Starting phenix.real_space_refine on Mon Aug 25 19:21:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8egs_28129/08_2025/8egs_28129.cif Found real_map, /net/cci-nas-00/data/ceres_data/8egs_28129/08_2025/8egs_28129.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8egs_28129/08_2025/8egs_28129.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8egs_28129/08_2025/8egs_28129.map" model { file = "/net/cci-nas-00/data/ceres_data/8egs_28129/08_2025/8egs_28129.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8egs_28129/08_2025/8egs_28129.cif" } resolution = 3.92 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 19506 2.51 5 N 5154 2.21 5 O 5928 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 234 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30696 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 153 Classifications: {'peptide': 20} Link IDs: {'PTRANS': 1, 'TRANS': 18} Chain: "B" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 153 Classifications: {'peptide': 20} Link IDs: {'PTRANS': 1, 'TRANS': 18} Chain: "C" Number of atoms: 4810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 586, 4810 Classifications: {'peptide': 586} Link IDs: {'PTRANS': 22, 'TRANS': 563} Restraints were copied for chains: D, G, J, L, O, E, H, I, M, P, F, K, N, Q, Y Time building chain proxies: 4.56, per 1000 atoms: 0.15 Number of scatterers: 30696 At special positions: 0 Unit cell: (110.224, 110.224, 171.312, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 5928 8.00 N 5154 7.00 C 19506 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=60, symmetry=0 Number of additional bonds: simple=60, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.37 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 476.8 nanoseconds 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7224 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 48 sheets defined 27.3% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'Y' and resid 28 through 38 Processing helix chain 'Y' and resid 67 through 72 Processing helix chain 'Y' and resid 110 through 116 Processing helix chain 'Y' and resid 119 through 124 Processing helix chain 'Y' and resid 135 through 148 Proline residue: Y 144 - end of helix Processing helix chain 'Y' and resid 200 through 204 removed outlier: 4.389A pdb=" N TYR Y 203 " --> pdb=" O THR Y 200 " (cutoff:3.500A) Processing helix chain 'Y' and resid 214 through 226 removed outlier: 4.138A pdb=" N ASN Y 219 " --> pdb=" O ARG Y 215 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASN Y 220 " --> pdb=" O GLU Y 216 " (cutoff:3.500A) Processing helix chain 'Y' and resid 228 through 234 removed outlier: 3.562A pdb=" N THR Y 232 " --> pdb=" O TYR Y 228 " (cutoff:3.500A) Processing helix chain 'Y' and resid 283 through 291 Processing helix chain 'Y' and resid 295 through 302 removed outlier: 4.578A pdb=" N HIS Y 300 " --> pdb=" O GLU Y 297 " (cutoff:3.500A) Processing helix chain 'Y' and resid 398 through 406 Processing helix chain 'Y' and resid 417 through 420 removed outlier: 4.004A pdb=" N ASN Y 420 " --> pdb=" O ASN Y 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 417 through 420' Processing helix chain 'Y' and resid 425 through 438 Processing helix chain 'Y' and resid 445 through 450 removed outlier: 3.716A pdb=" N SER Y 449 " --> pdb=" O THR Y 445 " (cutoff:3.500A) Processing helix chain 'Y' and resid 454 through 462 removed outlier: 3.599A pdb=" N ARG Y 462 " --> pdb=" O TYR Y 458 " (cutoff:3.500A) Processing helix chain 'Y' and resid 482 through 488 removed outlier: 3.515A pdb=" N ILE Y 486 " --> pdb=" O ASN Y 482 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN Y 488 " --> pdb=" O PHE Y 484 " (cutoff:3.500A) Processing helix chain 'Y' and resid 501 through 516 Processing helix chain 'Y' and resid 550 through 564 Processing helix chain 'Y' and resid 580 through 584 Processing helix chain 'C' and resid 28 through 38 Processing helix chain 'C' and resid 67 through 72 Processing helix chain 'C' and resid 110 through 116 Processing helix chain 'C' and resid 119 through 124 Processing helix chain 'C' and resid 135 through 148 Proline residue: C 144 - end of helix Processing helix chain 'C' and resid 200 through 204 removed outlier: 4.389A pdb=" N TYR C 203 " --> pdb=" O THR C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 226 removed outlier: 4.138A pdb=" N ASN C 219 " --> pdb=" O ARG C 215 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASN C 220 " --> pdb=" O GLU C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 234 removed outlier: 3.562A pdb=" N THR C 232 " --> pdb=" O TYR C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 291 Processing helix chain 'C' and resid 295 through 302 removed outlier: 4.578A pdb=" N HIS C 300 " --> pdb=" O GLU C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 406 Processing helix chain 'C' and resid 417 through 420 removed outlier: 4.004A pdb=" N ASN C 420 " --> pdb=" O ASN C 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 417 through 420' Processing helix chain 'C' and resid 425 through 438 Processing helix chain 'C' and resid 445 through 450 removed outlier: 3.716A pdb=" N SER C 449 " --> pdb=" O THR C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 462 removed outlier: 3.599A pdb=" N ARG C 462 " --> pdb=" O TYR C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 488 removed outlier: 3.515A pdb=" N ILE C 486 " --> pdb=" O ASN C 482 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN C 488 " --> pdb=" O PHE C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 516 Processing helix chain 'C' and resid 550 through 564 Processing helix chain 'C' and resid 580 through 584 Processing helix chain 'F' and resid 28 through 38 Processing helix chain 'F' and resid 67 through 72 Processing helix chain 'F' and resid 110 through 116 Processing helix chain 'F' and resid 119 through 124 Processing helix chain 'F' and resid 135 through 148 Proline residue: F 144 - end of helix Processing helix chain 'F' and resid 200 through 204 removed outlier: 4.389A pdb=" N TYR F 203 " --> pdb=" O THR F 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 226 removed outlier: 4.138A pdb=" N ASN F 219 " --> pdb=" O ARG F 215 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASN F 220 " --> pdb=" O GLU F 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 234 removed outlier: 3.562A pdb=" N THR F 232 " --> pdb=" O TYR F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 283 through 291 Processing helix chain 'F' and resid 295 through 302 removed outlier: 4.578A pdb=" N HIS F 300 " --> pdb=" O GLU F 297 " (cutoff:3.500A) Processing helix chain 'F' and resid 398 through 406 Processing helix chain 'F' and resid 417 through 420 removed outlier: 4.003A pdb=" N ASN F 420 " --> pdb=" O ASN F 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 417 through 420' Processing helix chain 'F' and resid 425 through 438 Processing helix chain 'F' and resid 445 through 450 removed outlier: 3.716A pdb=" N SER F 449 " --> pdb=" O THR F 445 " (cutoff:3.500A) Processing helix chain 'F' and resid 454 through 462 removed outlier: 3.600A pdb=" N ARG F 462 " --> pdb=" O TYR F 458 " (cutoff:3.500A) Processing helix chain 'F' and resid 482 through 488 removed outlier: 3.516A pdb=" N ILE F 486 " --> pdb=" O ASN F 482 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN F 488 " --> pdb=" O PHE F 484 " (cutoff:3.500A) Processing helix chain 'F' and resid 501 through 516 Processing helix chain 'F' and resid 550 through 564 Processing helix chain 'F' and resid 580 through 584 Processing helix chain 'K' and resid 28 through 38 Processing helix chain 'K' and resid 67 through 72 Processing helix chain 'K' and resid 110 through 116 Processing helix chain 'K' and resid 119 through 124 Processing helix chain 'K' and resid 135 through 148 Proline residue: K 144 - end of helix Processing helix chain 'K' and resid 200 through 204 removed outlier: 4.389A pdb=" N TYR K 203 " --> pdb=" O THR K 200 " (cutoff:3.500A) Processing helix chain 'K' and resid 214 through 226 removed outlier: 4.138A pdb=" N ASN K 219 " --> pdb=" O ARG K 215 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASN K 220 " --> pdb=" O GLU K 216 " (cutoff:3.500A) Processing helix chain 'K' and resid 228 through 234 removed outlier: 3.562A pdb=" N THR K 232 " --> pdb=" O TYR K 228 " (cutoff:3.500A) Processing helix chain 'K' and resid 283 through 291 Processing helix chain 'K' and resid 295 through 302 removed outlier: 4.578A pdb=" N HIS K 300 " --> pdb=" O GLU K 297 " (cutoff:3.500A) Processing helix chain 'K' and resid 398 through 406 Processing helix chain 'K' and resid 417 through 420 removed outlier: 4.004A pdb=" N ASN K 420 " --> pdb=" O ASN K 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 417 through 420' Processing helix chain 'K' and resid 425 through 438 Processing helix chain 'K' and resid 445 through 450 removed outlier: 3.716A pdb=" N SER K 449 " --> pdb=" O THR K 445 " (cutoff:3.500A) Processing helix chain 'K' and resid 454 through 462 removed outlier: 3.599A pdb=" N ARG K 462 " --> pdb=" O TYR K 458 " (cutoff:3.500A) Processing helix chain 'K' and resid 482 through 488 removed outlier: 3.515A pdb=" N ILE K 486 " --> pdb=" O ASN K 482 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN K 488 " --> pdb=" O PHE K 484 " (cutoff:3.500A) Processing helix chain 'K' and resid 501 through 516 Processing helix chain 'K' and resid 550 through 564 Processing helix chain 'K' and resid 580 through 584 Processing helix chain 'N' and resid 28 through 38 Processing helix chain 'N' and resid 67 through 72 Processing helix chain 'N' and resid 110 through 116 Processing helix chain 'N' and resid 119 through 124 Processing helix chain 'N' and resid 135 through 148 Proline residue: N 144 - end of helix Processing helix chain 'N' and resid 200 through 204 removed outlier: 4.389A pdb=" N TYR N 203 " --> pdb=" O THR N 200 " (cutoff:3.500A) Processing helix chain 'N' and resid 214 through 226 removed outlier: 4.138A pdb=" N ASN N 219 " --> pdb=" O ARG N 215 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASN N 220 " --> pdb=" O GLU N 216 " (cutoff:3.500A) Processing helix chain 'N' and resid 228 through 234 removed outlier: 3.562A pdb=" N THR N 232 " --> pdb=" O TYR N 228 " (cutoff:3.500A) Processing helix chain 'N' and resid 283 through 291 Processing helix chain 'N' and resid 295 through 302 removed outlier: 4.578A pdb=" N HIS N 300 " --> pdb=" O GLU N 297 " (cutoff:3.500A) Processing helix chain 'N' and resid 398 through 406 Processing helix chain 'N' and resid 417 through 420 removed outlier: 4.004A pdb=" N ASN N 420 " --> pdb=" O ASN N 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 417 through 420' Processing helix chain 'N' and resid 425 through 438 Processing helix chain 'N' and resid 445 through 450 removed outlier: 3.716A pdb=" N SER N 449 " --> pdb=" O THR N 445 " (cutoff:3.500A) Processing helix chain 'N' and resid 454 through 462 removed outlier: 3.600A pdb=" N ARG N 462 " --> pdb=" O TYR N 458 " (cutoff:3.500A) Processing helix chain 'N' and resid 482 through 488 removed outlier: 3.515A pdb=" N ILE N 486 " --> pdb=" O ASN N 482 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN N 488 " --> pdb=" O PHE N 484 " (cutoff:3.500A) Processing helix chain 'N' and resid 501 through 516 Processing helix chain 'N' and resid 550 through 564 Processing helix chain 'N' and resid 580 through 584 Processing helix chain 'Q' and resid 28 through 38 Processing helix chain 'Q' and resid 67 through 72 Processing helix chain 'Q' and resid 110 through 116 Processing helix chain 'Q' and resid 119 through 124 Processing helix chain 'Q' and resid 135 through 148 Proline residue: Q 144 - end of helix Processing helix chain 'Q' and resid 200 through 204 removed outlier: 4.389A pdb=" N TYR Q 203 " --> pdb=" O THR Q 200 " (cutoff:3.500A) Processing helix chain 'Q' and resid 214 through 226 removed outlier: 4.138A pdb=" N ASN Q 219 " --> pdb=" O ARG Q 215 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASN Q 220 " --> pdb=" O GLU Q 216 " (cutoff:3.500A) Processing helix chain 'Q' and resid 228 through 234 removed outlier: 3.562A pdb=" N THR Q 232 " --> pdb=" O TYR Q 228 " (cutoff:3.500A) Processing helix chain 'Q' and resid 283 through 291 Processing helix chain 'Q' and resid 295 through 302 removed outlier: 4.578A pdb=" N HIS Q 300 " --> pdb=" O GLU Q 297 " (cutoff:3.500A) Processing helix chain 'Q' and resid 398 through 406 Processing helix chain 'Q' and resid 417 through 420 removed outlier: 4.003A pdb=" N ASN Q 420 " --> pdb=" O ASN Q 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 417 through 420' Processing helix chain 'Q' and resid 425 through 438 Processing helix chain 'Q' and resid 445 through 450 removed outlier: 3.716A pdb=" N SER Q 449 " --> pdb=" O THR Q 445 " (cutoff:3.500A) Processing helix chain 'Q' and resid 454 through 462 removed outlier: 3.600A pdb=" N ARG Q 462 " --> pdb=" O TYR Q 458 " (cutoff:3.500A) Processing helix chain 'Q' and resid 482 through 488 removed outlier: 3.516A pdb=" N ILE Q 486 " --> pdb=" O ASN Q 482 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN Q 488 " --> pdb=" O PHE Q 484 " (cutoff:3.500A) Processing helix chain 'Q' and resid 501 through 516 Processing helix chain 'Q' and resid 550 through 564 Processing helix chain 'Q' and resid 580 through 584 Processing sheet with id=1, first strand: chain 'Y' and resid 44 through 46 removed outlier: 4.327A pdb=" N TYR Y 76 " --> pdb=" O PHE Y 12 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'Y' and resid 22 through 25 removed outlier: 6.394A pdb=" N THR Y 23 " --> pdb=" O TRP Y 568 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE Y 567 " --> pdb=" O ASN Y 536 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'Y' and resid 61 through 63 removed outlier: 3.753A pdb=" N LEU Y 63 " --> pdb=" O THR Y 103 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR Y 103 " --> pdb=" O LEU Y 63 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL Y 102 " --> pdb=" O VAL Y 98 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL Y 98 " --> pdb=" O VAL Y 102 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'Y' and resid 158 through 165 removed outlier: 6.603A pdb=" N ILE Y 497 " --> pdb=" O LEU Y 161 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ASN Y 163 " --> pdb=" O MET Y 495 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N MET Y 495 " --> pdb=" O ASN Y 163 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'Y' and resid 235 through 237 removed outlier: 3.667A pdb=" N LYS Y 237 " --> pdb=" O GLN Y 176 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'Y' and resid 235 through 237 removed outlier: 3.667A pdb=" N LYS Y 237 " --> pdb=" O GLN Y 176 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N LEU Y 210 " --> pdb=" O LEU Y 266 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU Y 266 " --> pdb=" O LEU Y 210 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'Y' and resid 281 through 282 removed outlier: 3.680A pdb=" N VAL Y 282 " --> pdb=" O VAL Y 332 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'Y' and resid 413 through 415 Processing sheet with id=9, first strand: chain 'C' and resid 44 through 46 removed outlier: 4.327A pdb=" N TYR C 76 " --> pdb=" O PHE C 12 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'C' and resid 22 through 25 removed outlier: 6.394A pdb=" N THR C 23 " --> pdb=" O TRP C 568 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE C 567 " --> pdb=" O ASN C 536 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'C' and resid 61 through 63 removed outlier: 3.753A pdb=" N LEU C 63 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR C 103 " --> pdb=" O LEU C 63 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL C 102 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL C 98 " --> pdb=" O VAL C 102 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'C' and resid 158 through 165 removed