Starting phenix.real_space_refine on Sun Jul 5 21:36:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8bdc_15981/07_2026/8bdc_15981.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bdc_15981/07_2026/8bdc_15981.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8bdc_15981/07_2026/8bdc_15981.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8bdc_15981/07_2026/8bdc_15981.cif" model { file = "/net/cci-nas-00/data/ceres_data/8bdc_15981/07_2026/8bdc_15981.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bdc_15981/07_2026/8bdc_15981.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8bdc_15981/07_2026/8bdc_15981.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bdc_15981/07_2026/8bdc_15981.map" } resolution = 2.65 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= 0.007 sd= 0.075 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: 6 Type Number sf(0) Gaussians P 4 5.49 5 S 136 5.16 5 Na 8 4.78 5 C 19852 2.51 5 N 4928 2.21 5 O 5204 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30132 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 963, 7412 Classifications: {'peptide': 963} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 126} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 938} Chain breaks: 8 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 480 Unresolved non-hydrogen angles: 583 Unresolved non-hydrogen dihedrals: 396 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'ASN:plan1': 8, 'ASP:plan': 14, 'GLU:plan': 26, 'GLN:plan1': 8, 'HIS:plan': 2, 'TYR:plan': 1, 'PHE:plan': 2, 'ARG:plan': 11, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 295 Chain: "A" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 121 Unusual residues: {' NA': 2, 'POV': 1, 'UND': 1, 'Y01': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: B, C, D Time building chain proxies: 9.38, per 1000 atoms: 0.31 Number of scatterers: 30132 At special positions: 0 Unit cell: (159.9, 159.9, 145.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 136 16.00 P 4 15.00 Na 8 11.00 O 5204 8.00 N 4928 7.00 C 19852 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 68 " distance=2.04 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 68 " distance=2.04 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 68 " distance=2.04 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 68 " distance=2.04 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: 2.69 Conformation dependent library (CDL) restraints added in 1.4 seconds 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7328 Finding SS restraints... Secondary structure from input PDB file: 188 helices and 12 sheets defined 69.5% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 41 through 49 Processing helix chain 'A' and resid 125 through 135 removed outlier: 3.652A pdb=" N LEU A 129 " --> pdb=" O ASP A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 176 Processing helix chain 'A' and resid 187 through 203 Processing helix chain 'A' and resid 218 through 220 No H-bonds generated for 'chain 'A' and resid 218 through 220' Processing helix chain 'A' and resid 274 through 288 Processing helix chain 'A' and resid 309 through 322 Processing helix chain 'A' and resid 333 through 345 removed outlier: 3.518A pdb=" N ASP A 337 " --> pdb=" O GLY A 333 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL A 338 " --> pdb=" O GLN A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 362 removed outlier: 3.547A pdb=" N VAL A 354 " --> pdb=" O THR A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 369 Processing helix chain 'A' and resid 370 through 387 removed outlier: 3.879A pdb=" N CYS A 387 " --> pdb=" O GLU A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 418 Processing helix chain 'A' and resid 419 through 424 removed outlier: 3.640A pdb=" N LYS A 423 " --> pdb=" O GLU A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 436 Processing helix chain 'A' and resid 438 through 445 Processing helix chain 'A' and resid 454 through 457 Processing helix chain 'A' and resid 458 through 468 Processing helix chain 'A' and resid 470 through 480 Processing helix chain 'A' and resid 483 through 488 Processing helix chain 'A' and resid 489 through 499 Processing helix chain 'A' and resid 502 through 516 Processing helix chain 'A' and resid 518 through 533 Processing helix chain 'A' and resid 559 through 571 removed outlier: 3.757A pdb=" N GLN A 571 " --> pdb=" O TRP A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 582 Processing helix chain 'A' and resid 586 through 602 Processing helix chain 'A' and resid 607 through 636 Processing helix chain 'A' and resid 637 through 645 Processing helix chain 'A' and resid 648 through 652 removed outlier: 3.815A pdb=" N TRP A 651 " --> pdb=" O CYS A 648 