Starting phenix.real_space_refine on Thu Jun 26 03:25:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8egs_28129/06_2025/8egs_28129.cif Found real_map, /net/cci-nas-00/data/ceres_data/8egs_28129/06_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_28129/06_2025/8egs_28129.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8egs_28129/06_2025/8egs_28129.map" model { file = "/net/cci-nas-00/data/ceres_data/8egs_28129/06_2025/8egs_28129.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8egs_28129/06_2025/8egs_28129.cif" } resolution = 3.92 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 13.05, per 1000 atoms: 0.43 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: 7.91 Conformation dependent library (CDL) restraints added in 3.9 seconds 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: 3.73 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: 10.05 Time building geometry restraints manager: 9.17 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: 3.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.110 Check model and map are aligned: 0.210 Set scattering table: 0.270 Process input model: 59.700 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.100 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:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.540 ------------------------------------------------------------------------------- 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 : 27.78 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (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 TRP 0.007 0.001 TRP K 275 HIS 0.004 0.001 HIS K 101 PHE 0.018 0.002 PHE Q 432 TYR 0.011 0.001 TYR K 455 ARG 0.006 0.001 ARG Y 56 Details of bonding type rmsd hydrogen bonds : bond 0.17647 ( 876) hydrogen bonds : angle 7.52582 ( 2250) covalent geometry : bond 0.00344 (31362) covalent geometry : angle 0.56950 (42528) 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 : 4.547 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: 0.4587 time to fit residues: 392.8781 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 : 3.830 ------------------------------------------------------------------------------- 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 314 optimal weight: 0.9980 chunk 281 optimal weight: 2.9990 chunk 156 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 chunk 190 optimal weight: 5.9990 chunk 150 optimal weight: 2.9990 chunk 291 optimal weight: 8.9990 chunk 112 optimal weight: 0.9990 chunk 177 optimal weight: 0.0770 chunk 217 optimal weight: 3.9990 chunk 337 optimal weight: 0.7980 overall best weight: 0.7742 ------------------------------------------------------------------------------- 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 354 ASN ** 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 441 ASN 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: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.115457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.095678 restraints weight = 51943.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.099301 restraints weight = 27197.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.101781 restraints weight = 17324.181| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2152 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= 0.179 Angle : 0.698 9.942 42528 Z= 0.369 Chirality : 0.045 0.220 4644 Planarity : 0.007 0.160 5568 Dihedral : 5.673 36.988 4106 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.54 % Allowed : 16.49 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.13), residues: 3720 helix: 0.23 (0.18), residues: 840 sheet: 0.06 (0.20), residues: 714 loop : -1.13 (0.13), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 568 HIS 0.005 0.001 HIS Q 300 PHE 0.012 0.002 PHE Y 586 TYR 0.029 0.002 TYR N 457 ARG 0.009 0.001 ARG K 541 Details of bonding type rmsd hydrogen bonds : bond 0.04348 ( 876) hydrogen bonds : angle 6.23444 ( 2250) covalent geometry : bond 0.00395 (31362) covalent geometry : angle 0.69802 (42528) Misc. bond : bond 0.00552 ( 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 660 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 538 time to evaluate : 3.158 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: 0.8437 (OUTLIER) cc_final: 0.7950 (p) REVERT: Y 194 GLU cc_start: 0.5888 (tp30) cc_final: 0.5679 (tp30) REVERT: Y 213 MET cc_start: 0.8808 (ptm) cc_final: 0.8436 (ptm) REVERT: Y 340 ILE cc_start: 0.9308 (OUTLIER) cc_final: 0.8996 (tp) REVERT: A 180 SER cc_start: 0.8460 (OUTLIER) cc_final: 0.8039 (p) REVERT: A 185 ASP cc_start: 0.8385 (t0) cc_final: 0.8074 (t0) REVERT: C 83 PHE cc_start: 0.8546 (OUTLIER) cc_final: 0.8040 (m-10) REVERT: C 105 MET cc_start: 0.8675 (mtp) cc_final: 0.8317 (mtp) REVERT: C 194 GLU cc_start: 0.5887 (tp30) cc_final: 0.5613 (tp30) REVERT: C 219 ASN cc_start: 0.7404 (m-40) cc_final: 0.7138 (m-40) REVERT: C 344 ASN cc_start: 0.9145 (OUTLIER) cc_final: 0.8502 (m-40) REVERT: C 375 SER cc_start: 0.9080 (m) cc_final: 0.8854 (t) REVERT: D 180 SER cc_start: 0.8354 (OUTLIER) cc_final: 0.8087 (p) REVERT: F 344 ASN cc_start: 0.8851 (OUTLIER) cc_final: 0.8533 (m-40) REVERT: G 180 SER cc_start: 0.8432 (OUTLIER) cc_final: 0.7941 (p) REVERT: K 194 GLU cc_start: 0.5890 (tp30) cc_final: 0.5677 (tp30) REVERT: K 213 MET cc_start: 0.8805 (ptm) cc_final: 0.8438 (ptm) REVERT: K 340 ILE cc_start: 0.9309 (OUTLIER) cc_final: 0.8993 (tp) REVERT: K 354 ASN cc_start: 0.9090 (OUTLIER) cc_final: 0.8805 (t0) REVERT: L 180 SER cc_start: 0.8457 (OUTLIER) cc_final: 0.8034 (p) REVERT: L 185 ASP cc_start: 0.8384 (t0) cc_final: 0.8075 (t0) REVERT: N 83 PHE cc_start: 0.8545 (OUTLIER) cc_final: 0.8041 (m-10) REVERT: N 105 MET cc_start: 0.8671 (mtp) cc_final: 0.8321 (mtp) REVERT: N 194 GLU cc_start: 0.5885 (tp30) cc_final: 0.5614 (tp30) REVERT: N 219 ASN cc_start: 0.7409 (m-40) cc_final: 0.7143 (m-40) REVERT: N 344 ASN cc_start: 0.9147 (OUTLIER) cc_final: 0.8496 (m-40) REVERT: N 375 SER cc_start: 0.9082 (m) cc_final: 0.8851 (t) REVERT: O 180 SER cc_start: 0.8359 (OUTLIER) cc_final: 0.8099 (p) REVERT: Q 344 ASN cc_start: 0.8848 (OUTLIER) cc_final: 0.8527 (m-40) outliers start: 122 outliers final: 47 residues processed: 618 average time/residue: 0.4547 time to fit residues: 450.7504 Evaluate side-chains 505 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 443 time to evaluate : 3.519 ------------------------------------------------------------------------------- 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 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 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 344 ASN 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 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 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 344 ASN 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 347 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 248 optimal weight: 4.9990 chunk 145 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 245 optimal weight: 0.7980 chunk 164 optimal weight: 6.9990 chunk 262 optimal weight: 3.9990 chunk 28 optimal weight: 0.0970 chunk 185 optimal weight: 0.3980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 72 GLN Y 93 ASN ** Y 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN C 93 ASN ** C 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 GLN F 93 ASN ** F 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 72 GLN K 93 ASN ** K 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 72 GLN N 93 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 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.113347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.094200 restraints weight = 53091.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.097734 restraints weight = 27695.