outlier: 6.604A pdb=" N ILE C 497 " --> pdb=" O LEU C 161 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ASN C 163 " --> pdb=" O MET C 495 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N MET C 495 " --> pdb=" O ASN C 163 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'C' and resid 235 through 237 removed outlier: 3.667A pdb=" N LYS C 237 " --> pdb=" O GLN C 176 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'C' and resid 235 through 237 removed outlier: 3.667A pdb=" N LYS C 237 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LEU C 210 " --> pdb=" O LEU C 266 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU C 266 " --> pdb=" O LEU C 210 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'C' and resid 281 through 282 removed outlier: 3.679A pdb=" N VAL C 282 " --> pdb=" O VAL C 332 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'C' and resid 413 through 415 Processing sheet with id=17, first strand: chain 'F' and resid 44 through 46 removed outlier: 4.328A pdb=" N TYR F 76 " --> pdb=" O PHE F 12 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'F' and resid 22 through 25 removed outlier: 6.394A pdb=" N THR F 23 " --> pdb=" O TRP F 568 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE F 567 " --> pdb=" O ASN F 536 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'F' and resid 61 through 63 removed outlier: 3.753A pdb=" N LEU F 63 " --> pdb=" O THR F 103 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR F 103 " --> pdb=" O LEU F 63 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL F 102 " --> pdb=" O VAL F 98 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL F 98 " --> pdb=" O VAL F 102 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'F' and resid 158 through 165 removed outlier: 6.603A pdb=" N ILE F 497 " --> pdb=" O LEU F 161 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ASN F 163 " --> pdb=" O MET F 495 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N MET F 495 " --> pdb=" O ASN F 163 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'F' and resid 235 through 237 removed outlier: 3.666A pdb=" N LYS F 237 " --> pdb=" O GLN F 176 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'F' and resid 235 through 237 removed outlier: 3.666A pdb=" N LYS F 237 " --> pdb=" O GLN F 176 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LEU F 210 " --> pdb=" O LEU F 266 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU F 266 " --> pdb=" O LEU F 210 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'F' and resid 281 through 282 removed outlier: 3.679A pdb=" N VAL F 282 " --> pdb=" O VAL F 332 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'F' and resid 413 through 415 Processing sheet with id=25, first strand: chain 'K' and resid 44 through 46 removed outlier: 4.327A pdb=" N TYR K 76 " --> pdb=" O PHE K 12 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'K' and resid 22 through 25 removed outlier: 6.394A pdb=" N THR K 23 " --> pdb=" O TRP K 568 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE K 567 " --> pdb=" O ASN K 536 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'K' and resid 61 through 63 removed outlier: 3.753A pdb=" N LEU K 63 " --> pdb=" O THR K 103 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR K 103 " --> pdb=" O LEU K 63 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL K 102 " --> pdb=" O VAL K 98 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL K 98 " --> pdb=" O VAL K 102 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'K' and resid 158 through 165 removed outlier: 6.603A pdb=" N ILE K 497 " --> pdb=" O LEU K 161 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ASN K 163 " --> pdb=" O MET K 495 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N MET K 495 " --> pdb=" O ASN K 163 " (cutoff:3.500A) Processing sheet with id=29, first strand: chain 'K' and resid 235 through 237 removed outlier: 3.667A pdb=" N LYS K 237 " --> pdb=" O GLN K 176 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'K' and resid 235 through 237 removed outlier: 3.667A pdb=" N LYS K 237 " --> pdb=" O GLN K 176 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N LEU K 210 " --> pdb=" O LEU K 266 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU K 266 " --> pdb=" O LEU K 210 " (cutoff:3.500A) Processing sheet with id=31, first strand: chain 'K' and resid 281 through 282 removed outlier: 3.680A pdb=" N VAL K 282 " --> pdb=" O VAL K 332 " (cutoff:3.500A) Processing sheet with id=32, first strand: chain 'K' and resid 413 through 415 Processing sheet with id=33, first strand: chain 'N' and resid 44 through 46 removed outlier: 4.327A pdb=" N TYR N 76 " --> pdb=" O PHE N 12 " (cutoff:3.500A) Processing sheet with id=34, first strand: chain 'N' and resid 22 through 25 removed outlier: 6.394A pdb=" N THR N 23 " --> pdb=" O TRP N 568 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE N 567 " --> pdb=" O ASN N 536 " (cutoff:3.500A) Processing sheet with id=35, first strand: chain 'N' and resid 61 through 63 removed outlier: 3.753A pdb=" N LEU N 63 " --> pdb=" O THR N 103 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR N 103 " --> pdb=" O LEU N 63 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL N 102 " --> pdb=" O VAL N 98 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL N 98 " --> pdb=" O VAL N 102 " (cutoff:3.500A) Processing sheet with id=36, first strand: chain 'N' and resid 158 through 165 removed outlier: 6.604A pdb=" N ILE N 497 " --> pdb=" O LEU N 161 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ASN N 163 " --> pdb=" O MET N 495 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N MET N 495 " --> pdb=" O ASN N 163 " (cutoff:3.500A) Processing sheet with id=37, first strand: chain 'N' and resid 235 through 237 removed outlier: 3.667A pdb=" N LYS N 237 " --> pdb=" O GLN N 176 " (cutoff:3.500A) Processing sheet with id=38, first strand: chain 'N' and resid 235 through 237 removed outlier: 3.667A pdb=" N LYS N 237 " --> pdb=" O GLN N 176 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LEU N 210 " --> pdb=" O LEU N 266 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU N 266 " --> pdb=" O LEU N 210 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain 'N' and resid 281 through 282 removed outlier: 3.679A pdb=" N VAL N 282 " --> pdb=" O VAL N 332 " (cutoff:3.500A) Processing sheet with id=40, first strand: chain 'N' and resid 413 through 415 Processing sheet with id=41, first strand: chain 'Q' and resid 44 through 46 removed outlier: 4.328A pdb=" N TYR Q 76 " --> pdb=" O PHE Q 12 " (cutoff:3.500A) Processing sheet with id=42, first strand: chain 'Q' and resid 22 through 25 removed outlier: 6.394A pdb=" N THR Q 23 " --> pdb=" O TRP Q 568 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE Q 567 " --> pdb=" O ASN Q 536 " (cutoff:3.500A) Processing sheet with id=43, first strand: chain 'Q' and resid 61 through 63 removed outlier: 3.753A pdb=" N LEU Q 63 " --> pdb=" O THR Q 103 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR Q 103 " --> pdb=" O LEU Q 63 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL Q 102 " --> pdb=" O VAL Q 98 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL Q 98 " --> pdb=" O VAL Q 102 " (cutoff:3.500A) Processing sheet with id=44, first strand: chain 'Q' and resid 158 through 165 removed outlier: 6.603A pdb=" N ILE Q 497 " --> pdb=" O LEU Q 161 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ASN Q 163 " --> pdb=" O MET Q 495 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N MET Q 495 " --> pdb=" O ASN Q 163 " (cutoff:3.500A) Processing sheet with id=45, first strand: chain 'Q' and resid 235 through 237 removed outlier: 3.666A pdb=" N LYS Q 237 " --> pdb=" O GLN Q 176 " (cutoff:3.500A) Processing sheet with id=46, first strand: chain 'Q' and resid 235 through 237 removed outlier: 3.666A pdb=" N LYS Q 237 " --> pdb=" O GLN Q 176 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LEU Q 210 " --> pdb=" O LEU Q 266 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU Q 266 " --> pdb=" O LEU Q 210 " (cutoff:3.500A) Processing sheet with id=47, first strand: chain 'Q' and resid 281 through 282 removed outlier: 3.679A pdb=" N VAL Q 282 " --> pdb=" O VAL Q 332 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain 'Q' and resid 413 through 415 882 hydrogen bonds defined for protein. 2250 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.01 Time building geometry restraints manager: 3.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 10092 1.34 - 1.46: 6743 1.46 - 1.58: 14317 1.58 - 1.69: 6 1.69 - 1.81: 204 Bond restraints: 31362 Sorted by residual: bond pdb=" CB PRO B 178 " pdb=" CG PRO B 178 " ideal model delta sigma weight residual 1.492 1.627 -0.135 5.00e-02 4.00e+02 7.31e+00 bond pdb=" CB PRO M 178 " pdb=" CG PRO M 178 " ideal model delta sigma weight residual 1.492 1.627 -0.135 5.00e-02 4.00e+02 7.31e+00 bond pdb=" CB PRO E 178 " pdb=" CG PRO E 178 " ideal model delta sigma weight residual 1.492 1.627 -0.135 5.00e-02 4.00e+02 7.30e+00 bond pdb=" CB PRO P 178 " pdb=" CG PRO P 178 " ideal model delta sigma weight residual 1.492 1.627 -0.135 5.00e-02 4.00e+02 7.30e+00 bond pdb=" CB PRO I 178 " pdb=" CG PRO I 178 " ideal model delta sigma weight residual 1.492 1.627 -0.135 5.00e-02 4.00e+02 7.30e+00 ... (remaining 31357 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 41757 1.75 - 3.49: 651 3.49 - 5.24: 108 5.24 - 6.99: 6 6.99 - 8.74: 6 Bond angle restraints: 42528 Sorted by residual: angle pdb=" CA PRO E 178 " pdb=" N PRO E 178 " pdb=" CD PRO E 178 " ideal model delta sigma weight residual 112.00 103.26 8.74 1.40e+00 5.10e-01 3.89e+01 angle pdb=" CA PRO P 178 " pdb=" N PRO P 178 " pdb=" CD PRO P 178 " ideal model delta sigma weight residual 112.00 103.26 8.74 1.40e+00 5.10e-01 3.89e+01 angle pdb=" CA PRO H 178 " pdb=" N PRO H 178 " pdb=" CD PRO H 178 " ideal model delta sigma weight residual 112.00 103.28 8.72 1.40e+00 5.10e-01 3.88e+01 angle pdb=" CA PRO I 178 " pdb=" N PRO I 178 " pdb=" CD PRO I 178 " ideal model delta sigma weight residual 112.00 103.28 8.72 1.40e+00 5.10e-01 3.88e+01 angle pdb=" CA PRO B 178 " pdb=" N PRO B 178 " pdb=" CD PRO B 178 " ideal model delta sigma weight residual 112.00 103.28 8.72 1.40e+00 5.10e-01 3.88e+01 ... (remaining 42523 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 16616 17.98 - 35.96: 1864 35.96 - 53.93: 336 53.93 - 71.91: 48 71.91 - 89.89: 12 Dihedral angle restraints: 18876 sinusoidal: 7698 harmonic: 11178 Sorted by residual: dihedral pdb=" CA TYR C 312 " pdb=" C TYR C 312 " pdb=" N SER C 313 " pdb=" CA SER C 313 " ideal model delta harmonic sigma weight residual 180.00 161.62 18.38 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA TYR N 312 " pdb=" C TYR N 312 " pdb=" N SER N 313 " pdb=" CA SER N 313 " ideal model delta harmonic sigma weight residual 180.00 161.62 18.38 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA TYR Q 312 " pdb=" C TYR Q 312 " pdb=" N SER Q 313 " pdb=" CA SER Q 313 " ideal model delta harmonic sigma weight residual 180.00 161.64 18.36 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 18873 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 3047 0.029 - 0.059: 1077 0.059 - 0.088: 213 0.088 - 0.117: 231 0.117 - 0.146: 76 Chirality restraints: 4644 Sorted by residual: chirality pdb=" CA ILE C 95 " pdb=" N ILE C 95 " pdb=" C ILE C 95 " pdb=" CB ILE C 95 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.35e-01 chirality pdb=" CA ILE N 95 " pdb=" N ILE N 95 " pdb=" C ILE N 95 " pdb=" CB ILE N 95 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.35e-01 chirality pdb=" CA ILE K 95 " pdb=" N ILE K 95 " pdb=" C ILE K 95 " pdb=" CB ILE K 95 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.15e-01 ... (remaining 4641 not shown) Planarity restraints: 5568 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU P 177 " 0.058 5.00e-02 4.00e+02 8.24e-02 1.09e+01 pdb=" N PRO P 178 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO P 178 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO P 178 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 177 " 0.058 5.00e-02 4.00e+02 8.24e-02 1.09e+01 pdb=" N PRO E 178 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO E 178 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO E 178 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU H 177 " -0.058 5.00e-02 4.00e+02 8.22e-02 1.08e+01 pdb=" N PRO H 178 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO H 178 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO H 178 " -0.045 5.00e-02 4.00e+02 ... (remaining 5565 not shown) Histogram of nonbonded interaction distances: 0.36 - 1.27: 180 1.27 - 2.17: 738 2.17 - 3.08: 25488 3.08 - 3.99: 77655 3.99 - 4.90: 145092 Warning: very small nonbonded interaction distances. Nonbonded interactions: 249153 Sorted by model distance: nonbonded pdb=" CD LYS D 181 " pdb=" CD2 TYR H 193 " model vdw 0.357 3.740 nonbonded pdb=" CD2 TYR I 193 " pdb=" CD LYS O 181 " model vdw 0.357 3.740 nonbonded pdb=" CD LYS L 181 " pdb=" CD2 TYR P 193 " model vdw 0.357 3.740 nonbonded pdb=" CD LYS A 181 " pdb=" CD2 TYR E 193 " model vdw 0.357 3.740 nonbonded pdb=" CD LYS J 181 " pdb=" CD2 TYR B 193 " model vdw 0.358 3.740 ... (remaining 249148 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'D' selection = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'K' selection = chain 'N' selection = chain 'Q' selection = chain 'Y' } 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: 4.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 22.990 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 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 : 0.021 1.009 31422 Z= 2.079 Angle : 0.570 8.737 42528 Z= 0.323 Chirality : 0.039 0.146 4644 Planarity : 0.004 0.082 5568 Dihedral : 14.973 89.889 11652 Min Nonbonded Distance : 0.357 Molprobity Statistics. All-atom Clashscore : 27.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.35 % Allowed : 19.30 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.14), residues: 3720 helix: 1.32 (0.20), residues: 792 sheet: 0.46 (0.22), residues: 684 loop : -0.90 (0.13), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG Y 56 TYR 0.011 0.001 TYR K 455 PHE 0.018 0.002 PHE Q 432 TRP 0.007 0.001 TRP K 275 HIS 0.004 0.001 HIS K 101 Details of bonding type rmsd covalent geometry : bond 0.00344 (31362) covalent geometry : angle 0.56950 (42528) hydrogen bonds : bond 0.17647 ( 876) hydrogen bonds : angle 7.52582 ( 2250) Misc. bond : bond 0.47456 ( 60) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 502 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 577 MET cc_start: 0.7311 (ttm) cc_final: 0.7053 (ttm) REVERT: C 338 SER cc_start: 0.8612 (m) cc_final: 0.8214 (p) REVERT: K 577 MET cc_start: 0.7292 (ttm) cc_final: 0.7041 (ttm) REVERT: N 338 SER cc_start: 0.8623 (m) cc_final: 0.8226 (p) outliers start: 12 outliers final: 4 residues processed: 514 average time/residue: 0.1600 time to fit residues: 137.5128 Evaluate side-chains 438 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 434 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 55 ILE Chi-restraints excluded: chain Y residue 354 ASN Chi-restraints excluded: chain K residue 55 ILE Chi-restraints excluded: chain K residue 354 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 72 GLN Y 126 ASN Y 343 HIS ** Y 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 441 ASN Y 509 GLN B 179 GLN C 72 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 ASN C 343 HIS ** C 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 441 ASN C 509 GLN E 179 GLN F 72 GLN ** F 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 126 ASN F 343 HIS ** F 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 441 ASN F 509 GLN K 72 GLN K 126 ASN K 343 HIS ** K 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 509 GLN M 179 GLN N 72 GLN ** N 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 126 ASN N 343 HIS ** N 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 509 GLN P 179 GLN Q 72 GLN ** Q 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 126 ASN Q 343 HIS ** Q 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 441 ASN Q 509 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.106217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.086592 restraints weight = 54333.