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY A 652 " --> pdb=" O GLU A 649 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 648 through 652' Processing helix chain 'A' and resid 655 through 663 Processing helix chain 'A' and resid 665 through 670 Processing helix chain 'A' and resid 671 through 684 Processing helix chain 'A' and resid 691 through 701 Processing helix chain 'A' and resid 702 through 708 removed outlier: 3.776A pdb=" N GLY A 708 " --> pdb=" O VAL A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 732 Processing helix chain 'A' and resid 733 through 759 Processing helix chain 'A' and resid 765 through 790 Processing helix chain 'A' and resid 791 through 794 removed outlier: 3.574A pdb=" N PHE A 794 " --> pdb=" O VAL A 791 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 791 through 794' Processing helix chain 'A' and resid 798 through 818 removed outlier: 3.638A pdb=" N HIS A 818 " --> pdb=" O VAL A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 852 Processing helix chain 'A' and resid 856 through 889 removed outlier: 3.532A pdb=" N ILE A 865 " --> pdb=" O GLN A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 912 Proline residue: A 907 - end of helix Processing helix chain 'A' and resid 955 through 980 Processing helix chain 'A' and resid 981 through 983 No H-bonds generated for 'chain 'A' and resid 981 through 983' Processing helix chain 'A' and resid 991 through 1007 Processing helix chain 'A' and resid 1015 through 1030 removed outlier: 3.951A pdb=" N ALA A1019 " --> pdb=" O PHE A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1072 Processing helix chain 'A' and resid 1078 through 1104 Processing helix chain 'B' and resid 42 through 49 Processing helix chain 'B' and resid 125 through 135 removed outlier: 3.651A pdb=" N LEU B 129 " --> pdb=" O ASP B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 176 Processing helix chain 'B' and resid 187 through 203 Processing helix chain 'B' and resid 218 through 220 No H-bonds generated for 'chain 'B' and resid 218 through 220' Processing helix chain 'B' and resid 274 through 288 Processing helix chain 'B' and resid 309 through 322 Processing helix chain 'B' and resid 333 through 345 removed outlier: 3.518A pdb=" N ASP B 337 " --> pdb=" O GLY B 333 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL B 338 " --> pdb=" O GLN B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 362 removed outlier: 3.547A pdb=" N VAL B 354 " --> pdb=" O THR B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 369 Processing helix chain 'B' and resid 370 through 387 removed outlier: 3.879A pdb=" N CYS B 387 " --> pdb=" O GLU B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 418 Processing helix chain 'B' and resid 419 through 424 removed outlier: 3.639A pdb=" N LYS B 423 " --> pdb=" O GLU B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 436 Processing helix chain 'B' and resid 438 through 445 Processing helix chain 'B' and resid 454 through 457 Processing helix chain 'B' and resid 458 through 468 Processing helix chain 'B' and resid 470 through 480 Processing helix chain 'B' and resid 483 through 488 Processing helix chain 'B' and resid 489 through 499 Processing helix chain 'B' and resid 502 through 516 Processing helix chain 'B' and resid 518 through 533 Processing helix chain 'B' and resid 559 through 571 removed outlier: 3.757A pdb=" N GLN B 571 " --> pdb=" O TRP B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 582 Processing helix chain 'B' and resid 586 through 602 Processing helix chain 'B' and resid 607 through 636 Processing helix chain 'B' and resid 637 through 645 Processing helix chain 'B' and resid 648 through 652 removed outlier: 3.815A pdb=" N TRP B 651 " --> pdb=" O CYS B 648 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY B 652 " --> pdb=" O GLU B 649 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 648 through 652' Processing helix chain 'B' and resid 655 through 663 Processing helix chain 'B' and resid 665 through 670 Processing helix chain 'B' and resid 671 through 684 Processing helix chain 'B' and resid 691 through 701 Processing helix chain 'B' and resid 702 through 708 removed outlier: 3.776A pdb=" N GLY B 708 " --> pdb=" O VAL B 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 732 Processing helix chain 'B' and resid 733 through 759 Processing helix chain 'B' and resid 765 through 790 Processing helix chain 'B' and resid 791 through 794 removed outlier: 3.574A pdb=" N PHE B 794 " --> pdb=" O VAL B 791 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 791 through 794' Processing helix chain 'B' and resid 798 through 818 removed outlier: 3.638A pdb=" N HIS B 818 " --> pdb=" O VAL B 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 852 