Starting phenix.real_space_refine on Thu Mar 5 14:24:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pbx_20294/03_2026/6pbx_20294.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pbx_20294/03_2026/6pbx_20294.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6pbx_20294/03_2026/6pbx_20294.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pbx_20294/03_2026/6pbx_20294.map" model { file = "/net/cci-nas-00/data/ceres_data/6pbx_20294/03_2026/6pbx_20294.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pbx_20294/03_2026/6pbx_20294.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 128 5.16 5 C 14880 2.51 5 N 3836 2.21 5 O 4184 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 108 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23028 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 648, 4897 Classifications: {'peptide': 648} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PTRANS': 17, 'TRANS': 630} Chain breaks: 6 Unresolved non-hydrogen bonds: 369 Unresolved non-hydrogen angles: 443 Unresolved non-hydrogen dihedrals: 301 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLU:plan': 14, 'ARG:plan': 14, 'ASN:plan1': 4, 'ASP:plan': 9, 'GLN:plan1': 11, 'HIS:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 225 Chain: "B" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 860 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 2, 'TRANS': 137} Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 300 Unresolved non-hydrogen dihedrals: 186 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 13, 'PHE:plan': 1, 'ASP:plan': 10, 'ARG:plan': 5, 'ASN:plan1': 4} Unresolved non-hydrogen planarities: 141 Restraints were copied for chains: C, E, G, D, F, H Time building chain proxies: 4.91, per 1000 atoms: 0.21 Number of scatterers: 23028 At special positions: 0 Unit cell: (157, 157, 142, 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 128 16.00 O 4184 8.00 N 3836 7.00 C 14880 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.92 Conformation dependent library (CDL) restraints added in 980.4 milliseconds 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5984 Finding SS restraints... Secondary structure from input PDB file: 152 helices and 16 sheets defined 64.0% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 16 through 26 removed outlier: 3.805A pdb=" N ILE A 21 " --> pdb=" O PHE A 17 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ASN A 26 " --> pdb=" O VAL A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 54 Processing helix chain 'A' and resid 56 through 61 Processing helix chain 'A' and resid 67 through 71 Processing helix chain 'A' and resid 76 through 90 Processing helix chain 'A' and resid 133 through 138 Processing helix chain 'A' and resid 146 through 158 Processing helix chain 'A' and resid 158 through 163 removed outlier: 3.541A pdb=" N ARG A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 193 Processing helix chain 'A' and resid 215 through 241 Proline residue: A 236 - end of helix Processing helix chain 'A' and resid 248 through 271 Processing helix chain 'A' and resid 285 through 295 Processing helix chain 'A' and resid 295 through 303 removed outlier: 4.070A pdb=" N CYS A 303 " --> pdb=" O ASP A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 335 removed outlier: 3.634A pdb=" N LYS A 327 " --> pdb=" O SER A 324 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A 334 " --> pdb=" O LEU A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 342 removed outlier: 3.991A pdb=" N LYS A 340 " --> pdb=" O ARG A 336 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 379 removed outlier: 3.808A pdb=" N LEU A 352 " --> pdb=" O GLY A 348 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL A 353 " --> pdb=" O ALA A 349 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N PHE A 379 " --> pdb=" O ASP A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 400 Processing helix chain 'A' and resid 418 through 435 Processing helix chain 'A' and resid 446 through 499 removed outlier: 3.692A pdb=" N LEU A 462 " --> pdb=" O MET A 458 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N THR A 482 " --> pdb=" O MET A 478 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N TYR A 485 " --> pdb=" O ASN A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 520 Processing helix chain 'A' and resid 524 through 532 Processing helix chain 'A' and resid 533 through 545 Processing helix chain 'A' and resid 545 through 550 Processing helix chain 'A' and resid 559 through 568 Processing helix chain 'A' and resid 620 through 625 removed outlier: 3.828A pdb=" N GLU A 624 " --> pdb=" O VAL A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 657 Processing helix chain 'A' and resid 657 through 668 removed outlier: 3.848A pdb=" N HIS A 662 " --> pdb=" O THR A 658 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N SER A 663 " --> pdb=" O ALA A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 692 Processing helix chain 'A' and resid 707 through 720 removed outlier: 3.716A pdb=" N ARG A 712 " --> pdb=" O HIS A 708 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU A 713 " --> pdb=" O PRO A 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 11 No H-bonds generated for 'chain 'B' and resid 9 through 11' Processing helix chain 'B' and resid 12 through 20 removed outlier: 3.667A pdb=" N PHE B 16 " --> pdb=" O PHE B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 39 Processing helix chain 'B' and resid 44 through 56 Processing helix chain 'B' and resid 64 through 75 removed outlier: 3.956A pdb=" N THR B 70 " --> pdb=" O PRO B 66 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N MET B 71 " --> pdb=" O GLU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 93 Processing helix chain 'B' and resid 101 through 113 Processing helix chain 'B' and resid 117 through 129 Processing helix chain 'B' and resid 137 through 147 removed outlier: 3.599A pdb=" N MET B 144 " --> pdb=" O GLU B 140 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ALA B 147 " --> pdb=" O GLN B 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 26 removed outlier: 3.805A pdb=" N ILE C 21 " --> pdb=" O PHE C 17 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ASN C 26 " --> pdb=" O VAL C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 54 Processing helix chain 'C' and resid 56 through 61 Processing helix chain 'C' and resid 67 through 71 Processing helix chain 'C' and resid 76 through 90 Processing helix chain 'C' and resid 133 through 138 Processing helix chain 'C' and resid 146 through 158 Processing helix chain 'C' and resid 158 through 163 removed outlier: 3.541A pdb=" N ARG C 162 " --> pdb=" O LEU C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 193 Processing helix chain 'C' and resid 215 through 241 Proline residue: C 236 - end of helix Processing helix chain 'C' and resid 248 through 271 Processing helix chain 'C' and resid 285 through 295 Processing helix chain 'C' and resid 295 through 303 removed outlier: 4.070A pdb=" N CYS C 303 " --> pdb=" O ASP C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 335 removed outlier: 3.635A pdb=" N LYS C 327 " --> pdb=" O SER C 324 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU C 334 " --> pdb=" O LEU C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 342 removed outlier: 3.991A pdb=" N LYS C 340 " --> pdb=" O ARG C 336 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP C 342 " --> pdb=" O ALA C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 379 removed outlier: 3.808A pdb=" N LEU C 352 " --> pdb=" O GLY C 348 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL C 353 " --> pdb=" O ALA C 349 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N PHE C 379 " --> pdb=" O ASP C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 400 Processing helix chain 'C' and resid 418 through 435 Processing helix chain 'C' and resid 446 through 499 removed outlier: 3.693A pdb=" N LEU C 462 " --> pdb=" O MET C 458 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N THR C 482 " --> pdb=" O MET C 478 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N TYR C 485 " --> pdb=" O ASN C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 520 Processing helix chain 'C' and resid 524 through 532 Processing helix chain 'C' and resid 533 through 545 Processing helix chain 'C' and resid 545 through 550 Processing helix chain 'C' and resid 559 through 568 Processing helix chain 'C' and resid 620 through 625 removed outlier: 3.829A pdb=" N GLU C 624 " --> pdb=" O VAL C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 657 Processing helix chain 'C' and resid 657 through 668 removed outlier: 3.849A pdb=" N HIS C 662 " --> pdb=" O THR C 658 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N SER