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.089857 restraints weight = 29600.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.092074 restraints weight = 19449.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.093646 restraints weight = 14415.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.094750 restraints weight = 11616.823| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 31422 Z= 0.192 Angle : 0.713 11.980 42528 Z= 0.377 Chirality : 0.045 0.209 4644 Planarity : 0.008 0.166 5568 Dihedral : 5.714 36.987 4106 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.59 % Allowed : 16.52 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.13), residues: 3720 helix: 0.24 (0.18), residues: 840 sheet: 0.07 (0.20), residues: 714 loop : -1.12 (0.13), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 347 TYR 0.033 0.002 TYR K 457 PHE 0.012 0.002 PHE K 586 TRP 0.007 0.001 TRP Q 568 HIS 0.005 0.001 HIS Q 300 Details of bonding type rmsd covalent geometry : bond 0.00411 (31362) covalent geometry : angle 0.71268 (42528) hydrogen bonds : bond 0.04439 ( 876) hydrogen bonds : angle 6.28471 ( 2250) Misc. bond : bond 0.00454 ( 60) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 528 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 180 SER cc_start: 0.8442 (OUTLIER) cc_final: 0.7944 (p) REVERT: Y 213 MET cc_start: 0.8806 (ptm) cc_final: 0.8408 (ptm) REVERT: Y 340 ILE cc_start: 0.9314 (OUTLIER) cc_final: 0.9009 (tp) REVERT: Y 354 ASN cc_start: 0.9068 (OUTLIER) cc_final: 0.8803 (t0) REVERT: A 180 SER cc_start: 0.8461 (OUTLIER) cc_final: 0.7964 (p) REVERT: A 185 ASP cc_start: 0.8497 (t0) cc_final: 0.8194 (t0) REVERT: C 83 PHE cc_start: 0.8591 (OUTLIER) cc_final: 0.8208 (m-10) REVERT: C 105 MET cc_start: 0.8692 (mtp) cc_final: 0.8334 (mtp) REVERT: C 219 ASN cc_start: 0.7315 (m-40) cc_final: 0.7018 (m-40) REVERT: C 344 ASN cc_start: 0.9081 (OUTLIER) cc_final: 0.7549 (m-40) REVERT: C 345 GLU cc_start: 0.8486 (tt0) cc_final: 0.8187 (mp0) REVERT: C 540 MET cc_start: 0.8746 (mtp) cc_final: 0.8457 (ttm) REVERT: D 180 SER cc_start: 0.8298 (OUTLIER) cc_final: 0.7935 (p) REVERT: F 168 PHE cc_start: 0.8078 (OUTLIER) cc_final: 0.7091 (p90) REVERT: G 180 SER cc_start: 0.8441 (OUTLIER) cc_final: 0.7937 (p) REVERT: K 213 MET cc_start: 0.8809 (ptm) cc_final: 0.8415 (ptm) REVERT: K 340 ILE cc_start: 0.9314 (OUTLIER) cc_final: 0.9004 (tp) REVERT: K 354 ASN cc_start: 0.9071 (OUTLIER) cc_final: 0.8804 (t0) REVERT: L 180 SER cc_start: 0.8459 (OUTLIER) cc_final: 0.7960 (p) REVERT: L 185 ASP cc_start: 0.8497 (t0) cc_final: 0.8191 (t0) REVERT: N 83 PHE cc_start: 0.8592 (OUTLIER) cc_final: 0.8206 (m-10) REVERT: N 105 MET cc_start: 0.8686 (mtp) cc_final: 0.8335 (mtp) REVERT: N 219 ASN cc_start: 0.7312 (m-40) cc_final: 0.7015 (m-40) REVERT: N 344 ASN cc_start: 0.9086 (OUTLIER) cc_final: 0.7544 (m-40) REVERT: N 345 GLU cc_start: 0.8496 (tt0) cc_final: 0.8182 (mp0) REVERT: N 540 MET cc_start: 0.8734 (mtp) cc_final: 0.8454 (ttm) REVERT: O 180 SER cc_start: 0.8299 (OUTLIER) cc_final: 0.7957 (p) REVERT: Q 168 PHE cc_start: 0.8074 (OUTLIER) cc_final: 0.7092 (p90) outliers start: 124 outliers final: 48 residues processed: 610 average time/residue: 0.2111 time to fit residues: 205.5638 Evaluate side-chains 497 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 433 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 180 SER Chi-restraints excluded: chain Y residue 55 ILE Chi-restraints excluded: chain Y residue 83 PHE Chi-restraints excluded: chain Y residue 123 THR Chi-restraints excluded: chain Y residue 152 VAL Chi-restraints excluded: chain Y residue 168 PHE Chi-restraints excluded: chain Y residue 232 THR Chi-restraints excluded: chain Y residue 340 ILE Chi-restraints excluded: chain Y residue 344 ASN Chi-restraints excluded: chain Y residue 354 ASN Chi-restraints excluded: chain Y residue 563 THR Chi-restraints excluded: chain Y residue 565 VAL Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain C residue 83 PHE Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 344 ASN Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 565 VAL Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain F residue 168 PHE Chi-restraints excluded: chain F residue 204 ILE Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain F residue 391 ILE Chi-restraints excluded: chain F residue 563 THR Chi-restraints excluded: chain F residue 565 VAL Chi-restraints excluded: chain G residue 180 SER Chi-restraints excluded: chain K residue 55 ILE Chi-restraints excluded: chain K residue 83 PHE Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 152 VAL Chi-restraints excluded: chain K residue 168 PHE Chi-restraints excluded: chain K residue 232 THR Chi-restraints excluded: chain K residue 340 ILE Chi-restraints excluded: chain K residue 344 ASN Chi-restraints excluded: chain K residue 354 ASN Chi-restraints excluded: chain K residue 563 THR Chi-restraints excluded: chain K residue 565 VAL Chi-restraints excluded: chain L residue 180 SER Chi-restraints excluded: chain N residue 83 PHE Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 153 ILE Chi-restraints excluded: chain N residue 168 PHE Chi-restraints excluded: chain N residue 204 ILE Chi-restraints excluded: chain N residue 212 VAL Chi-restraints excluded: chain N residue 232 THR Chi-restraints excluded: chain N residue 344 ASN Chi-restraints excluded: chain N residue 563 THR Chi-restraints excluded: chain N residue 565 VAL Chi-restraints excluded: chain O residue 180 SER Chi-restraints excluded: chain Q residue 168 PHE Chi-restraints excluded: chain Q residue 204 ILE Chi-restraints excluded: chain Q residue 212 VAL Chi-restraints excluded: chain Q residue 232 THR Chi-restraints excluded: chain Q residue 241 ILE Chi-restraints excluded: chain Q residue 391 ILE Chi-restraints excluded: chain Q residue 563 THR Chi-restraints excluded: chain Q residue 565 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 98 optimal weight: 0.0170 chunk 219 optimal weight: 0.9980 chunk 282 optimal weight: 3.9990 chunk 298 optimal weight: 3.9990 chunk 330 optimal weight: 2.9990 chunk 324 optimal weight: 4.9990 chunk 88 optimal weight: 0.4980 chunk 61 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 130 optimal weight: 0.0980 overall best weight: 0.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 219 ASN ** Y 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN C 99 ASN ** C 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 520 ASN F 72 GLN F 99 ASN ** F 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 471 GLN K 219 ASN ** K 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 72 GLN ** N 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 72 GLN Q 99 ASN ** Q 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 471 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.114029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.094242 restraints weight = 53180.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.097864 restraints weight = 27820.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.100323 restraints weight = 17649.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.102030 restraints weight = 12708.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.103213 restraints weight = 10006.456| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 31422 Z= 0.146 Angle : 0.617 9.483 42528 Z= 0.325 Chirality : 0.042 0.134 4644 Planarity : 0.012 0.480 5568 Dihedral : 7.354 151.126 4106 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 5.13 % Allowed : 15.10 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.99 (0.13), residues: 3720 helix: 0.02 (0.17), residues: 870 sheet: 0.03 (0.20), residues: 714 loop : -1.20 (0.13), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG Y 510 TYR 0.025 0.001 TYR Y 457 PHE 0.022 0.001 PHE Q 54 TRP 0.006 0.001 TRP K 568 HIS 0.005 0.001 HIS Q 343 Details of bonding type rmsd covalent geometry : bond 0.00325 (31362) covalent geometry : angle 0.61733 (42528) hydrogen bonds : bond 0.04062 ( 876) hydrogen bonds : angle 5.88298 ( 2250) Misc. bond : bond 0.00468 ( 60) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 505 time to evaluate : 1.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 185 ASP cc_start: 0.8477 (t0) cc_final: 0.8252 (t0) REVERT: Y 6 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.9096 (mm) REVERT: Y 115 TYR cc_start: 0.8883 (m-80) cc_final: 0.8611 (m-10) REVERT: Y 159 TYR cc_start: 0.8730 (OUTLIER) cc_final: 0.7944 (p90) REVERT: Y 213 MET cc_start: 0.8768 (ptm) cc_final: 0.8425 (ptm) REVERT: Y 219 ASN cc_start: 0.7076 (m-40) cc_final: 0.6518 (m-40) REVERT: Y 340 ILE cc_start: 0.9443 (OUTLIER) cc_final: 0.9170 (tp) REVERT: Y 354 ASN cc_start: 0.9092 (OUTLIER) cc_final: 0.8851 (t0) REVERT: Y 388 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7745 (mm-30) REVERT: Y 519 THR cc_start: 0.9343 (OUTLIER) cc_final: 0.9013 (p) REVERT: Y 540 MET cc_start: 0.8746 (mtp) cc_final: 0.8486 (mtp) REVERT: A 185 ASP cc_start: 0.8603 (t0) cc_final: 0.8319 (t0) REVERT: C 19 ASP cc_start: 0.8310 (t0) cc_final: 0.8030 (t0) REVERT: C 83 PHE cc_start: 0.8677 (OUTLIER) cc_final: 0.8360 (m-80) REVERT: C 159 TYR cc_start: 0.8802 (OUTLIER) cc_final: 0.8145 (p90) REVERT: C 213 MET cc_start: 0.8834 (OUTLIER) cc_final: 0.8438 (ptm) REVERT: C 219 ASN cc_start: 0.7796 (m-40) cc_final: 0.7247 (m-40) REVERT: C 290 MET cc_start: 0.9135 (mtm) cc_final: 0.8859 (mtm) REVERT: C 344 ASN cc_start: 0.9186 (OUTLIER) cc_final: 0.8602 (m-40) REVERT: C 515 LEU cc_start: 0.9458 (mm) cc_final: 0.9206 (mm) REVERT: C 562 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7545 (mt-10) REVERT: C 577 MET cc_start: 0.9103 (mmm) cc_final: 0.8894 (mmt) REVERT: F 19 ASP cc_start: 0.8302 (t0) cc_final: 0.7950 (t0) REVERT: F 168 PHE cc_start: 0.8008 (OUTLIER) cc_final: 0.6763 (p90) REVERT: F 175 PHE cc_start: 0.7437 (t80) cc_final: 0.7230 (t80) REVERT: F 213 MET cc_start: 0.8957 (ptp) cc_final: 0.8604 (ptm) REVERT: F 345 GLU cc_start: 0.8424 (tt0) cc_final: 0.7653 (mt-10) REVERT: F 388 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7806 (mm-30) REVERT: F 455 TYR cc_start: 0.7694 (t80) cc_final: 0.7340 (t80) REVERT: F 519 THR cc_start: 0.9311 (OUTLIER) cc_final: 0.8930 (p) REVERT: F 562 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7417 (mt-10) REVERT: F 577 MET cc_start: 0.9057 (mmt) cc_final: 0.8611 (mmt) REVERT: G 185 ASP cc_start: 0.8476 (t0) cc_final: 0.8254 (t0) REVERT: K 115 TYR cc_start: 0.8884 (m-80) cc_final: 0.8607 (m-10) REVERT: K 159 TYR cc_start: 0.8721 (OUTLIER) cc_final: 0.7942 (p90) REVERT: K 213 MET cc_start: 0.8768 (ptm) cc_final: 0.8442 (ptm) REVERT: K 219 ASN cc_start: 0.7072 (m-40) cc_final: 0.6479 (m-40) REVERT: K 340 ILE cc_start: 0.9446 (OUTLIER) cc_final: 0.9170 (tp) REVERT: K 354 ASN cc_start: 0.9093 (OUTLIER) cc_final: 0.8855 (t0) REVERT: K 459 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7996 (mmmm) REVERT: K 519 THR cc_start: 0.9345 (OUTLIER) cc_final: 0.9014 (p) REVERT: K 540 MET cc_start: 0.8740 (mtp) cc_final: 0.8485 (mtp) REVERT: K 577 MET cc_start: 0.9039 (mmm) cc_final: 0.8777 (mmt) REVERT: L 185 ASP cc_start: 0.8602 (t0) cc_final: 0.8318 (t0) REVERT: N 19 ASP cc_start: 0.8302 (t0) cc_final: 0.8023 (t0) REVERT: N 83 PHE cc_start: 0.8676 (OUTLIER) cc_final: 0.8358 (m-80) REVERT: N 159 TYR cc_start: 0.8804 (OUTLIER) cc_final: 0.8146 (p90) REVERT: N 213 MET cc_start: 0.8846 (OUTLIER) cc_final: 0.8450 (ptm) REVERT: N 219 ASN cc_start: 0.7796 (m-40) cc_final: 0.7248 (m-40) REVERT: N 290 MET cc_start: 0.9137 (mtm) cc_final: 0.8855 (mtm) REVERT: N 344 ASN cc_start: 0.9186 (OUTLIER) cc_final: 0.8608 (m-40) REVERT: N 515 LEU cc_start: 0.9457 (mm) cc_final: 0.9205 (mm) REVERT: N 562 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7534 (mt-10) REVERT: N 577 MET cc_start: 0.9100 (mmm) cc_final: 0.8892 (mmt) REVERT: O 180 SER cc_start: 0.8340 (OUTLIER) cc_final: 0.7877 (p) REVERT: Q 19 ASP cc_start: 0.8160 (t0) cc_final: 0.7705 (t70) REVERT: Q 168 PHE cc_start: 0.8014 (OUTLIER) cc_final: 0.6766 (p90) REVERT: Q 175 PHE cc_start: 0.7435 (t80) cc_final: 0.7230 (t80) REVERT: Q 213 MET cc_start: 0.8955 (ptp) cc_final: 0.8607 (ptm) REVERT: Q 388 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7794 (mm-30) REVERT: Q 455 TYR cc_start: 0.7695 (t80) cc_final: 0.7295 (t80) REVERT: Q 519 THR cc_start: 0.9317 (OUTLIER) cc_final: 0.8935 (p) REVERT: Q 577 MET cc_start: 0.9052 (mmt) cc_final: 0.8609 (mmt) outliers start: 177 outliers final: 82 residues processed: 617 average time/residue: 0.1938 time to fit residues: 197.3024 Evaluate side-chains 558 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 450 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 177 LEU Chi-restraints excluded: chain J residue 179 GLN Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 83 PHE Chi-restraints excluded: chain Y residue 123 THR Chi-restraints excluded: chain Y residue 152 VAL Chi-restraints excluded: chain Y residue 159 TYR Chi-restraints excluded: chain Y residue 168 PHE Chi-restraints excluded: chain Y residue 205 THR Chi-restraints excluded: chain Y residue 232 THR Chi-restraints excluded: chain Y residue 340 ILE Chi-restraints excluded: chain Y residue 344 ASN Chi-restraints excluded: chain Y residue 354 ASN Chi-restraints excluded: chain Y residue 375 SER Chi-restraints excluded: chain Y residue 388 GLU Chi-restraints excluded: chain Y residue 519 THR Chi-restraints excluded: chain Y residue 522 GLN Chi-restraints excluded: chain Y residue 563 THR Chi-restraints excluded: chain Y residue 565 VAL Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain B residue 179 GLN Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 83 PHE Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 159 TYR Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 213 MET Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 255 LYS Chi-restraints excluded: chain C residue 344 ASN Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 565 VAL Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 179 GLN Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 83 PHE Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 159 TYR Chi-restraints excluded: chain F residue 168 PHE Chi-restraints excluded: chain F residue 204 ILE Chi-restraints excluded: chain F residue 205 THR Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 388 GLU Chi-restraints excluded: chain F residue 391 ILE Chi-restraints excluded: chain F residue 519 THR Chi-restraints excluded: chain F residue 563 THR Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain G residue 179 GLN Chi-restraints excluded: chain K residue 83 PHE Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 152 VAL Chi-restraints excluded: chain K residue 159 TYR Chi-restraints excluded: chain K residue 168 PHE Chi-restraints excluded: chain K residue 205 THR Chi-restraints excluded: chain K residue 232 THR Chi-restraints excluded: chain K residue 340 ILE Chi-restraints excluded: chain K residue 344 ASN Chi-restraints excluded: chain K residue 354 ASN Chi-restraints excluded: chain K residue 375 SER Chi-restraints excluded: chain K residue 459 LYS Chi-restraints excluded: chain K residue 519 THR Chi-restraints excluded: chain K residue 522 GLN Chi-restraints excluded: chain K residue 563 THR Chi-restraints excluded: chain K residue 565 VAL Chi-restraints excluded: chain L residue 177 LEU Chi-restraints excluded: chain M residue 179 GLN Chi-restraints excluded: chain N residue 83 PHE Chi-restraints excluded: chain N residue 95 ILE Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 153 ILE Chi-restraints excluded: chain N residue 159 TYR Chi-restraints excluded: chain N residue 168 PHE Chi-restraints excluded: chain N residue 205 THR Chi-restraints excluded: chain N residue 212 VAL Chi-restraints excluded: chain N residue 213 MET Chi-restraints excluded: chain N residue 232 THR Chi-restraints excluded: chain N residue 241 ILE Chi-restraints excluded: chain N residue 255 LYS Chi-restraints excluded: chain N residue 344 ASN Chi-restraints excluded: chain N residue 375 SER Chi-restraints excluded: chain N residue 391 ILE Chi-restraints excluded: chain N residue 519 THR Chi-restraints excluded: chain N residue 563 THR Chi-restraints excluded: chain N residue 565 VAL Chi-restraints excluded: chain O residue 177 LEU Chi-restraints excluded: chain O residue 180 SER Chi-restraints excluded: chain Q residue 77 CYS Chi-restraints excluded: chain Q residue 83 PHE Chi-restraints excluded: chain Q residue 95 ILE Chi-restraints excluded: chain Q residue 159 TYR Chi-restraints excluded: chain Q residue 168 PHE Chi-restraints excluded: chain Q residue 204 ILE Chi-restraints excluded: chain Q residue 212 VAL Chi-restraints excluded: chain Q residue 232 THR Chi-restraints excluded: chain Q residue 388 GLU Chi-restraints excluded: chain Q residue 391 ILE Chi-restraints excluded: chain Q residue 519 THR Chi-restraints excluded: chain Q residue 563 THR Chi-restraints excluded: chain Q residue 565 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 45 optimal weight: 5.9990 chunk 366 optimal weight: 2.9990 chunk 324 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 298 optimal weight: 0.5980 chunk 244 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 90 optimal weight: 0.0980 chunk 75 optimal weight: 0.7980 chunk 167 optimal weight: 8.9990 chunk 269 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 93 ASN ** Y 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 183 ASN C 93 ASN ** C 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 520 ASN F 72 GLN F 93 ASN F 343 HIS ** F 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 93 ASN ** K 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 183 ASN N 93 ASN N 99 ASN ** N 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 72 GLN Q 93 ASN Q 343 HIS ** Q 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.112918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.093539 restraints weight = 52902.