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.100133 restraints weight = 17479.204| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 31422 Z= 0.147 Angle : 0.612 9.760 42528 Z= 0.322 Chirality : 0.042 0.131 4644 Planarity : 0.009 0.234 5568 Dihedral : 7.945 156.098 4104 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 5.19 % Allowed : 15.33 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.13), residues: 3720 helix: 0.01 (0.17), residues: 870 sheet: 0.00 (0.20), residues: 708 loop : -1.21 (0.13), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 568 HIS 0.003 0.001 HIS F 343 PHE 0.022 0.001 PHE Q 54 TYR 0.030 0.002 TYR Q 342 ARG 0.029 0.001 ARG K 510 Details of bonding type rmsd hydrogen bonds : bond 0.04130 ( 876) hydrogen bonds : angle 5.83647 ( 2250) covalent geometry : bond 0.00324 (31362) covalent geometry : angle 0.61150 (42528) Misc. bond : bond 0.00417 ( 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 687 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 508 time to evaluate : 3.584 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: J 185 ASP cc_start: 0.8512 (t0) cc_final: 0.8276 (t0) REVERT: Y 6 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.9064 (mm) REVERT: Y 19 ASP cc_start: 0.8149 (t0) cc_final: 0.7879 (t0) REVERT: Y 64 GLU cc_start: 0.8316 (mt-10) cc_final: 0.7994 (mt-10) REVERT: Y 115 TYR cc_start: 0.8892 (m-80) cc_final: 0.8630 (m-10) REVERT: Y 159 TYR cc_start: 0.8715 (OUTLIER) cc_final: 0.7931 (p90) REVERT: Y 194 GLU cc_start: 0.6191 (tp30) cc_final: 0.5908 (tp30) REVERT: Y 213 MET cc_start: 0.8789 (ptm) cc_final: 0.8406 (ptm) REVERT: Y 219 ASN cc_start: 0.7410 (m-40) cc_final: 0.7155 (m-40) REVERT: Y 222 MET cc_start: 0.9165 (tpp) cc_final: 0.8746 (tpp) REVERT: Y 340 ILE cc_start: 0.9414 (OUTLIER) cc_final: 0.9204 (tp) REVERT: Y 480 MET cc_start: 0.8851 (mmm) cc_final: 0.8515 (mmm) REVERT: Y 519 THR cc_start: 0.9292 (OUTLIER) cc_final: 0.8950 (p) REVERT: A 185 ASP cc_start: 0.8627 (t0) cc_final: 0.8320 (t0) REVERT: C 19 ASP cc_start: 0.8295 (t0) cc_final: 0.7949 (t0) REVERT: C 83 PHE cc_start: 0.8644 (OUTLIER) cc_final: 0.8315 (m-80) REVERT: C 159 TYR cc_start: 0.8764 (OUTLIER) cc_final: 0.8133 (p90) REVERT: C 213 MET cc_start: 0.8951 (ptp) cc_final: 0.8461 (ptm) REVERT: C 219 ASN cc_start: 0.7556 (m-40) cc_final: 0.6998 (m-40) REVERT: C 290 MET cc_start: 0.9156 (mtm) cc_final: 0.8876 (mtm) REVERT: C 344 ASN cc_start: 0.9233 (OUTLIER) cc_final: 0.8550 (m-40) REVERT: C 375 SER cc_start: 0.8950 (m) cc_final: 0.8694 (t) REVERT: C 386 PHE cc_start: 0.7997 (m-80) cc_final: 0.7668 (m-80) REVERT: C 515 LEU cc_start: 0.9437 (mm) cc_final: 0.9222 (mm) REVERT: C 577 MET cc_start: 0.9126 (mmm) cc_final: 0.8910 (mmt) REVERT: F 19 ASP cc_start: 0.8314 (t0) cc_final: 0.7899 (t0) REVERT: F 168 PHE cc_start: 0.8041 (OUTLIER) cc_final: 0.6973 (p90) REVERT: F 213 MET cc_start: 0.8947 (ptp) cc_final: 0.8625 (ptm) REVERT: F 219 ASN cc_start: 0.7113 (m-40) cc_final: 0.6884 (m-40) REVERT: F 388 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7739 (mm-30) REVERT: F 461 LEU cc_start: 0.8907 (tp) cc_final: 0.8628 (tp) REVERT: F 514 MET cc_start: 0.8516 (mtm) cc_final: 0.8151 (mtp) REVERT: F 519 THR cc_start: 0.9287 (OUTLIER) cc_final: 0.8909 (p) REVERT: F 562 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7530 (tp30) REVERT: F 577 MET cc_start: 0.9087 (mmt) cc_final: 0.8625 (mmt) REVERT: G 185 ASP cc_start: 0.8514 (t0) cc_final: 0.8275 (t0) REVERT: K 19 ASP cc_start: 0.8149 (t0) cc_final: 0.7856 (t0) REVERT: K 115 TYR cc_start: 0.8906 (m-80) cc_final: 0.8631 (m-10) REVERT: K 159 TYR cc_start: 0.8709 (OUTLIER) cc_final: 0.7926 (p90) REVERT: K 194 GLU cc_start: 0.6164 (tp30) cc_final: 0.5882 (tp30) REVERT: K 213 MET cc_start: 0.8789 (ptm) cc_final: 0.8413 (ptm) REVERT: K 219 ASN cc_start: 0.7411 (m-40) cc_final: 0.7109 (m-40) REVERT: K 222 MET cc_start: 0.9161 (tpp) cc_final: 0.8756 (tpp) REVERT: K 340 ILE cc_start: 0.9416 (OUTLIER) cc_final: 0.9207 (tp) REVERT: K 354 ASN cc_start: 0.9095 (OUTLIER) cc_final: 0.8878 (t0) REVERT: K 388 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.8126 (tm-30) REVERT: K 519 THR cc_start: 0.9290 (OUTLIER) cc_final: 0.8947 (p) REVERT: L 185 ASP cc_start: 0.8632 (t0) cc_final: 0.8323 (t0) REVERT: N 19 ASP cc_start: 0.8286 (t0) cc_final: 0.7939 (t0) REVERT: N 83 PHE cc_start: 0.8639 (OUTLIER) cc_final: 0.8308 (m-80) REVERT: N 159 TYR cc_start: 0.8779 (OUTLIER) cc_final: 0.8134 (p90) REVERT: N 213 MET cc_start: 0.8964 (ptp) cc_final: 0.8471 (ptm) REVERT: N 219 ASN cc_start: 0.7554 (m-40) cc_final: 0.6994 (m-40) REVERT: N 290 MET cc_start: 0.9157 (mtm) cc_final: 0.8874 (mtm) REVERT: N 344 ASN cc_start: 0.9228 (OUTLIER) cc_final: 0.8540 (m-40) REVERT: N 375 SER cc_start: 0.8947 (m) cc_final: 0.8689 (t) REVERT: N 386 PHE cc_start: 0.7998 (m-80) cc_final: 0.7666 (m-80) REVERT: N 515 LEU cc_start: 0.9439 (mm) cc_final: 0.9221 (mm) REVERT: N 577 MET cc_start: 0.9127 (mmm) cc_final: 0.8912 (mmt) REVERT: O 180 SER cc_start: 0.8326 (OUTLIER) cc_final: 0.6634 (p) REVERT: Q 19 ASP cc_start: 0.8306 (t0) cc_final: 0.7877 (t0) REVERT: Q 168 PHE cc_start: 0.8035 (OUTLIER) cc_final: 0.6969 (p90) REVERT: Q 213 MET cc_start: 0.8951 (ptp) cc_final: 0.8627 (ptm) REVERT: Q 219 ASN cc_start: 0.7139 (m-40) cc_final: 0.6910 (m-40) REVERT: Q 388 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7745 (mm-30) REVERT: Q 461 LEU cc_start: 0.8902 (tp) cc_final: 0.8625 (tp) REVERT: Q 514 MET cc_start: 0.8519 (mtm) cc_final: 0.8160 (mtp) REVERT: Q 519 THR cc_start: 0.9283 (OUTLIER) cc_final: 0.8898 (p) REVERT: Q 577 MET cc_start: 0.9094 (mmt) cc_final: 0.8633 (mmt) outliers start: 179 outliers final: 84 residues processed: 618 average time/residue: 0.4097 time to fit residues: 419.6480 Evaluate side-chains 556 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 450 time to evaluate : 3.486 ------------------------------------------------------------------------------- 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 61 VAL 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 375 SER 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 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 212 VAL 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 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 153 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 417 ASN Chi-restraints excluded: chain F residue 519 THR Chi-restraints excluded: chain F residue 522 GLN 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 61 VAL 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 354 ASN Chi-restraints excluded: chain K residue 375 SER Chi-restraints excluded: chain K residue 388 GLU 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 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 212 VAL 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 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 95 ILE Chi-restraints excluded: chain Q residue 153 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 417 ASN 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 168 optimal weight: 6.9990 chunk 225 optimal weight: 3.9990 chunk 207 optimal weight: 6.9990 chunk 360 optimal weight: 7.9990 chunk 49 optimal weight: 0.4980 chunk 291 optimal weight: 0.4980 chunk 338 optimal weight: 4.9990 chunk 302 optimal weight: 0.9990 chunk 144 optimal weight: 3.9990 chunk 367 optimal weight: 4.9990 chunk 279 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 343 HIS ** Y 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 183 ASN C 72 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 GLN ** F 99 ASN ** 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 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 343 HIS ** K 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 441 ASN L 183 ASN N 72 GLN ** N 99 ASN ** 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 72 GLN ** Q 99 ASN ** 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** Q 522 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.109776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.089840 restraints weight = 53573.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.093370 restraints weight = 28133.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.095719 restraints weight = 17993.409| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 31422 Z= 0.202 Angle : 0.668 16.793 42528 Z= 0.348 Chirality : 0.043 0.212 4644 Planarity : 0.010 0.328 5568 Dihedral : 8.051 175.144 4100 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 4.93 % Allowed : 14.23 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.13), residues: 3720 helix: -0.03 (0.17), residues: 876 sheet: -0.05 (0.20), residues: 738 loop : -1.37 (0.13), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Q 568 HIS 0.005 0.001 HIS K 343 PHE 0.022 0.002 PHE Q 128 TYR 0.044 0.002 TYR I 193 ARG 0.022 0.001 ARG Y 510 Details of bonding type rmsd hydrogen bonds : bond 0.04051 ( 876) hydrogen bonds : angle 5.82090 ( 2250) covalent geometry : bond 0.00462 (31362) covalent geometry : angle 0.66781 (42528) Misc. bond : bond 0.00568 ( 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 657 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 487 time to evaluate : 3.757 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: J 181 LYS cc_start: 0.7470 (tppt) cc_final: 0.7147 (tppt) REVERT: J 185 ASP cc_start: 0.8577 (t0) cc_final: 0.8329 (t0) REVERT: Y 6 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9109 (mm) REVERT: Y 64 GLU cc_start: 0.8309 (mt-10) cc_final: 0.8106 (mt-10) REVERT: Y 115 TYR cc_start: 0.9030 (m-80) cc_final: 0.8715 (m-10) REVERT: Y 159 TYR cc_start: 0.8827 (OUTLIER) cc_final: 0.8128 (p90) REVERT: Y 194 GLU cc_start: 0.6021 (tp30) cc_final: 0.5786 (tp30) REVERT: Y 213 MET cc_start: 0.8864 (ptm) cc_final: 0.8410 (ptm) REVERT: Y 340 ILE cc_start: 0.9446 (OUTLIER) cc_final: 0.9147 (tp) REVERT: Y 345 GLU cc_start: 0.8519 (tt0) cc_final: 0.7900 (mt-10) REVERT: Y 519 THR cc_start: 0.9261 (OUTLIER) cc_final: 0.8863 (p) REVERT: Y 577 MET cc_start: 0.9159 (mmt) cc_final: 0.8916 (mmt) REVERT: A 181 LYS cc_start: 0.7701 (tppt) cc_final: 0.7392 (tppt) REVERT: A 185 ASP cc_start: 0.8805 (t0) cc_final: 0.8490 (t0) REVERT: C 83 PHE cc_start: 0.8900 (OUTLIER) cc_final: 0.8508 (m-80) REVERT: C 159 TYR cc_start: 0.8911 (OUTLIER) cc_final: 0.8367 (p90) REVERT: C 194 GLU cc_start: 0.5955 (tp30) cc_final: 0.5645 (tp30) REVERT: C 213 MET cc_start: 0.9020 (ptp) cc_final: 0.8529 (ptm) REVERT: C 219 ASN cc_start: 0.7838 (m-40) cc_final: 0.7196 (m-40) REVERT: C 305 GLU cc_start: 0.8762 (tm-30) cc_final: 0.8530 (tm-30) REVERT: C 344 ASN cc_start: 0.9245 (OUTLIER) cc_final: 0.8522 (m-40) REVERT: C 457 TYR cc_start: 0.6762 (m-10) cc_final: 0.6536 (m-10) REVERT: C 480 MET cc_start: 0.9286 (tpt) cc_final: 0.8829 (tpp) REVERT: C 515 LEU cc_start: 0.9449 (mm) cc_final: 0.9242 (mm) REVERT: D 181 LYS cc_start: 0.7620 (tppt) cc_final: 0.7120 (tppt) REVERT: E 177 LEU cc_start: 0.9215 (tp) cc_final: 0.9012 (tt) REVERT: F 19 ASP cc_start: 0.8242 (t0) cc_final: 0.8001 (t0) REVERT: F 83 PHE cc_start: 0.9026 (OUTLIER) cc_final: 0.8629 (m-10) REVERT: F 168 PHE cc_start: 0.8117 (OUTLIER) cc_final: 0.6534 (p90) REVERT: F 213 MET cc_start: 0.9060 (ptp) cc_final: 0.8733 (ptm) REVERT: F 219 ASN cc_start: 0.7381 (m-40) cc_final: 0.7044 (m-40) REVERT: F 222 MET cc_start: 0.9131 (mmm) cc_final: 0.8525 (tpp) REVERT: F 388 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7909 (mm-30) REVERT: F 519 THR cc_start: 0.9340 (OUTLIER) cc_final: 0.9014 (p) REVERT: F 577 MET cc_start: 0.9127 (mmt) cc_final: 0.8690 (mmt) REVERT: G 181 LYS cc_start: 0.7467 (tppt) cc_final: 0.7142 (tppt) REVERT: G 185 ASP cc_start: 0.8575 (t0) cc_final: 0.8334 (t0) REVERT: K 115 TYR cc_start: 0.9034 (m-80) cc_final: 0.8719 (m-10) REVERT: K 159 TYR cc_start: 0.8829 (OUTLIER) cc_final: 0.8130 (p90) REVERT: K 194 GLU cc_start: 0.6019 (tp30) cc_final: 0.5780 (tp30) REVERT: K 213 MET cc_start: 0.8861 (ptm) cc_final: 0.8388 (ptm) REVERT: K 219 ASN cc_start: 0.7358 (m-40) cc_final: 0.7158 (m-40) REVERT: K 222 MET cc_start: 0.9177 (tpp) cc_final: 0.8863 (mmt) REVERT: K 340 ILE cc_start: 0.9458 (OUTLIER) cc_final: 0.9167 (tp) REVERT: K 345 GLU cc_start: 0.8524 (tt0) cc_final: 0.7900 (mt-10) REVERT: K 519 THR cc_start: 0.9257 (OUTLIER) cc_final: 0.8859 (p) REVERT: K 577 MET cc_start: 0.9160 (mmt) cc_final: 0.8913 (mmt) REVERT: L 181 LYS cc_start: 0.7710 (tppt) cc_final: 0.7392 (tppt) REVERT: L 185 ASP cc_start: 0.8808 (t0) cc_final: 0.8488 (t0) REVERT: N 83 PHE cc_start: 0.8896 (OUTLIER) cc_final: 0.8504 (m-80) REVERT: N 159 TYR cc_start: 0.8926 (OUTLIER) cc_final: 0.8385 (p90) REVERT: N 194 GLU cc_start: 0.5954 (tp30) cc_final: 0.5645 (tp30) REVERT: N 213 MET cc_start: 0.9025 (ptp) cc_final: 0.8542 (ptm) REVERT: N 219 ASN cc_start: 0.7836 (m-40) cc_final: 0.7186 (m-40) REVERT: N 305 GLU cc_start: 0.8758 (tm-30) cc_final: 0.8525 (tm-30) REVERT: N 344 ASN cc_start: 0.9246 (OUTLIER) cc_final: 0.8513 (m-40) REVERT: N 457 TYR cc_start: 0.6771 (m-10) cc_final: 0.6547 (m-10) REVERT: N 480 MET cc_start: 0.9288 (tpt) cc_final: 0.8804 (tpp) REVERT: N 515 LEU cc_start: 0.9448 (mm) cc_final: 0.9241 (mm) REVERT: Q 83 PHE cc_start: 0.9035 (OUTLIER) cc_final: 0.8638 (m-10) REVERT: Q 168 PHE cc_start: 0.8118 (OUTLIER) cc_final: 0.6540 (p90) REVERT: Q 213 MET cc_start: 0.9066 (ptp) cc_final: 0.8742 (ptm) REVERT: Q 219 ASN cc_start: 0.7389 (m-40) cc_final: 0.7045 (m-40) REVERT: Q 222 MET cc_start: 0.9132 (mmm) cc_final: 0.8526 (tpp) REVERT: Q 345 GLU cc_start: 0.8578 (tt0) cc_final: 0.8373 (tt0) REVERT: Q 388 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7926 (mm-30) REVERT: Q 519 THR cc_start: 0.9348 (OUTLIER) cc_final: 0.9034 (p) REVERT: Q 577 MET cc_start: 0.9129 (mmt) cc_final: 0.8692 (mmt) outliers start: 170 outliers final: 107 residues processed: 594 average time/residue: 0.3944 time to fit residues: 386.3610 Evaluate side-chains 576 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 448 time to evaluate : 3.318 ------------------------------------------------------------------------------- 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 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 232 THR Chi-restraints excluded: chain Y residue 336 THR Chi-restraints excluded: chain Y residue 340 ILE Chi-restraints excluded: chain Y residue 343 HIS Chi-restraints excluded: chain Y residue 344 ASN Chi-restraints excluded: chain Y residue 375 SER Chi-restraints excluded: chain Y residue 415 ILE 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 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 369 ILE Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 415 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 E residue 186 VAL 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 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 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 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 153 ILE 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 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 343 HIS 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 389 VAL Chi-restraints excluded: chain K residue 415 ILE 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 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 369 ILE Chi-restraints excluded: chain N residue 391 ILE Chi-restraints excluded: chain N residue 415 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 P residue 186 VAL 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 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 344 ASN 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 553 LEU Chi-restraints excluded: chain Q residue 563 THR Chi-restraints excluded: chain Q residue 565 VAL 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 224 optimal weight: 0.6980 chunk 254 optimal weight: 5.9990 chunk 340 optimal weight: 5.9990 chunk 285 optimal weight: 0.6980 chunk 116 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 257 optimal weight: 4.9990 chunk 226 optimal weight: 0.5980 chunk 250 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 126 ASN Y 343 HIS ** Y 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** 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 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 343 HIS ** F 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 126 ASN K 343 HIS ** K 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 179 GLN ** Q 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.110888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.091048 restraints weight = 53098.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.094559 restraints weight = 28333.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.096915 restraints weight = 18237.521| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 31422 Z= 0.153 Angle : 0.611 10.594 42528 Z= 0.321 Chirality : 0.042 0.145 4644 Planarity : 0.006 0.224 5568 Dihedral : 8.461 179.164 4100 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 4.70 % Allowed : 16.67 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.13), residues: 3720 helix: 0.17 (0.18), residues: 870 sheet: 0.07 (0.20), residues: 708 loop : -1.42 (0.13), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Q 230 HIS 0.009 0.001 HIS Y 343 PHE 0.019 0.002 PHE C 586 TYR 0.027 0.001 TYR F 342 ARG 0.016 0.001 ARG Y 510 Details of bonding type rmsd hydrogen bonds : bond 0.03678 ( 876) hydrogen bonds : angle 5.66679 ( 2250) covalent geometry : bond 0.00347 (31362) covalent geometry : angle 0.61133 (42528) Misc. bond : bond 0.00429 ( 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 650 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 488 time to evaluate : 3.637 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 185 ASP cc_start: 0.8594 (t0) cc_final: 0.8317 (t0) REVERT: Y 6 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9128 (mm) REVERT: Y 19 ASP cc_start: 0.7791 (t0) cc_final: 0.6704 (t0) REVERT: Y 115 TYR cc_start: 0.9037 (m-80) cc_final: 0.8693 (m-10) REVERT: Y 159 TYR cc_start: 0.8817 (OUTLIER) cc_final: 0.8151 (p90) REVERT: Y 194 GLU cc_start: 0.6424 (tp30) cc_final: 0.6183 (tp30) REVERT: Y 213 MET cc_start: 0.8846 (ptm) cc_final: 0.8319 (ptm) REVERT: Y 222 MET cc_start: 0.9292 (tpp) cc_final: 0.8718 (mmt) REVERT: Y 388 GLU cc_start: 0.8293 (mt-10) cc_final: 0.8069 (mt-10) REVERT: Y 519 THR cc_start: 0.9265 (OUTLIER) cc_final: 0.8872 (p) REVERT: Y 577 MET cc_start: 0.9141 (mmt) cc_final: 0.8768 (mmt) REVERT: A 179 GLN cc_start: 0.8326 (mt0) cc_final: 0.8057 (pt0) REVERT: A 185 ASP cc_start: 0.8726 (t0) cc_final: 0.8307 (t0) REVERT: C 159 TYR cc_start: 0.8887 (OUTLIER) cc_final: 0.8431 (p90) REVERT: C 213 MET cc_start: 0.8971 (OUTLIER) cc_final: 0.8504 (ptm) REVERT: C 219 ASN cc_start: 0.7758 (m-40) cc_final: 0.7298 (m-40) REVERT: C 290 MET cc_start: 0.9108 (mtm) cc_final: 0.8866 (mtm) REVERT: C 375 SER cc_start: 0.8941 (m) cc_final: 0.8668 (t) REVERT: C 376 PHE cc_start: 0.9126 (t80) cc_final: 0.8449 (t80) REVERT: E 177 LEU cc_start: 0.9188 (tp) cc_final: 0.8924 (tt) REVERT: F 83 PHE cc_start: 0.9014 (OUTLIER) cc_final: 0.8729 (m-10) REVERT: F 168 PHE cc_start: 0.8006 (OUTLIER) cc_final: 0.6420 (p90) REVERT: F 213 MET cc_start: 0.9052 (OUTLIER) cc_final: 0.8752 (ptm) REVERT: F 219 ASN cc_start: 0.7670 (m-40) cc_final: 0.7314 (m-40) REVERT: F 519 THR cc_start: 0.9310 (OUTLIER) cc_final: 0.8985 (p) REVERT: F 577 MET cc_start: 0.8973 (mmt) cc_final: 0.8508 (mmt) REVERT: G 185 ASP cc_start: 0.8596 (t0) cc_final: 0.8320 (t0) REVERT: K 61 VAL cc_start: 0.8525 (OUTLIER) cc_final: 0.8168 (p) REVERT: K 115 TYR cc_start: 0.9040 (m-80) cc_final: 0.8691 (m-10) REVERT: K 159 TYR cc_start: 0.8814 (OUTLIER) cc_final: 0.8148 (p90) REVERT: K 194 GLU cc_start: 0.6435 (tp30) cc_final: 0.6188 (tp30) REVERT: K 213 MET cc_start: 0.8851 (ptm) cc_final: 0.8402 (ptm) REVERT: K 345 GLU cc_start: 0.8447 (tt0) cc_final: 0.8123 (tt0) REVERT: K 519 THR cc_start: 0.9262 (OUTLIER) cc_final: 0.8866 (p) REVERT: K 577 MET cc_start: 0.9140 (mmt) cc_final: 0.8767 (mmt) REVERT: L 179 GLN cc_start: 0.8338 (mt0) cc_final: 0.8049 (pt0) REVERT: L 185 ASP cc_start: 0.8726 (t0) cc_final: 0.8300 (t0) REVERT: N 159 TYR cc_start: 0.8901 (OUTLIER) cc_final: 0.8375 (p90) REVERT: N 213 MET cc_start: 0.8983 (OUTLIER) cc_final: 0.8515 (ptm) REVERT: N 219 ASN cc_start: 0.7760 (m-40) cc_final: 0.7297 (m-40) REVERT: N 290 MET cc_start: 0.9108 (mtm) cc_final: 0.8865 (mtm) REVERT: N 375 SER cc_start: 0.8927 (m) cc_final: 0.8658 (t) REVERT: N 376 PHE cc_start: 0.9125 (t80) cc_final: 0.8456 (t80) REVERT: Q 83 PHE cc_start: 0.9025 (OUTLIER) cc_final: 0.8743 (m-10) REVERT: Q 168 PHE cc_start: 0.8012 (OUTLIER) cc_final: 0.6432 (p90) REVERT: Q 213 MET cc_start: 0.9066 (OUTLIER) cc_final: 0.8757 (ptm) REVERT: Q 219 ASN cc_start: 0.7694 (m-40) cc_final: 0.7330 (m-40) REVERT: Q 519 THR cc_start: 0.9306 (OUTLIER) cc_final: 0.8980 (p) REVERT: Q 577 MET cc_start: 0.8968 (mmt) cc_final: 0.8509 (mmt) outliers start: 162 outliers final: 102 residues processed: 590 average time/residue: 0.3784 time to fit residues: 367.0673 Evaluate side-chains 565 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 445 time to evaluate : 3.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 177 LEU Chi-restraints excluded: chain Y residue 6 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 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 475 VAL 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 336 THR Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 400 GLN Chi-restraints excluded: chain C residue 475 VAL 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 E residue 186 VAL 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 102 VAL 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 241 ILE 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 510 ARG 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 61 VAL 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 354 ASN Chi-restraints excluded: chain K residue 375 SER Chi-restraints excluded: chain K residue 389 VAL Chi-restraints excluded: chain K residue 415 ILE Chi-restraints excluded: chain K residue 475 VAL Chi-restraints excluded: chain K residue 519 THR 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 336 THR Chi-restraints excluded: chain N residue 391 ILE Chi-restraints excluded: chain N residue 400 GLN Chi-restraints excluded: chain N residue 475 VAL 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 P residue 186 VAL 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 102 VAL 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 510 ARG 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 253 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 chunk 135 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 120 optimal weight: 1.9990 chunk 213 optimal weight: 3.9990 chunk 345 optimal weight: 4.9990 chunk 207 optimal weight: 4.9990 chunk 250 optimal weight: 3.9990 chunk 86 optimal weight: 0.0970 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 179 GLN ** Y 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 ASN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 179 GLN ** K 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 93 ASN ** N 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 126 ASN ** 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 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 402 GLN ** 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 = 0.3251 r_free = 0.3251 target = 0.110221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.090888 restraints weight = 53645.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.094355 restraints weight = 28606.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.096703 restraints weight = 18388.054| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 31422 Z= 0.177 Angle : 0.653 12.952 42528 Z= 0.340 Chirality : 0.043 0.222 4644 Planarity : 0.006 0.198 5568 Dihedral : 7.221 177.893 4100 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 4.99 % Allowed : 17.59 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.13), residues: 3720 helix: 0.06 (0.18), residues: 876 sheet: 0.07 (0.20), residues: 738 loop : -1.42 (0.13), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Y 230 HIS 0.003 0.001 HIS F 343 PHE 0.019 0.002 PHE C 586 TYR 0.032 0.001 TYR K 457 ARG 0.018 0.001 ARG Q 215 Details of bonding type rmsd hydrogen bonds : bond 0.03837 ( 876) hydrogen bonds : angle 5.62050 ( 2250) covalent geometry : bond 0.00403 (31362) covalent geometry : angle 0.65309 (42528) Misc. bond : bond 0.00519 ( 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 647 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 475 time to evaluate : 4.401 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: J 179 GLN cc_start: 0.8771 (pt0) cc_final: 0.8479 (pt0) REVERT: J 185 ASP cc_start: 0.8580 (t0) cc_final: 0.8351 (t0) REVERT: Y 60 MET cc_start: 0.8554 (ttm) cc_final: 0.8343 (mtp) REVERT: Y 115 TYR cc_start: 0.9044 (m-80) cc_final: 0.8693 (m-10) REVERT: Y 159 TYR cc_start: 0.8903 (OUTLIER) cc_final: 0.8231 (p90) REVERT: Y 213 MET cc_start: 0.8862 (ptm) cc_final: 0.8297 (ptm) REVERT: Y 222 MET cc_start: 0.9185 (tpp) cc_final: 0.8911 (tpp) REVERT: Y 340 ILE cc_start: 0.9488 (OUTLIER) cc_final: 0.9253 (tp) REVERT: Y 345 GLU cc_start: 0.8404 (tt0) cc_final: 0.7928 (mt-10) REVERT: Y 388 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7782 (mt-10) REVERT: Y 519 THR cc_start: 0.9354 (OUTLIER) cc_final: 0.8976 (p) REVERT: Y 577 MET cc_start: 0.9042 (mmt) cc_final: 0.8721 (mmt) REVERT: A 185 ASP cc_start: 0.8736 (t0) cc_final: 0.8519 (t0) REVERT: B 193 TYR cc_start: 0.5975 (m-80) cc_final: 0.5138 (m-80) REVERT: C 159 TYR cc_start: 0.9009 (OUTLIER) cc_final: 0.8602 (p90) REVERT: C 194 GLU cc_start: 0.6074 (tp30) cc_final: 0.5841 (tp30) REVERT: C 213 MET cc_start: 0.9032 (OUTLIER) cc_final: 0.8623 (ptm) REVERT: C 219 ASN cc_start: 0.7937 (m-40) cc_final: 0.7584 (m-40) REVERT: C 290 MET cc_start: 0.9112 (mtm) cc_final: 0.8861 (mtm) REVERT: C 344 ASN cc_start: 0.9106 (OUTLIER) cc_final: 0.8486 (m-40) REVERT: C 375 SER cc_start: 0.8926 (m) cc_final: 0.8661 (t) REVERT: C 376 PHE cc_start: 0.9117 (t80) cc_final: 0.8441 (t80) REVERT: E 193 TYR cc_start: 0.6289 (m-80) cc_final: 0.5483 (m-80) REVERT: F 83 PHE cc_start: 0.9062 (OUTLIER) cc_final: 0.8744 (m-10) REVERT: F 168 PHE cc_start: 0.8087 (OUTLIER) cc_final: 0.6392 (p90) REVERT: F 175 PHE cc_start: 0.7816 (OUTLIER) cc_final: 0.6863 (m-80) REVERT: F 213 MET cc_start: 0.9082 (OUTLIER) cc_final: 0.8700 (ptm) REVERT: F 219 ASN cc_start: 0.7886 (m-40) cc_final: 0.7454 (m-40) REVERT: F 519 THR cc_start: 0.9387 (OUTLIER) cc_final: 0.9056 (p) REVERT: F 577 MET cc_start: 0.8936 (mmt) cc_final: 0.8545 (mmt) REVERT: G 179 GLN cc_start: 0.8766 (pt0) cc_final: 0.8479 (pt0) REVERT: G 185 ASP cc_start: 0.8590 (t0) cc_final: 0.8362 (t0) REVERT: K 115 TYR cc_start: 0.9041 (m-80) cc_final: 0.8692 (m-10) REVERT: K 159 TYR cc_start: 0.8898 (OUTLIER) cc_final: 0.8222 (p90) REVERT: K 213 MET cc_start: 0.8938 (ptm) cc_final: 0.8407 (ptm) REVERT: K 519 THR cc_start: 0.9371 (OUTLIER) cc_final: 0.9001 (p) REVERT: K 577 MET cc_start: 0.9070 (mmt) cc_final: 0.8519 (mmt) REVERT: L 185 ASP cc_start: 0.8746 (t0) cc_final: 0.8528 (t0) REVERT: M 193 TYR cc_start: 0.5972 (m-80) cc_final: 0.5136 (m-80) REVERT: N 159 TYR cc_start: 0.9065 (OUTLIER) cc_final: 0.8612 (p90) REVERT: N 194 GLU cc_start: 0.6081 (tp30) cc_final: 0.5848 (tp30) REVERT: N 213 MET cc_start: 0.9044 (OUTLIER) cc_final: 0.8621 (ptm) REVERT: N 219 ASN cc_start: 0.7941 (m-40) cc_final: 0.7591 (m-40) REVERT: N 290 MET cc_start: 0.9108 (mtm) cc_final: 0.8856 (mtm) REVERT: N 344 ASN cc_start: 0.9112 (OUTLIER) cc_final: 0.8485 (m-40) REVERT: N 375 SER cc_start: 0.8908 (m) cc_final: 0.8652 (t) REVERT: N 376 PHE cc_start: 0.9119 (t80) cc_final: 0.8452 (t80) REVERT: N 577 MET cc_start: 0.8815 (mmt) cc_final: 0.8615 (mmt) REVERT: P 193 TYR cc_start: 0.6313 (m-80) cc_final: 0.5508 (m-80) REVERT: Q 83 PHE cc_start: 0.9071 (OUTLIER) cc_final: 0.8748 (m-10) REVERT: Q 168 PHE cc_start: 0.8098 (OUTLIER) cc_final: 0.6396 (p90) REVERT: Q 175 PHE cc_start: 0.7802 (OUTLIER) cc_final: 0.6862 (m-80) REVERT: Q 213 MET cc_start: 0.9077 (OUTLIER) cc_final: 0.8715 (ptm) REVERT: Q 219 ASN cc_start: 0.7891 (m-40) cc_final: 0.7461 (m-40) REVERT: Q 519 THR cc_start: 0.9395 (OUTLIER) cc_final: 0.9106 (p) REVERT: Q 577 MET cc_start: 0.8933 (mmt) cc_final: 0.8543 (mmt) outliers start: 172 outliers final: 113 residues processed: 590 average time/residue: 0.5339 time to fit residues: 528.1310 Evaluate side-chains 572 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 438 time to evaluate : 5.