 0.7831 (tpp) cc_final: 0.7275 (tpp) outliers start: 30 outliers final: 19 residues processed: 99 average time/residue: 0.2868 time to fit residues: 50.2391 Evaluate side-chains 99 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 76 time to evaluate : 2.474 ------------------------------------------------------------------------------- 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 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 307 ASP 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 364 THR 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 75 optimal weight: 20.0000 chunk 29 optimal weight: 9.9990 chunk 109 optimal weight: 20.0000 chunk 154 optimal weight: 0.9990 chunk 30 optimal weight: 20.0000 chunk 286 optimal weight: 10.0000 chunk 226 optimal weight: 3.9990 chunk 147 optimal weight: 0.9980 chunk 12 optimal weight: 20.0000 chunk 55 optimal weight: 20.0000 chunk 287 optimal weight: 5.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- 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 = 0.3211 r_free = 0.3211 target = 0.040144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.032282 restraints weight = 151458.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.033061 restraints weight = 64159.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.033631 restraints weight = 36296.222| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 24260 Z= 0.186 Angle : 0.500 8.962 32890 Z= 0.270 Chirality : 0.043 0.145 3448 Planarity : 0.003 0.034 4300 Dihedral : 4.151 19.006 3290 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.81 % Favored : 95.12 % Rotamer: Outliers : 1.63 % Allowed : 8.53 % Favored : 89.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.15), residues: 2972 helix: 0.82 (0.36), residues: 218 sheet: 0.66 (0.15), residues: 1222 loop : -0.76 (0.16), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 685 HIS 0.005 0.001 HIS E 71 PHE 0.015 0.001 PHE I 758 TYR 0.014 0.001 TYR I 422 ARG 0.002 0.000 ARG I 345 Details of bonding type rmsd hydrogen bonds : bond 0.02741 ( 1044) hydrogen bonds : angle 4.81312 ( 2922) covalent geometry : bond 0.00408 (24260) covalent geometry : angle 0.50048 (32890) *********************** 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 117 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 76 time to evaluate : 2.442 Fit side-chains REVERT: E 216 MET cc_start: 0.8252 (mmm) cc_final: 0.7777 (tpp) REVERT: E 229 MET cc_start: 0.9164 (mmm) cc_final: 0.8621 (ttm) REVERT: E 307 ASP cc_start: 0.8703 (OUTLIER) cc_final: 0.7995 (p0) REVERT: E 384 VAL cc_start: 0.9349 (OUTLIER) cc_final: 0.9087 (p) REVERT: M 216 MET cc_start: 0.8391 (mmm) cc_final: 0.7951 (tpp) REVERT: M 307 ASP cc_start: 0.8717 (OUTLIER) cc_final: 0.8043 (p0) REVERT: M 384 VAL cc_start: 0.9344 (OUTLIER) cc_final: 0.9085 (p) REVERT: A 241 MET cc_start: 0.9038 (ttt) cc_final: 0.8803 (ttm) REVERT: A 427 MET cc_start: 0.7923 (OUTLIER) cc_final: 0.7343 (mmm) REVERT: A 561 MET cc_start: 0.8106 (tmm) cc_final: 0.7723 (tmm) REVERT: A 968 MET cc_start: 0.7842 (tpp) cc_final: 0.7461 (tpt) REVERT: I 241 MET cc_start: 0.9037 (ttt) cc_final: 0.8778 (ttt) REVERT: I 561 MET cc_start: 0.8122 (tmm) cc_final: 0.7710 (tmm) REVERT: I 968 MET cc_start: 0.7708 (tpp) cc_final: 0.7151 (tpp) outliers start: 41 outliers final: 22 residues processed: 110 average time/residue: 0.2928 time to fit residues: 56.9457 Evaluate side-chains 103 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 76 time to evaluate : 2.543 ------------------------------------------------------------------------------- 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 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 307 ASP 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 364 THR Chi-restraints excluded: chain A residue 427 MET 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 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 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 79 optimal weight: 20.0000 