C 663 " --> pdb=" O ALA C 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 682 through 692 Processing helix chain 'C' and resid 707 through 720 removed outlier: 3.716A pdb=" N ARG C 712 " --> pdb=" O HIS C 708 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LEU C 713 " --> pdb=" O PRO C 709 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 26 removed outlier: 3.806A pdb=" N ILE E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ASN E 26 " --> pdb=" O VAL E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 54 Processing helix chain 'E' and resid 56 through 61 Processing helix chain 'E' and resid 67 through 71 Processing helix chain 'E' and resid 76 through 90 Processing helix chain 'E' and resid 133 through 138 Processing helix chain 'E' and resid 146 through 158 Processing helix chain 'E' and resid 158 through 163 removed outlier: 3.541A pdb=" N ARG E 162 " --> pdb=" O LEU E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 193 Processing helix chain 'E' and resid 215 through 241 Proline residue: E 236 - end of helix Processing helix chain 'E' and resid 248 through 271 Processing helix chain 'E' and resid 285 through 295 Processing helix chain 'E' and resid 295 through 303 removed outlier: 4.070A pdb=" N CYS E 303 " --> pdb=" O ASP E 299 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 335 removed outlier: 3.634A pdb=" N LYS E 327 " --> pdb=" O SER E 324 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU E 334 " --> pdb=" O LEU E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 342 removed outlier: 3.991A pdb=" N LYS E 340 " --> pdb=" O ARG E 336 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP E 342 " --> pdb=" O ALA E 338 " (cutoff:3.500A) Processing helix chain 'E' and resid 348 through 379 removed outlier: 3.808A pdb=" N LEU E 352 " --> pdb=" O GLY E 348 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL E 353 " --> pdb=" O ALA E 349 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N PHE E 379 " --> pdb=" O ASP E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 390 through 400 Processing helix chain 'E' and resid 418 through 435 Processing helix chain 'E' and resid 446 through 499 removed outlier: 3.692A pdb=" N LEU E 462 " --> pdb=" O MET E 458 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N THR E 482 " --> pdb=" O MET E 478 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N TYR E 485 " --> pdb=" O ASN E 481 " (cutoff:3.500A) Processing helix chain 'E' and resid 502 through 520 Processing helix chain 'E' and resid 524 through 532 Processing helix chain 'E' and resid 533 through 545 Processing helix chain 'E' and resid 545 through 550 Processing helix chain 'E' and resid 559 through 568 Processing helix chain 'E' and resid 620 through 625 removed outlier: 3.828A pdb=" N GLU E 624 " --> pdb=" O VAL E 620 " (cutoff:3.500A) Processing helix chain 'E' and resid 647 through 657 Processing helix chain 'E' and resid 657 through 668 removed outlier: 3.849A pdb=" N HIS E 662 " --> pdb=" O THR E 658 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N SER E 663 " --> pdb=" O ALA E 659 " (cutoff:3.500A) Processing helix chain 'E' and resid 682 through 692 Processing helix chain 'E' and resid 707 through 720 removed outlier: 3.716A pdb=" N ARG E 712 " --> pdb=" O HIS E 708 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU E 713 " --> pdb=" O PRO E 709 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 26 removed outlier: 3.804A pdb=" N ILE G 21 " --> pdb=" O PHE G 17 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ASN G 26 " --> pdb=" O VAL G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 54 Processing helix chain 'G' and resid 56 through 61 Processing helix chain 'G' and resid 67 through 71 Processing helix chain 'G' and resid 76 through 90 Processing helix chain 'G' and resid 133 through 138 Processing helix chain 'G' and resid 146 through 158 Processing helix chain 'G' and resid 158 through 163 removed outlier: 3.541A pdb=" N ARG G 162 " --> pdb=" O LEU G 158 " (cutoff:3.500A) Processing helix chain 'G' and resid 178 through 193 Processing helix chain 'G' and resid 215 through 241 Proline residue: G 236 - end of helix Processing helix chain 'G' and resid 248 through 271 Processing helix chain 'G' and resid 285 through 295 Processing helix chain 'G' and resid 295 through 303 removed outlier: 4.070A pdb=" N CYS G 303 " --> pdb=" O ASP G 299 " (cutoff:3.500A) Processing helix chain 'G' and resid 324 through 335 removed outlier: 3.634A pdb=" N LYS G 327 " --> pdb=" O SER G 324 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU G 334 " --> pdb=" O LEU G 331 " (cutoff:3.500A) Processing helix chain 'G' and resid 336 through 342 removed outlier: 3.991A pdb=" N LYS G 340 " --> pdb=" O ARG G 336 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP G 342 " --> pdb=" O ALA G 338 " (cutoff:3.500A) Processing helix chain 'G' and resid 348 through 379 removed outlier: 3.807A pdb=" N LEU G 352 " --> pdb=" O GLY G 348 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL G 353 " --> pdb=" O ALA G 349 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N PHE G 379 " --> pdb=" O ASP G 375 " (cutoff:3.500A) Processing helix chain 'G' and resid 390 through 400 Processing helix chain 'G' and resid 418 through 435 Processing helix chain 'G' and resid 446 through 499 removed outlier: 3.692A pdb=" N LEU G 462 " --> pdb=" O MET G 458 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N THR G 482 " --> pdb=" O MET G 478 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N TYR G 485 " --> pdb=" O ASN G 481 " (cutoff:3.500A) Processing helix chain 'G' and resid 502 through 520 Processing helix chain 'G' and resid 524 through 532 Processing helix chain 'G' and resid 533 through 545 Processing helix chain 'G' and resid 545 through 550 Processing helix chain 'G' and resid 559 through 568 Processing helix chain 'G' and resid 620 through 625 removed outlier: 3.828A pdb=" N GLU G 624 " --> pdb=" O VAL G 620 " (cutoff:3.500A) Processing helix chain 'G' and resid 647 through 657 Processing helix chain 'G' and resid 657 through 668 removed outlier: 3.849A pdb=" N HIS G 662 " --> pdb=" O THR G 658 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N SER G 663 " --> pdb=" O ALA G 659 " (cutoff:3.500A) Processing helix chain 'G' and resid 682 through 692 Processing helix chain 'G' and resid 707 through 720 removed outlier: 3.716A pdb=" N ARG G 712 " --> pdb=" O HIS G 708 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU G 713 " --> pdb=" O PRO G 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 11 No H-bonds generated for 'chain 'D' and resid 9 through 11' Processing helix chain 'D' and resid 12 through 20 removed outlier: 3.667A pdb=" N PHE D 16 " --> pdb=" O PHE D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 39 Processing helix chain 'D' and resid 44 through 56 Processing helix chain 'D' and resid 64 through 75 removed outlier: 3.956A pdb=" N THR D 70 " --> pdb=" O PRO D 66 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N MET D 71 " --> pdb=" O GLU D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 93 Processing helix chain 'D' and resid 101 through 113 Processing helix chain 'D' and resid 117 through 129 Processing helix chain 'D' and resid 137 through 147 removed outlier: 3.599A pdb=" N MET D 144 " --> pdb=" O GLU D 140 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ALA D 147 " --> pdb=" O GLN D 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 11 No H-bonds generated for 'chain 'F' and resid 9 through 11' Processing helix chain 'F' and resid 12 through 20 removed outlier: 3.667A pdb=" N PHE F 16 " --> pdb=" O PHE F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 39 Processing helix chain 'F' and resid 44 through 56 Processing helix chain 'F' and resid 64 through 75 removed outlier: 3.956A pdb=" N THR F 70 " --> pdb=" O PRO F 66 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N MET F 71 " --> pdb=" O GLU F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 93 Processing helix chain 'F' and resid 101 through 113 Processing helix chain 'F' and resid 117 through 129 Processing helix chain 'F' and resid 137 through 147 removed outlier: 3.598A pdb=" N MET F 144 " --> pdb=" O GLU F 140 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ALA F 147 " --> pdb=" O GLN F 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 11 No H-bonds generated for 'chain 'H' and resid 9 through 11' Processing helix chain 'H' and resid 12 through 20 removed outlier: 3.667A pdb=" N PHE H 16 " --> pdb=" O PHE H 12 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 39 Processing helix chain 'H' and resid 44 through 56 Processing helix chain 'H' and resid 64 through 75 removed outlier: 3.956A pdb=" N THR H 70 " --> pdb=" O