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 177 LEU Chi-restraints excluded: chain I residue 176 THR 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 400 GLN Chi-restraints excluded: chain Y residue 415 ILE Chi-restraints excluded: chain Y residue 475 VAL 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 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 204 ILE 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 339 ILE Chi-restraints excluded: chain C residue 344 ASN Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 400 GLN Chi-restraints excluded: chain C residue 415 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 179 GLN Chi-restraints excluded: chain E residue 186 VAL 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 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 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 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 159 TYR Chi-restraints excluded: chain K residue 168 PHE Chi-restraints excluded: chain K residue 204 ILE 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 354 ASN Chi-restraints excluded: chain K residue 375 SER Chi-restraints excluded: chain K residue 389 VAL Chi-restraints excluded: chain K residue 415 ILE Chi-restraints excluded: chain K residue 475 VAL Chi-restraints excluded: chain K residue 519 THR 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 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 204 ILE 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 339 ILE Chi-restraints excluded: chain N residue 344 ASN Chi-restraints excluded: chain N residue 391 ILE Chi-restraints excluded: chain N residue 400 GLN Chi-restraints excluded: chain N residue 415 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 P residue 186 VAL 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 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 241 ILE 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 103 optimal weight: 2.9990 chunk 190 optimal weight: 4.9990 chunk 172 optimal weight: 1.9990 chunk 332 optimal weight: 0.0070 chunk 35 optimal weight: 4.9990 chunk 321 optimal weight: 2.9990 chunk 243 optimal weight: 0.8980 chunk 126 optimal weight: 0.0980 chunk 88 optimal weight: 3.9990 chunk 2 optimal weight: 0.0030 chunk 338 optimal weight: 3.9990 overall best weight: 0.6010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 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** ** K 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 179 GLN ** N 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 99 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 = 0.3285 r_free = 0.3285 target = 0.112271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.092443 restraints weight = 52942.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.095991 restraints weight = 28278.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.098413 restraints weight = 18190.317| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 31422 Z= 0.142 Angle : 0.672 19.139 42528 Z= 0.349 Chirality : 0.042 0.264 4644 Planarity : 0.010 0.478 5568 Dihedral : 5.585 94.006 4100 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 4.58 % Allowed : 18.67 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.13), residues: 3720 helix: 0.07 (0.18), residues: 876 sheet: 0.07 (0.20), residues: 720 loop : -1.43 (0.13), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Q 532 HIS 0.002 0.000 HIS F 343 PHE 0.016 0.001 PHE F 175 TYR 0.025 0.001 TYR M 193 ARG 0.045 0.001 ARG C 215 Details of bonding type rmsd hydrogen bonds : bond 0.03378 ( 876) hydrogen bonds : angle 5.41376 ( 2250) covalent geometry : bond 0.00310 (31362) covalent geometry : angle 0.67218 (42528) Misc. bond : bond 0.00646 ( 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 669 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 511 time to evaluate : 5.272 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: J 179 GLN cc_start: 0.8731 (pt0) cc_final: 0.8416 (pt0) REVERT: J 185 ASP cc_start: 0.8601 (t0) cc_final: 0.8163 (t0) REVERT: J 189 THR cc_start: 0.8444 (m) cc_final: 0.8150 (m) REVERT: Y 60 MET cc_start: 0.8613 (ttm) cc_final: 0.8254 (mtp) REVERT: Y 115 TYR cc_start: 0.9003 (m-80) cc_final: 0.8623 (m-10) REVERT: Y 159 TYR cc_start: 0.8788 (OUTLIER) cc_final: 0.8176 (p90) REVERT: Y 213 MET cc_start: 0.8840 (ptm) cc_final: 0.8210 (ptm) REVERT: Y 345 GLU cc_start: 0.8342 (tt0) cc_final: 0.8123 (mt-10) REVERT: Y 388 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7555 (mt-10) REVERT: Y 480 MET cc_start: 0.8839 (mmm) cc_final: 0.8581 (mmt) REVERT: Y 577 MET cc_start: 0.9081 (mmt) cc_final: 0.8761 (mmt) REVERT: A 185 ASP cc_start: 0.8759 (t0) cc_final: 0.8474 (t0) REVERT: C 159 TYR cc_start: 0.8958 (OUTLIER) cc_final: 0.8555 (p90) REVERT: C 175 PHE cc_start: 0.7675 (OUTLIER) cc_final: 0.7199 (m-80) REVERT: C 194 GLU cc_start: 0.5954 (tp30) cc_final: 0.5723 (tp30) REVERT: C 213 MET cc_start: 0.8907 (OUTLIER) cc_final: 0.8478 (ptm) REVERT: C 305 GLU cc_start: 0.8645 (tm-30) cc_final: 0.8415 (tm-30) REVERT: C 375 SER cc_start: 0.9023 (m) cc_final: 0.8791 (t) REVERT: C 376 PHE cc_start: 0.9056 (t80) cc_final: 0.8459 (t80) REVERT: C 515 LEU cc_start: 0.9457 (mm) cc_final: 0.9197 (mm) REVERT: F 83 PHE cc_start: 0.8997 (OUTLIER) cc_final: 0.8633 (m-10) REVERT: F 168 PHE cc_start: 0.8082 (OUTLIER) cc_final: 0.6187 (p90) REVERT: F 175 PHE cc_start: 0.7797 (OUTLIER) cc_final: 0.6864 (m-80) REVERT: F 213 MET cc_start: 0.8825 (OUTLIER) cc_final: 0.8459 (ptm) REVERT: F 219 ASN cc_start: 0.8131 (m-40) cc_final: 0.7803 (m-40) REVERT: F 577 MET cc_start: 0.8916 (mmt) cc_final: 0.8510 (mmt) REVERT: G 179 GLN cc_start: 0.8741 (pt0) cc_final: 0.8423 (pt0) REVERT: G 185 ASP cc_start: 0.8605 (t0) cc_final: 0.8169 (t0) REVERT: G 189 THR cc_start: 0.8456 (m) cc_final: 0.8167 (m) REVERT: K 115 TYR cc_start: 0.9001 (m-80) cc_final: 0.8625 (m-10) REVERT: K 159 TYR cc_start: 0.8818 (OUTLIER) cc_final: 0.8135 (p90) REVERT: K 213 MET cc_start: 0.8789 (ptm) cc_final: 0.8194 (ptm) REVERT: K 376 PHE cc_start: 0.9248 (t80) cc_final: 0.8265 (t80) REVERT: K 388 GLU cc_start: 0.8310 (mt-10) cc_final: 0.7451 (mt-10) REVERT: K 577 MET cc_start: 0.9050 (mmt) cc_final: 0.8726 (mmt) REVERT: L 185 ASP cc_start: 0.8764 (t0) cc_final: 0.8480 (t0) REVERT: N 159 TYR cc_start: 0.8975 (OUTLIER) cc_final: 0.8569 (p90) REVERT: N 175 PHE cc_start: 0.7778 (OUTLIER) cc_final: 0.7283 (m-80) REVERT: N 194 GLU cc_start: 0.5971 (tp30) cc_final: 0.5735 (tp30) REVERT: N 213 MET cc_start: 0.8914 (OUTLIER) cc_final: 0.8481 (ptm) REVERT: N 305 GLU cc_start: 0.8621 (tm-30) cc_final: 0.8407 (tm-30) REVERT: N 375 SER cc_start: 0.9015 (m) cc_final: 0.8794 (t) REVERT: N 376 PHE cc_start: 0.9051 (t80) cc_final: 0.8462 (t80) REVERT: N 515 LEU cc_start: 0.9459 (mm) cc_final: 0.9197 (mm) REVERT: N 577 MET cc_start: 0.8754 (mmt) cc_final: 0.8495 (mmt) REVERT: Q 83 PHE cc_start: 0.9002 (OUTLIER) cc_final: 0.8676 (m-10) REVERT: Q 168 PHE cc_start: 0.8081 (OUTLIER) cc_final: 0.6186 (p90) REVERT: Q 175 PHE cc_start: 0.7786 (OUTLIER) cc_final: 0.6875 (m-80) REVERT: Q 185 PHE cc_start: 0.7761 (m-80) cc_final: 0.7397 (m-80) REVERT: Q 213 MET cc_start: 0.8828 (OUTLIER) cc_final: 0.8467 (ptm) REVERT: Q 219 ASN cc_start: 0.8140 (m-40) cc_final: 0.7813 (m-40) REVERT: Q 577 MET cc_start: 0.8904 (mmt) cc_final: 0.8520 (mmt) outliers start: 158 outliers final: 107 residues processed: 614 average time/residue: 0.4268 time to fit residues: 435.2599 Evaluate side-chains 574 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 451 time to evaluate : 3.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 176 THR 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 362 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 475 VAL 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 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 175 PHE Chi-restraints excluded: chain C residue 204 ILE 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 391 ILE Chi-restraints excluded: chain C residue 400 GLN 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 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 83 PHE 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 519 THR Chi-restraints excluded: chain F residue 563 THR 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 168 PHE Chi-restraints excluded: chain K residue 204 ILE 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 354 ASN Chi-restraints excluded: chain K residue 375 SER Chi-restraints excluded: chain K residue 389 VAL Chi-restraints excluded: chain K residue 415 ILE 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 L residue 177 LEU 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 175 PHE Chi-restraints excluded: chain N residue 204 ILE 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 391 ILE Chi-restraints excluded: chain N residue 400 GLN 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 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 83 PHE 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 479 GLN Chi-restraints excluded: chain Q residue 563 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 122 optimal weight: 4.9990 chunk 130 optimal weight: 0.9980 chunk 194 optimal weight: 0.5980 chunk 201 optimal weight: 0.7980 chunk 113 optimal weight: 4.9990 chunk 162 optimal weight: 3.9990 chunk 169 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 347 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 GLN ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 179 GLN ** N 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 72 GLN Q 126 ASN ** 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 = 0.3267 r_free = 0.3267 target = 0.111103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.091025 restraints weight = 53714.