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.097076 restraints weight = 27888.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.099484 restraints weight = 17719.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.101167 restraints weight = 12767.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.102295 restraints weight = 10032.558| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 31422 Z= 0.149 Angle : 0.639 16.903 42528 Z= 0.330 Chirality : 0.042 0.129 4644 Planarity : 0.010 0.308 5568 Dihedral : 6.948 141.278 4102 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 4.55 % Allowed : 14.96 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.03 (0.13), residues: 3720 helix: 0.08 (0.17), residues: 864 sheet: 0.05 (0.20), residues: 708 loop : -1.28 (0.13), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG N 510 TYR 0.040 0.001 TYR I 193 PHE 0.015 0.001 PHE Q 128 TRP 0.007 0.001 TRP F 568 HIS 0.005 0.001 HIS Q 343 Details of bonding type rmsd covalent geometry : bond 0.00331 (31362) covalent geometry : angle 0.63871 (42528) hydrogen bonds : bond 0.03726 ( 876) hydrogen bonds : angle 5.65985 ( 2250) Misc. bond : bond 0.00474 ( 60) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 510 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 185 ASP cc_start: 0.8506 (t0) cc_final: 0.8266 (t0) REVERT: Y 19 ASP cc_start: 0.8054 (t0) cc_final: 0.6158 (t0) REVERT: Y 115 TYR cc_start: 0.8974 (m-80) cc_final: 0.8594 (m-10) REVERT: Y 159 TYR cc_start: 0.8674 (OUTLIER) cc_final: 0.7837 (p90) REVERT: Y 194 GLU cc_start: 0.6801 (tt0) cc_final: 0.6315 (tp30) REVERT: Y 213 MET cc_start: 0.8811 (ptm) cc_final: 0.8446 (ptm) REVERT: Y 219 ASN cc_start: 0.7505 (m-40) cc_final: 0.7078 (m-40) REVERT: Y 222 MET cc_start: 0.9268 (tpp) cc_final: 0.8762 (mmt) REVERT: Y 340 ILE cc_start: 0.9428 (OUTLIER) cc_final: 0.9113 (tp) REVERT: Y 519 THR cc_start: 0.9312 (OUTLIER) cc_final: 0.8952 (p) REVERT: A 185 ASP cc_start: 0.8792 (t0) cc_final: 0.8361 (t0) REVERT: C 83 PHE cc_start: 0.8781 (OUTLIER) cc_final: 0.8422 (m-80) REVERT: C 159 TYR cc_start: 0.8819 (OUTLIER) cc_final: 0.8155 (p90) REVERT: C 213 MET cc_start: 0.8999 (OUTLIER) cc_final: 0.8670 (ptm) REVERT: C 219 ASN cc_start: 0.7573 (m-40) cc_final: 0.7008 (m-40) REVERT: C 290 MET cc_start: 0.9153 (mtm) cc_final: 0.8900 (mtm) REVERT: C 344 ASN cc_start: 0.9222 (OUTLIER) cc_final: 0.8532 (m-40) REVERT: C 376 PHE cc_start: 0.9205 (t80) cc_final: 0.8509 (t80) REVERT: C 457 TYR cc_start: 0.6521 (m-10) cc_final: 0.6295 (m-10) REVERT: C 480 MET cc_start: 0.9233 (tpt) cc_final: 0.8881 (tpp) REVERT: C 515 LEU cc_start: 0.9460 (mm) cc_final: 0.9251 (mm) REVERT: C 577 MET cc_start: 0.9143 (mmm) cc_final: 0.8905 (mmt) REVERT: F 19 ASP cc_start: 0.8219 (t0) cc_final: 0.6546 (t0) REVERT: F 168 PHE cc_start: 0.8081 (OUTLIER) cc_final: 0.6542 (p90) REVERT: F 213 MET cc_start: 0.8987 (ptp) cc_final: 0.8669 (ptm) REVERT: F 388 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7662 (mm-30) REVERT: F 455 TYR cc_start: 0.7775 (t80) cc_final: 0.7427 (t80) REVERT: F 519 THR cc_start: 0.9335 (OUTLIER) cc_final: 0.9020 (p) REVERT: F 577 MET cc_start: 0.9058 (mmt) cc_final: 0.8603 (mmt) REVERT: G 185 ASP cc_start: 0.8509 (t0) cc_final: 0.8270 (t0) REVERT: K 115 TYR cc_start: 0.8979 (m-80) cc_final: 0.8595 (m-10) REVERT: K 159 TYR cc_start: 0.8672 (OUTLIER) cc_final: 0.7829 (p90) REVERT: K 194 GLU cc_start: 0.6800 (tt0) cc_final: 0.6316 (tp30) REVERT: K 213 MET cc_start: 0.8811 (ptm) cc_final: 0.8361 (ptm) REVERT: K 219 ASN cc_start: 0.7564 (m-40) cc_final: 0.6971 (m-40) REVERT: K 222 MET cc_start: 0.9269 (tpp) cc_final: 0.8767 (mmt) REVERT: K 340 ILE cc_start: 0.9426 (OUTLIER) cc_final: 0.9122 (tp) REVERT: K 519 THR cc_start: 0.9310 (OUTLIER) cc_final: 0.8945 (p) REVERT: L 185 ASP cc_start: 0.8789 (t0) cc_final: 0.8354 (t0) REVERT: N 83 PHE cc_start: 0.8776 (OUTLIER) cc_final: 0.8409 (m-80) REVERT: N 159 TYR cc_start: 0.8814 (OUTLIER) cc_final: 0.8143 (p90) REVERT: N 213 MET cc_start: 0.8999 (OUTLIER) cc_final: 0.8676 (ptm) REVERT: N 219 ASN cc_start: 0.7571 (m-40) cc_final: 0.7002 (m-40) REVERT: N 290 MET cc_start: 0.9155 (mtm) cc_final: 0.8901 (mtm) REVERT: N 344 ASN cc_start: 0.9221 (OUTLIER) cc_final: 0.8527 (m-40) REVERT: N 376 PHE cc_start: 0.9208 (t80) cc_final: 0.8514 (t80) REVERT: N 457 TYR cc_start: 0.6524 (m-10) cc_final: 0.6308 (m-10) REVERT: N 480 MET cc_start: 0.9239 (tpt) cc_final: 0.8889 (tpp) REVERT: N 515 LEU cc_start: 0.9460 (mm) cc_final: 0.9254 (mm) REVERT: N 577 MET cc_start: 0.9148 (mmm) cc_final: 0.8912 (mmt) REVERT: Q 19 ASP cc_start: 0.8100 (t0) cc_final: 0.7898 (t70) REVERT: Q 168 PHE cc_start: 0.8081 (OUTLIER) cc_final: 0.6682 (p90) REVERT: Q 194 GLU cc_start: 0.6088 (tp30) cc_final: 0.5875 (tp30) REVERT: Q 213 MET cc_start: 0.8988 (ptp) cc_final: 0.8672 (ptm) REVERT: Q 388 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7660 (mm-30) REVERT: Q 455 TYR cc_start: 0.7725 (t80) cc_final: 0.7388 (t80) REVERT: Q 519 THR cc_start: 0.9357 (OUTLIER) cc_final: 0.8996 (p) outliers start: 157 outliers final: 87 residues processed: 616 average time/residue: 0.1929 time to fit residues: 196.1738 Evaluate side-chains 559 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 452 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 177 LEU Chi-restraints excluded: chain J residue 179 GLN Chi-restraints excluded: chain Y residue 83 PHE Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 123 THR Chi-restraints excluded: chain Y residue 152 VAL Chi-restraints excluded: chain Y residue 159 TYR Chi-restraints excluded: chain Y residue 168 PHE Chi-restraints excluded: chain Y residue 205 THR Chi-restraints excluded: chain Y residue 232 THR Chi-restraints excluded: chain Y residue 336 THR Chi-restraints excluded: chain Y residue 340 ILE Chi-restraints excluded: chain Y residue 375 SER Chi-restraints excluded: chain Y residue 519 THR Chi-restraints excluded: chain Y residue 563 THR Chi-restraints excluded: chain Y residue 565 VAL Chi-restraints excluded: chain Y residue 586 PHE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain B residue 179 GLN Chi-restraints excluded: chain C residue 83 PHE Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 159 TYR Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 213 MET Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 255 LYS Chi-restraints excluded: chain C residue 339 ILE Chi-restraints excluded: chain C residue 344 ASN Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 565 VAL Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 179 GLN Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 168 PHE Chi-restraints excluded: chain F residue 204 ILE Chi-restraints excluded: chain F residue 205 THR Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 336 THR Chi-restraints excluded: chain F residue 388 GLU Chi-restraints excluded: chain F residue 391 ILE Chi-restraints excluded: chain F residue 519 THR Chi-restraints excluded: chain F residue 563 THR Chi-restraints excluded: chain F residue 586 PHE Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain G residue 179 GLN Chi-restraints excluded: chain K residue 83 PHE Chi-restraints excluded: chain K residue 102 VAL Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 152 VAL Chi-restraints excluded: chain K residue 159 TYR Chi-restraints excluded: chain K residue 168 PHE Chi-restraints excluded: chain K residue 205 THR Chi-restraints excluded: chain K residue 232 THR Chi-restraints excluded: chain K residue 336 THR Chi-restraints excluded: chain K residue 340 ILE Chi-restraints excluded: chain K residue 375 SER Chi-restraints excluded: chain K residue 519 THR Chi-restraints excluded: chain K residue 563 THR Chi-restraints excluded: chain K residue 565 VAL Chi-restraints excluded: chain K residue 586 PHE Chi-restraints excluded: chain L residue 177 LEU Chi-restraints excluded: chain M residue 179 GLN Chi-restraints excluded: chain N residue 83 PHE Chi-restraints excluded: chain N residue 95 ILE Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 153 ILE Chi-restraints excluded: chain N residue 159 TYR Chi-restraints excluded: chain N residue 168 PHE Chi-restraints excluded: chain N residue 205 THR Chi-restraints excluded: chain N residue 213 MET Chi-restraints excluded: chain N residue 232 THR Chi-restraints excluded: chain N residue 255 LYS Chi-restraints excluded: chain N residue 339 ILE Chi-restraints excluded: chain N residue 344 ASN Chi-restraints excluded: chain N residue 375 SER Chi-restraints excluded: chain N residue 391 ILE Chi-restraints excluded: chain N residue 519 THR Chi-restraints excluded: chain N residue 563 THR Chi-restraints excluded: chain N residue 565 VAL Chi-restraints excluded: chain O residue 177 LEU Chi-restraints excluded: chain O residue 179 GLN Chi-restraints excluded: chain Q residue 77 CYS Chi-restraints excluded: chain Q residue 95 ILE Chi-restraints excluded: chain Q residue 102 VAL Chi-restraints excluded: chain Q residue 153 ILE Chi-restraints excluded: chain Q residue 168 PHE Chi-restraints excluded: chain Q residue 204 ILE Chi-restraints excluded: chain Q residue 212 VAL Chi-restraints excluded: chain Q residue 232 THR Chi-restraints excluded: chain Q residue 336 THR Chi-restraints excluded: chain Q residue 388 GLU Chi-restraints excluded: chain Q residue 391 ILE Chi-restraints excluded: chain Q residue 519 THR Chi-restraints excluded: chain Q residue 563 THR Chi-restraints excluded: chain Q residue 586 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 65 optimal weight: 1.9990 chunk 93 optimal weight: 7.9990 chunk 115 optimal weight: 5.9990 chunk 228 optimal weight: 5.9990 chunk 143 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 324 optimal weight: 0.6980 chunk 277 optimal weight: 4.9990 chunk 222 optimal weight: 0.0770 chunk 363 optimal weight: 6.9990 chunk 270 optimal weight: 20.0000 overall best weight: 1.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 126 ASN ** Y 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 126 ASN ** K 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 99 ASN ** Q 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.111811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.091947 restraints weight = 53523.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.095500 restraints weight = 28556.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.097942 restraints weight = 18359.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.099659 restraints weight = 13347.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.100852 restraints weight = 10563.515| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 31422 Z= 0.160 Angle : 0.624 10.903 42528 Z= 0.325 Chirality : 0.042 0.156 4644 Planarity : 0.006 0.197 5568 Dihedral : 6.949 178.977 4098 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 5.10 % Allowed : 15.65 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.13), residues: 3720 helix: 0.23 (0.18), residues: 870 sheet: 0.10 (0.20), residues: 708 loop : -1.42 (0.13), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG K 510 TYR 0.028 0.001 TYR F 457 PHE 0.018 0.002 PHE C 586 TRP 0.006 0.001 TRP Y 568 HIS 0.003 0.001 HIS K 343 Details of bonding type rmsd covalent geometry : bond 0.00364 (31362) covalent geometry : angle 0.62450 (42528) hydrogen bonds : bond 0.03671 ( 876) hydrogen bonds : angle 5.55034 ( 2250) Misc. bond : bond 0.00504 ( 60) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 483 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 185 ASP cc_start: 0.8565 (t0) cc_final: 0.8281 (t0) REVERT: Y 19 ASP cc_start: 0.7848 (t0) cc_final: 0.7210 (t0) REVERT: Y 115 TYR cc_start: 0.9036 (m-80) cc_final: 0.8698 (m-10) REVERT: Y 159 TYR cc_start: 0.8799 (OUTLIER) cc_final: 0.8035 (p90) REVERT: Y 194 GLU cc_start: 0.6757 (tt0) cc_final: 0.6299 (tp30) REVERT: Y 213 MET cc_start: 0.8788 (ptm) cc_final: 0.8297 (ptm) REVERT: Y 219 ASN cc_start: 0.7826 (m-40) cc_final: 0.7467 (m-40) REVERT: Y 222 MET cc_start: 0.9170 (tpp) cc_final: 0.8858 (mmt) REVERT: Y 340 ILE cc_start: 0.9414 (OUTLIER) cc_final: 0.9148 (tp) REVERT: Y 345 GLU cc_start: 0.8435 (tt0) cc_final: 0.8234 (mt-10) REVERT: Y 388 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7997 (mt-10) REVERT: Y 519 THR cc_start: 0.9365 (OUTLIER) cc_final: 0.8934 (p) REVERT: Y 577 MET cc_start: 0.8836 (mmt) cc_final: 0.8458 (mmt) REVERT: A 185 ASP cc_start: 0.8661 (t0) cc_final: 0.8434 (t0) REVERT: C 159 TYR cc_start: 0.8840 (OUTLIER) cc_final: 0.8301 (p90) REVERT: C 213 MET cc_start: 0.8876 (OUTLIER) cc_final: 0.8470 (ptm) REVERT: C 219 ASN cc_start: 0.7768 (m-40) cc_final: 0.7291 (m-40) REVERT: C 344 ASN cc_start: 0.9191 (OUTLIER) cc_final: 0.8534 (m-40) REVERT: C 376 PHE cc_start: 0.9232 (t80) cc_final: 0.8504 (t80) REVERT: C 388 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7727 (mt-10) REVERT: C 480 MET cc_start: 0.9317 (tpt) cc_final: 0.8932 (tpp) REVERT: C 515 LEU cc_start: 0.9510 (mm) cc_final: 0.9243 (mm) REVERT: F 168 PHE cc_start: 0.8102 (OUTLIER) cc_final: 0.6584 (p90) REVERT: F 213 MET cc_start: 0.9040 (OUTLIER) cc_final: 0.8728 (ptm) REVERT: F 345 GLU cc_start: 0.8509 (tt0) cc_final: 0.8259 (tt0) REVERT: F 388 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7643 (mm-30) REVERT: F 455 TYR cc_start: 0.7702 (t80) cc_final: 0.7304 (t80) REVERT: F 519 THR cc_start: 0.9401 (OUTLIER) cc_final: 0.9079 (p) REVERT: F 577 MET cc_start: 0.8955 (mmt) cc_final: 0.8533 (mmt) REVERT: G 185 ASP cc_start: 0.8565 (t0) cc_final: 0.8279 (t0) REVERT: K 115 TYR cc_start: 0.9032 (m-80) cc_final: 0.8695 (m-10) REVERT: K 159 TYR cc_start: 0.8788 (OUTLIER) cc_final: 