PRO H 66 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N MET H 71 " --> pdb=" O GLU H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 93 Processing helix chain 'H' and resid 101 through 113 Processing helix chain 'H' and resid 117 through 129 Processing helix chain 'H' and resid 137 through 147 removed outlier: 3.599A pdb=" N MET H 144 " --> pdb=" O GLU H 140 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ALA H 147 " --> pdb=" O GLN H 143 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 45 removed outlier: 6.432A pdb=" N LEU A 32 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N SER A 45 " --> pdb=" O PHE A 30 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N PHE A 30 " --> pdb=" O SER A 45 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ASN A 29 " --> pdb=" O PHE A 130 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU A 125 " --> pdb=" O ILE A 116 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 571 through 575 removed outlier: 6.237A pdb=" N ASP A 641 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASP A 615 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY A 618 " --> pdb=" O TYR A 672 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 587 through 588 removed outlier: 4.398A pdb=" N ALA A 628 " --> pdb=" O VAL A 588 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 607 through 611 removed outlier: 6.564A pdb=" N VAL A 601 " --> pdb=" O VAL A 608 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ILE A 610 " --> pdb=" O LEU A 599 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU A 599 " --> pdb=" O ILE A 610 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 42 through 45 removed outlier: 6.431A pdb=" N LEU C 32 " --> pdb=" O VAL C 43 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N SER C 45 " --> pdb=" O PHE C 30 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N PHE C 30 " --> pdb=" O SER C 45 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ASN C 29 " --> pdb=" O PHE C 130 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU C 125 " --> pdb=" O ILE C 116 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 571 through 575 removed outlier: 6.237A pdb=" N ASP C 641 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASP C 615 " --> pdb=" O VAL C 594 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY C 618 " --> pdb=" O TYR C 672 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 587 through 588 removed outlier: 4.397A pdb=" N ALA C 628 " --> pdb=" O VAL C 588 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 607 through 611 removed outlier: 6.564A pdb=" N VAL C 601 " --> pdb=" O VAL C 608 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ILE C 610 " --> pdb=" O LEU C 599 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU C 599 " --> pdb=" O ILE C 610 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 42 through 45 removed outlier: 6.432A pdb=" N LEU E 32 " --> pdb=" O VAL E 43 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N SER E 45 " --> pdb=" O PHE E 30 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N PHE E 30 " --> pdb=" O SER E 45 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ASN E 29 " --> pdb=" O PHE E 130 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU E 125 " --> pdb=" O ILE E 116 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 571 through 575 removed outlier: 6.236A pdb=" N ASP E 641 " --> pdb=" O VAL E 595 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASP E 615 " --> pdb=" O VAL E 594 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY E 618 " --> pdb=" O TYR E 672 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 587 through 588 removed outlier: 4.397A pdb=" N ALA E 628 " --> pdb=" O VAL E 588 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 607 through 611 removed outlier: 6.563A pdb=" N VAL E 601 " --> pdb=" O VAL E 608 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ILE E 610 " --> pdb=" O LEU E 599 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU E 599 " --> pdb=" O ILE E 610 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 42 through 45 removed outlier: 6.431A pdb=" N LEU G 32 " --> pdb=" O VAL G 43 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N SER G 45 " --> pdb=" O PHE G 30 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N PHE G 30 " --> pdb=" O SER G 45 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ASN G 29 " --> pdb=" O PHE G 130 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU G 125 " --> pdb=" O ILE G 116 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 571 through 575 removed outlier: 6.237A pdb=" N ASP G 641 " --> pdb=" O VAL G 595 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASP G 615 " --> pdb=" O VAL G 594 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY G 618 " --> pdb=" O TYR G 672 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 587 through 588 removed outlier: 4.398A pdb=" N ALA G 628 " --> pdb=" O VAL G 588 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 607 through 611 removed outlier: 6.563A pdb=" N VAL G 601 " --> pdb=" O VAL G 608 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILE G 610 " --> pdb=" O LEU G 599 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU G 599 " --> pdb=" O ILE G 610 " (cutoff:3.500A) 1472 hydrogen bonds defined for protein. 4236 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: 4.58 Time building geometry restraints manager: 2.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7379 1.34 - 1.46: 5112 1.46 - 1.58: 10837 1.58 - 1.69: 0 1.69 - 1.81: 196 Bond restraints: 23524 Sorted by residual: bond pdb=" C LEU C 195 " pdb=" N PRO C 196 " ideal model delta sigma weight residual 1.335 1.359 -0.024 1.28e-02 6.10e+03 3.52e+00 bond pdb=" C LEU A 195 " pdb=" N PRO A 196 " ideal model delta sigma weight residual 1.335 1.358 -0.024 1.28e-02 6.10e+03 3.43e+00 bond pdb=" CG1 ILE C 224 " pdb=" CD1 ILE C 224 " ideal model delta sigma weight residual 1.513 1.441 0.072 3.90e-02 6.57e+02 3.41e+00 bond pdb=" C LEU G 195 " pdb=" N PRO G 196 " ideal model delta sigma weight residual 1.335 1.358 -0.024 1.28e-02 6.10e+03 3.39e+00 bond pdb=" CG1 ILE A 224 " pdb=" CD1 ILE A 224 " ideal model delta sigma weight residual 1.513 1.442 0.071 3.90e-02 6.57e+02 3.33e+00 ... (remaining 23519 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 31343 2.27 - 4.54: 639 4.54 - 6.81: 82 6.81 - 9.07: 28 9.07 - 11.34: 8 Bond angle restraints: 32100 Sorted by residual: angle pdb=" N LEU C 195 " pdb=" CA LEU C 195 " pdb=" C LEU C 195 " ideal model delta sigma weight residual 109.81 119.83 -10.02 2.21e+00 2.05e-01 2.06e+01 angle pdb=" N LEU A 195 " pdb=" CA LEU A 195 " pdb=" C LEU A 195 " ideal model delta sigma weight residual 109.81 119.81 -10.00 2.21e+00 2.05e-01 2.05e+01 angle pdb=" N LEU E 195 " pdb=" CA LEU E 195 " pdb=" C LEU E 195 " ideal model delta sigma weight residual 109.81 119.79 -9.98 2.21e+00 2.05e-01 2.04e+01 angle pdb=" N LEU G 195 " pdb=" CA LEU G 195 " pdb=" C LEU G 195 " ideal model delta sigma weight residual 109.81 119.79 -9.98 2.21e+00 2.05e-01 2.04e+01 angle pdb=" CA PRO G 196 " pdb=" N PRO G 196 " pdb=" CD PRO G 196 " ideal model delta sigma weight residual 112.00 106.68 5.32 1.40e+00 5.10e-01 1.44e+01 ... (remaining 32095 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.35: 12216 16.35 - 32.69: 1068 32.69 - 49.04: 284 49.04 - 65.39: 44 65.39 - 81.74: 8 Dihedral angle restraints: 13620 sinusoidal: 4404 harmonic: 9216 Sorted by residual: dihedral pdb=" CA PRO G 502 " pdb=" C PRO G 502 " pdb=" N LYS G 503 " pdb=" CA LYS G 503 " ideal model delta harmonic sigma weight residual -180.00 -158.51 -21.49 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA PRO E 502 " pdb=" C PRO E 502 " pdb=" N LYS E 503 " pdb=" CA LYS E 503 " ideal model delta harmonic sigma weight residual -180.00 -158.52 -21.48 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA PRO A 502 " pdb=" C PRO A 502 " pdb=" N LYS A 503 " pdb=" CA LYS A 503 " ideal model delta harmonic sigma weight residual -180.00 -158.56 -21.44 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 13617 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2618 0.045 - 0.090: 851 0.090 - 0.134: 253 0.134 - 0.179: 50 0.179 - 0.224: 16 Chirality restraints: 3788 Sorted by residual: chirality pdb=" CB THR E 228 " pdb=" CA THR E 228 " pdb=" OG1 THR E 228 " pdb=" CG2 THR E 228 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CB THR G 228 " pdb=" CA THR G 228 " pdb=" OG1 THR G 228 " pdb=" CG2 THR G 228 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CB THR A 432 " pdb=" CA THR A 432 " pdb=" OG1 THR A 432 " pdb=" CG2 THR A 432 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 3785 not shown) Planarity restraints: 4076 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 