Processing helix chain 'B' and resid 856 through 889 removed outlier: 3.531A pdb=" N ILE B 865 " --> pdb=" O GLN B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 896 through 912 Proline residue: B 907 - end of helix Processing helix chain 'B' and resid 955 through 980 Processing helix chain 'B' and resid 981 through 983 No H-bonds generated for 'chain 'B' and resid 981 through 983' Processing helix chain 'B' and resid 991 through 1007 Processing helix chain 'B' and resid 1015 through 1030 removed outlier: 3.951A pdb=" N ALA B1019 " --> pdb=" O PHE B1015 " (cutoff:3.500A) Processing helix chain 'B' and resid 1050 through 1072 Processing helix chain 'B' and resid 1078 through 1104 Processing helix chain 'C' and resid 42 through 49 Processing helix chain 'C' and resid 125 through 135 removed outlier: 3.652A pdb=" N LEU C 129 " --> pdb=" O ASP C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 176 Processing helix chain 'C' and resid 187 through 203 Processing helix chain 'C' and resid 218 through 220 No H-bonds generated for 'chain 'C' and resid 218 through 220' Processing helix chain 'C' and resid 274 through 288 Processing helix chain 'C' and resid 309 through 322 Processing helix chain 'C' and resid 333 through 345 removed outlier: 3.518A pdb=" N ASP C 337 " --> pdb=" O GLY C 333 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL C 338 " --> pdb=" O GLN C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 362 removed outlier: 3.548A pdb=" N VAL C 354 " --> pdb=" O THR C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 369 Processing helix chain 'C' and resid 370 through 387 removed outlier: 3.879A pdb=" N CYS C 387 " --> pdb=" O GLU C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 418 Processing helix chain 'C' and resid 419 through 424 removed outlier: 3.640A pdb=" N LYS C 423 " --> pdb=" O GLU C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 436 Processing helix chain 'C' and resid 438 through 445 Processing helix chain 'C' and resid 454 through 457 Processing helix chain 'C' and resid 458 through 468 Processing helix chain 'C' and resid 470 through 480 Processing helix chain 'C' and resid 483 through 488 Processing helix chain 'C' and resid 489 through 499 Processing helix chain 'C' and resid 502 through 516 Processing helix chain 'C' and resid 518 through 533 Processing helix chain 'C' and resid 559 through 571 removed outlier: 3.757A pdb=" N GLN C 571 " --> pdb=" O TRP C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 582 Processing helix chain 'C' and resid 586 through 602 Processing helix chain 'C' and resid 607 through 636 Processing helix chain 'C' and resid 637 through 645 Processing helix chain 'C' and resid 648 through 652 removed outlier: 3.814A pdb=" N TRP C 651 " --> pdb=" O CYS C 648 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY C 652 " --> pdb=" O GLU C 649 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 648 through 652' Processing helix chain 'C' and resid 655 through 663 Processing helix chain 'C' and resid 665 through 670 Processing helix chain 'C' and resid 671 through 684 Processing helix chain 'C' and resid 691 through 701 Processing helix chain 'C' and resid 702 through 708 removed outlier: 3.776A pdb=" N GLY C 708 " --> pdb=" O VAL C 705 " (cutoff:3.500A) Processing helix chain 'C' and resid 724 through 732 Processing helix chain 'C' and resid 733 through 759 Processing helix chain 'C' and resid 765 through 790 Processing helix chain 'C' and resid 791 through 794 removed outlier: 3.574A pdb=" N PHE C 794 " --> pdb=" O VAL C 791 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 791 through 794' Processing helix chain 'C' and resid 798 through 818 removed outlier: 3.638A pdb=" N HIS C 818 " --> pdb=" O VAL C 814 " (cutoff:3.500A) Processing helix chain 'C' and resid 821 through 852 Processing helix chain 'C' and resid 856 through 889 removed outlier: 3.530A pdb=" N ILE C 865 " --> pdb=" O GLN C 861 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 912 Proline residue: C 907 - end of helix Processing helix chain 'C' and resid 955 through 980 Processing helix chain 'C' and resid 981 through 983 No H-bonds generated for 'chain 'C' and resid 981 through 983' Processing helix chain 'C' and resid 991 through 1007 Processing helix chain 'C' and resid 1015 through 1030 removed outlier: 3.951A pdb=" N ALA C1019 " --> pdb=" O PHE C1015 " (cutoff:3.500A) Processing helix chain 'C' and resid 1050 through 1072 Processing helix chain 'C' and resid 1078 through 1104 Processing helix chain 'D' and resid 42 through 49 Processing helix chain 'D' and resid 125 through 135 removed outlier: 3.650A pdb=" N LEU D 129 " --> pdb=" O ASP D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 176 Processing helix chain 'D' and