chunk 16 optimal weight: 9.9990 chunk 56 optimal weight: 0.9990 chunk 232 optimal weight: 6.9990 chunk 279 optimal weight: 1.9990 chunk 83 optimal weight: 20.0000 chunk 29 optimal weight: 9.9990 chunk 35 optimal weight: 0.0980 chunk 107 optimal weight: 5.9990 chunk 274 optimal weight: 9.9990 chunk 73 optimal weight: 20.0000 overall best weight: 3.2188 ------------------------------------------------------------------------------- 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 = 0.3221 r_free = 0.3221 target = 0.040347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.032539 restraints weight = 152548.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.033347 restraints weight = 64709.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.033760 restraints weight = 36597.657| |-----------------------------------------------------------------------------| r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 24260 Z= 0.145 Angle : 0.489 9.485 32890 Z= 0.264 Chirality : 0.043 0.152 3448 Planarity : 0.003 0.033 4300 Dihedral : 4.083 19.816 3290 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.31 % Favored : 95.63 % Rotamer: Outliers : 1.51 % Allowed : 8.89 % Favored : 89.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.15), residues: 2972 helix: 0.89 (0.36), residues: 218 sheet: 0.71 (0.15), residues: 1204 loop : -0.74 (0.16), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 878 HIS 0.006 0.001 HIS M 71 PHE 0.014 0.001 PHE I 758 TYR 0.013 0.001 TYR A 422 ARG 0.002 0.000 ARG I 345 Details of bonding type rmsd hydrogen bonds : bond 0.02595 ( 1044) hydrogen bonds : angle 4.72977 ( 2922) covalent geometry : bond 0.00315 (24260) covalent geometry : angle 0.48900 (32890) *********************** 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 114 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 76 time to evaluate : 2.701 Fit side-chains REVERT: E 216 MET cc_start: 0.8321 (mmm) cc_final: 0.7896 (tpp) REVERT: E 229 MET cc_start: 0.9085 (mmm) cc_final: 0.8539 (ttm) REVERT: E 384 VAL cc_start: 0.9330 (OUTLIER) cc_final: 0.9067 (p) REVERT: T 22 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8424 (mt) REVERT: M 216 MET cc_start: 0.8391 (mmm) cc_final: 0.7988 (tpp) REVERT: M 307 ASP cc_start: 0.8645 (OUTLIER) cc_final: 0.7940 (p0) REVERT: M 384 VAL cc_start: 0.9319 (OUTLIER) cc_final: 0.9059 (p) REVERT: A 241 MET cc_start: 0.9032 (ttt) cc_final: 0.8790 (ttt) REVERT: A 561 MET cc_start: 0.8082 (tmm) cc_final: 0.7687 (tmm) REVERT: A 968 MET cc_start: 0.7777 (tpp) cc_final: 0.7463 (tpt) REVERT: I 241 MET cc_start: 0.9005 (ttt) cc_final: 0.8760 (ttt) REVERT: I 561 MET cc_start: 0.8116 (tmm) cc_final: 0.7684 (tmm) REVERT: I 968 MET cc_start: 0.7653 (tpp) cc_final: 0.7193 (tpp) outliers start: 38 outliers final: 25 residues processed: 103 average time/residue: 0.2964 time to fit residues: 53.9528 Evaluate side-chains 105 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 76 time to evaluate : 2.779 ------------------------------------------------------------------------------- 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 E residue 479 MET 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 307 ASP 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 487 MET Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 770 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 356 ILE 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 509 MET Chi-restraints excluded: chain I residue 574 THR Chi-restraints excluded: chain I residue 595 VAL Chi-restraints excluded: chain I residue 770 THR Chi-restraints excluded: chain I residue 796 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 94 optimal weight: 30.0000 chunk 206 optimal weight: 0.9990 chunk 169 optimal weight: 9.9990 chunk 266 optimal weight: 4.9990 chunk 93 optimal weight: 0.0670 chunk 191 optimal weight: 5.9990 chunk 4 optimal weight: 0.0670 chunk 134 optimal weight: 6.9990 chunk 84 optimal weight: 10.0000 chunk 214 optimal weight: 7.9990 chunk 104 optimal weight: 0.6980 overall best weight: 1.3660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.040684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.032910 restraints weight = 152144.