169 " -0.047 5.00e-02 4.00e+02 6.92e-02 7.66e+00 pdb=" N PRO A 170 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO A 170 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 170 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 169 " -0.046 5.00e-02 4.00e+02 6.90e-02 7.61e+00 pdb=" N PRO C 170 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO C 170 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 170 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA G 169 " -0.046 5.00e-02 4.00e+02 6.90e-02 7.61e+00 pdb=" N PRO G 170 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO G 170 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO G 170 " -0.039 5.00e-02 4.00e+02 ... (remaining 4073 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 6400 2.79 - 3.32: 22457 3.32 - 3.85: 40104 3.85 - 4.37: 43824 4.37 - 4.90: 73821 Nonbonded interactions: 186606 Sorted by model distance: nonbonded pdb=" O VAL E 172 " pdb=" OG SER F 38 " model vdw 2.264 3.040 nonbonded pdb=" OH TYR C 582 " pdb=" OG SER C 590 " model vdw 2.280 3.040 nonbonded pdb=" OH TYR A 582 " pdb=" OG SER A 590 " model vdw 2.280 3.040 nonbonded pdb=" OH TYR G 582 " pdb=" OG SER G 590 " model vdw 2.280 3.040 nonbonded pdb=" OH TYR E 582 " pdb=" OG SER E 590 " model vdw 2.281 3.040 ... (remaining 186601 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } 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: 2.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 21.300 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 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 : 0.006 0.072 23524 Z= 0.289 Angle : 0.825 11.343 32100 Z= 0.454 Chirality : 0.050 0.224 3788 Planarity : 0.006 0.069 4076 Dihedral : 14.043 81.736 7636 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.07 (0.12), residues: 3088 helix: -2.01 (0.09), residues: 1760 sheet: -2.23 (0.33), residues: 204 loop : -1.70 (0.17), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 24 TYR 0.017 0.002 TYR C 44 PHE 0.017 0.002 PHE F 68 TRP 0.013 0.002 TRP E 370 HIS 0.010 0.002 HIS G 543 Details of bonding type rmsd covalent geometry : bond 0.00610 (23524) covalent geometry : angle 0.82502 (32100) hydrogen bonds : bond 0.12723 ( 1472) hydrogen bonds : angle 6.65020 ( 4236) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 2804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 484 time to evaluate : 0.885 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: A 59 GLU cc_start: 0.9324 (mt-10) cc_final: 0.9083 (mp0) REVERT: A 468 PHE cc_start: 0.8574 (m-80) cc_final: 0.8372 (m-10) REVERT: A 470 ASN cc_start: 0.9215 (t0) cc_final: 0.9014 (t0) REVERT: A 519 MET cc_start: 0.8441 (ttm) cc_final: 0.7910 (tmm) REVERT: A 652 LYS cc_start: 0.8859 (mttt) cc_final: 0.8347 (mmtm) REVERT: B 32 LEU cc_start: 0.8035 (tp) cc_final: 0.7815 (mt) REVERT: B 123 GLU cc_start: 0.8476 (tp30) cc_final: 0.8270 (tp30) REVERT: B 144 MET cc_start: 0.8239 (tpt) cc_final: 0.7686 (tpt) REVERT: C 59 GLU cc_start: 0.9299 (mt-10) cc_final: 0.9063 (mp0) REVERT: C 99 MET cc_start: 0.8998 (mtp) cc_final: 0.8383 (mtp) REVERT: C 468 PHE cc_start: 0.8455 (m-80) cc_final: 0.8193 (m-10) REVERT: C 470 ASN cc_start: 0.9197 (t0) cc_final: 0.8987 (t0) REVERT: C 519 MET cc_start: 0.8459 (ttm) cc_final: 0.7996 (tmm) REVERT: C 651 GLN cc_start: 0.8796 (mt0) cc_final: 0.8553 (mt0) REVERT: C 652 LYS cc_start: 0.8829 (mttt) cc_final: 0.8618 (mmtm) REVERT: E 59 GLU cc_start: 0.9299 (mt-10) cc_final: 0.9052 (mp0) REVERT: E 99 MET cc_start: 0.8988 (mtp) cc_final: 0.8360 (mtp) REVERT: E 470 ASN cc_start: 0.9164 (t0) cc_final: 0.8935 (t0) REVERT: E 519 MET cc_start: 0.8470 (ttm) cc_final: 0.8031 (tmm) REVERT: E 651 GLN cc_start: 0.8823 (mt0) cc_final: 0.8579 (mt0) REVERT: E 652 LYS cc_start: 0.8827 (mttt) cc_final: 0.8617 (mmtm) REVERT: G 60 VAL cc_start: 0.9278 (t) cc_final: 0.9073 (p) REVERT: G 463 LEU cc_start: 0.9183 (mt) cc_final: 0.8960 (mt) REVERT: G 468 PHE cc_start: 0.8441 (m-80) cc_final: 0.7997 (m-80) REVERT: G 470 ASN cc_start: 0.9256 (t0) cc_final: 0.8894 (t0) REVERT: G 519 MET cc_start: 0.8443 (ttm) cc_final: 0.7842 (tmm) REVERT: G 536 MET cc_start: 0.8806 (mmp) cc_final: 0.8212 (mtp) REVERT: G 652 LYS cc_start: 0.8868 (mttt) cc_final: 0.8392 (mmtm) REVERT: D 32 LEU cc_start: 0.8061 (tp) cc_final: 0.7809 (mt) REVERT: D 123 GLU cc_start: 0.8517 (tp30) cc_final: 0.8311 (tp30) REVERT: D 136 VAL cc_start: 0.7757 (t) cc_final: 0.7537 (t) REVERT: D 139 GLU cc_start: 0.9241 (mp0) cc_final: 0.8757 (pm20) REVERT: D 144 MET cc_start: 0.8203 (tpt) cc_final: 0.7661 (tpt) REVERT: F 32 LEU cc_start: 0.8253 (tp) cc_final: 0.8026 (mt) REVERT: F 119 GLU cc_start: 0.8445 (tm-30) cc_final: 0.8155 (tm-30) REVERT: F 123 GLU cc_start: 0.8518 (tp30) cc_final: 0.8313 (mm-30) REVERT: F 139 GLU cc_start: 0.9275 (mp0) cc_final: 0.8801 (pm20) REVERT: F 144 MET cc_start: 0.8165 (tpt) cc_final: 0.7693 (tpt) REVERT: H 139 GLU cc_start: 0.9250 (mp0) cc_final: 0.8790 (pm20) REVERT: H 144 MET cc_start: 0.8137 (tpt) cc_final: 0.7636 (tpt) outliers start: 0 outliers final: 0 residues processed: 484 average time/residue: 0.1491 time to fit residues: 114.8309 Evaluate side-chains 326 residues out of total 2804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 326 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 30.0000 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 GLN A 651 GLN A 673 ASN ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 477 GLN E 673 ASN G 477 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.102500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.080413 restraints weight = 88022.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.081831 restraints weight = 58422.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.081947 restraints weight = 40701.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.082194 restraints weight = 39524.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.082332 restraints weight = 37849.779| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23524 Z= 0.139 Angle : 0.564 8.255 32100 Z= 0.301 Chirality : 0.040 0.203 3788 Planarity : 0.004 0.044 4076 Dihedral : 4.583 16.867 3328 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.94 % Allowed : 13.09 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.14), residues: 3088 helix: -0.15 (0.11), residues: 1848 sheet: -1.35 (0.36), residues: 204 loop : -1.19 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 508 TYR 0.017 0.002 TYR A 512 PHE 0.022 0.001 PHE E 468 TRP 0.008 0.001 TRP G 370 HIS 0.005 0.001 HIS G 543 Details of bonding type rmsd covalent geometry : bond 0.00294 (23524) covalent geometry : angle 0.56425 (32100) hydrogen bonds : bond 0.03645 ( 1472) hydrogen bonds : angle 4.72514 ( 4236) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 372 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 MET cc_start: 0.7136 (OUTLIER) cc_final: 0.6651 (mtp) REVERT: A 478 MET cc_start: 0.8262 (mtp) cc_final: 0.7996 (ttm) REVERT: A 510 MET cc_start: 0.9008 (mmm) cc_final: 0.8749 (tpt) REVERT: A 519 MET cc_start: 0.8157 (ttm) cc_final: 0.7921 (tmm) REVERT: A 534 LYS cc_start: 0.8837 (tppt) cc_final: 0.8546 (tppt) REVERT: A 652 LYS cc_start: 0.8802 (mttt) cc_final: 0.8080 (mmtm) REVERT: B 123 GLU cc_start: 0.8268 (tp30) cc_final: 0.7975 (tp30) REVERT: B 144 MET cc_start: 0.7700 (tpt) cc_final: 0.7166 (tpt) REVERT: C 457 MET cc_start: 0.8751 (mtp) cc_final: 0.8363 (mtm) REVERT: C 478 MET cc_start: 0.8271 (mtp) cc_final: 0.8030 (ttm) REVERT: C 510 MET cc_start: 0.9051 (mmm) cc_final: 0.8847 (tpt) REVERT: C 519 MET cc_start: 0.8184 (ttm) cc_final: 0.7924 (tmm) REVERT: E 478 MET cc_start: 0.8254 (mtp) cc_final: 0.8013 (ttm) REVERT: E 510 MET cc_start: 0.9096 (mmm) cc_final: 0.8877 (tpt) REVERT: E 519 MET cc_start: 0.8289 (ttm) cc_final: 0.7977 (tmm) REVERT: E 534 LYS cc_start: 0.8821 (tppt) cc_final: 0.8482 (tppt) REVERT: G 223 ILE cc_start: 0.9206 (tp) cc_final: 0.8992 (pt) REVERT: G 258 ASP cc_start: 0.7278 (m-30) cc_final: 0.7021 (t0) REVERT: G 463 LEU cc_start: 0.9284 (mt) cc_final: 0.8990 (mt) REVERT: G 468 PHE cc_start: 0.8738 (m-80) cc_final: 0.8315 (m-80) REVERT: G 557 LEU cc_start: 0.8268 (mt) cc_final: 0.7960 (tt) REVERT: D 123 GLU cc_start: 0.8223 (tp30) cc_final: 0.7965 (tp30) REVERT: D 139 GLU cc_start: 0.8698 (mp0) cc_final: 0.8374 (pm20) REVERT: D 141 PHE cc_start: 0.8738 (t80) cc_final: 0.8284 (t80) REVERT: D 144 MET cc_start: 0.7710 (tpt) cc_final: 0.7318 (tpt) REVERT: F 65 PHE cc_start: 0.6073 (t80) cc_final: 0.5744 (t80) REVERT: F 119 GLU cc_start: 0.9038 (tm-30) cc_final: 0.8816 (tm-30) REVERT: F 141 PHE cc_start: 0.8918 (t80) cc_final: 0.8619 (t80) REVERT: F 144 MET cc_start: 0.7998 (tpt) cc_final: 0.7264 (tpt) REVERT: H 65 PHE cc_start: 0.5657 (t80) cc_final: 0.5400 (t80) REVERT: H 141 PHE cc_start: 0.8910 (t80) cc_final: 0.8572 (t80) REVERT: H 144 MET cc_start: 0.7923 (tpt) cc_final: 0.7169 (tpt) outliers start: 20 outliers final: 2 residues processed: 381 average time/residue: 0.1290 time to fit residues: 81.7729 Evaluate side-chains 311 residues out of total 2804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 308 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 347 TYR Chi-restraints excluded: chain G residue 353 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 100 optimal weight: 7.9990 chunk 241 optimal weight: 10.0000 chunk 99 optimal weight: 0.8980 chunk 131 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 43 optimal weight: 0.3980 chunk 38 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 259 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 470 ASN ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 477 GLN ** E 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 470 ASN ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 470 ASN G 651 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.112679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.092420 restraints weight = 103474.