resid 187 through 203 Processing helix chain 'D' and resid 218 through 220 No H-bonds generated for 'chain 'D' and resid 218 through 220' Processing helix chain 'D' and resid 274 through 288 Processing helix chain 'D' and resid 309 through 322 Processing helix chain 'D' and resid 333 through 345 removed outlier: 3.518A pdb=" N ASP D 337 " --> pdb=" O GLY D 333 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL D 338 " --> pdb=" O GLN D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 362 removed outlier: 3.548A pdb=" N VAL D 354 " --> pdb=" O THR D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 369 Processing helix chain 'D' and resid 370 through 387 removed outlier: 3.878A pdb=" N CYS D 387 " --> pdb=" O GLU D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 418 Processing helix chain 'D' and resid 419 through 424 removed outlier: 3.640A pdb=" N LYS D 423 " --> pdb=" O GLU D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 436 Processing helix chain 'D' and resid 438 through 445 Processing helix chain 'D' and resid 454 through 457 Processing helix chain 'D' and resid 458 through 468 Processing helix chain 'D' and resid 470 through 480 Processing helix chain 'D' and resid 483 through 488 Processing helix chain 'D' and resid 489 through 499 Processing helix chain 'D' and resid 502 through 516 Processing helix chain 'D' and resid 518 through 533 Processing helix chain 'D' and resid 559 through 571 removed outlier: 3.757A pdb=" N GLN D 571 " --> pdb=" O TRP D 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 582 Processing helix chain 'D' and resid 586 through 602 Processing helix chain 'D' and resid 607 through 636 Processing helix chain 'D' and resid 637 through 645 Processing helix chain 'D' and resid 648 through 652 removed outlier: 3.815A pdb=" N TRP D 651 " --> pdb=" O CYS D 648 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY D 652 " --> pdb=" O GLU D 649 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 648 through 652' Processing helix chain 'D' and resid 655 through 663 Processing helix chain 'D' and resid 665 through 670 Processing helix chain 'D' and resid 671 through 684 Processing helix chain 'D' and resid 691 through 701 Processing helix chain 'D' and resid 702 through 708 removed outlier: 3.775A pdb=" N GLY D 708 " --> pdb=" O VAL D 705 " (cutoff:3.500A) Processing helix chain 'D' and resid 724 through 732 Processing helix chain 'D' and resid 733 through 759 Processing helix chain 'D' and resid 765 through 790 Processing helix chain 'D' and resid 791 through 794 removed outlier: 3.575A pdb=" N PHE D 794 " --> pdb=" O VAL D 791 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 791 through 794' Processing helix chain 'D' and resid 798 through 818 removed outlier: 3.638A pdb=" N HIS D 818 " --> pdb=" O VAL D 814 " (cutoff:3.500A) Processing helix chain 'D' and resid 821 through 852 Processing helix chain 'D' and resid 856 through 889 removed outlier: 3.532A pdb=" N ILE D 865 " --> pdb=" O GLN D 861 " (cutoff:3.500A) Processing helix chain 'D' and resid 896 through 912 Proline residue: D 907 - end of helix Processing helix chain 'D' and resid 955 through 980 Processing helix chain 'D' and resid 981 through 983 No H-bonds generated for 'chain 'D' and resid 981 through 983' Processing helix chain 'D' and resid 991 through 1007 Processing helix chain 'D' and resid 1015 through 1030 removed outlier: 3.951A pdb=" N ALA D1019 " --> pdb=" O PHE D1015 " (cutoff:3.500A) Processing helix chain 'D' and resid 1050 through 1072 Processing helix chain 'D' and resid 1078 through 1104 Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 54 removed outlier: 3.650A pdb=" N LYS A 96 " --> pdb=" O GLU A 53 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 57 Processing sheet with id=AA3, first strand: chain 'A' and resid 237 through 239 removed outlier: 6.763A pdb=" N LYS A 116 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N LEU A 262 " --> pdb=" O LYS A 116 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE A 118 " --> pdb=" O LEU A 262 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ASP A 264 " --> pdb=" O ILE A 118 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N LEU A 120 " --> pdb=" O ASP A 264 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ILE A 179 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE A 214 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N THR A 181 " --> pdb=" O ILE A 214 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N ALA A 216 " --> pdb=" O THR A 181 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE A 146 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLN A 306 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N VAL A 327 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N