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.094573 restraints weight = 28857.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.096975 restraints weight = 18652.547| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 31422 Z= 0.165 Angle : 0.697 29.605 42528 Z= 0.358 Chirality : 0.043 0.270 4644 Planarity : 0.015 0.485 5568 Dihedral : 6.221 131.463 4100 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 4.29 % Allowed : 19.97 % Favored : 75.74 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.13), residues: 3720 helix: 0.03 (0.18), residues: 882 sheet: 0.03 (0.20), residues: 720 loop : -1.50 (0.12), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Q 532 HIS 0.004 0.001 HIS F 343 PHE 0.041 0.002 PHE Q 376 TYR 0.022 0.001 TYR K 457 ARG 0.045 0.001 ARG Q 215 Details of bonding type rmsd hydrogen bonds : bond 0.03415 ( 876) hydrogen bonds : angle 5.54981 ( 2250) covalent geometry : bond 0.00377 (31362) covalent geometry : angle 0.69727 (42528) Misc. bond : bond 0.00512 ( 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 638 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 490 time to evaluate : 6.429 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: 0.8680 (pt0) cc_final: 0.8335 (pt0) REVERT: J 185 ASP cc_start: 0.8637 (t0) cc_final: 0.8246 (t0) REVERT: J 189 THR cc_start: 0.8476 (m) cc_final: 0.8191 (m) REVERT: Y 60 MET cc_start: 0.8565 (ttm) cc_final: 0.8217 (mtp) REVERT: Y 115 TYR cc_start: 0.9028 (m-80) cc_final: 0.8672 (m-10) REVERT: Y 159 TYR cc_start: 0.8815 (OUTLIER) cc_final: 0.8059 (p90) REVERT: Y 213 MET cc_start: 0.8860 (ptm) cc_final: 0.8269 (ptm) REVERT: Y 388 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7610 (mt-10) REVERT: Y 577 MET cc_start: 0.9089 (mmt) cc_final: 0.8568 (mmt) REVERT: B 183 ASN cc_start: 0.8341 (t0) cc_final: 0.8018 (t0) REVERT: C 159 TYR cc_start: 0.8940 (OUTLIER) cc_final: 0.8645 (p90) REVERT: C 175 PHE cc_start: 0.7643 (OUTLIER) cc_final: 0.7205 (m-80) REVERT: C 194 GLU cc_start: 0.5943 (tp30) cc_final: 0.5667 (tp30) REVERT: C 213 MET cc_start: 0.8997 (OUTLIER) cc_final: 0.8649 (ptm) REVERT: C 305 GLU cc_start: 0.8703 (tm-30) cc_final: 0.8466 (tm-30) REVERT: C 344 ASN cc_start: 0.9104 (OUTLIER) cc_final: 0.8532 (m-40) REVERT: C 375 SER cc_start: 0.9016 (m) cc_final: 0.8791 (t) REVERT: C 376 PHE cc_start: 0.9095 (t80) cc_final: 0.8481 (t80) REVERT: C 515 LEU cc_start: 0.9484 (mm) cc_final: 0.9250 (mm) REVERT: F 66 MET cc_start: 0.8633 (ttm) cc_final: 0.8422 (ttm) REVERT: F 83 PHE cc_start: 0.8997 (OUTLIER) cc_final: 0.8676 (m-10) REVERT: F 168 PHE cc_start: 0.8095 (OUTLIER) cc_final: 0.6483 (p90) REVERT: F 175 PHE cc_start: 0.7829 (OUTLIER) cc_final: 0.6915 (m-80) REVERT: F 185 PHE cc_start: 0.7823 (m-80) cc_final: 0.7448 (m-10) REVERT: F 213 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.8599 (ptm) REVERT: F 219 ASN cc_start: 0.8466 (m-40) cc_final: 0.8174 (m-40) REVERT: F 519 THR cc_start: 0.9423 (OUTLIER) cc_final: 0.9148 (p) REVERT: F 577 MET cc_start: 0.8943 (mmt) cc_final: 0.8541 (mmt) REVERT: G 179 GLN cc_start: 0.8687 (pt0) cc_final: 0.8348 (pt0) REVERT: G 185 ASP cc_start: 0.8641 (t0) cc_final: 0.8252 (t0) REVERT: G 189 THR cc_start: 0.8481 (m) cc_final: 0.8196 (m) REVERT: K 115 TYR cc_start: 0.9037 (m-80) cc_final: 0.8679 (m-10) REVERT: K 159 TYR cc_start: 0.8823 (OUTLIER) cc_final: 0.8163 (p90) REVERT: K 213 MET cc_start: 0.8851 (ptm) cc_final: 0.8262 (ptm) REVERT: K 376 PHE cc_start: 0.9263 (t80) cc_final: 0.8273 (t80) REVERT: K 388 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7861 (mt-10) REVERT: K 577 MET cc_start: 0.9117 (mmt) cc_final: 0.8568 (mmt) REVERT: M 183 ASN cc_start: 0.8340 (t0) cc_final: 0.8021 (t0) REVERT: N 159 TYR cc_start: 0.8970 (OUTLIER) cc_final: 0.8619 (p90) REVERT: N 175 PHE cc_start: 0.7664 (OUTLIER) cc_final: 0.7164 (m-80) REVERT: N 194 GLU cc_start: 0.5946 (tp30) cc_final: 0.5668 (tp30) REVERT: N 213 MET cc_start: 0.9007 (OUTLIER) cc_final: 0.8649 (ptm) REVERT: N 305 GLU cc_start: 0.8702 (tm-30) cc_final: 0.8450 (tm-30) REVERT: N 344 ASN cc_start: 0.9105 (OUTLIER) cc_final: 0.8529 (m-40) REVERT: N 375 SER cc_start: 0.9007 (m) cc_final: 0.8791 (t) REVERT: N 376 PHE cc_start: 0.9097 (t80) cc_final: 0.8493 (t80) REVERT: N 515 LEU cc_start: 0.9484 (mm) cc_final: 0.9251 (mm) REVERT: N 577 MET cc_start: 0.8785 (mmt) cc_final: 0.8414 (mmt) REVERT: O 179 GLN cc_start: 0.8782 (pt0) cc_final: 0.7892 (pm20) REVERT: Q 83 PHE cc_start: 0.8998 (OUTLIER) cc_final: 0.8652 (m-10) REVERT: Q 168 PHE cc_start: 0.8093 (OUTLIER) cc_final: 0.6484 (p90) REVERT: Q 175 PHE cc_start: 0.7825 (OUTLIER) cc_final: 0.6974 (m-80) REVERT: Q 185 PHE cc_start: 0.7820 (m-80) cc_final: 0.7451 (m-10) REVERT: Q 213 MET cc_start: 0.8970 (OUTLIER) cc_final: 0.8591 (ptm) REVERT: Q 219 ASN cc_start: 0.8457 (m-40) cc_final: 0.8170 (m-40) REVERT: Q 577 MET cc_start: 0.8932 (mmt) cc_final: 0.8546 (mmt) outliers start: 148 outliers final: 102 residues processed: 588 average time/residue: 0.5875 time to fit residues: 581.9028 Evaluate side-chains 570 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 449 time to evaluate : 5.588 ------------------------------------------------------------------------------- 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 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 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 400 GLN Chi-restraints excluded: chain Y residue 415 ILE Chi-restraints excluded: chain Y residue 475 VAL 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 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 175 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 344 ASN Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 400 GLN Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 83 PHE 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 255 LYS Chi-restraints excluded: chain F residue 336 THR Chi-restraints excluded: chain F residue 343 HIS 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 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 153 ILE 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 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 354 ASN Chi-restraints excluded: chain K residue 369 ILE Chi-restraints excluded: chain K residue 375 SER Chi-restraints excluded: chain K residue 389 VAL Chi-restraints excluded: chain K residue 415 ILE Chi-restraints excluded: chain K residue 475 VAL Chi-restraints excluded: chain K residue 480 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 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 175 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 344 ASN Chi-restraints excluded: chain N residue 391 ILE Chi-restraints excluded: chain N residue 400 GLN Chi-restraints excluded: chain N residue 475 VAL Chi-restraints excluded: chain N residue 519 THR Chi-restraints excluded: chain N residue 563 THR Chi-restraints excluded: chain O residue 177 LEU Chi-restraints excluded: chain P residue 186 VAL Chi-restraints excluded: chain Q residue 77 CYS Chi-restraints excluded: chain Q residue 83 PHE 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 183 optimal weight: 2.9990 chunk 260 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 313 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 307 optimal weight: 0.8980 chunk 24 optimal weight: 0.4980 chunk 345 optimal weight: 2.9990 chunk 225 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 ASN ** C 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 GLN 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** ** K 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 126 ASN ** N 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 402 GLN ** 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** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.108815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.088793 restraints weight = 53734.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.092258 restraints weight = 28895.