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.093538 restraints weight = 69418.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.093639 restraints weight = 51178.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.093677 restraints weight = 49893.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.093741 restraints weight = 48176.431| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23524 Z= 0.130 Angle : 0.542 8.795 32100 Z= 0.285 Chirality : 0.039 0.132 3788 Planarity : 0.003 0.036 4076 Dihedral : 4.225 16.320 3328 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.22 % Allowed : 15.76 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.15), residues: 3088 helix: 0.73 (0.12), residues: 1860 sheet: -0.80 (0.37), residues: 200 loop : -0.93 (0.20), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 508 TYR 0.015 0.001 TYR C 55 PHE 0.021 0.001 PHE E 468 TRP 0.006 0.001 TRP G 517 HIS 0.004 0.001 HIS G 543 Details of bonding type rmsd covalent geometry : bond 0.00274 (23524) covalent geometry : angle 0.54230 (32100) hydrogen bonds : bond 0.03399 ( 1472) hydrogen bonds : angle 4.33471 ( 4236) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 325 time to evaluate : 0.899 Fit side-chains revert: symmetry clash REVERT: A 70 MET cc_start: 0.8190 (ptm) cc_final: 0.7971 (ptm) REVERT: A 510 MET cc_start: 0.8772 (mmm) cc_final: 0.8558 (tpt) REVERT: A 519 MET cc_start: 0.8182 (ttm) cc_final: 0.7824 (tmm) REVERT: B 123 GLU cc_start: 0.8373 (tp30) cc_final: 0.7873 (tm-30) REVERT: B 144 MET cc_start: 0.8023 (tpt) cc_final: 0.7459 (tpt) REVERT: C 70 MET cc_start: 0.8124 (ttm) cc_final: 0.7921 (ptm) REVERT: C 99 MET cc_start: 0.7266 (OUTLIER) cc_final: 0.7035 (mtp) REVERT: C 427 LEU cc_start: 0.9623 (tp) cc_final: 0.9413 (tp) REVERT: C 457 MET cc_start: 0.8699 (mtp) cc_final: 0.8320 (mtm) REVERT: C 468 PHE cc_start: 0.8661 (m-10) cc_final: 0.8279 (m-10) REVERT: C 510 MET cc_start: 0.8783 (mmm) cc_final: 0.8568 (tpt) REVERT: C 519 MET cc_start: 0.8250 (ttm) cc_final: 0.7837 (tmm) REVERT: E 99 MET cc_start: 0.7165 (OUTLIER) cc_final: 0.6918 (mtp) REVERT: E 510 MET cc_start: 0.8727 (mmm) cc_final: 0.8472 (tpt) REVERT: E 519 MET cc_start: 0.8252 (ttm) cc_final: 0.7859 (tmm) REVERT: G 463 LEU cc_start: 0.9162 (mt) cc_final: 0.8813 (mt) REVERT: G 464 TYR cc_start: 0.8577 (OUTLIER) cc_final: 0.7918 (t80) REVERT: G 468 PHE cc_start: 0.8394 (m-80) cc_final: 0.7562 (m-80) REVERT: D 123 GLU cc_start: 0.8400 (tp30) cc_final: 0.7948 (tm-30) REVERT: D 139 GLU cc_start: 0.8767 (mp0) cc_final: 0.8336 (pm20) REVERT: D 144 MET cc_start: 0.8050 (tpt) cc_final: 0.7517 (tpt) REVERT: F 65 PHE cc_start: 0.6048 (t80) cc_final: 0.5708 (t80) REVERT: F 119 GLU cc_start: 0.9073 (tm-30) cc_final: 0.8849 (tm-30) REVERT: F 141 PHE cc_start: 0.9057 (t80) cc_final: 0.8643 (t80) REVERT: F 144 MET cc_start: 0.8196 (tpt) cc_final: 0.7471 (tpt) REVERT: H 65 PHE cc_start: 0.5917 (t80) cc_final: 0.5683 (t80) REVERT: H 141 PHE cc_start: 0.9061 (t80) cc_final: 0.8734 (t80) REVERT: H 144 MET cc_start: 0.8177 (tpt) cc_final: 0.7370 (tpt) outliers start: 26 outliers final: 12 residues processed: 342 average time/residue: 0.1312 time to fit residues: 75.1715 Evaluate side-chains 306 residues out of total 2804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 291 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 347 TYR Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain E residue 99 MET Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 353 VAL Chi-restraints excluded: chain G residue 464 TYR Chi-restraints excluded: chain G residue 654 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 61 optimal weight: 10.0000 chunk 242 optimal weight: 5.9990 chunk 173 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 230 optimal weight: 9.9990 chunk 182 optimal weight: 2.9990 chunk 167 optimal weight: 0.7980 chunk 304 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 chunk 24 optimal weight: 6.9990 chunk 265 optimal weight: 4.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 486 HIS ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 673 ASN ** E 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 441 ASN ** 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 = 0.4017 r_free = 0.4017 target = 0.111714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.091385 restraints weight = 104457.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.092508 restraints weight = 71978.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.092500 restraints weight = 51519.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.092524 restraints weight = 52938.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.092687 restraints weight = 50305.060| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23524 Z= 0.150 Angle : 0.552 9.630 32100 Z= 0.289 Chirality : 0.040 0.148 3788 Planarity : 0.003 0.037 4076 Dihedral : 4.083 15.788 3328 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.41 % Allowed : 17.35 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.16), residues: 3088 helix: 1.16 (0.12), residues: 1864 sheet: -0.66 (0.37), residues: 200 loop : -0.75 (0.21), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 484 TYR 0.017 0.001 TYR C 464 PHE 0.024 0.001 PHE E 468 TRP 0.008 0.001 TRP G 517 HIS 0.005 0.001 HIS C 543 Details of bonding type rmsd covalent geometry : bond 0.00322 (23524) covalent geometry : angle 0.55224 (32100) hydrogen bonds : bond 0.03372 ( 1472) hydrogen bonds : angle 4.28956 ( 4236) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 314 time to evaluate : 0.773 Fit side-chains revert: symmetry clash REVERT: A 510 MET cc_start: 0.8794 (mmm) cc_final: 0.8588 (tpt) REVERT: A 519 MET cc_start: 0.8228 (ttm) cc_final: 0.7801 (tmm) REVERT: B 123 GLU cc_start: 0.8358 (tp30) cc_final: 0.7933 (tm-30) REVERT: B 144 MET cc_start: 0.8108 (tpt) cc_final: 0.7545 (tpp) REVERT: C 468 PHE cc_start: 0.8548 (m-10) cc_final: 0.8166 (m-10) REVERT: C 519 MET cc_start: 0.8202 (ttm) cc_final: 0.7792 (tmm) REVERT: C 534 LYS cc_start: 0.8775 (tppt) cc_final: 0.8551 (pttp) REVERT: E 70 MET cc_start: 0.8292 (ptm) cc_final: 0.8072 (ptm) REVERT: E 519 MET cc_start: 0.8285 (ttm) cc_final: 0.7869 (tmm) REVERT: G 464 TYR cc_start: 0.8616 (OUTLIER) cc_final: 0.8071 (t80) REVERT: G 468 PHE cc_start: 0.8500 (m-80) cc_final: 0.7790 (m-80) REVERT: G 534 LYS cc_start: 0.8658 (tppt) cc_final: 0.8415 (ptmt) REVERT: D 36 MET cc_start: 0.8674 (mmm) cc_final: 0.8443 (mpp) REVERT: D 123 GLU cc_start: 0.8329 (tp30) cc_final: 0.7907 (tm-30) REVERT: D 139 GLU cc_start: 0.8770 (mp0) cc_final: 0.8353 (pm20) REVERT: D 144 MET cc_start: 0.8104 (tpt) cc_final: 0.7591 (tpt) REVERT: F 65 PHE cc_start: 0.6053 (t80) cc_final: 0.5730 (t80) REVERT: F 119 GLU cc_start: 0.9097 (tm-30) cc_final: 0.8882 (tm-30) REVERT: F 141 PHE cc_start: 0.9058 (t80) cc_final: 0.8199 (t80) REVERT: F 144 MET cc_start: 0.8159 (tpt) cc_final: 0.7426 (tpt) REVERT: H 65 PHE cc_start: 0.5924 (t80) cc_final: 0.5678 (t80) REVERT: H 141 PHE cc_start: 0.9082 (t80) cc_final: 0.8767 (t80) REVERT: H 144 MET cc_start: 0.8081 (tpt) cc_final: 0.7411 (tpp) outliers start: 30 outliers final: 18 residues processed: 339 average time/residue: 0.1294 time to fit residues: 74.0965 Evaluate side-chains 314 residues out of total 2804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 295 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 347 TYR Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 513 ILE Chi-restraints excluded: chain E residue 644 VAL Chi-restraints excluded: chain G residue 99 MET Chi-restraints excluded: chain G residue 102 LYS Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 426 SER Chi-restraints excluded: chain G residue 464 TYR Chi-restraints excluded: chain G residue 644 VAL Chi-restraints excluded: chain G residue 654 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 183 optimal weight: 5.9990 chunk 150 optimal weight: 9.9990 chunk 174 optimal weight: 8.9990 chunk 309 optimal weight: 0.9990 chunk 284 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 chunk 122 optimal weight: 9.9990 chunk 108 optimal weight: 0.7980 chunk 180 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 245 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 470 ASN G 15 ASN ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 651 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.112386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.092098 restraints weight = 103457.