CYS A 303 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N VAL A 329 " --> pdb=" O CYS A 303 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N ALA A 305 " --> pdb=" O VAL A 329 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 50 through 54 removed outlier: 3.649A pdb=" N LYS B 96 " --> pdb=" O GLU B 53 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 56 through 57 Processing sheet with id=AA6, first strand: chain 'B' and resid 237 through 239 removed outlier: 6.763A pdb=" N LYS B 116 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N LEU B 262 " --> pdb=" O LYS B 116 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ILE B 118 " --> pdb=" O LEU B 262 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ASP B 264 " --> pdb=" O ILE B 118 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N LEU B 120 " --> pdb=" O ASP B 264 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ILE B 179 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE B 214 " --> pdb=" O ILE B 179 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N THR B 181 " --> pdb=" O ILE B 214 " (cutoff:3.500A) removed outlier: 8.463A pdb=" N ALA B 216 " --> pdb=" O THR B 181 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE B 146 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLN B 306 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N VAL B 327 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N CYS B 303 " --> pdb=" O VAL B 327 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N VAL B 329 " --> pdb=" O CYS B 303 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N ALA B 305 " --> pdb=" O VAL B 329 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 50 through 54 removed outlier: 3.650A pdb=" N LYS C 96 " --> pdb=" O GLU C 53 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 56 through 57 Processing sheet with id=AA9, first strand: chain 'C' and resid 237 through 239 removed outlier: 6.762A pdb=" N LYS C 116 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N LEU C 262 " --> pdb=" O LYS C 116 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ILE C 118 " --> pdb=" O LEU C 262 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ASP C 264 " --> pdb=" O ILE C 118 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N LEU C 120 " --> pdb=" O ASP C 264 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ILE C 179 " --> pdb=" O ILE C 212 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE C 214 " --> pdb=" O ILE C 179 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N THR C 181 " --> pdb=" O ILE C 214 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N ALA C 216 " --> pdb=" O THR C 181 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE C 146 " --> pdb=" O LEU C 180 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLN C 306 " --> pdb=" O THR C 149 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N VAL C 327 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N CYS C 303 " --> pdb=" O VAL C 327 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N VAL C 329 " --> pdb=" O CYS C 303 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N ALA C 305 " --> pdb=" O VAL C 329 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 50 through 54 removed outlier: 3.649A pdb=" N LYS D 96 " --> pdb=" O GLU D 53 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 56 through 57 Processing sheet with id=AB3, first strand: chain 'D' and resid 237 through 239 removed outlier: 6.762A pdb=" N LYS D 116 " --> pdb=" O LEU D 260 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N LEU D 262 " --> pdb=" O LYS D 116 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE D 118 " --> pdb=" O LEU D 262 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ASP D 264 " --> pdb=" O ILE D 118 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N LEU D 120 " --> pdb=" O ASP D 264 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ILE D 179 " --> pdb=" O ILE D 212 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE D 214 " --> pdb=" O ILE D 179 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N THR D 181 " --> pdb=" O ILE D 214 " (cutoff:3.500A) removed outlier: 8.463A pdb=" N ALA D 216 " --> pdb=" O THR D 181 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE D 146 " --> pdb=" O LEU D 180 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLN D 306 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N VAL D 327 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N CYS D 303 " --> pdb=" O VAL D 327 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N VAL D 329 " --> pdb=" O CYS D 303 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N ALA D 305 " --> pdb=" O VAL D 329 " (cutoff:3.500A) 1965 hydrogen bonds defined for protein. 