0.8094 (p90) REVERT: K 194 GLU cc_start: 0.6755 (tt0) cc_final: 0.6300 (tp30) REVERT: K 213 MET cc_start: 0.8816 (ptm) cc_final: 0.8374 (ptm) REVERT: K 219 ASN cc_start: 0.7938 (m-40) cc_final: 0.7571 (m-40) REVERT: K 340 ILE cc_start: 0.9462 (OUTLIER) cc_final: 0.9248 (tp) REVERT: K 388 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7525 (mt-10) REVERT: K 518 GLU cc_start: 0.8322 (tm-30) cc_final: 0.8107 (tm-30) REVERT: K 577 MET cc_start: 0.9178 (mmm) cc_final: 0.8961 (mmt) REVERT: L 185 ASP cc_start: 0.8657 (t0) cc_final: 0.8431 (t0) REVERT: N 159 TYR cc_start: 0.8833 (OUTLIER) cc_final: 0.8296 (p90) REVERT: N 213 MET cc_start: 0.8885 (OUTLIER) cc_final: 0.8473 (ptm) REVERT: N 219 ASN cc_start: 0.7777 (m-40) cc_final: 0.7288 (m-40) REVERT: N 344 ASN cc_start: 0.9196 (OUTLIER) cc_final: 0.8535 (m-40) REVERT: N 376 PHE cc_start: 0.9234 (t80) cc_final: 0.8508 (t80) REVERT: N 388 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7484 (mt-10) REVERT: N 480 MET cc_start: 0.9320 (tpt) cc_final: 0.8943 (tpp) REVERT: N 515 LEU cc_start: 0.9509 (mm) cc_final: 0.9243 (mm) REVERT: Q 19 ASP cc_start: 0.8060 (t0) cc_final: 0.7853 (t70) REVERT: Q 168 PHE cc_start: 0.8089 (OUTLIER) cc_final: 0.6567 (p90) REVERT: Q 213 MET cc_start: 0.9034 (OUTLIER) cc_final: 0.8718 (ptm) REVERT: Q 388 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7639 (mm-30) REVERT: Q 455 TYR cc_start: 0.7788 (t80) cc_final: 0.7403 (t80) REVERT: Q 577 MET cc_start: 0.8967 (mmt) cc_final: 0.8510 (mmt) outliers start: 176 outliers final: 106 residues processed: 602 average time/residue: 0.1942 time to fit residues: 193.0289 Evaluate side-chains 568 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 444 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 177 LEU Chi-restraints excluded: chain Y residue 83 PHE Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 123 THR Chi-restraints excluded: chain Y residue 152 VAL Chi-restraints excluded: chain Y residue 153 ILE Chi-restraints excluded: chain Y residue 159 TYR Chi-restraints excluded: chain Y residue 168 PHE Chi-restraints excluded: chain Y residue 205 THR Chi-restraints excluded: chain Y residue 232 THR Chi-restraints excluded: chain Y residue 336 THR Chi-restraints excluded: chain Y residue 340 ILE Chi-restraints excluded: chain Y residue 375 SER Chi-restraints excluded: chain Y residue 415 ILE Chi-restraints excluded: chain Y residue 461 LEU Chi-restraints excluded: chain Y residue 475 VAL Chi-restraints excluded: chain Y residue 495 MET Chi-restraints excluded: chain Y residue 519 THR Chi-restraints excluded: chain Y residue 563 THR Chi-restraints excluded: chain Y residue 586 PHE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain B residue 179 GLN Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 159 TYR Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 213 MET Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 255 LYS Chi-restraints excluded: chain C residue 339 ILE Chi-restraints excluded: chain C residue 344 ASN Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain C residue 540 MET Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 565 VAL Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 179 GLN Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 168 PHE Chi-restraints excluded: chain F residue 204 ILE Chi-restraints excluded: chain F residue 205 THR Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 213 MET Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 336 THR Chi-restraints excluded: chain F residue 388 GLU Chi-restraints excluded: chain F residue 391 ILE Chi-restraints excluded: chain F residue 475 VAL Chi-restraints excluded: chain F residue 519 THR Chi-restraints excluded: chain F residue 553 LEU Chi-restraints excluded: chain F residue 563 THR Chi-restraints excluded: chain F residue 586 PHE Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain K residue 83 PHE Chi-restraints excluded: chain K residue 102 VAL Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 152 VAL Chi-restraints excluded: chain K residue 153 ILE Chi-restraints excluded: chain K residue 159 TYR Chi-restraints excluded: chain K residue 168 PHE Chi-restraints excluded: chain K residue 205 THR Chi-restraints excluded: chain K residue 232 THR Chi-restraints excluded: chain K residue 336 THR Chi-restraints excluded: chain K residue 340 ILE Chi-restraints excluded: chain K residue 375 SER Chi-restraints excluded: chain K residue 400 GLN Chi-restraints excluded: chain K residue 415 ILE Chi-restraints excluded: chain K residue 461 LEU Chi-restraints excluded: chain K residue 475 VAL Chi-restraints excluded: chain K residue 495 MET Chi-restraints excluded: chain K residue 563 THR Chi-restraints excluded: chain K residue 586 PHE Chi-restraints excluded: chain L residue 177 LEU Chi-restraints excluded: chain M residue 179 GLN Chi-restraints excluded: chain N residue 95 ILE Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 153 ILE Chi-restraints excluded: chain N residue 159 TYR Chi-restraints excluded: chain N residue 168 PHE Chi-restraints excluded: chain N residue 205 THR Chi-restraints excluded: chain N residue 213 MET Chi-restraints excluded: chain N residue 232 THR Chi-restraints excluded: chain N residue 241 ILE Chi-restraints excluded: chain N residue 255 LYS Chi-restraints excluded: chain N residue 339 ILE Chi-restraints excluded: chain N residue 344 ASN Chi-restraints excluded: chain N residue 375 SER Chi-restraints excluded: chain N residue 391 ILE Chi-restraints excluded: chain N residue 475 VAL Chi-restraints excluded: chain N residue 519 THR Chi-restraints excluded: chain N residue 540 MET Chi-restraints excluded: chain N residue 563 THR Chi-restraints excluded: chain N residue 565 VAL Chi-restraints excluded: chain O residue 177 LEU Chi-restraints excluded: chain O residue 179 GLN Chi-restraints excluded: chain Q residue 77 CYS Chi-restraints excluded: chain Q residue 95 ILE Chi-restraints excluded: chain Q residue 102 VAL Chi-restraints excluded: chain Q residue 153 ILE Chi-restraints excluded: chain Q residue 168 PHE Chi-restraints excluded: chain Q residue 204 ILE Chi-restraints excluded: chain Q residue 212 VAL Chi-restraints excluded: chain Q residue 213 MET Chi-restraints excluded: chain Q residue 232 THR Chi-restraints excluded: chain Q residue 255 LYS Chi-restraints excluded: chain Q residue 336 THR Chi-restraints excluded: chain Q residue 388 GLU Chi-restraints excluded: chain Q residue 391 ILE Chi-restraints excluded: chain Q residue 475 VAL Chi-restraints excluded: chain Q residue 519 THR Chi-restraints excluded: chain Q residue 553 LEU Chi-restraints excluded: chain Q residue 563 THR Chi-restraints excluded: chain Q residue 586 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 68 optimal weight: 5.9990 chunk 174 optimal weight: 4.9990 chunk 285 optimal weight: 2.9990 chunk 289 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 250 optimal weight: 0.0770 chunk 70 optimal weight: 0.7980 chunk 271 optimal weight: 5.9990 overall best weight: 1.5342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 179 GLN ** Y 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 ASN ** C 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 126 ASN ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 179 GLN ** K 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 93 ASN ** N 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 343 HIS ** Q 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.109083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.089147 restraints weight = 53654.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.092582 restraints weight = 28906.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.094878 restraints weight = 18808.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.096518 restraints weight = 13815.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.097672 restraints weight = 11018.517| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 31422 Z= 0.193 Angle : 0.662 10.107 42528 Z= 0.343 Chirality : 0.043 0.180 4644 Planarity : 0.012 0.442 5568 Dihedral : 6.221 115.219 4098 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 5.22 % Allowed : 16.61 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.13), residues: 3720 helix: 0.06 (0.18), residues: 870 sheet: 0.02 (0.20), residues: 738 loop : -1.45 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG C 510 TYR 0.030 0.002 TYR C 457 PHE 0.018 0.002 PHE C 586 TRP 0.007 0.001 TRP F 230 HIS 0.003 0.001 HIS K 343 Details of bonding type rmsd covalent geometry : bond 0.00441 (31362) covalent geometry : angle 0.66199 (42528) hydrogen bonds : bond 0.03826 ( 876) hydrogen bonds : angle 5.63046 ( 2250) Misc. bond : bond 0.00504 ( 60) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 470 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 179 GLN cc_start: 0.8742 (pt0) cc_final: 0.8441 (pt0) REVERT: J 185 ASP cc_start: 0.8564 (t0) cc_final: 0.8334 (t0) REVERT: Y 66 MET cc_start: 0.8538 (ttm) cc_final: 0.8327 (ttm) REVERT: Y 115 TYR cc_start: 0.9040 (m-80) cc_final: 0.8658 (m-10) REVERT: Y 159 TYR cc_start: 0.8835 (OUTLIER) cc_final: 0.8152 (p90) REVERT: Y 213 MET cc_start: 0.8828 (ptm) cc_final: 0.8286 (ptm) REVERT: Y 219 ASN cc_start: 0.8147 (m-40) cc_final: 0.7722 (m-40) REVERT: Y 340 ILE cc_start: 0.9413 (OUTLIER) cc_final: 0.9162 (tp) REVERT: Y 376 PHE cc_start: 0.9293 (t80) cc_final: 0.8258 (t80) REVERT: Y 388 GLU cc_start: 0.8302 (mm-30) cc_final: 0.7937 (mt-10) REVERT: Y 519 THR cc_start: 0.9363 (OUTLIER) cc_final: 0.8943 (p) REVERT: Y 577 MET cc_start: 0.8857 (mmt) cc_final: 0.8269 (mmt) REVERT: A 185 ASP cc_start: 0.8747 (t0) cc_final: 0.8534 (t0) REVERT: C 159 TYR cc_start: 0.8923 (OUTLIER) cc_final: 0.8502 (p90) REVERT: C 213 MET cc_start: 0.8919 (OUTLIER) cc_final: 0.8606 (ptm) REVERT: C 290 MET cc_start: 0.9168 (mtm) cc_final: 0.8921 (mtm) REVERT: C 305 GLU cc_start: 0.8677 (tm-30) cc_final: 0.8470 (tm-30) REVERT: C 344 ASN cc_start: 0.9207 (OUTLIER) cc_final: 0.8530 (m-40) REVERT: C 376 PHE cc_start: 0.9266 (t80) cc_final: 0.8507 (t80) REVERT: C 388 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7656 (mt-10) REVERT: C 480 MET cc_start: 0.9339 (tpt) cc_final: 0.8961 (tpp) REVERT: C 515 LEU cc_start: 0.9493 (mm) cc_final: 0.9190 (mm) REVERT: D 187 ASP cc_start: 0.7791 (OUTLIER) cc_final: 0.7446 (t0) REVERT: E 193 TYR cc_start: 0.6280 (m-80) cc_final: 0.5692 (m-80) REVERT: F 60 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.8273 (mtp) REVERT: F 168 PHE cc_start: 0.8168 (OUTLIER) cc_final: 0.6532 (p90) REVERT: F 213 MET cc_start: 0.9149 (OUTLIER) cc_final: 0.8835 (ptm) REVERT: F 519 THR cc_start: 0.9423 (OUTLIER) cc_final: 0.9101 (p) REVERT: F 577 MET cc_start: 0.8964 (mmt) cc_final: 0.8495 (mmt) REVERT: G 179 GLN cc_start: 0.8731 (pt0) cc_final: 0.8406 (pt0) REVERT: G 185 ASP cc_start: 0.8565 (t0) cc_final: 0.8343 (t0) REVERT: K 115 TYR cc_start: 0.9031 (m-80) cc_final: 0.8704 (m-10) REVERT: K 159 TYR cc_start: 0.8830 (OUTLIER) cc_final: 0.8141 (p90) REVERT: K 213 MET cc_start: 0.8938 (ptm) cc_final: 0.8317 (ptm) REVERT: K 219 ASN cc_start: 0.8034 (m-40) cc_final: 0.7727 (m-40) REVERT: K 340 ILE cc_start: 0.9425 (OUTLIER) cc_final: 0.9172 (tp) REVERT: K 388 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7598 (mt-10) REVERT: K 518 GLU cc_start: 0.8427 (tm-30) cc_final: 0.8181 (tm-30) REVERT: K 577 MET cc_start: 0.9251 (mmm) cc_final: 0.8917 (mmt) REVERT: L 185 ASP cc_start: 0.8747 (t0) cc_final: 0.8531 (t0) REVERT: N 159 TYR cc_start: 0.8921 (OUTLIER) cc_final: 0.8505 (p90) REVERT: N 213 MET cc_start: 0.8924 (OUTLIER) cc_final: 0.8601 (ptm) REVERT: N 290 MET cc_start: 0.9168 (mtm) cc_final: 0.8917 (mtm) REVERT: N 344 ASN cc_start: 0.9211 (OUTLIER) cc_final: 0.8585 (m110) REVERT: N 376 PHE cc_start: 0.9267 (t80) cc_final: 0.8517 (t80) REVERT: N 388 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7403 (mt-10) REVERT: N 400 GLN cc_start: 0.8397 (tp40) cc_final: 0.8183 (tp40) REVERT: P 193 TYR cc_start: 0.6282 (m-80) cc_final: 0.5695 (m-80) REVERT: Q 19 ASP cc_start: 0.8141 (t0) cc_final: 0.7896 (t70) REVERT: Q 60 MET cc_start: 0.8491 (OUTLIER) cc_final: 0.8257 (mtp) REVERT: Q 168 PHE cc_start: 0.8161 (OUTLIER) cc_final: 0.6517 (p90) REVERT: Q 194 GLU cc_start: 0.6243 (tp30) cc_final: 0.6007 (tp30) REVERT: Q 213 MET cc_start: 0.9145 (OUTLIER) cc_final: 0.8835 (ptm) REVERT: Q 345 GLU cc_start: 0.8665 (tt0) cc_final: 0.8277 (mt-10) REVERT: Q 562 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7628 (mt-10) REVERT: Q 577 MET cc_start: 0.8978 (mmt) cc_final: 0.8497 (mmt) outliers start: 180 outliers final: 111 residues processed: 592 average time/residue: 0.1947 time to fit residues: 190.5212 Evaluate side-chains 565 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 435 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 177 LEU Chi-restraints excluded: chain Y residue 78 THR Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 123 THR Chi-restraints excluded: chain Y residue 152 VAL Chi-restraints excluded: chain Y residue 153 ILE Chi-restraints excluded: chain Y residue 159 TYR Chi-restraints excluded: chain Y residue 168 PHE Chi-restraints excluded: chain Y residue 204 ILE Chi-restraints excluded: chain Y residue 205 THR Chi-restraints excluded: chain Y residue 212 VAL Chi-restraints excluded: chain Y residue 232 THR Chi-restraints excluded: chain Y residue 336 THR Chi-restraints excluded: chain Y residue 340 ILE Chi-restraints excluded: chain Y residue 375 SER Chi-restraints excluded: chain Y residue 415 ILE Chi-restraints excluded: chain Y residue 461 LEU Chi-restraints excluded: chain Y residue 475 VAL Chi-restraints excluded: chain Y residue 480 MET Chi-restraints excluded: chain Y residue 495 MET Chi-restraints excluded: chain Y residue 519 THR Chi-restraints excluded: chain Y residue 563 THR Chi-restraints excluded: chain Y residue 586 PHE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain C residue 8 HIS Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 159 TYR Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 213 MET Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 255 LYS Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 339 ILE Chi-restraints excluded: chain C residue 344 ASN Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 479 GLN Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 565 VAL Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain F residue 60 MET Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 168 PHE Chi-restraints excluded: chain F residue 204 ILE Chi-restraints excluded: chain F residue 205 THR Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 213 MET Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 336 THR Chi-restraints excluded: chain F residue 339 ILE Chi-restraints excluded: chain F residue 391 ILE Chi-restraints excluded: chain F residue 475 VAL Chi-restraints excluded: chain F residue 519 THR Chi-restraints excluded: chain F residue 553 LEU Chi-restraints excluded: chain F residue 563 THR Chi-restraints excluded: chain F residue 586 PHE Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 102 VAL Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 152 VAL Chi-restraints excluded: chain K residue 153 ILE Chi-restraints excluded: chain K residue 159 TYR Chi-restraints excluded: chain K residue 168 PHE Chi-restraints excluded: chain K residue 205 THR Chi-restraints excluded: chain K residue 212 VAL Chi-restraints excluded: chain K residue 232 THR Chi-restraints excluded: chain K residue 336 THR Chi-restraints excluded: chain K residue 340 ILE Chi-restraints excluded: chain K residue 375 SER Chi-restraints excluded: chain K residue 400 GLN Chi-restraints excluded: chain K residue 415 ILE Chi-restraints excluded: chain K residue 475 VAL Chi-restraints excluded: chain K residue 495 MET Chi-restraints excluded: chain K residue 563 THR Chi-restraints excluded: chain K residue 586 PHE Chi-restraints excluded: chain L residue 177 LEU Chi-restraints excluded: chain N residue 8 HIS Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 95 ILE Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 153 ILE Chi-restraints excluded: chain N residue 159 TYR Chi-restraints excluded: chain N residue 168 PHE Chi-restraints excluded: chain N residue 205 THR Chi-restraints excluded: chain N residue 213 MET Chi-restraints excluded: chain N residue 241 ILE Chi-restraints excluded: chain N residue 255 LYS Chi-restraints excluded: chain N residue 336 THR Chi-restraints excluded: chain N residue 339 ILE Chi-restraints excluded: chain N residue 344 ASN Chi-restraints excluded: chain N residue 375 SER Chi-restraints excluded: chain N residue 391 ILE Chi-restraints excluded: chain N residue 475 VAL Chi-restraints excluded: chain N residue 479 GLN Chi-restraints excluded: chain N residue 519 THR Chi-restraints excluded: chain N residue 563 THR Chi-restraints excluded: chain N residue 565 VAL Chi-restraints excluded: chain O residue 177 LEU Chi-restraints excluded: chain O residue 179 GLN Chi-restraints excluded: chain O residue 187 ASP Chi-restraints excluded: chain Q residue 60 MET Chi-restraints excluded: chain Q residue 77 CYS Chi-restraints excluded: chain Q residue 95 ILE Chi-restraints excluded: chain Q residue 102 VAL Chi-restraints excluded: chain Q residue 153 ILE Chi-restraints excluded: chain Q residue 168 PHE Chi-restraints excluded: chain Q residue 204 ILE Chi-restraints excluded: chain Q residue 212 VAL Chi-restraints excluded: chain Q residue 213 MET Chi-restraints excluded: chain Q residue 232 THR Chi-restraints excluded: chain Q residue 336 THR Chi-restraints excluded: chain Q residue 391 ILE Chi-restraints excluded: chain Q residue 475 VAL Chi-restraints excluded: chain Q residue 519 THR Chi-restraints excluded: chain Q residue 553 LEU Chi-restraints excluded: chain Q residue 563 THR Chi-restraints excluded: chain Q residue 586 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 323 optimal weight: 0.2980 chunk 147 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 136 optimal weight: 0.6980 chunk 199 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 342 optimal weight: 0.0870 chunk 251 optimal weight: 0.7980 chunk 288 optimal weight: 0.0060 chunk 344 optimal weight: 0.8980 chunk 312 optimal weight: 5.9990 overall best weight: 0.3574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN ** F 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 179 GLN ** Q 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.114963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.095171 restraints weight = 52843.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.098771 restraints weight = 28257.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.101231 restraints weight = 18102.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.102965 restraints weight = 13114.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.104175 restraints weight = 10321.304| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 31422 Z= 0.135 Angle : 0.687 15.503 42528 Z= 0.353 Chirality : 0.043 0.278 4644 Planarity : 0.008 0.304 5568 Dihedral : 5.793 142.212 4098 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 4.46 % Allowed : 18.55 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.10 (0.13), residues: 3720 helix: 0.17 (0.18), residues: 864 sheet: -0.00 (0.20), residues: 720 loop : -1.41 (0.13), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.046 0.001 ARG N 215 TYR 0.025 0.001 TYR E 193 PHE 0.033 0.001 PHE C 235 TRP 0.005 0.001 TRP K 568 HIS 0.002 0.000 HIS Y 343 Details of bonding type rmsd covalent geometry : bond 0.00291 (31362) covalent geometry : angle 0.68658 (42528) hydrogen bonds : bond 0.03252 ( 876) hydrogen bonds : angle 5.36405 ( 2250) Misc. bond : bond 0.00661 ( 60) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 516 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 179 GLN cc_start: 0.8573 (pt0) cc_final: 0.8265 (pt0) REVERT: J 185 ASP cc_start: 0.8604 (t0) cc_final: 0.8160 (t0) REVERT: J 189 THR cc_start: 0.8299 (m) cc_final: 0.8002 (m) REVERT: Y 115 TYR cc_start: 0.8973 (m-80) cc_final: 0.8591 (m-10) REVERT: Y 159 TYR cc_start: 0.8755 (OUTLIER) cc_final: 0.8059 (p90) REVERT: Y 210 LEU cc_start: 0.9173 (mt) cc_final: 0.8931 (mp) REVERT: Y 219 ASN cc_start: 0.8193 (m-40) cc_final: 0.7819 (m-40) REVERT: Y 340 ILE cc_start: 0.9405 (OUTLIER) cc_final: 0.9116 (tp) REVERT: Y 345 GLU cc_start: 0.8329 (tt0) cc_final: 0.7713 (mt-10) REVERT: Y 388 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7355 (mt-10) REVERT: Y 515 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.9079 (mm) REVERT: Y 577 MET cc_start: 0.8807 (mmt) cc_final: 0.8121 (mmt) REVERT: A 185 ASP cc_start: 0.8775 (t0) cc_final: 0.8264 (t0) REVERT: C 19 ASP cc_start: 0.7876 (t0) cc_final: 0.7207 (t0) REVERT: C 83 PHE cc_start: 0.8890 (OUTLIER) cc_final: 0.8539 (m-80) REVERT: C 159 TYR cc_start: 0.8892 (OUTLIER) cc_final: 0.8477 (p90) REVERT: C 213 MET cc_start: 0.8957 (OUTLIER) cc_final: 0.8653 (ptm) REVERT: C 305 GLU cc_start: 0.8617 (tm-30) cc_final: 0.8371 (tm-30) REVERT: C 376 PHE cc_start: 0.9158 (t80) cc_final: 0.8450 (t80) REVERT: C 388 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7897 (mt-10) REVERT: C 515 LEU cc_start: 0.9451 (mm) cc_final: 0.9152 (mm) REVERT: D 187 ASP cc_start: 0.7757 (OUTLIER) cc_final: 0.7391 (t0) REVERT: F 168 PHE cc_start: 0.8017 (OUTLIER) cc_final: 0.6651 (p90) REVERT: F 175 PHE cc_start: 0.7570 (OUTLIER) cc_final: 0.6708 (m-80) REVERT: F 194 GLU cc_start: 0.6214 (tp30) cc_final: 0.5917 (tp30) REVERT: F 213 MET cc_start: 0.8973 (OUTLIER) cc_final: 0.8605 (ptm) REVERT: F 345 GLU cc_start: 0.8629 (tt0) cc_final: 0.8335 (mt-10) REVERT: F 459 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7961 (mttm) REVERT: F 519 THR cc_start: 0.9483 (OUTLIER) cc_final: 0.9170 (p) REVERT: F 577 MET cc_start: 0.8935 (mmt) cc_final: 0.8531 (mmt) REVERT: G 179 GLN cc_start: 0.8567 (pt0) cc_final: 0.8325 (pt0) REVERT: G 185 ASP cc_start: 0.8593 (t0) cc_final: 0.8165 (t0) REVERT: G 189 THR cc_start: 0.8336 (m) cc_final: 0.8033 (m) REVERT: K 115 TYR cc_start: 0.8975 (m-80) cc_final: 0.8589 (m-10) REVERT: K 159 TYR cc_start: 0.8717 (OUTLIER) cc_final: 0.8008 (p90) REVERT: K 210 LEU cc_start: 0.9067 (mt) cc_final: 0.8779 (mp) REVERT: K 213 MET cc_start: 0.8827 (ptm) cc_final: 0.8357 (ptm) REVERT: K 344 ASN cc_start: 0.8417 (OUTLIER) cc_final: 0.7719 (m-40) REVERT: K 345 GLU cc_start: 0.8359 (tt0) cc_final: 0.7772 (mt-10) REVERT: K 388 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7718 (mt-10) REVERT: L 185 ASP cc_start: 0.8775 (t0) cc_final: 0.8263 (t0) REVERT: N 6 LEU cc_start: 0.9294 (mt) cc_final: 0.9093 (mt) REVERT: N 19 ASP cc_start: 0.7888 (t0) cc_final: 0.7225 (t0) REVERT: N 83 PHE cc_start: 0.8888 (OUTLIER) cc_final: 0.8540 (m-80) REVERT: N 159 TYR cc_start: 0.8885 (OUTLIER) cc_final: 0.8467 (p90) REVERT: N 210 LEU cc_start: 0.8925 (mp) cc_final: 0.8557 (mt) REVERT: N 213 MET cc_start: 0.8975 (OUTLIER) cc_final: 0.8667 (ptm) REVERT: N 376 PHE cc_start: 0.9161 (t80) cc_final: 0.8452 (t80) REVERT: N 388 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7550 (mt-10) REVERT: N 515 LEU cc_start: 0.9425 (mm) cc_final: 0.9103 (mm) REVERT: O 187 ASP cc_start: 0.7970 (OUTLIER) cc_final: 0.7541 (t0) REVERT: Q 19 ASP cc_start: 0.8125 (t0) cc_final: 0.7645 (t70) REVERT: Q 168 PHE cc_start: 0.8012 (OUTLIER) cc_final: 0.6501 (p90) REVERT: Q 175 PHE cc_start: 0.7575 (OUTLIER) cc_final: 0.6717 (m-80) REVERT: Q 194 GLU cc_start: 0.6044 (tp30) cc_final: 0.5784 (tp30) REVERT: Q 213 MET cc_start: 0.8967 (OUTLIER) cc_final: 0.8603 (ptm) REVERT: Q 459 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7926 (mttm) REVERT: Q 577 MET cc_start: 0.8937 (mmt) cc_final: 0.8503 (mmt) outliers start: 154 outliers final: 93 residues processed: 613 average time/residue: 0.1905 time to fit residues: 195.8639 Evaluate side-chains 570 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 455 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 78 THR Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 123 THR Chi-restraints excluded: chain Y residue 152 VAL Chi-restraints excluded: chain Y residue 159 TYR Chi-restraints excluded: chain Y residue 168 PHE Chi-restraints excluded: chain Y residue 204 ILE Chi-restraints excluded: chain Y residue 205 THR Chi-restraints excluded: chain Y residue 232 THR Chi-restraints excluded: chain Y residue 336 THR Chi-restraints excluded: chain Y residue 340 ILE Chi-restraints excluded: chain Y residue 375 SER Chi-restraints excluded: chain Y residue 415 ILE Chi-restraints excluded: chain Y residue 461 LEU Chi-restraints excluded: chain Y residue 475 VAL Chi-restraints excluded: chain Y residue 480 MET Chi-restraints excluded: chain Y residue 515 LEU Chi-restraints excluded: chain Y residue 586 PHE Chi-restraints excluded: chain B residue 179 GLN Chi-restraints excluded: chain C residue 83 PHE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 159 TYR Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 213 MET Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 255 LYS Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 339 ILE Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 565 VAL Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 168 PHE Chi-restraints excluded: chain F residue 175 PHE Chi-restraints excluded: chain F residue 204 ILE Chi-restraints excluded: chain F residue 205 THR Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 213 MET Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 255 LYS Chi-restraints excluded: chain F residue 336 THR Chi-restraints excluded: chain F residue 391 ILE Chi-restraints excluded: chain F residue 415 ILE Chi-restraints excluded: chain F residue 459 LYS Chi-restraints excluded: chain F residue 475 VAL Chi-restraints excluded: chain F residue 519 THR Chi-restraints excluded: chain F residue 586 PHE Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 102 VAL Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 152 VAL Chi-restraints excluded: chain K residue 159 TYR Chi-restraints excluded: chain K residue 168 PHE Chi-restraints excluded: chain K residue 204 ILE Chi-restraints excluded: chain K residue 232 THR Chi-restraints excluded: chain K residue 336 THR Chi-restraints excluded: chain K residue 340 ILE Chi-restraints excluded: chain K residue 344 ASN Chi-restraints excluded: chain K residue 375 SER Chi-restraints excluded: chain K residue 400 GLN Chi-restraints excluded: chain K residue 415 ILE Chi-restraints excluded: chain K residue 475 VAL Chi-restraints excluded: chain K residue 586 PHE Chi-restraints excluded: chain M residue 179 GLN Chi-restraints excluded: chain N residue 83 PHE Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 153 ILE Chi-restraints excluded: chain N residue 159 TYR Chi-restraints excluded: chain N residue 168 PHE Chi-restraints excluded: chain N residue 204 ILE Chi-restraints excluded: chain N residue 213 MET Chi-restraints excluded: chain N residue 241 ILE Chi-restraints excluded: chain N residue 255 LYS Chi-restraints excluded: chain N residue 327 THR Chi-restraints excluded: chain N residue 336 THR Chi-restraints excluded: chain N residue 339 ILE Chi-restraints excluded: chain N residue 375 SER Chi-restraints excluded: chain N residue 391 ILE Chi-restraints excluded: chain N residue 438 ILE Chi-restraints excluded: chain N residue 475 VAL Chi-restraints excluded: chain N residue 479 GLN Chi-restraints excluded: chain N residue 563 THR Chi-restraints excluded: chain N residue 565 VAL Chi-restraints excluded: chain O residue 177 LEU Chi-restraints excluded: chain O residue 179 GLN Chi-restraints excluded: chain O residue 187 ASP Chi-restraints excluded: chain P residue 186 VAL Chi-restraints excluded: chain Q residue 77 CYS Chi-restraints excluded: chain Q residue 102 VAL Chi-restraints excluded: chain Q residue 168 PHE Chi-restraints excluded: chain Q residue 175 PHE Chi-restraints excluded: chain Q residue 204 ILE Chi-restraints excluded: chain Q residue 205 THR Chi-restraints excluded: chain Q residue 212 VAL Chi-restraints excluded: chain Q residue 213 MET Chi-restraints excluded: chain Q residue 232 THR Chi-restraints excluded: chain Q residue 255 LYS Chi-restraints excluded: chain Q residue 336 THR Chi-restraints excluded: chain Q residue 391 ILE Chi-restraints excluded: chain Q residue 415 ILE Chi-restraints excluded: chain Q residue 459 LYS Chi-restraints excluded: chain Q residue 475 VAL Chi-restraints excluded: chain Q residue 586 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 170 optimal weight: 6.9990 chunk 338 optimal weight: 3.9990 chunk 297 optimal weight: 0.9980 chunk 310 optimal weight: 0.4980 chunk 164 optimal weight: 0.0670 chunk 96 optimal weight: 4.9990 chunk 298 optimal weight: 0.0870 chunk 68 optimal weight: 2.9990 chunk 208 optimal weight: 2.9990 chunk 180 optimal weight: 0.7980 chunk 204 optimal weight: 3.9990 overall best weight: 0.4896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 GLN ** C 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 GLN F 343 HIS ** F 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 72 GLN ** K 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 179 GLN ** N 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 358 ASN ** N 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 72 GLN Q 126 ASN ** Q 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.121717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.102429 restraints weight = 53488.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.105882 restraints weight = 28328.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.108337 restraints weight = 18141.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.110070 restraints weight = 13114.