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.093294 restraints weight = 74759.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.093589 restraints weight = 52274.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.093597 restraints weight = 50628.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.093711 restraints weight = 49084.918| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23524 Z= 0.128 Angle : 0.546 11.434 32100 Z= 0.282 Chirality : 0.040 0.193 3788 Planarity : 0.003 0.036 4076 Dihedral : 3.957 15.817 3328 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.64 % Allowed : 18.67 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.16), residues: 3088 helix: 1.42 (0.13), residues: 1860 sheet: -0.58 (0.38), residues: 200 loop : -0.65 (0.21), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 126 TYR 0.015 0.001 TYR C 464 PHE 0.030 0.001 PHE E 17 TRP 0.007 0.001 TRP C 517 HIS 0.004 0.001 HIS A 543 Details of bonding type rmsd covalent geometry : bond 0.00277 (23524) covalent geometry : angle 0.54635 (32100) hydrogen bonds : bond 0.03238 ( 1472) hydrogen bonds : angle 4.13007 ( 4236) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 321 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 510 MET cc_start: 0.8816 (mmm) cc_final: 0.8577 (tpt) REVERT: A 519 MET cc_start: 0.8272 (ttm) cc_final: 0.7804 (tmm) REVERT: A 534 LYS cc_start: 0.8767 (tppt) cc_final: 0.8518 (pttp) REVERT: B 123 GLU cc_start: 0.8280 (tp30) cc_final: 0.7860 (tm-30) REVERT: B 144 MET cc_start: 0.8067 (tpt) cc_final: 0.7634 (tpp) REVERT: C 70 MET cc_start: 0.8533 (ttm) cc_final: 0.7400 (ttt) REVERT: C 468 PHE cc_start: 0.8553 (m-10) cc_final: 0.8174 (m-10) REVERT: C 519 MET cc_start: 0.8282 (ttm) cc_final: 0.7853 (tmm) REVERT: C 534 LYS cc_start: 0.8740 (tppt) cc_final: 0.8516 (pttp) REVERT: E 519 MET cc_start: 0.8267 (ttm) cc_final: 0.7845 (tmm) REVERT: E 534 LYS cc_start: 0.8778 (tppt) cc_final: 0.8518 (pttp) REVERT: G 464 TYR cc_start: 0.8656 (OUTLIER) cc_final: 0.8140 (t80) REVERT: G 468 PHE cc_start: 0.8520 (m-80) cc_final: 0.7835 (m-80) REVERT: G 510 MET cc_start: 0.8735 (mmm) cc_final: 0.8500 (tpp) REVERT: D 123 GLU cc_start: 0.8314 (tp30) cc_final: 0.7913 (tm-30) REVERT: D 139 GLU cc_start: 0.8707 (mp0) cc_final: 0.8346 (pm20) REVERT: D 144 MET cc_start: 0.8143 (tpt) cc_final: 0.7629 (tpt) REVERT: F 65 PHE cc_start: 0.6059 (t80) cc_final: 0.5759 (t80) REVERT: F 119 GLU cc_start: 0.9148 (tm-30) cc_final: 0.8944 (tm-30) REVERT: F 141 PHE cc_start: 0.9059 (t80) cc_final: 0.8149 (t80) REVERT: F 144 MET cc_start: 0.8113 (tpt) cc_final: 0.7513 (tpt) REVERT: H 65 PHE cc_start: 0.5967 (t80) cc_final: 0.5717 (t80) REVERT: H 141 PHE cc_start: 0.9069 (t80) cc_final: 0.8660 (t80) REVERT: H 144 MET cc_start: 0.8102 (tpt) cc_final: 0.7457 (tpp) outliers start: 35 outliers final: 20 residues processed: 349 average time/residue: 0.1347 time to fit residues: 78.6381 Evaluate side-chains 323 residues out of total 2804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 302 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 347 TYR Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 691 GLU Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 470 ASN Chi-restraints excluded: chain E residue 644 VAL Chi-restraints excluded: chain E residue 691 GLU Chi-restraints excluded: chain G residue 99 MET Chi-restraints excluded: chain G residue 102 LYS Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 353 VAL Chi-restraints excluded: chain G residue 426 SER Chi-restraints excluded: chain G residue 464 TYR Chi-restraints excluded: chain G residue 644 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 37 optimal weight: 1.9990 chunk 168 optimal weight: 20.0000 chunk 35 optimal weight: 7.9990 chunk 92 optimal weight: 20.0000 chunk 198 optimal weight: 0.0030 chunk 187 optimal weight: 9.9990 chunk 226 optimal weight: 9.9990 chunk 64 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 174 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 overall best weight: 1.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 470 ASN ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 470 ASN ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 470 ASN G 545 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.111987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.091469 restraints weight = 104524.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.092945 restraints weight = 71984.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.093074 restraints weight = 51360.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.092993 restraints weight = 47427.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.093101 restraints weight = 49699.667| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23524 Z= 0.138 Angle : 0.565 12.247 32100 Z= 0.290 Chirality : 0.040 0.221 3788 Planarity : 0.003 0.032 4076 Dihedral : 3.930 15.653 3328 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.50 % Allowed : 20.68 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.16), residues: 3088 helix: 1.55 (0.13), residues: 1860 sheet: -0.50 (0.37), residues: 200 loop : -0.62 (0.21), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 126 TYR 0.013 0.001 TYR G 512 PHE 0.028 0.001 PHE C 17 TRP 0.008 0.001 TRP G 365 HIS 0.007 0.001 HIS E 364 Details of bonding type rmsd covalent geometry : bond 0.00302 (23524) covalent geometry : angle 0.56478 (32100) hydrogen bonds : bond 0.03216 ( 1472) hydrogen bonds : angle 4.09021 ( 4236) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 324 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 510 MET cc_start: 0.8682 (mmm) cc_final: 0.8402 (tpt) REVERT: B 123 GLU cc_start: 0.8222 (tp30) cc_final: 0.7825 (tm-30) REVERT: B 144 MET cc_start: 0.8040 (tpt) cc_final: 0.7625 (tpp) REVERT: C 70 MET cc_start: 0.8378 (ttm) cc_final: 0.7687 (ttm) REVERT: C 468 PHE cc_start: 0.8417 (m-10) cc_final: 0.8086 (m-10) REVERT: E 519 MET cc_start: 0.8189 (ttm) cc_final: 0.7792 (tmm) REVERT: G 464 TYR cc_start: 0.8481 (OUTLIER) cc_final: 0.8014 (t80) REVERT: G 468 PHE cc_start: 0.8421 (m-80) cc_final: 0.7757 (m-80) REVERT: D 139 GLU cc_start: 0.8592 (mp0) cc_final: 0.8283 (pm20) REVERT: D 144 MET cc_start: 0.8120 (tpt) cc_final: 0.7638 (tpt) REVERT: F 65 PHE cc_start: 0.6031 (t80) cc_final: 0.5739 (t80) REVERT: F 123 GLU cc_start: 0.8643 (mm-30) cc_final: 0.7943 (tm-30) REVERT: F 141 PHE cc_start: 0.9013 (t80) cc_final: 0.8134 (t80) REVERT: F 144 MET cc_start: 0.8101 (tpt) cc_final: 0.7516 (tpt) REVERT: H 65 PHE cc_start: 0.5969 (t80) cc_final: 0.5723 (t80) REVERT: H 141 PHE cc_start: 0.8975 (t80) cc_final: 0.8680 (t80) REVERT: H 144 MET cc_start: 0.7978 (tpt) cc_final: 0.7444 (tpp) outliers start: 32 outliers final: 30 residues processed: 346 average time/residue: 0.1284 time to fit residues: 74.3850 Evaluate side-chains 325 residues out of total 2804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 294 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 347 TYR Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 470 ASN Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 691 GLU Chi-restraints excluded: chain E residue 99 MET Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 451 ILE Chi-restraints excluded: chain E residue 456 ILE Chi-restraints excluded: chain E residue 470 ASN Chi-restraints excluded: chain E residue 644 VAL Chi-restraints excluded: chain E residue 691 GLU Chi-restraints excluded: chain G residue 99 MET Chi-restraints excluded: chain G residue 102 LYS Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 426 SER Chi-restraints excluded: chain G residue 456 ILE Chi-restraints excluded: chain G residue 464 TYR Chi-restraints excluded: chain G residue 470 ASN Chi-restraints excluded: chain G residue 644 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 292 optimal weight: 0.9990 chunk 247 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 218 optimal weight: 4.9990 chunk 311 optimal weight: 8.9990 chunk 281 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 203 optimal weight: 3.9990 chunk 234 optimal weight: 0.7980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 470 ASN C 15 ASN ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 470 ASN ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 470 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.112712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.094216 restraints weight = 103876.