5811 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.80 Time building geometry restraints manager: 3.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5111 1.33 - 1.45: 8429 1.45 - 1.58: 17108 1.58 - 1.70: 8 1.70 - 1.83: 200 Bond restraints: 30856 Sorted by residual: bond pdb=" CAX Y01 C1203 " pdb=" OAH Y01 C1203 " ideal model delta sigma weight residual 1.248 1.308 -0.060 2.00e-02 2.50e+03 9.06e+00 bond pdb=" CAX Y01 A1201 " pdb=" OAH Y01 A1201 " ideal model delta sigma weight residual 1.248 1.308 -0.060 2.00e-02 2.50e+03 9.04e+00 bond pdb=" CAX Y01 B1201 " pdb=" OAH Y01 B1201 " ideal model delta sigma weight residual 1.248 1.308 -0.060 2.00e-02 2.50e+03 9.04e+00 bond pdb=" CAX Y01 B1203 " pdb=" OAH Y01 B1203 " ideal model delta sigma weight residual 1.248 1.308 -0.060 2.00e-02 2.50e+03 9.04e+00 bond pdb=" CAX Y01 C1201 " pdb=" OAH Y01 C1201 " ideal model delta sigma weight residual 1.248 1.308 -0.060 2.00e-02 2.50e+03 8.93e+00 ... (remaining 30851 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 41492 1.42 - 2.84: 400 2.84 - 4.26: 88 4.26 - 5.68: 28 5.68 - 7.10: 8 Bond angle restraints: 42016 Sorted by residual: angle pdb=" N THR A 795 " pdb=" CA THR A 795 " pdb=" C THR A 795 " ideal model delta sigma weight residual 114.56 110.70 3.86 1.27e+00 6.20e-01 9.23e+00 angle pdb=" N THR D 795 " pdb=" CA THR D 795 " pdb=" C THR D 795 " ideal model delta sigma weight residual 114.56 110.72 3.84 1.27e+00 6.20e-01 9.15e+00 angle pdb=" N THR C 795 " pdb=" CA THR C 795 " pdb=" C THR C 795 " ideal model delta sigma weight residual 114.56 110.75 3.81 1.27e+00 6.20e-01 9.01e+00 angle pdb=" N THR B 795 " pdb=" CA THR B 795 " pdb=" C THR B 795 " ideal model delta sigma weight residual 114.56 110.76 3.80 1.27e+00 6.20e-01 8.96e+00 angle pdb=" CA THR B 795 " pdb=" C THR B 795 " pdb=" N ASP B 796 " ideal model delta sigma weight residual 119.26 116.93 2.33 1.14e+00 7.69e-01 4.17e+00 ... (remaining 42011 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 15558 17.97 - 35.93: 1603 35.93 - 53.90: 514 53.90 - 71.87: 93 71.87 - 89.84: 36 Dihedral angle restraints: 17804 sinusoidal: 6508 harmonic: 11296 Sorted by residual: dihedral pdb=" CG ARG B 784 " pdb=" CD ARG B 784 " pdb=" NE ARG B 784 " pdb=" CZ ARG B 784 " ideal model delta sinusoidal sigma weight residual -90.00 -134.98 44.98 2 1.50e+01 4.44e-03 1.07e+01 dihedral pdb=" CG ARG C 784 " pdb=" CD ARG C 784 " pdb=" NE ARG C 784 " pdb=" CZ ARG C 784 " ideal model delta sinusoidal sigma weight residual -90.00 -134.97 44.97 2 1.50e+01 4.44e-03 1.07e+01 dihedral pdb=" CG ARG A 784 " pdb=" CD ARG A 784 " pdb=" NE ARG A 784 " pdb=" CZ ARG A 784 " ideal model delta sinusoidal sigma weight residual -90.00 -134.96 44.96 2 1.50e+01 4.44e-03 1.07e+01 ... (remaining 17801 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 3173 0.028 - 0.056: 1022 0.056 - 0.083: 463 0.083 - 0.111: 179 0.111 - 0.139: 19 Chirality restraints: 4856 Sorted by residual: chirality pdb=" CA ILE A1011 " pdb=" N ILE A1011 " pdb=" C ILE A1011 " pdb=" CB ILE A1011 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.83e-01 chirality pdb=" CA ILE B1011 " pdb=" N ILE B1011 " pdb=" C ILE B1011 " pdb=" CB ILE B1011 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.55e-01 chirality pdb=" CA ILE C1011 " pdb=" N ILE C1011 " pdb=" C ILE C1011 " pdb=" CB ILE C1011 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.48e-01 ... (remaining 4853 not shown) Planarity restraints: 5164 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 763 " -0.025 5.00e-02 4.00e+02 3.82e-02 2.34e+00 pdb=" N PRO B 764 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO B 764 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 764 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 763 " 0.025 5.00e-02 4.00e+02 3.82e-02 2.33e+00 pdb=" N PRO D 764 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO D 764 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 764 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 763 " -0.025 5.00e-02 4.00e+02 3.81e-02 2.32e+00 pdb=" N PRO A 764 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 764 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 764 " -0.021 5.00e-02 4.00e+02 ... (remaining 5161 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 8346 2.81 - 3.33: 29305 3.33 - 3.85: 52609 3.85 - 4.38: 58914 4.38 - 4.90: 103004 Nonbonded interactions: 252178 Sorted by model distance: nonbonded pdb=" OH TYR A 117 " pdb=" O LEU A 226 " model vdw 2.285 3.040 nonbonded pdb=" OH TYR D 117 " pdb=" O LEU D 226 " model vdw 2.285 3.040 nonbonded pdb=" OH TYR B 117 " pdb=" O LEU B 226 " model vdw 2.286 3.040 nonbonded pdb=" OH TYR C 117 " pdb=" O LEU C 226 " model vdw 2.286 3.040 nonbonded pdb=" O VAL C 728 " pdb=" OG1 THR C 732 " model vdw 2.296 3.040 ... (remaining 252173 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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 individual isotropic 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: 6.