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.094625 restraints weight = 18772.781| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 31422 Z= 0.206 Angle : 0.708 19.167 42528 Z= 0.368 Chirality : 0.044 0.297 4644 Planarity : 0.012 0.445 5568 Dihedral : 5.945 66.708 4100 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 4.09 % Allowed : 20.46 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.13), residues: 3720 helix: 0.05 (0.18), residues: 876 sheet: 0.03 (0.20), residues: 738 loop : -1.47 (0.13), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Q 532 HIS 0.005 0.001 HIS C 343 PHE 0.028 0.002 PHE Q 376 TYR 0.032 0.002 TYR M 193 ARG 0.058 0.002 ARG F 215 Details of bonding type rmsd hydrogen bonds : bond 0.03670 ( 876) hydrogen bonds : angle 5.69490 ( 2250) covalent geometry : bond 0.00476 (31362) covalent geometry : angle 0.70808 (42528) Misc. bond : bond 0.00558 ( 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 589 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 448 time to evaluate : 3.216 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: J 179 GLN cc_start: 0.8795 (pt0) cc_final: 0.8536 (pt0) REVERT: J 185 ASP cc_start: 0.8678 (t0) cc_final: 0.8382 (t0) REVERT: Y 60 MET cc_start: 0.8556 (ttm) cc_final: 0.8220 (mtp) REVERT: Y 115 TYR cc_start: 0.9045 (m-80) cc_final: 0.8719 (m-10) REVERT: Y 159 TYR cc_start: 0.8893 (OUTLIER) cc_final: 0.8247 (p90) REVERT: Y 213 MET cc_start: 0.8853 (ptm) cc_final: 0.8620 (ptm) REVERT: Y 345 GLU cc_start: 0.8306 (tt0) cc_final: 0.7834 (mt-10) REVERT: Y 388 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7535 (mt-10) REVERT: Y 480 MET cc_start: 0.9274 (mmt) cc_final: 0.9046 (mmp) REVERT: Y 577 MET cc_start: 0.9122 (mmt) cc_final: 0.8667 (mmt) REVERT: A 179 GLN cc_start: 0.8805 (pt0) cc_final: 0.7928 (pm20) REVERT: B 183 ASN cc_start: 0.8451 (t0) cc_final: 0.8139 (t0) REVERT: C 159 TYR cc_start: 0.9052 (OUTLIER) cc_final: 0.8844 (p90) REVERT: C 175 PHE cc_start: 0.7666 (OUTLIER) cc_final: 0.7156 (m-80) REVERT: C 213 MET cc_start: 0.9067 (OUTLIER) cc_final: 0.8663 (ptm) REVERT: C 305 GLU cc_start: 0.8827 (tm-30) cc_final: 0.8593 (tm-30) REVERT: C 344 ASN cc_start: 0.9194 (OUTLIER) cc_final: 0.8476 (m-40) REVERT: C 375 SER cc_start: 0.9118 (m) cc_final: 0.8854 (t) REVERT: C 376 PHE cc_start: 0.9138 (t80) cc_final: 0.8488 (t80) REVERT: C 386 PHE cc_start: 0.8237 (m-80) cc_final: 0.8014 (m-80) REVERT: C 515 LEU cc_start: 0.9473 (mm) cc_final: 0.9218 (mm) REVERT: C 574 ASN cc_start: 0.8819 (m-40) cc_final: 0.7987 (t0) REVERT: D 179 GLN cc_start: 0.8426 (pt0) cc_final: 0.7082 (pm20) REVERT: F 6 LEU cc_start: 0.9286 (mm) cc_final: 0.8867 (mt) REVERT: F 60 MET cc_start: 0.8607 (mmm) cc_final: 0.8277 (mmm) REVERT: F 83 PHE cc_start: 0.9021 (OUTLIER) cc_final: 0.8606 (m-10) REVERT: F 168 PHE cc_start: 0.8147 (OUTLIER) cc_final: 0.6482 (p90) REVERT: F 175 PHE cc_start: 0.7730 (OUTLIER) cc_final: 0.6949 (m-80) REVERT: F 185 PHE cc_start: 0.8079 (m-80) cc_final: 0.7739 (m-10) REVERT: F 213 MET cc_start: 0.8889 (OUTLIER) cc_final: 0.8390 (ptm) REVERT: F 388 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7334 (mt-10) REVERT: F 519 THR cc_start: 0.9385 (OUTLIER) cc_final: 0.9108 (p) REVERT: F 577 MET cc_start: 0.8982 (mmt) cc_final: 0.8601 (mmt) REVERT: G 179 GLN cc_start: 0.8801 (pt0) cc_final: 0.8537 (pt0) REVERT: G 185 ASP cc_start: 0.8686 (t0) cc_final: 0.8394 (t0) REVERT: K 115 TYR cc_start: 0.9055 (m-80) cc_final: 0.8718 (m-10) REVERT: K 159 TYR cc_start: 0.8897 (OUTLIER) cc_final: 0.8255 (p90) REVERT: K 213 MET cc_start: 0.8838 (ptm) cc_final: 0.8179 (ptm) REVERT: K 480 MET cc_start: 0.9094 (OUTLIER) cc_final: 0.8644 (mpp) REVERT: K 577 MET cc_start: 0.9122 (mmt) cc_final: 0.8660 (mmt) REVERT: M 183 ASN cc_start: 0.8455 (t0) cc_final: 0.8138 (t0) REVERT: N 159 TYR cc_start: 0.9064 (OUTLIER) cc_final: 0.8859 (p90) REVERT: N 175 PHE cc_start: 0.7657 (OUTLIER) cc_final: 0.7157 (m-80) REVERT: N 213 MET cc_start: 0.9069 (OUTLIER) cc_final: 0.8651 (ptm) REVERT: N 305 GLU cc_start: 0.8812 (tm-30) cc_final: 0.8557 (tm-30) REVERT: N 344 ASN cc_start: 0.9199 (OUTLIER) cc_final: 0.8470 (m-40) REVERT: N 375 SER cc_start: 0.9109 (m) cc_final: 0.8857 (t) REVERT: N 376 PHE cc_start: 0.9142 (t80) cc_final: 0.8499 (t80) REVERT: N 386 PHE cc_start: 0.8259 (m-80) cc_final: 0.8046 (m-80) REVERT: N 515 LEU cc_start: 0.9476 (mm) cc_final: 0.9218 (mm) REVERT: N 577 MET cc_start: 0.8912 (mmt) cc_final: 0.8491 (mmt) REVERT: Q 6 LEU cc_start: 0.9307 (mm) cc_final: 0.8854 (mt) REVERT: Q 60 MET cc_start: 0.8589 (mmm) cc_final: 0.8306 (mmm) REVERT: Q 83 PHE cc_start: 0.9025 (OUTLIER) cc_final: 0.8593 (m-10) REVERT: Q 168 PHE cc_start: 0.8133 (OUTLIER) cc_final: 0.6464 (p90) REVERT: Q 175 PHE cc_start: 0.7706 (OUTLIER) cc_final: 0.6965 (m-80) REVERT: Q 185 PHE cc_start: 0.8076 (m-80) cc_final: 0.7740 (m-10) REVERT: Q 213 MET cc_start: 0.9074 (OUTLIER) cc_final: 0.8723 (ptm) REVERT: Q 345 GLU cc_start: 0.8577 (tt0) cc_final: 0.8349 (tt0) REVERT: Q 577 MET cc_start: 0.9021 (mmt) cc_final: 0.8632 (mmt) outliers start: 141 outliers final: 102 residues processed: 548 average time/residue: 0.4006 time to fit residues: 369.0723 Evaluate side-chains 552 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 430 time to evaluate : 3.212 ------------------------------------------------------------------------------- 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 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 212 VAL Chi-restraints excluded: chain Y residue 232 THR Chi-restraints excluded: chain Y residue 336 THR 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 475 VAL 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 92 VAL 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 175 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 344 ASN Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 400 GLN 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 563 THR Chi-restraints excluded: chain E residue 186 VAL 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 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 255 LYS Chi-restraints excluded: chain F residue 336 THR Chi-restraints excluded: chain F residue 343 HIS Chi-restraints excluded: chain F residue 358 ASN 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 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 204 ILE 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 354 ASN Chi-restraints excluded: chain K residue 375 SER Chi-restraints excluded: chain K residue 389 VAL Chi-restraints excluded: chain K residue 415 ILE Chi-restraints excluded: chain K residue 475 VAL Chi-restraints excluded: chain K residue 480 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 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 175 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 344 ASN Chi-restraints excluded: chain N residue 391 ILE Chi-restraints excluded: chain N residue 400 GLN 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 563 THR Chi-restraints excluded: chain O residue 177 LEU Chi-restraints excluded: chain P residue 186 VAL Chi-restraints excluded: chain Q residue 77 CYS Chi-restraints excluded: chain Q residue 83 PHE 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 255 LYS Chi-restraints excluded: chain Q residue 336 THR Chi-restraints excluded: chain Q residue 391 ILE Chi-restraints excluded: chain Q residue 400 GLN Chi-restraints excluded: chain Q residue 475 VAL Chi-restraints excluded: chain Q residue 519 THR Chi-restraints excluded: chain Q residue 563 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 296 optimal weight: 0.9980 chunk 232 optimal weight: 10.0000 chunk 189 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 321 optimal weight: 0.9990 chunk 370 optimal weight: 0.2980 chunk 217 optimal weight: 4.9990 chunk 149 optimal weight: 1.9990 chunk 246 optimal weight: 3.9990 chunk 328 optimal weight: 1.9990 chunk 275 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** 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** ** K 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 354 ASN K 400 GLN ** 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 157 ASN ** 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 = 0.3267 r_free = 0.3267 target = 0.111067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.090892 restraints weight = 53504.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.094428 restraints weight = 28913.