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.033719 restraints weight = 63941.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.034037 restraints weight = 36447.650| |-----------------------------------------------------------------------------| r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 24260 Z= 0.092 Angle : 0.459 9.612 32890 Z= 0.249 Chirality : 0.043 0.137 3448 Planarity : 0.003 0.034 4300 Dihedral : 3.853 16.932 3290 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.24 % Favored : 95.69 % Rotamer: Outliers : 1.23 % Allowed : 9.33 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.15), residues: 2972 helix: 1.07 (0.37), residues: 218 sheet: 0.81 (0.15), residues: 1202 loop : -0.73 (0.16), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 878 HIS 0.007 0.001 HIS E 71 PHE 0.013 0.001 PHE I 758 TYR 0.010 0.001 TYR A 424 ARG 0.002 0.000 ARG G 48 Details of bonding type rmsd hydrogen bonds : bond 0.02366 ( 1044) hydrogen bonds : angle 4.53432 ( 2922) covalent geometry : bond 0.00195 (24260) covalent geometry : angle 0.45920 (32890) *********************** 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 107 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 76 time to evaluate : 2.531 Fit side-chains REVERT: E 44 MET cc_start: 0.8403 (tpp) cc_final: 0.7754 (mmt) REVERT: E 215 MET cc_start: 0.6533 (mmt) cc_final: 0.6246 (mmt) REVERT: E 229 MET cc_start: 0.9099 (mmm) cc_final: 0.8482 (ttm) REVERT: E 307 ASP cc_start: 0.8680 (OUTLIER) cc_final: 0.8056 (p0) REVERT: E 384 VAL cc_start: 0.9373 (OUTLIER) cc_final: 0.9123 (p) REVERT: T 22 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8441 (mt) REVERT: M 44 MET cc_start: 0.8378 (tpp) cc_final: 0.7755 (mmt) REVERT: M 216 MET cc_start: 0.8453 (mmm) cc_final: 0.8085 (tpp) REVERT: M 229 MET cc_start: 0.9112 (mmm) cc_final: 0.8555 (ttm) REVERT: M 384 VAL cc_start: 0.9361 (OUTLIER) cc_final: 0.9112 (p) REVERT: A 241 MET cc_start: 0.8972 (ttt) cc_final: 0.8734 (ttm) REVERT: A 561 MET cc_start: 0.8045 (tmm) cc_final: 0.7646 (tmm) REVERT: A 968 MET cc_start: 0.7792 (tpp) cc_final: 0.7452 (tpt) REVERT: I 561 MET cc_start: 0.8073 (tmm) cc_final: 0.7674 (tmm) REVERT: I 968 MET cc_start: 0.7697 (tpp) cc_final: 0.7295 (tpp) outliers start: 31 outliers final: 23 residues processed: 98 average time/residue: 0.2938 time to fit residues: 50.9813 Evaluate side-chains 103 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 76 time to evaluate : 2.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 307 ASP Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 479 MET 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 M residue 479 MET 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 364 THR Chi-restraints excluded: chain A residue 427 MET 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 356 ILE 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 770 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 11 optimal weight: 7.9990 chunk 152 optimal weight: 9.9990 chunk 208 optimal weight: 0.1980 chunk 156 optimal weight: 7.9990 chunk 77 optimal weight: 20.0000 chunk 80 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 111 optimal weight: 0.0470 chunk 247 optimal weight: 6.9990 chunk 154 optimal weight: 0.5980 chunk 293 optimal weight: 10.0000 overall best weight: 1.7682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.040610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.032867 restraints weight = 151854.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.033639 restraints weight = 65846.