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.094275 restraints weight = 70462.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.094851 restraints weight = 52964.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.094944 restraints weight = 43460.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.094960 restraints weight = 43867.263| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23524 Z= 0.124 Angle : 0.578 12.823 32100 Z= 0.293 Chirality : 0.040 0.219 3788 Planarity : 0.003 0.031 4076 Dihedral : 3.877 15.739 3328 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.92 % Allowed : 21.67 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.16), residues: 3088 helix: 1.62 (0.13), residues: 1860 sheet: -0.43 (0.37), residues: 200 loop : -0.58 (0.21), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 126 TYR 0.012 0.001 TYR E 512 PHE 0.027 0.001 PHE G 17 TRP 0.009 0.001 TRP C 365 HIS 0.007 0.001 HIS E 364 Details of bonding type rmsd covalent geometry : bond 0.00271 (23524) covalent geometry : angle 0.57772 (32100) hydrogen bonds : bond 0.03199 ( 1472) hydrogen bonds : angle 4.07724 ( 4236) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 319 time to evaluate : 0.840 Fit side-chains revert: symmetry clash REVERT: B 123 GLU cc_start: 0.7979 (tp30) cc_final: 0.7549 (tm-30) REVERT: B 144 MET cc_start: 0.7725 (tpt) cc_final: 0.7461 (tpp) REVERT: C 468 PHE cc_start: 0.8436 (m-10) cc_final: 0.8091 (m-10) REVERT: G 464 TYR cc_start: 0.8405 (OUTLIER) cc_final: 0.7953 (t80) REVERT: G 468 PHE cc_start: 0.8394 (m-80) cc_final: 0.7788 (m-80) REVERT: D 123 GLU cc_start: 0.7936 (tm-30) cc_final: 0.7452 (tm-30) REVERT: D 144 MET cc_start: 0.7844 (tpt) cc_final: 0.7608 (tpp) REVERT: F 65 PHE cc_start: 0.5511 (t80) cc_final: 0.5278 (t80) REVERT: F 123 GLU cc_start: 0.8378 (mm-30) cc_final: 0.7932 (tm-30) REVERT: F 141 PHE cc_start: 0.8815 (t80) cc_final: 0.7958 (t80) REVERT: F 144 MET cc_start: 0.7761 (tpt) cc_final: 0.7318 (tpt) REVERT: H 141 PHE cc_start: 0.8780 (t80) cc_final: 0.8559 (t80) REVERT: H 144 MET cc_start: 0.7749 (tpt) cc_final: 0.7341 (tpp) outliers start: 41 outliers final: 29 residues processed: 351 average time/residue: 0.1318 time to fit residues: 77.2301 Evaluate side-chains 330 residues out of total 2804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 300 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 347 TYR Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 470 ASN Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 588 VAL Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 691 GLU Chi-restraints excluded: chain E residue 99 MET Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 456 ILE Chi-restraints excluded: chain E residue 470 ASN Chi-restraints excluded: chain E residue 588 VAL Chi-restraints excluded: chain E residue 644 VAL Chi-restraints excluded: chain E residue 691 GLU Chi-restraints excluded: chain G residue 99 MET Chi-restraints excluded: chain G residue 102 LYS Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 426 SER Chi-restraints excluded: chain G residue 456 ILE Chi-restraints excluded: chain G residue 464 TYR Chi-restraints excluded: chain G residue 470 ASN Chi-restraints excluded: chain G residue 644 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 32 optimal weight: 10.0000 chunk 139 optimal weight: 9.9990 chunk 76 optimal weight: 8.9990 chunk 181 optimal weight: 0.6980 chunk 279 optimal weight: 8.9990 chunk 178 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 10 optimal weight: 20.0000 chunk 211 optimal weight: 8.9990 chunk 192 optimal weight: 2.9990 chunk 297 optimal weight: 9.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 486 HIS C 545 ASN ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 486 HIS E 545 ASN ** G 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 486 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.108208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.088680 restraints weight = 104759.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.088874 restraints weight = 73774.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.088869 restraints weight = 63722.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.089176 restraints weight = 57128.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.089237 restraints weight = 54214.592| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 23524 Z= 0.276 Angle : 0.707 13.473 32100 Z= 0.369 Chirality : 0.044 0.271 3788 Planarity : 0.004 0.032 4076 Dihedral : 4.305 17.151 3328 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.88 % Allowed : 22.37 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.16), residues: 3088 helix: 1.31 (0.12), residues: 1864 sheet: -0.63 (0.37), residues: 196 loop : -0.72 (0.21), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 126 TYR 0.020 0.002 TYR G 237 PHE 0.026 0.002 PHE A 468 TRP 0.016 0.002 TRP E 517 HIS 0.009 0.002 HIS E 543 Details of bonding type rmsd covalent geometry : bond 0.00594 (23524) covalent geometry : angle 0.70723 (32100) hydrogen bonds : bond 0.03948 ( 1472) hydrogen bonds : angle 4.55404 ( 4236) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 311 time to evaluate : 0.622 Fit side-chains revert: symmetry clash REVERT: B 123 GLU cc_start: 0.8344 (tp30) cc_final: 0.7981 (tm-30) REVERT: B 144 MET cc_start: 0.8082 (tpt) cc_final: 0.7625 (tpp) REVERT: C 468 PHE cc_start: 0.8540 (m-10) cc_final: 0.8302 (m-10) REVERT: E 70 MET cc_start: 0.8007 (ptm) cc_final: 0.7737 (ppp) REVERT: D 123 GLU cc_start: 0.8139 (tm-30) cc_final: 0.7668 (tm-30) REVERT: D 144 MET cc_start: 0.8184 (tpt) cc_final: 0.7565 (tpt) REVERT: F 65 PHE cc_start: 0.6126 (t80) cc_final: 0.5870 (t80) REVERT: F 144 MET cc_start: 0.8091 (tpt) cc_final: 0.7466 (tpt) REVERT: H 119 GLU cc_start: 0.9082 (tm-30) cc_final: 0.8876 (tm-30) REVERT: H 126 ARG cc_start: 0.8248 (mmm160) cc_final: 0.8023 (mtp180) REVERT: H 144 MET cc_start: 0.8010 (tpt) cc_final: 0.7448 (tpp) outliers start: 40 outliers final: 37 residues processed: 339 average time/residue: 0.1326 time to fit residues: 74.8101 Evaluate side-chains 323 residues out of total 2804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 286 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 347 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain C residue 588 VAL Chi-restraints excluded: chain C residue 654 LEU Chi-restraints excluded: chain C residue 691 GLU Chi-restraints excluded: chain E residue 99 MET Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 451 ILE Chi-restraints excluded: chain E residue 456 ILE Chi-restraints excluded: chain E residue 462 LEU Chi-restraints excluded: chain E residue 588 VAL Chi-restraints excluded: chain E residue 654 LEU Chi-restraints excluded: chain E residue 691 GLU Chi-restraints excluded: chain G residue 99 MET Chi-restraints excluded: chain G residue 102 LYS Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 426 SER Chi-restraints excluded: chain G residue 430 THR Chi-restraints excluded: chain G residue 451 ILE Chi-restraints excluded: chain G residue 456 ILE Chi-restraints excluded: chain G residue 644 VAL Chi-restraints excluded: chain G residue 654 LEU Chi-restraints excluded: chain G residue 674 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 56 optimal weight: 6.9990 chunk 181 optimal weight: 0.8980 chunk 28 optimal weight: 0.3980 chunk 307 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 157 optimal weight: 10.0000 chunk 264 optimal weight: 9.9990 chunk 150 optimal weight: 10.0000 chunk 166 optimal weight: 8.9990 chunk 220 optimal weight: 0.7980 chunk 149 optimal weight: 0.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 583 HIS ** C 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 583 HIS E 15 ASN ** E 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 583 HIS ** G 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 583 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.102150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.079769 restraints weight = 89063.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.081143 restraints weight = 54608.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.082022 restraints weight = 40562.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.082491 restraints weight = 34343.