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.096846 restraints weight = 18800.870| |-----------------------------------------------------------------------------| r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.4066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 31422 Z= 0.174 Angle : 0.697 15.615 42528 Z= 0.360 Chirality : 0.043 0.206 4644 Planarity : 0.012 0.427 5568 Dihedral : 6.599 133.367 4100 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 3.59 % Allowed : 21.13 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.13), residues: 3720 helix: -0.04 (0.18), residues: 894 sheet: -0.05 (0.20), residues: 720 loop : -1.52 (0.13), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Y 230 HIS 0.004 0.001 HIS Y 343 PHE 0.031 0.002 PHE Y 376 TYR 0.024 0.001 TYR K 457 ARG 0.049 0.001 ARG N 215 Details of bonding type rmsd hydrogen bonds : bond 0.03441 ( 876) hydrogen bonds : angle 5.65976 ( 2250) covalent geometry : bond 0.00397 (31362) covalent geometry : angle 0.69740 (42528) Misc. bond : bond 0.00518 ( 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 566 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 442 time to evaluate : 6.755 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: J 179 GLN cc_start: 0.8733 (pt0) cc_final: 0.7854 (pm20) REVERT: J 185 ASP cc_start: 0.8667 (t0) cc_final: 0.8351 (t0) REVERT: Y 115 TYR cc_start: 0.9028 (m-80) cc_final: 0.8700 (m-10) REVERT: Y 159 TYR cc_start: 0.8882 (OUTLIER) cc_final: 0.8315 (p90) REVERT: Y 345 GLU cc_start: 0.8356 (tt0) cc_final: 0.7925 (mt-10) REVERT: Y 388 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7643 (mt-10) REVERT: Y 577 MET cc_start: 0.9115 (mmt) cc_final: 0.8657 (mmt) REVERT: A 179 GLN cc_start: 0.8718 (pt0) cc_final: 0.7965 (pm20) REVERT: B 183 ASN cc_start: 0.8382 (t0) cc_final: 0.8083 (t0) REVERT: C 138 VAL cc_start: 0.9094 (m) cc_final: 0.8843 (p) REVERT: C 159 TYR cc_start: 0.9031 (OUTLIER) cc_final: 0.8786 (p90) REVERT: C 175 PHE cc_start: 0.7666 (OUTLIER) cc_final: 0.7192 (m-80) REVERT: C 213 MET cc_start: 0.9101 (OUTLIER) cc_final: 0.8656 (ptm) REVERT: C 305 GLU cc_start: 0.8863 (tm-30) cc_final: 0.8646 (tm-30) REVERT: C 344 ASN cc_start: 0.9097 (OUTLIER) cc_final: 0.8421 (m-40) REVERT: C 375 SER cc_start: 0.9094 (m) cc_final: 0.8844 (t) REVERT: C 376 PHE cc_start: 0.9153 (t80) cc_final: 0.8527 (t80) REVERT: C 386 PHE cc_start: 0.8256 (m-80) cc_final: 0.8033 (m-80) REVERT: C 388 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7767 (mt-10) REVERT: C 514 MET cc_start: 0.8540 (mtp) cc_final: 0.8315 (mtp) REVERT: C 515 LEU cc_start: 0.9464 (mm) cc_final: 0.9153 (mm) REVERT: C 574 ASN cc_start: 0.8823 (m-40) cc_final: 0.7974 (t0) REVERT: D 179 GLN cc_start: 0.8405 (pt0) cc_final: 0.7092 (pm20) REVERT: F 6 LEU cc_start: 0.9294 (mm) cc_final: 0.8901 (mt) REVERT: F 60 MET cc_start: 0.8610 (mmm) cc_final: 0.8293 (mmm) REVERT: F 83 PHE cc_start: 0.9021 (OUTLIER) cc_final: 0.8609 (m-10) REVERT: F 168 PHE cc_start: 0.8093 (OUTLIER) cc_final: 0.6269 (p90) REVERT: F 175 PHE cc_start: 0.7697 (OUTLIER) cc_final: 0.6964 (m-80) REVERT: F 185 PHE cc_start: 0.8036 (m-80) cc_final: 0.7653 (m-10) REVERT: F 213 MET cc_start: 0.9087 (OUTLIER) cc_final: 0.8613 (ptm) REVERT: F 388 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7376 (mt-10) REVERT: F 519 THR cc_start: 0.9335 (OUTLIER) cc_final: 0.9100 (p) REVERT: F 577 MET cc_start: 0.8976 (mmt) cc_final: 0.8567 (mmt) REVERT: G 179 GLN cc_start: 0.8733 (pt0) cc_final: 0.7859 (pm20) REVERT: G 185 ASP cc_start: 0.8668 (t0) cc_final: 0.8348 (t0) REVERT: K 115 TYR cc_start: 0.9027 (m-80) cc_final: 0.8691 (m-10) REVERT: K 159 TYR cc_start: 0.8901 (OUTLIER) cc_final: 0.8322 (p90) REVERT: K 213 MET cc_start: 0.8895 (ptm) cc_final: 0.8253 (ptm) REVERT: K 388 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7694 (mt-10) REVERT: K 480 MET cc_start: 0.9050 (OUTLIER) cc_final: 0.8744 (mpp) REVERT: K 577 MET cc_start: 0.9114 (mmt) cc_final: 0.8655 (mmt) REVERT: L 179 GLN cc_start: 0.8761 (pt0) cc_final: 0.7942 (pm20) REVERT: M 183 ASN cc_start: 0.8378 (t0) cc_final: 0.8078 (t0) REVERT: N 60 MET cc_start: 0.8691 (mmm) cc_final: 0.8487 (mmm) REVERT: N 138 VAL cc_start: 0.9100 (m) cc_final: 0.8854 (p) REVERT: N 159 TYR cc_start: 0.9031 (OUTLIER) cc_final: 0.8795 (p90) REVERT: N 175 PHE cc_start: 0.7604 (OUTLIER) cc_final: 0.7116 (m-80) REVERT: N 213 MET cc_start: 0.9091 (OUTLIER) cc_final: 0.8646 (ptm) REVERT: N 305 GLU cc_start: 0.8858 (tm-30) cc_final: 0.8637 (tm-30) REVERT: N 344 ASN cc_start: 0.9096 (OUTLIER) cc_final: 0.8426 (m-40) REVERT: N 375 SER cc_start: 0.9093 (m) cc_final: 0.8847 (t) REVERT: N 376 PHE cc_start: 0.9151 (t80) cc_final: 0.8532 (t80) REVERT: N 386 PHE cc_start: 0.8235 (m-80) cc_final: 0.8008 (m-80) REVERT: N 514 MET cc_start: 0.8550 (mtp) cc_final: 0.8318 (mtp) REVERT: N 515 LEU cc_start: 0.9444 (mm) cc_final: 0.9140 (mm) REVERT: N 577 MET cc_start: 0.8913 (mmt) cc_final: 0.8454 (mmt) REVERT: O 179 GLN cc_start: 0.8682 (pt0) cc_final: 0.8117 (pm20) REVERT: Q 6 LEU cc_start: 0.9305 (mm) cc_final: 0.8872 (mt) REVERT: Q 60 MET cc_start: 0.8613 (mmm) cc_final: 0.8204 (tpp) REVERT: Q 83 PHE cc_start: 0.9085 (OUTLIER) cc_final: 0.8656 (m-10) REVERT: Q 168 PHE cc_start: 0.8091 (OUTLIER) cc_final: 0.6273 (p90) REVERT: Q 175 PHE cc_start: 0.7644 (OUTLIER) cc_final: 0.6990 (m-80) REVERT: Q 185 PHE cc_start: 0.8031 (m-80) cc_final: 0.7724 (m-10) REVERT: Q 213 MET cc_start: 0.9134 (OUTLIER) cc_final: 0.8803 (ptm) REVERT: Q 345 GLU cc_start: 0.8395 (tt0) cc_final: 0.8175 (mt-10) REVERT: Q 577 MET cc_start: 0.9002 (mmt) cc_final: 0.8618 (mmt) outliers start: 124 outliers final: 99 residues processed: 526 average time/residue: 0.5797 time to fit residues: 523.7277 Evaluate side-chains 546 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 427 time to evaluate : 7.621 ------------------------------------------------------------------------------- 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 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 212 VAL Chi-restraints excluded: chain Y residue 232 THR Chi-restraints excluded: chain Y residue 336 THR 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 455 TYR Chi-restraints excluded: chain Y residue 475 VAL 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 92 VAL 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 175 PHE 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 344 ASN Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 400 GLN 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 563 THR Chi-restraints excluded: chain E residue 186 VAL 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 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 255 LYS Chi-restraints excluded: chain F residue 336 THR Chi-restraints excluded: chain F residue 343 HIS Chi-restraints excluded: chain F residue 358 ASN 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 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 204 ILE 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 369 ILE Chi-restraints excluded: chain K residue 375 SER Chi-restraints excluded: chain K residue 415 ILE Chi-restraints excluded: chain K residue 475 VAL Chi-restraints excluded: chain K residue 480 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 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 175 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 344 ASN Chi-restraints excluded: chain N residue 391 ILE Chi-restraints excluded: chain N residue 400 GLN Chi-restraints excluded: chain N residue 438 ILE Chi-restraints excluded: chain N residue 475 VAL Chi-restraints excluded: chain N residue 495 MET Chi-restraints excluded: chain N residue 519 THR Chi-restraints excluded: chain N residue 563 THR Chi-restraints excluded: chain O residue 177 LEU Chi-restraints excluded: chain P residue 186 VAL 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 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 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 563 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 260 optimal weight: 4.9990 chunk 175 optimal weight: 0.0470 chunk 319 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 192 optimal weight: 1.9990 chunk 128 optimal weight: 0.7980 chunk 306 optimal weight: 0.9980 chunk 248 optimal weight: 0.9980 chunk 314 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 176 optimal weight: 0.9990 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 402 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** ** K 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 179 GLN ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.112956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.093178 restraints weight = 53655.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.096774 restraints weight = 28867.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.099256 restraints weight = 18612.502| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31422 Z= 0.139 Angle : 0.675 14.579 42528 Z= 0.346 Chirality : 0.043 0.237 4644 Planarity : 0.011 0.343 5568 Dihedral : 6.457 142.050 4098 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 3.94 % Allowed : 20.81 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.13), residues: 3720 helix: 0.01 (0.18), residues: 900 sheet: -0.06 (0.19), residues: 720 loop : -1.47 (0.13), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 230 HIS 0.003 0.001 HIS Q 343 PHE 0.032 0.001 PHE Y 376 TYR 0.019 0.001 TYR K 457 ARG 0.056 0.002 ARG Q 215 Details of bonding type rmsd hydrogen bonds : bond 0.03370 ( 876) hydrogen bonds : angle 5.55762 ( 2250) covalent geometry : bond 0.00311 (31362) covalent geometry : angle 0.67550 (42528) Misc. bond : bond 0.00495 ( 60) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10583.64 seconds wall clock time: 194 minutes 37.07 seconds (11677.07 seconds total)