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.610 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 31.780 Find NCS groups from input model: 0.320 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: 0.010 Load rotamer database and sin/cos tables:6.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 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 : 0.003 0.060 30860 Z= 0.133 Angle : 0.411 7.095 42024 Z= 0.213 Chirality : 0.036 0.139 4856 Planarity : 0.003 0.038 5164 Dihedral : 16.980 89.835 10464 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.15 % Allowed : 22.54 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 2.17 (0.14), residues: 3780 helix: 2.37 (0.10), residues: 2520 sheet: -1.23 (0.36), residues: 212 loop : -0.28 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 998 TYR 0.015 0.001 TYR D 621 PHE 0.013 0.001 PHE A 165 TRP 0.012 0.001 TRP D 877 HIS 0.002 0.000 HIS A 500 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (30856) covalent geometry : angle 0.41042 / 0.21 (42016) SS BOND : bond 0.00560 / 0.28 ( 4) SS BOND : angle 1.58990 / 0.66 ( 8) hydrogen bonds : bond 0.10883 / 7.08 ( 1965) hydrogen bonds : angle 4.38402 / 3.11 ( 5811) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 607 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 194 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7558 (mt-10) REVERT: A 219 MET cc_start: 0.8308 (mmm) cc_final: 0.8053 (mmt) REVERT: A 396 MET cc_start: 0.7663 (mtm) cc_final: 0.7124 (mtp) REVERT: A 462 MET cc_start: 0.8876 (tpt) cc_final: 0.8561 (tpt) REVERT: A 655 ASN cc_start: 0.8165 (t0) cc_final: 0.7714 (t0) REVERT: B 98 PHE cc_start: 0.7479 (m-80) cc_final: 0.7276 (m-80) REVERT: B 101 ASP cc_start: 0.7887 (p0) cc_final: 0.7595 (p0) REVERT: B 194 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7542 (mt-10) REVERT: B 219 MET cc_start: 0.8282 (mmm) cc_final: 0.8013 (mmt) REVERT: B 396 MET cc_start: 0.7660 (mtm) cc_final: 0.7136 (mtp) REVERT: B 655 ASN cc_start: 0.8182 (t0) cc_final: 0.7704 (t0) REVERT: C 98 PHE cc_start: 0.7421 (m-80) cc_final: 0.7213 (m-80) REVERT: C 101 ASP cc_start: 0.7913 (p0) cc_final: 0.7628 (p0) REVERT: C 194 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7565 (mt-10) REVERT: C 219 MET cc_start: 0.8281 (mmm) cc_final: 0.8020 (mmt) REVERT: C 396 MET cc_start: 0.7677 (mtm) cc_final: 0.7109 (mtp) REVERT: C 462 MET cc_start: 0.8872 (tpt) cc_final: 0.8553 (tpt) REVERT: C 655 ASN cc_start: 0.8112 (t0) cc_final: 0.7613 (t0) REVERT: D 194 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7533 (mt-10) REVERT: D 219 MET cc_start: 0.8300 (mmm) cc_final: 0.8046 (mmt) REVERT: D 396 MET cc_start: 0.7674 (mtm) cc_final: 0.7131 (mtp) REVERT: D 462 MET cc_start: 0.8879 (tpt) cc_final: 0.8631 (tpt) REVERT: D 655 ASN cc_start: 0.8090 (t0) cc_final: 0.7625 (t0) outliers start: 63 outliers final: 52 residues processed: 662 average time/residue: 0.6057 time to fit residues: 481.1050 Evaluate side-chains 541 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 489 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ASN Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 808 TYR Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 898 TRP Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 676 ASN Chi-restraints excluded: chain B residue 763 VAL Chi-restraints excluded: chain B residue 808 TYR Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 898 TRP Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 1052 THR Chi-restraints excluded: chain C residue 143 ASN Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 676 ASN Chi-restraints excluded: chain C residue 763 VAL Chi-restraints excluded: chain C residue 808 TYR Chi-restraints excluded: chain C residue 825 LEU Chi-restraints excluded: chain C residue 903 VAL Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 1052 THR Chi-restraints excluded: chain D residue 143 ASN Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 676 ASN Chi-restraints excluded: chain D residue 763 VAL Chi-restraints excluded: chain D residue 808 TYR Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 903 VAL Chi-restraints excluded: chain D residue 955 ILE Chi-restraints excluded: chain D residue 1052 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 197 optimal weight: 0.0370 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 0.5980 chunk 298 optimal weight: 0.4980 overall best weight: 0.7460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 222 ASN A 294 ASN A 437 ASN A 671 GLN B 222 ASN B 294 ASN B 437 ASN B 671 GLN B 765 HIS