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.034162 restraints weight = 38067.886| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 24260 Z= 0.100 Angle : 0.466 14.882 32890 Z= 0.249 Chirality : 0.043 0.144 3448 Planarity : 0.003 0.033 4300 Dihedral : 3.820 17.519 3290 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.34 % Favored : 95.59 % Rotamer: Outliers : 1.35 % Allowed : 9.25 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.15), residues: 2972 helix: 1.08 (0.37), residues: 218 sheet: 0.85 (0.15), residues: 1200 loop : -0.72 (0.16), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 878 HIS 0.006 0.001 HIS M 71 PHE 0.013 0.001 PHE I 758 TYR 0.010 0.001 TYR A 422 ARG 0.002 0.000 ARG A 124 Details of bonding type rmsd hydrogen bonds : bond 0.02388 ( 1044) hydrogen bonds : angle 4.47076 ( 2922) covalent geometry : bond 0.00214 (24260) covalent geometry : angle 0.46649 (32890) *********************** 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 110 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 76 time to evaluate : 2.525 Fit side-chains REVERT: E 215 MET cc_start: 0.6978 (mmt) cc_final: 0.6379 (mmt) REVERT: E 216 MET cc_start: 0.8242 (mmm) cc_final: 0.7837 (tpp) REVERT: E 229 MET cc_start: 0.9081 (mmm) cc_final: 0.8523 (ttm) REVERT: E 307 ASP cc_start: 0.8652 (OUTLIER) cc_final: 0.8039 (p0) REVERT: E 384 VAL cc_start: 0.9336 (OUTLIER) cc_final: 0.9086 (p) REVERT: T 22 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8451 (mt) REVERT: M 213 MET cc_start: 0.8562 (mtp) cc_final: 0.8151 (mtp) REVERT: M 215 MET cc_start: 0.7336 (mmm) cc_final: 0.6924 (mmm) REVERT: M 216 MET cc_start: 0.8609 (mmm) cc_final: 0.8252 (tpp) REVERT: M 229 MET cc_start: 0.9067 (mmm) cc_final: 0.8511 (ttm) REVERT: M 384 VAL cc_start: 0.9325 (OUTLIER) cc_final: 0.9075 (p) REVERT: A 561 MET cc_start: 0.8057 (tmm) cc_final: 0.7654 (tmm) REVERT: A 968 MET cc_start: 0.7689 (tpp) cc_final: 0.7384 (tpt) REVERT: I 561 MET cc_start: 0.8066 (tmm) cc_final: 0.7673 (tmm) REVERT: I 968 MET cc_start: 0.7683 (tpp) cc_final: 0.7260 (tpp) outliers start: 34 outliers final: 26 residues processed: 102 average time/residue: 0.2921 time to fit residues: 52.6953 Evaluate side-chains 106 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 76 time to evaluate : 2.488 ------------------------------------------------------------------------------- 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 307 ASP Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 479 MET 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 M residue 479 MET 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 364 THR 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 A residue 770 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 356 ILE 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 595 VAL Chi-restraints excluded: chain I residue 770 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 225 optimal weight: 4.9990 chunk 264 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 chunk 146 optimal weight: 10.0000 chunk 82 optimal weight: 8.9990 chunk 251 optimal weight: 3.9990 chunk 45 optimal weight: 20.0000 chunk 281 optimal weight: 8.9990 chunk 141 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.040419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.032581 restraints weight = 153251.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.033383 restraints weight = 64078.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.033902 restraints weight = 37041.492| |-----------------------------------------------------------------------------| r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 24260 Z= 0.130 Angle : 0.480 13.720 32890 Z= 0.256 Chirality : 0.043 0.149 3448 Planarity : 0.003 0.032 4300 Dihedral : 3.887 16.830 3290 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.41 % Favored : 95.52 % Rotamer: Outliers : 1.31 % Allowed : 9.40 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.15), residues: 2972 helix: 1.04 (0.37), residues: 218 sheet: 0.83 (0.15), residues: 1198 loop : -0.71 (0.16), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 878 HIS 0.005 0.001 HIS M 71 PHE 0.013 0.001 PHE I 758 TYR 0.012 0.001 TYR A 422 ARG 