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.111322 restraints weight = 10321.274| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.4009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31422 Z= 0.139 Angle : 0.676 14.478 42528 Z= 0.349 Chirality : 0.043 0.245 4644 Planarity : 0.010 0.366 5568 Dihedral : 7.056 170.915 4098 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 4.58 % Allowed : 19.22 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.13), residues: 3720 helix: 0.20 (0.18), residues: 864 sheet: 0.29 (0.20), residues: 678 loop : -1.44 (0.12), residues: 2178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.039 0.001 ARG F 215 TYR 0.023 0.001 TYR C 342 PHE 0.040 0.002 PHE Q 376 TRP 0.005 0.001 TRP Y 568 HIS 0.002 0.000 HIS N 343 Details of bonding type rmsd covalent geometry : bond 0.00301 (31362) covalent geometry : angle 0.67611 (42528) hydrogen bonds : bond 0.03268 ( 876) hydrogen bonds : angle 5.38485 ( 2250) Misc. bond : bond 0.00670 ( 60) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 662 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 504 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 179 GLN cc_start: 0.8746 (pt0) cc_final: 0.8358 (pt0) REVERT: J 185 ASP cc_start: 0.8622 (t0) cc_final: 0.8190 (t0) REVERT: J 189 THR cc_start: 0.8294 (m) cc_final: 0.7998 (m) REVERT: I 183 ASN cc_start: 0.8011 (t0) cc_final: 0.7490 (t0) REVERT: Y 60 MET cc_start: 0.8616 (ttm) cc_final: 0.8086 (mmm) REVERT: Y 115 TYR cc_start: 0.8974 (m-80) cc_final: 0.8582 (m-10) REVERT: Y 159 TYR cc_start: 0.8785 (OUTLIER) cc_final: 0.8041 (p90) REVERT: Y 219 ASN cc_start: 0.8070 (m-40) cc_final: 0.7323 (m-40) REVERT: Y 340 ILE cc_start: 0.9402 (OUTLIER) cc_final: 0.9120 (tp) REVERT: Y 577 MET cc_start: 0.8842 (mmt) cc_final: 0.8076 (mmt) REVERT: C 83 PHE cc_start: 0.8810 (OUTLIER) cc_final: 0.8464 (m-80) REVERT: C 213 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.8581 (ptm) REVERT: C 376 PHE cc_start: 0.9172 (t80) cc_final: 0.8451 (t80) REVERT: C 515 LEU cc_start: 0.9426 (mm) cc_final: 0.9202 (mm) REVERT: D 179 GLN cc_start: 0.8064 (pt0) cc_final: 0.6877 (pm20) REVERT: F 6 LEU cc_start: 0.8955 (mm) cc_final: 0.8715 (mt) REVERT: F 97 TYR cc_start: 0.9177 (t80) cc_final: 0.8952 (t80) REVERT: F 168 PHE cc_start: 0.8054 (OUTLIER) cc_final: 0.6406 (p90) REVERT: F 175 PHE cc_start: 0.7608 (OUTLIER) cc_final: 0.6798 (m-80) REVERT: F 185 PHE cc_start: 0.7570 (m-80) cc_final: 0.7204 (m-80) REVERT: F 213 MET cc_start: 0.8872 (OUTLIER) cc_final: 0.8569 (ptm) REVERT: F 345 GLU cc_start: 0.8601 (tt0) cc_final: 0.8348 (tt0) REVERT: F 459 LYS cc_start: 0.8160 (mttm) cc_final: 0.7866 (mttp) REVERT: F 515 LEU cc_start: 0.9526 (OUTLIER) cc_final: 0.9263 (mm) REVERT: F 519 THR cc_start: 0.9448 (OUTLIER) cc_final: 0.9162 (p) REVERT: F 577 MET cc_start: 0.8951 (mmt) cc_final: 0.8526 (mmt) REVERT: G 179 GLN cc_start: 0.8780 (pt0) cc_final: 0.8475 (pt0) REVERT: G 185 ASP cc_start: 0.8608 (t0) cc_final: 0.8185 (t0) REVERT: G 189 THR cc_start: 0.8308 (m) cc_final: 0.8027 (m) REVERT: H 183 ASN cc_start: 0.7927 (t0) cc_final: 0.7417 (t0) REVERT: K 63 LEU cc_start: 0.9427 (mp) cc_final: 0.9224 (mp) REVERT: K 115 TYR cc_start: 0.8972 (m-80) cc_final: 0.8582 (m-10) REVERT: K 159 TYR cc_start: 0.8732 (OUTLIER) cc_final: 0.8043 (p90) REVERT: K 210 LEU cc_start: 0.9030 (mt) cc_final: 0.8736 (mp) REVERT: K 213 MET cc_start: 0.8454 (ptm) cc_final: 0.8052 (ptm) REVERT: K 214 ASN cc_start: 0.8625 (OUTLIER) cc_final: 0.8011 (t0) REVERT: K 345 GLU cc_start: 0.8283 (tt0) cc_final: 0.7747 (mt-10) REVERT: K 388 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7669 (mt-10) REVERT: N 159 TYR cc_start: 0.8861 (OUTLIER) cc_final: 0.8491 (p90) REVERT: N 213 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.8599 (ptm) REVERT: N 376 PHE cc_start: 0.9162 (t80) cc_final: 0.8454 (t80) REVERT: N 388 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7441 (mt-10) REVERT: N 515 LEU cc_start: 0.9436 (mm) cc_final: 0.9201 (mm) REVERT: O 187 ASP cc_start: 0.7938 (OUTLIER) cc_final: 0.7573 (t0) REVERT: Q 6 LEU cc_start: 0.8971 (mm) cc_final: 0.8736 (mt) REVERT: Q 97 TYR cc_start: 0.9180 (t80) cc_final: 0.8954 (t80) REVERT: Q 168 PHE cc_start: 0.8041 (OUTLIER) cc_final: 0.6390 (p90) REVERT: Q 175 PHE cc_start: 0.7623 (OUTLIER) cc_final: 0.6815 (m-80) REVERT: Q 185 PHE cc_start: 0.7730 (m-80) cc_final: 0.7416 (m-80) REVERT: Q 194 GLU cc_start: 0.6036 (tp30) cc_final: 0.5777 (tp30) REVERT: Q 213 MET cc_start: 0.8900 (OUTLIER) cc_final: 0.8618 (ptm) REVERT: Q 400 GLN cc_start: 0.8341 (mm-40) cc_final: 0.8139 (mm-40) REVERT: Q 455 TYR cc_start: 0.7206 (t80) cc_final: 0.6796 (t80) REVERT: Q 459 LYS cc_start: 0.8155 (mttm) cc_final: 0.7797 (mttp) REVERT: Q 515 LEU cc_start: 0.9544 (mm) cc_final: 0.9271 (mm) REVERT: Q 519 THR cc_start: 0.9372 (OUTLIER) cc_final: 0.9067 (p) REVERT: Q 577 MET cc_start: 0.8968 (mmt) cc_final: 0.8521 (mmt) outliers start: 158 outliers final: 106 residues processed: 611 average time/residue: 0.1814 time to fit residues: 188.0072 Evaluate side-chains 582 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 458 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 78 THR Chi-restraints excluded: chain Y residue 83 PHE Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 123 THR Chi-restraints excluded: chain Y residue 152 VAL Chi-restraints excluded: chain Y residue 159 TYR Chi-restraints excluded: chain Y residue 205 THR Chi-restraints excluded: chain Y residue 232 THR Chi-restraints excluded: chain Y residue 336 THR Chi-restraints excluded: chain Y residue 340 ILE Chi-restraints excluded: chain Y residue 369 ILE Chi-restraints excluded: chain Y residue 375 SER Chi-restraints excluded: chain Y residue 415 ILE Chi-restraints excluded: chain Y residue 438 ILE Chi-restraints excluded: chain Y residue 461 LEU Chi-restraints excluded: chain Y residue 475 VAL Chi-restraints excluded: chain Y residue 480 MET Chi-restraints excluded: chain Y residue 586 PHE Chi-restraints excluded: chain B residue 179 GLN Chi-restraints excluded: chain C residue 8 HIS Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 83 PHE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 213 MET Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 255 LYS Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 339 ILE Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 479 GLN Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain C residue 540 MET Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 168 PHE Chi-restraints excluded: chain F residue 175 PHE Chi-restraints excluded: chain F residue 204 ILE Chi-restraints excluded: chain F residue 205 THR Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 213 MET Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 255 LYS Chi-restraints excluded: chain F residue 336 THR Chi-restraints excluded: chain F residue 391 ILE Chi-restraints excluded: chain F residue 475 VAL Chi-restraints excluded: chain F residue 479 GLN Chi-restraints excluded: chain F residue 515 LEU Chi-restraints excluded: chain F residue 519 THR Chi-restraints excluded: chain F residue 586 PHE Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 83 PHE Chi-restraints excluded: chain K residue 102 VAL Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 152 VAL Chi-restraints excluded: chain K residue 159 TYR Chi-restraints excluded: chain K residue 212 VAL Chi-restraints excluded: chain K residue 214 ASN Chi-restraints excluded: chain K residue 232 THR Chi-restraints excluded: chain K residue 336 THR Chi-restraints excluded: chain K residue 340 ILE Chi-restraints excluded: chain K residue 369 ILE Chi-restraints excluded: chain K residue 375 SER Chi-restraints excluded: chain K residue 400 GLN Chi-restraints excluded: chain K residue 415 ILE Chi-restraints excluded: chain K residue 438 ILE Chi-restraints excluded: chain K residue 461 LEU Chi-restraints excluded: chain K residue 475 VAL Chi-restraints excluded: chain K residue 563 THR Chi-restraints excluded: chain K residue 586 PHE Chi-restraints excluded: chain M residue 179 GLN Chi-restraints excluded: chain N residue 8 HIS Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 153 ILE Chi-restraints excluded: chain N residue 159 TYR Chi-restraints excluded: chain N residue 168 PHE Chi-restraints excluded: chain N residue 213 MET Chi-restraints excluded: chain N residue 241 ILE Chi-restraints excluded: chain N residue 255 LYS Chi-restraints excluded: chain N residue 327 THR Chi-restraints excluded: chain N residue 336 THR Chi-restraints excluded: chain N residue 339 ILE Chi-restraints excluded: chain N residue 358 ASN Chi-restraints excluded: chain N residue 375 SER Chi-restraints excluded: chain N residue 391 ILE Chi-restraints excluded: chain N residue 438 ILE Chi-restraints excluded: chain N residue 475 VAL Chi-restraints excluded: chain N residue 519 THR Chi-restraints excluded: chain N residue 540 MET Chi-restraints excluded: chain N residue 563 THR Chi-restraints excluded: chain O residue 177 LEU Chi-restraints excluded: chain O residue 187 ASP Chi-restraints excluded: chain P residue 186 VAL Chi-restraints excluded: chain Q residue 77 CYS Chi-restraints excluded: chain Q residue 102 VAL Chi-restraints excluded: chain Q residue 153 ILE Chi-restraints excluded: chain Q residue 168 PHE Chi-restraints excluded: chain Q residue 175 PHE Chi-restraints excluded: chain Q residue 204 ILE Chi-restraints excluded: chain Q residue 205 THR Chi-restraints excluded: chain Q residue 212 VAL Chi-restraints excluded: chain Q residue 213 MET Chi-restraints excluded: chain Q residue 232 THR Chi-restraints excluded: chain Q residue 255 LYS Chi-restraints excluded: chain Q residue 336 THR Chi-restraints excluded: chain Q residue 391 ILE Chi-restraints excluded: chain Q residue 475 VAL Chi-restraints excluded: chain Q residue 519 THR Chi-restraints excluded: chain Q residue 563 THR Chi-restraints excluded: chain Q residue 586 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 109 optimal weight: 7.9990 chunk 364 optimal weight: 1.9990 chunk 210 optimal weight: 4.9990 chunk 206 optimal weight: 3.9990 chunk 269 optimal weight: 4.9990 chunk 369 optimal weight: 0.8980 chunk 143 optimal weight: 3.9990 chunk 227 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 179 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 GLN C 126 ASN ** C 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 179 GLN N 126 ASN N 358 ASN ** N 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.110881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.090581 restraints weight = 53546.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.094080 restraints weight = 28900.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.096418 restraints weight = 18804.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.098070 restraints weight = 13834.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.099243 restraints weight = 11069.242| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 31422 Z= 0.197 Angle : 0.722 24.733 42528 Z= 0.370 Chirality : 0.044 0.214 4644 Planarity : 0.013 0.383 5568 Dihedral : 6.674 155.438 4098 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 4.06 % Allowed : 20.32 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.13), residues: 3720 helix: 0.13 (0.18), residues: 870 sheet: 0.44 (0.21), residues: 684 loop : -1.50 (0.12), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.055 0.001 ARG F 215 TYR 0.032 0.002 TYR E 193 PHE 0.025 0.002 PHE F 376 TRP 0.008 0.001 TRP F 532 HIS 0.003 0.001 HIS C 343 Details of bonding type rmsd covalent geometry : bond 0.00452 (31362) covalent geometry : angle 0.72225 (42528) hydrogen bonds : bond 0.03632 ( 876) hydrogen bonds : angle 5.59217 ( 2250) Misc. bond : bond 0.00529 ( 60) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 472 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 179 GLN cc_start: 0.8862 (pt0) cc_final: 0.8102 (pm20) REVERT: J 185 ASP cc_start: 0.8666 (t0) cc_final: 0.8237 (t0) REVERT: J 189 THR cc_start: 0.8459 (m) cc_final: 0.8185 (m) REVERT: I 183 ASN cc_start: 0.8023 (t0) cc_final: 0.7255 (t0) REVERT: Y 64 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7832 (mt-10) REVERT: Y 115 TYR cc_start: 0.9031 (m-80) cc_final: 0.8658 (m-10) REVERT: Y 159 TYR cc_start: 0.8893 (OUTLIER) cc_final: 0.8222 (p90) REVERT: Y 194 GLU cc_start: 0.6766 (mm-30) cc_final: 0.6382 (tp30) REVERT: Y 219 ASN cc_start: 0.8251 (m-40) cc_final: 0.7816 (m-40) REVERT: Y 340 ILE cc_start: 0.9394 (OUTLIER) cc_final: 0.9134 (tp) REVERT: Y 345 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7784 (mt-10) REVERT: Y 514 MET cc_start: 0.8396 (ttm) cc_final: 0.8013 (mtp) REVERT: Y 577 MET cc_start: 0.8891 (mmt) cc_final: 0.8083 (mmt) REVERT: A 179 GLN cc_start: 0.8748 (pt0) cc_final: 0.7937 (pm20) REVERT: B 183 ASN cc_start: 0.8310 (t0) cc_final: 0.8014 (t0) REVERT: C 159 TYR cc_start: 0.8974 (OUTLIER) cc_final: 0.8730 (p90) REVERT: C 344 ASN cc_start: 0.9214 (OUTLIER) cc_final: 0.8156 (m110) REVERT: C 376 PHE cc_start: 0.9227 (t80) cc_final: 0.8558 (t80) REVERT: C 386 PHE cc_start: 0.8015 (m-80) cc_final: 0.7390 (m-80) REVERT: C 515 LEU cc_start: 0.9456 (mm) cc_final: 0.9251 (mm) REVERT: C 574 ASN cc_start: 0.8822 (m-40) cc_final: 0.8005 (t0) REVERT: D 187 ASP cc_start: 0.7778 (OUTLIER) cc_final: 0.7459 (t0) REVERT: F 168 PHE cc_start: 0.8188 (OUTLIER) cc_final: 0.6415 (p90) REVERT: F 175 PHE cc_start: 0.7951 (OUTLIER) cc_final: 0.7102 (m-80) REVERT: F 185 PHE cc_start: 0.7877 (m-80) cc_final: 0.7488 (m-10) REVERT: F 213 MET cc_start: 0.9038 (OUTLIER) cc_final: 0.8715 (ptm) REVERT: F 459 LYS cc_start: 0.7990 (mttm) cc_final: 0.7750 (mttp) REVERT: F 515 LEU cc_start: 0.9497 (OUTLIER) cc_final: 0.9226 (mm) REVERT: F 519 THR cc_start: 0.9401 (OUTLIER) cc_final: 0.9116 (p) REVERT: F 577 MET cc_start: 0.8964 (mmt) cc_final: 0.8574 (mmt) REVERT: G 179 GLN cc_start: 0.8861 (pt0) cc_final: 0.7988 (pm20) REVERT: G 185 ASP cc_start: 0.8671 (t0) cc_final: 0.8246 (t0) REVERT: G 189 THR cc_start: 0.8469 (m) cc_final: 0.8203 (m) REVERT: H 183 ASN cc_start: 0.7987 (t0) cc_final: 0.7224 (t0) REVERT: K 115 TYR cc_start: 0.9044 (m-80) cc_final: 0.8681 (m-10) REVERT: K 159 TYR cc_start: 0.8908 (OUTLIER) cc_final: 0.8227 (p90) REVERT: K 194 GLU cc_start: 0.6764 (mm-30) cc_final: 0.6386 (tp30) REVERT: K 213 MET cc_start: 0.8736 (ptm) cc_final: 0.8245 (ptm) REVERT: K 214 ASN cc_start: 0.8339 (OUTLIER) cc_final: 0.7803 (m-40) REVERT: K 345 GLU cc_start: 0.8305 (tt0) cc_final: 0.8021 (mt-10) REVERT: K 455 TYR cc_start: 0.7947 (t80) cc_final: 0.7713 (t80) REVERT: L 179 GLN cc_start: 0.8756 (pt0) cc_final: 0.7934 (pm20) REVERT: M 183 ASN cc_start: 0.8299 (t0) cc_final: 0.8005 (t0) REVERT: N 159 TYR cc_start: 0.8965 (OUTLIER) cc_final: 0.8678 (p90) REVERT: N 213 MET cc_start: 0.8905 (OUTLIER) cc_final: 0.8551 (ptm) REVERT: N 376 PHE cc_start: 0.9236 (t80) cc_final: 0.8527 (t80) REVERT: N 388 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7368 (mt-10) REVERT: N 400 GLN cc_start: 0.8517 (tp40) cc_final: 0.8275 (tp40) REVERT: N 515 LEU cc_start: 0.9462 (mm) cc_final: 0.9241 (mm) REVERT: O 179 GLN cc_start: 0.8674 (pt0) cc_final: 0.7895 (pm20) REVERT: O 187 ASP cc_start: 0.7957 (OUTLIER) cc_final: 0.7652 (t0) REVERT: Q 6 LEU cc_start: 0.9171 (mm) cc_final: 0.8963 (mt) REVERT: Q 168 PHE cc_start: 0.8188 (OUTLIER) cc_final: 0.6417 (p90) REVERT: Q 175 PHE cc_start: 0.7878 (OUTLIER) cc_final: 0.6926 (m-80) REVERT: Q 194 GLU cc_start: 0.6413 (tp30) cc_final: 0.6183 (tp30) REVERT: Q 213 MET cc_start: 0.9176 (OUTLIER) cc_final: 0.8846 (ptm) REVERT: Q 345 GLU cc_start: 0.8498 (tt0) cc_final: 0.8210 (mt-10) REVERT: Q 400 GLN cc_start: 0.8360 (mm-40) cc_final: 0.7143 (mm-40) REVERT: Q 459 LYS cc_start: 0.8001 (mttm) cc_final: 0.7633 (mttp) REVERT: Q 515 LEU cc_start: 0.9512 (OUTLIER) cc_final: 0.9233 (mm) REVERT: Q 577 MET cc_start: 0.8954 (mmt) cc_final: 0.8577 (mmt) outliers start: 140 outliers final: 100 residues processed: 560 average time/residue: 0.1914 time to fit residues: 179.1254 Evaluate side-chains 573 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 454 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 78 THR Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 123 THR Chi-restraints excluded: chain Y residue 152 VAL Chi-restraints excluded: chain Y residue 159 TYR Chi-restraints excluded: chain Y residue 168 PHE Chi-restraints excluded: chain Y residue 204 ILE Chi-restraints excluded: chain Y residue 212 VAL Chi-restraints excluded: chain Y residue 232 THR Chi-restraints excluded: chain Y residue 336 THR Chi-restraints excluded: chain Y residue 340 ILE Chi-restraints excluded: chain Y residue 369 ILE Chi-restraints excluded: chain Y residue 375 SER Chi-restraints excluded: chain Y residue 415 ILE Chi-restraints excluded: chain Y residue 438 ILE Chi-restraints excluded: chain Y residue 461 LEU Chi-restraints excluded: chain Y residue 475 VAL Chi-restraints excluded: chain Y residue 480 MET Chi-restraints excluded: chain Y residue 586 PHE Chi-restraints excluded: chain C residue 8 HIS Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 159 TYR Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 255 LYS Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 339 ILE Chi-restraints excluded: chain C residue 344 ASN Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 479 GLN Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain C residue 540 MET Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 168 PHE Chi-restraints excluded: chain F residue 175 PHE Chi-restraints excluded: chain F residue 204 ILE Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 213 MET Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 255 LYS Chi-restraints excluded: chain F residue 336 THR Chi-restraints excluded: chain F residue 391 ILE Chi-restraints excluded: chain F residue 475 VAL Chi-restraints excluded: chain F residue 479 GLN Chi-restraints excluded: chain F residue 515 LEU Chi-restraints excluded: chain F residue 519 THR Chi-restraints excluded: chain F residue 553 LEU Chi-restraints excluded: chain F residue 563 THR Chi-restraints excluded: chain F residue 586 PHE Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 102 VAL Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 152 VAL Chi-restraints excluded: chain K residue 159 TYR Chi-restraints excluded: chain K residue 168 PHE Chi-restraints excluded: chain K residue 204 ILE Chi-restraints excluded: chain K residue 214 ASN Chi-restraints excluded: chain K residue 232 THR Chi-restraints excluded: chain K residue 336 THR Chi-restraints excluded: chain K residue 340 ILE Chi-restraints excluded: chain K residue 369 ILE Chi-restraints excluded: chain K residue 375 SER Chi-restraints excluded: chain K residue 400 GLN Chi-restraints excluded: chain K residue 415 ILE Chi-restraints excluded: chain K residue 438 ILE Chi-restraints excluded: chain K residue 461 LEU Chi-restraints excluded: chain K residue 475 VAL Chi-restraints excluded: chain K residue 563 THR Chi-restraints excluded: chain K residue 586 PHE Chi-restraints excluded: chain N residue 8 HIS Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 153 ILE Chi-restraints excluded: chain N residue 159 TYR Chi-restraints excluded: chain N residue 168 PHE Chi-restraints excluded: chain N residue 204 ILE Chi-restraints excluded: chain N residue 213 MET Chi-restraints excluded: chain N residue 255 LYS Chi-restraints excluded: chain N residue 327 THR Chi-restraints excluded: chain N residue 339 ILE Chi-restraints excluded: chain N residue 375 SER Chi-restraints excluded: chain N residue 391 ILE Chi-restraints excluded: chain N residue 475 VAL Chi-restraints excluded: chain N residue 519 THR Chi-restraints excluded: chain N residue 540 MET Chi-restraints excluded: chain N residue 563 THR Chi-restraints excluded: chain O residue 177 LEU Chi-restraints excluded: chain O residue 187 ASP Chi-restraints excluded: chain P residue 186 VAL Chi-restraints excluded: chain Q residue 77 CYS Chi-restraints excluded: chain Q residue 102 VAL Chi-restraints excluded: chain Q residue 153 ILE Chi-restraints excluded: chain Q residue 168 PHE Chi-restraints excluded: chain Q residue 175 PHE Chi-restraints excluded: chain Q residue 204 ILE Chi-restraints excluded: chain Q residue 212 VAL Chi-restraints excluded: chain Q residue 213 MET Chi-restraints excluded: chain Q residue 232 THR Chi-restraints excluded: chain Q residue 255 LYS Chi-restraints excluded: chain Q residue 336 THR Chi-restraints excluded: chain Q residue 391 ILE Chi-restraints excluded: chain Q residue 475 VAL Chi-restraints excluded: chain Q residue 479 GLN Chi-restraints excluded: chain Q residue 515 LEU Chi-restraints excluded: chain Q residue 519 THR Chi-restraints excluded: chain Q residue 563 THR Chi-restraints excluded: chain Q residue 586 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 276 optimal weight: 0.7980 chunk 180 optimal weight: 5.9990 chunk 311 optimal weight: 0.0020 chunk 127 optimal weight: 0.8980 chunk 143 optimal weight: 3.9990 chunk 223 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 279 optimal weight: 0.9990 chunk 145 optimal weight: 4.9990 chunk 273 optimal weight: 0.0980 chunk 302 optimal weight: 0.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 520 ASN ** F 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 209 ASN F 400 GLN ** F 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.114700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.094719 restraints weight = 52914.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.098310 restraints weight = 28706.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.100727 restraints weight = 18591.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.102441 restraints weight = 13581.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.103662 restraints weight = 10795.831| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.4184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 31422 Z= 0.141 Angle : 0.787 31.514 42528 Z= 0.395 Chirality : 0.043 0.332 4644 Planarity : 0.012 0.377 5568 Dihedral : 5.771 50.124 4098 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.68 % Allowed : 20.72 % Favored : 75.59 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.12 (0.13), residues: 3720 helix: 0.12 (0.18), residues: 876 sheet: 0.28 (0.20), residues: 678 loop : -1.51 (0.12), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.058 0.002 ARG K 215 TYR 0.022 0.001 TYR F 342 PHE 0.031 0.001 PHE K 376 TRP 0.006 0.001 TRP Y 314 HIS 0.003 0.001 HIS F 343 Details of bonding type rmsd covalent geometry : bond 0.00314 (31362) covalent geometry : angle 0.78710 (42528) hydrogen bonds : bond 0.03467 ( 876) hydrogen bonds : angle 5.48931 ( 2250) Misc. bond : bond 0.00547 ( 60) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 491 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 179 GLN cc_start: 0.8752 (pt0) cc_final: 0.7825 (pm20) REVERT: J 185 ASP cc_start: 0.8640 (t0) cc_final: 0.8212 (t0) REVERT: J 189 THR cc_start: 0.8312 (m) cc_final: 0.8038 (m) REVERT: I 183 ASN cc_start: 0.7998 (t0) cc_final: 0.7180 (t0) REVERT: Y 115 TYR cc_start: 0.8977 (m-80) cc_final: 0.8629 (m-10) REVERT: Y 159 TYR cc_start: 0.8805 (OUTLIER) cc_final: 0.8143 (p90) REVERT: Y 194 GLU cc_start: 0.6700 (mm-30) cc_final: 0.6350 (tp30) REVERT: Y 264 MET cc_start: 0.8386 (mtt) cc_final: 0.8183 (mmm) REVERT: Y 344 ASN cc_start: 0.8429 (OUTLIER) cc_final: 0.6700 (m-40) REVERT: Y 345 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7736 (mt-10) REVERT: Y 386 PHE cc_start: 0.8250 (m-80) cc_final: 0.7482 (m-80) REVERT: Y 388 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7386 (mt-10) REVERT: Y 577 MET cc_start: 0.8874 (mmt) cc_final: 0.8048 (mmt) REVERT: A 179 GLN cc_start: 0.8589 (pt0) cc_final: 0.7867 (pm20) REVERT: B 183 ASN cc_start: 0.8292 (t0) cc_final: 0.7990 (t0) REVERT: C 159 TYR cc_start: 0.8966 (OUTLIER) cc_final: 0.8718 (p90) REVERT: C 213 MET cc_start: 0.8500 (ptm) cc_final: 0.8241 (ptm) REVERT: C 290 MET cc_start: 0.9134 (mtm) cc_final: 0.8883 (mtm) REVERT: C 376 PHE cc_start: 0.9182 (t80) cc_final: 0.8507 (t80) REVERT: C 386 PHE cc_start: 0.8130 (m-80) cc_final: 0.7436 (m-80) REVERT: C 574 ASN cc_start: 0.8819 (m-40) cc_final: 0.8034 (t0) REVERT: D 179 GLN cc_start: 0.8213 (pt0) cc_final: 0.6867 (pm20) REVERT: D 187 ASP cc_start: 0.7660 (OUTLIER) cc_final: 0.7368 (t0) REVERT: F 60 MET cc_start: 0.8540 (mmm) cc_final: 0.8252 (mmm) REVERT: F 168 PHE cc_start: 0.8091 (OUTLIER) cc_final: 0.6472 (p90) REVERT: F 175 PHE cc_start: 0.7806 (OUTLIER) cc_final: 0.6945 (m-80) REVERT: F 185 PHE cc_start: 0.7591 (m-80) cc_final: 0.7254 (m-10) REVERT: F 209 ASN cc_start: 0.8228 (OUTLIER) cc_final: 0.7036 (t0) REVERT: F 213 MET cc_start: 0.9023 (OUTLIER) cc_final: 0.8706 (ptm) REVERT: F 455 TYR cc_start: 0.7353 (t80) cc_final: 0.6784 (t80) REVERT: F 459 LYS cc_start: 0.8058 (mttm) cc_final: 0.7688 (mttp) REVERT: F 519 THR cc_start: 0.9433 (OUTLIER) cc_final: 0.9202 (p) REVERT: F 577 MET cc_start: 0.8909 (mmt) cc_final: 0.8547 (mmt) REVERT: G 179 GLN cc_start: 0.8764 (pt0) cc_final: 0.7834 (pm20) REVERT: G 185 ASP cc_start: 0.8641 (t0) cc_final: 0.8217 (t0) REVERT: G 189 THR cc_start: 0.8323 (m) cc_final: 0.8055 (m) REVERT: H 183 ASN cc_start: 0.7947 (t0) cc_final: 0.7157 (t0) REVERT: K 115 TYR cc_start: 0.8998 (m-80) cc_final: 0.8637 (m-10) REVERT: K 159 TYR cc_start: 0.8837 (OUTLIER) cc_final: 0.8233 (p90) REVERT: K 194 GLU cc_start: 0.6687 (mm-30) cc_final: 0.6345 (tp30) REVERT: K 213 MET cc_start: 0.8452 (ptm) cc_final: 0.8141 (ptm) REVERT: K 214 ASN cc_start: 0.8542 (OUTLIER) cc_final: 0.8144 (m-40) REVERT: K 340 ILE cc_start: 0.9430 (OUTLIER) cc_final: 0.9172 (tp) REVERT: K 345 GLU cc_start: 0.8263 (tt0) cc_final: 0.7678 (mt-10) REVERT: L 179 GLN cc_start: 0.8581 (pt0) cc_final: 0.7869 (pm20) REVERT: M 183 ASN cc_start: 0.8281 (t0) cc_final: 0.7982 (t0) REVERT: N 83 PHE cc_start: 0.8879 (OUTLIER) cc_final: 0.8536 (m-80) REVERT: N 138 VAL cc_start: 0.9082 (m) cc_final: 0.8835 (p) REVERT: N 159 TYR cc_start: 0.8958 (OUTLIER) cc_final: 0.8715 (p90) REVERT: N 213 MET cc_start: 0.8817 (OUTLIER) cc_final: 0.8615 (ptm) REVERT: N 290 MET cc_start: 0.9130 (mtm) cc_final: 0.8881 (mtm) REVERT: N 376 PHE cc_start: 0.9176 (t80) cc_final: 0.8502 (t80) REVERT: N 388 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7374 (mt-10) REVERT: N 400 GLN cc_start: 0.8431 (tp40) cc_final: 0.8188 (tp40) REVERT: N 574 ASN cc_start: 0.8809 (m-40) cc_final: 0.8024 (t0) REVERT: O 179 GLN cc_start: 0.8550 (pt0) cc_final: 0.7824 (pm20) REVERT: O 187 ASP cc_start: 0.7883 (OUTLIER) cc_final: 0.7605 (t0) REVERT: Q 60 MET cc_start: 0.8514 (mmm) cc_final: 0.8261 (mmm) REVERT: Q 168 PHE cc_start: 0.8086 (OUTLIER) cc_final: 0.6442 (p90) REVERT: Q 175 PHE cc_start: 0.7803 (OUTLIER) cc_final: 0.6971 (m-80) REVERT: Q 185 PHE cc_start: 0.7740 (m-80) cc_final: 0.7380 (m-10) REVERT: Q 194 GLU cc_start: 0.6327 (tp30) cc_final: 0.6112 (tp30) REVERT: Q 213 MET cc_start: 0.9140 (OUTLIER) cc_final: 0.8809 (ptm) REVERT: Q 455 TYR cc_start: 0.7344 (t80) cc_final: 0.7046 (t80) REVERT: Q 459 LYS cc_start: 0.8057 (mttm) cc_final: 0.7736 (mttp) REVERT: Q 519 THR cc_start: 0.9399 (OUTLIER) cc_final: 0.9124 (p) REVERT: Q 577 MET cc_start: 0.8956 (mmt) cc_final: 0.8533 (mmt) outliers start: 127 outliers final: 96 residues processed: 577 average time/residue: 0.1587 time to fit residues: 155.3638 Evaluate side-chains 570 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 454 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 78 THR Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 123 THR Chi-restraints excluded: chain Y residue 152 VAL Chi-restraints excluded: chain Y residue 159 TYR Chi-restraints excluded: chain Y residue 168 PHE Chi-restraints excluded: chain Y residue 204 ILE Chi-restraints excluded: chain Y residue 232 THR Chi-restraints excluded: chain Y residue 336 THR Chi-restraints excluded: chain Y residue 340 ILE Chi-restraints excluded: chain Y residue 344 ASN Chi-restraints excluded: chain Y residue 369 ILE Chi-restraints excluded: chain Y residue 375 SER Chi-restraints excluded: chain Y residue 400 GLN Chi-restraints excluded: chain Y residue 415 ILE Chi-restraints excluded: chain Y residue 438 ILE Chi-restraints excluded: chain Y residue 461 LEU Chi-restraints excluded: chain Y residue 475 VAL Chi-restraints excluded: chain Y residue 586 PHE Chi-restraints excluded: chain C residue 8 HIS Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 159 TYR Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 339 ILE Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain C residue 540 MET Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 168 PHE Chi-restraints excluded: chain F residue 175 PHE Chi-restraints excluded: chain F residue 204 ILE Chi-restraints excluded: chain F residue 205 THR Chi-restraints excluded: chain F residue 209 ASN Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 213 MET Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 255 LYS Chi-restraints excluded: chain F residue 336 THR Chi-restraints excluded: chain F residue 391 ILE Chi-restraints excluded: chain F residue 475 VAL Chi-restraints excluded: chain F residue 479 GLN Chi-restraints excluded: chain F residue 519 THR Chi-restraints excluded: chain F residue 586 PHE Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 102 VAL Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 152 VAL Chi-restraints excluded: chain K residue 159 TYR Chi-restraints excluded: chain K residue 168 PHE Chi-restraints excluded: chain K residue 212 VAL Chi-restraints excluded: chain K residue 214 ASN Chi-restraints excluded: chain K residue 232 THR Chi-restraints excluded: chain K residue 336 THR Chi-restraints excluded: chain K residue 340 ILE Chi-restraints excluded: chain K residue 343 HIS Chi-restraints excluded: chain K residue 369 ILE Chi-restraints excluded: chain K residue 375 SER Chi-restraints excluded: chain K residue 415 ILE Chi-restraints excluded: chain K residue 438 ILE Chi-restraints excluded: chain K residue 461 LEU Chi-restraints excluded: chain K residue 475 VAL Chi-restraints excluded: chain K residue 563 THR Chi-restraints excluded: chain K residue 586 PHE Chi-restraints excluded: chain N residue 8 HIS Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 83 PHE Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 153 ILE Chi-restraints excluded: chain N residue 159 TYR Chi-restraints excluded: chain N residue 168 PHE Chi-restraints excluded: chain N residue 204 ILE Chi-restraints excluded: chain N residue 213 MET Chi-restraints excluded: chain N residue 327 THR Chi-restraints excluded: chain N residue 339 ILE Chi-restraints excluded: chain N residue 375 SER Chi-restraints excluded: chain N residue 391 ILE Chi-restraints excluded: chain N residue 438 ILE Chi-restraints excluded: chain N residue 475 VAL Chi-restraints excluded: chain N residue 519 THR Chi-restraints excluded: chain N residue 540 MET Chi-restraints excluded: chain N residue 563 THR Chi-restraints excluded: chain O residue 177 LEU Chi-restraints excluded: chain O residue 187 ASP Chi-restraints excluded: chain P residue 186 VAL Chi-restraints excluded: chain Q residue 77 CYS Chi-restraints excluded: chain Q residue 102 VAL Chi-restraints excluded: chain Q residue 153 ILE Chi-restraints excluded: chain Q residue 168 PHE Chi-restraints excluded: chain Q residue 175 PHE Chi-restraints excluded: chain Q residue 204 ILE Chi-restraints excluded: chain Q residue 212 VAL Chi-restraints excluded: chain Q residue 213 MET Chi-restraints excluded: chain Q residue 232 THR Chi-restraints excluded: chain Q residue 255 LYS Chi-restraints excluded: chain Q residue 336 THR Chi-restraints excluded: chain Q residue 391 ILE Chi-restraints excluded: chain Q residue 475 VAL Chi-restraints excluded: chain Q residue 479 GLN Chi-restraints excluded: chain Q residue 515 LEU Chi-restraints excluded: chain Q residue 519 THR Chi-restraints excluded: chain Q residue 563 THR Chi-restraints excluded: chain Q residue 586 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 364 optimal weight: 0.8980 chunk 271 optimal weight: 3.9990 chunk 123 optimal weight: 0.5980 chunk 282 optimal weight: 4.9990 chunk 135 optimal weight: 0.8980 chunk 280 optimal weight: 3.9990 chunk 158 optimal weight: 4.9990 chunk 289 optimal weight: 0.9990 chunk 349 optimal weight: 0.9980 chunk 157 optimal weight: 0.0980 chunk 321 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 520 ASN ** F 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 209 ASN ** F 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.114651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.094631 restraints weight = 53478.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.098228 restraints weight = 29084.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.100639 restraints weight = 18883.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.102351 restraints weight = 13829.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.103561 restraints weight = 11001.052| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.4294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31422 Z= 0.140 Angle : 0.725 25.800 42528 Z= 0.368 Chirality : 0.043 0.199 4644 Planarity : 0.013 0.484 5568 Dihedral : 6.474 135.363 4098 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.68 % Allowed : 21.25 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.14 (0.13), residues: 3720 helix: 0.01 (0.18), residues: 876 sheet: 0.27 (0.20), residues: 678 loop : -1.47 (0.12), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.038 0.001 ARG C 215 TYR 0.016 0.001 TYR C 342 PHE 0.033 0.001 PHE K 376 TRP 0.006 0.001 TRP K 568 HIS 0.004 0.001 HIS F 343 Details of bonding type rmsd covalent geometry : bond 0.00313 (31362) covalent geometry : angle 0.72468 (42528) hydrogen bonds : bond 0.03448 ( 876) hydrogen bonds : angle 5.42890 ( 2250) Misc. bond : bond 0.00501 ( 60) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5114.04 seconds wall clock time: 90 minutes 5.10 seconds (5405.10 seconds total)