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.082625 restraints weight = 31239.840| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 23524 Z= 0.135 Angle : 0.628 13.203 32100 Z= 0.320 Chirality : 0.042 0.284 3788 Planarity : 0.003 0.031 4076 Dihedral : 4.047 16.932 3328 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.64 % Allowed : 23.73 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.16), residues: 3088 helix: 1.53 (0.13), residues: 1860 sheet: -0.59 (0.37), residues: 200 loop : -0.62 (0.21), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 126 TYR 0.017 0.001 TYR G 464 PHE 0.022 0.001 PHE C 17 TRP 0.015 0.001 TRP A 365 HIS 0.006 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00302 (23524) covalent geometry : angle 0.62789 (32100) hydrogen bonds : bond 0.03300 ( 1472) hydrogen bonds : angle 4.25736 ( 4236) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 307 time to evaluate : 0.897 Fit side-chains revert: symmetry clash REVERT: B 123 GLU cc_start: 0.7860 (tp30) cc_final: 0.7429 (tm-30) REVERT: B 126 ARG cc_start: 0.8038 (mmm160) cc_final: 0.7774 (tpt-90) REVERT: B 144 MET cc_start: 0.7813 (tpt) cc_final: 0.7517 (tpp) REVERT: C 468 PHE cc_start: 0.8490 (m-10) cc_final: 0.7709 (m-10) REVERT: E 468 PHE cc_start: 0.8505 (m-10) cc_final: 0.8282 (m-10) REVERT: D 36 MET cc_start: 0.8045 (mtm) cc_final: 0.7820 (mtm) REVERT: D 123 GLU cc_start: 0.7903 (tm-30) cc_final: 0.7469 (tm-30) REVERT: D 144 MET cc_start: 0.7848 (tpt) cc_final: 0.7457 (tpp) REVERT: F 65 PHE cc_start: 0.5753 (t80) cc_final: 0.5537 (t80) REVERT: F 123 GLU cc_start: 0.8272 (mm-30) cc_final: 0.7805 (tm-30) REVERT: F 144 MET cc_start: 0.7819 (tpt) cc_final: 0.7283 (tpt) REVERT: H 141 PHE cc_start: 0.8811 (t80) cc_final: 0.8561 (t80) REVERT: H 144 MET cc_start: 0.7849 (tpt) cc_final: 0.7328 (tpt) outliers start: 35 outliers final: 30 residues processed: 333 average time/residue: 0.1298 time to fit residues: 72.3779 Evaluate side-chains 324 residues out of total 2804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 294 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 347 TYR Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 588 VAL Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 654 LEU Chi-restraints excluded: chain C residue 691 GLU Chi-restraints excluded: chain E residue 99 MET Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain E residue 456 ILE Chi-restraints excluded: chain E residue 588 VAL Chi-restraints excluded: chain E residue 644 VAL Chi-restraints excluded: chain E residue 654 LEU Chi-restraints excluded: chain E residue 691 GLU Chi-restraints excluded: chain G residue 99 MET Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 426 SER Chi-restraints excluded: chain G residue 456 ILE Chi-restraints excluded: chain G residue 644 VAL Chi-restraints excluded: chain G residue 654 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 0.0980 chunk 212 optimal weight: 0.7980 chunk 242 optimal weight: 2.9990 chunk 67 optimal weight: 9.9990 chunk 261 optimal weight: 0.9980 chunk 148 optimal weight: 1.9990 chunk 228 optimal weight: 7.9990 chunk 231 optimal weight: 1.9990 chunk 135 optimal weight: 0.8980 chunk 200 optimal weight: 0.6980 chunk 24 optimal weight: 10.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 583 HIS C 364 HIS ** C 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 583 HIS ** E 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 583 HIS ** G 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 583 HIS D 137 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.103651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.081026 restraints weight = 89991.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.082823 restraints weight = 57577.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.082877 restraints weight = 40128.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.083268 restraints weight = 38072.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.083283 restraints weight = 36024.858| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 23524 Z= 0.118 Angle : 0.605 13.159 32100 Z= 0.308 Chirality : 0.042 0.289 3788 Planarity : 0.003 0.031 4076 Dihedral : 3.862 16.913 3328 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.45 % Allowed : 24.11 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.16), residues: 3088 helix: 1.68 (0.13), residues: 1860 sheet: -0.31 (0.38), residues: 196 loop : -0.61 (0.21), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 126 TYR 0.016 0.001 TYR G 464 PHE 0.015 0.001 PHE G 468 TRP 0.019 0.001 TRP G 365 HIS 0.007 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00262 (23524) covalent geometry : angle 0.60516 (32100) hydrogen bonds : bond 0.03157 ( 1472) hydrogen bonds : angle 4.13623 ( 4236) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 330 time to evaluate : 0.870 Fit side-chains revert: symmetry clash REVERT: B 123 GLU cc_start: 0.7929 (tp30) cc_final: 0.7603 (tm-30) REVERT: B 126 ARG cc_start: 0.8112 (mmm160) cc_final: 0.7901 (mtp180) REVERT: B 144 MET cc_start: 0.8014 (tpt) cc_final: 0.7637 (tpp) REVERT: C 99 MET cc_start: 0.7376 (ttt) cc_final: 0.6746 (ttt) REVERT: C 457 MET cc_start: 0.8826 (mtp) cc_final: 0.8552 (mtm) REVERT: C 468 PHE cc_start: 0.8428 (m-10) cc_final: 0.7718 (m-10) REVERT: D 36 MET cc_start: 0.7958 (mtm) cc_final: 0.7690 (mtm) REVERT: D 123 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7545 (tm-30) REVERT: D 144 MET cc_start: 0.8015 (tpt) cc_final: 0.7599 (tpp) REVERT: F 123 GLU cc_start: 0.8407 (mm-30) cc_final: 0.7803 (tm-30) REVERT: F 141 PHE cc_start: 0.8783 (t80) cc_final: 0.8576 (t80) REVERT: F 144 MET cc_start: 0.7917 (tpt) cc_final: 0.7605 (tpp) REVERT: F 145 MET cc_start: 0.7070 (mmm) cc_final: 0.5772 (tpt) REVERT: H 144 MET cc_start: 0.7961 (tpt) cc_final: 0.7554 (tpp) outliers start: 31 outliers final: 24 residues processed: 352 average time/residue: 0.1328 time to fit residues: 77.8399 Evaluate side-chains 324 residues out of total 2804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 300 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 347 TYR Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 588 VAL Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 691 GLU Chi-restraints excluded: chain E residue 99 MET Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 456 ILE Chi-restraints excluded: chain E residue 588 VAL Chi-restraints excluded: chain E residue 644 VAL Chi-restraints excluded: chain E residue 691 GLU Chi-restraints excluded: chain G residue 99 MET Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 456 ILE Chi-restraints excluded: chain G residue 644 VAL Chi-restraints excluded: chain G residue 654 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 184 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 212 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 232 optimal weight: 20.0000 chunk 76 optimal weight: 10.0000 chunk 66 optimal weight: 20.0000 chunk 79 optimal weight: 7.9990 chunk 30 optimal weight: 0.5980 chunk 80 optimal weight: 5.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 583 HIS ** C 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 583 HIS ** E 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 583 HIS ** G 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 583 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.111231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.092329 restraints weight = 104441.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.092710 restraints weight = 74198.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.092907 restraints weight = 53899.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.093078 restraints weight = 52153.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.093244 restraints weight = 51306.425| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 23524 Z= 0.163 Angle : 0.657 14.460 32100 Z= 0.333 Chirality : 0.043 0.320 3788 Planarity : 0.003 0.060 4076 Dihedral : 3.956 18.043 3328 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.74 % Allowed : 24.72 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.16), residues: 3088 helix: 1.67 (0.13), residues: 1856 sheet: -0.40 (0.37), residues: 196 loop : -0.53 (0.21), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 484 TYR 0.013 0.001 TYR A 71 PHE 0.016 0.001 PHE E 429 TRP 0.021 0.001 TRP G 365 HIS 0.009 0.001 HIS C 364 Details of bonding type rmsd covalent geometry : bond 0.00366 (23524) covalent geometry : angle 0.65662 (32100) hydrogen bonds : bond 0.03325 ( 1472) hydrogen bonds : angle 4.18213 ( 4236) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3671.16 seconds wall clock time: 64 minutes 9.75 seconds (3849.75 seconds total)