0.002 0.000 ARG I 426 Details of bonding type rmsd hydrogen bonds : bond 0.02492 ( 1044) hydrogen bonds : angle 4.53236 ( 2922) covalent geometry : bond 0.00281 (24260) covalent geometry : angle 0.47960 (32890) ********************** 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 111 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 78 time to evaluate : 2.542 Fit side-chains REVERT: E 215 MET cc_start: 0.7095 (mmt) cc_final: 0.6590 (mmt) REVERT: E 216 MET cc_start: 0.8323 (mmm) cc_final: 0.7915 (tpp) REVERT: E 229 MET cc_start: 0.9125 (mmm) cc_final: 0.8566 (ttm) REVERT: E 307 ASP cc_start: 0.8688 (OUTLIER) cc_final: 0.8058 (p0) REVERT: E 384 VAL cc_start: 0.9367 (OUTLIER) cc_final: 0.9107 (p) REVERT: T 22 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8481 (mt) REVERT: M 213 MET cc_start: 0.8547 (mtp) cc_final: 0.8102 (mtp) REVERT: M 215 MET cc_start: 0.7499 (mmm) cc_final: 0.7108 (mmm) REVERT: M 216 MET cc_start: 0.8620 (mmm) cc_final: 0.8289 (tpp) REVERT: M 229 MET cc_start: 0.9110 (mmm) cc_final: 0.8533 (ttm) REVERT: M 384 VAL cc_start: 0.9359 (OUTLIER) cc_final: 0.9111 (p) REVERT: A 561 MET cc_start: 0.8050 (tmm) cc_final: 0.7647 (tmm) REVERT: A 968 MET cc_start: 0.7774 (tpp) cc_final: 0.7402 (tpt) REVERT: I 561 MET cc_start: 0.8061 (tmm) cc_final: 0.7648 (tmm) REVERT: I 968 MET cc_start: 0.7727 (tpp) cc_final: 0.7279 (tpp) outliers start: 33 outliers final: 28 residues processed: 103 average time/residue: 0.2870 time to fit residues: 52.3445 Evaluate side-chains 109 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 77 time to evaluate : 2.516 ------------------------------------------------------------------------------- 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 307 ASP Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 479 MET 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 M residue 479 MET 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 364 THR 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 A residue 595 VAL Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain I residue 121 LEU Chi-restraints excluded: chain I residue 219 SER Chi-restraints excluded: chain I residue 356 ILE 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 595 VAL Chi-restraints excluded: chain I residue 770 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 153 optimal weight: 1.9990 chunk 231 optimal weight: 9.9990 chunk 109 optimal weight: 0.9990 chunk 245 optimal weight: 9.9990 chunk 77 optimal weight: 8.9990 chunk 273 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 280 optimal weight: 0.0020 chunk 262 optimal weight: 10.0000 chunk 240 optimal weight: 2.9990 chunk 272 optimal weight: 4.9990 overall best weight: 1.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.040245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.032326 restraints weight = 150252.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.033157 restraints weight = 59106.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.033533 restraints weight = 32136.792| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 24260 Z= 0.105 Angle : 0.469 13.645 32890 Z= 0.251 Chirality : 0.043 0.152 3448 Planarity : 0.003 0.032 4300 Dihedral : 3.839 17.535 3290 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.37 % Favored : 95.56 % Rotamer: Outliers : 1.39 % Allowed : 9.37 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.15), residues: 2972 helix: 1.08 (0.36), residues: 218 sheet: 0.86 (0.15), residues: 1198 loop : -0.70 (0.16), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 878 HIS 0.006 0.001 HIS M 71 PHE 0.013 0.001 PHE I 758 TYR 0.011 0.001 TYR A 422 ARG 0.001 0.000 ARG G 48 Details of bonding type rmsd hydrogen bonds : bond 0.02385 ( 1044) hydrogen bonds : angle 4.47999 ( 2922) covalent geometry : bond 0.00225 (24260) covalent geometry : angle 0.46927 (32890) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5703.66 seconds wall clock time: 102 minutes 0.05 seconds (6120.05 seconds total)