C 222 ASN C 294 ASN C 437 ASN C 671 GLN D 222 ASN D 294 ASN D 437 ASN D 671 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.138538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.107081 restraints weight = 47411.588| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.75 r_work: 0.3208 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 30860 Z= 0.124 Angle : 0.456 6.963 42024 Z= 0.241 Chirality : 0.038 0.177 4856 Planarity : 0.004 0.053 5164 Dihedral : 7.487 76.685 4430 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 5.57 % Allowed : 22.20 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 2.10 (0.14), residues: 3780 helix: 2.39 (0.10), residues: 2544 sheet: -1.55 (0.35), residues: 220 loop : -0.48 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 167 TYR 0.015 0.001 TYR D 621 PHE 0.014 0.001 PHE A 629 TRP 0.014 0.001 TRP C 426 HIS 0.002 0.001 HIS B 500 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (30856) covalent geometry : angle 0.45530 / 0.24 (42016) SS BOND : bond 0.00943 / 0.47 ( 4) SS BOND : angle 2.38986 / 1.03 ( 8) hydrogen bonds : bond 0.03471 / 2.33 ( 1965) hydrogen bonds : angle 3.77910 / 2.67 ( 5811) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 515 time to evaluate : 1.147 Fit side-chains REVERT: A 101 ASP cc_start: 0.7936 (p0) cc_final: 0.7648 (p0) REVERT: A 131 GLU cc_start: 0.8276 (tp30) cc_final: 0.7474 (tp30) REVERT: A 219 MET cc_start: 0.8630 (mmm) cc_final: 0.8372 (mmt) REVERT: A 378 ILE cc_start: 0.8232 (mm) cc_final: 0.7783 (mt) REVERT: A 383 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8212 (tp30) REVERT: A 655 ASN cc_start: 0.8094 (t0) cc_final: 0.7808 (t0) REVERT: A 851 ARG cc_start: 0.8919 (OUTLIER) cc_final: 0.6860 (tpt-90) REVERT: B 98 PHE cc_start: 0.7935 (m-80) cc_final: 0.7728 (m-80) REVERT: B 101 ASP cc_start: 0.8049 (p0) cc_final: 0.7761 (p0) REVERT: B 219 MET cc_start: 0.8613 (mmm) cc_final: 0.8352 (mmt) REVERT: B 378 ILE cc_start: 0.8168 (mm) cc_final: 0.7745 (mp) REVERT: B 655 ASN cc_start: 0.8066 (t0) cc_final: 0.7721 (t0) REVERT: B 851 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.6887 (tpt-90) REVERT: C 101 ASP cc_start: 0.8058 (p0) cc_final: 0.7755 (p0) REVERT: C 167 ARG cc_start: 0.7989 (mmm160) cc_final: 0.7664 (tpm-80) REVERT: C 219 MET cc_start: 0.8607 (mmm) cc_final: 0.8365 (mmt) REVERT: C 378 ILE cc_start: 0.8194 (mm) cc_final: 0.7769 (mp) REVERT: C 851 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.6873 (tpt-90) REVERT: D 101 ASP cc_start: 0.7894 (p0) cc_final: 0.7634 (p0) REVERT: D 167 ARG cc_start: 0.7990 (mmm160) cc_final: 0.7590 (tpm-80) REVERT: D 219 MET cc_start: 0.8642 (mmm) cc_final: 0.8394 (mmt) REVERT: D 378 ILE cc_start: 0.8229 (mm) cc_final: 0.7801 (mt) REVERT: D 655 ASN cc_start: 0.8081 (t0) cc_final: 0.7856 (t0) REVERT: D 851 ARG cc_start: 0.8905 (OUTLIER) cc_final: 0.6798 (tpt-90) outliers start: 163 outliers final: 50 residues processed: 623 average time/residue: 0.5940 time to fit residues: 445.0035 Evaluate side-chains 548 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 494 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 656 CYS Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 785 GLN Chi-restraints excluded: chain A residue 851 ARG Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 656 CYS Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 785 GLN Chi-restraints excluded: chain B residue 851 ARG Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 491 ASP Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 825 LEU Chi-restraints excluded: chain C residue 851 ARG Chi-restraints excluded: chain C residue 911 MET Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 491 ASP Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 758 MET Chi-restraints excluded: chain D residue 769 LEU Chi-restraints excluded: chain D residue 851 ARG Chi-restraints excluded: chain D residue 1024 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 93 optimal weight: 0.9980 chunk 318 optimal weight: 4.9990 chunk 4 optimal weight: 0.0770 chunk 285 optimal weight: 0.8980 chunk 242 optimal weight: 0.9980 chunk 203 optimal weight: 10.0000 chunk 142 optimal weight: 0.7980 chunk 153 optimal weight: 0.9980 chunk 34 optimal weight: 0.3980 chunk 51 optimal weight: 0.8980 chunk 105 optimal weight: 5.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 GLN B 671 GLN B1003 GLN C 671 GLN D 765 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.136603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.104316 restraints weight = 47800.213| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.74 r_work: 0.3213 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 30860 Z= 0.112 Angle : 0.437 7.134 42024 Z= 0.231 Chirality : 0.037 0.204 4856 Planarity : 0.003 0.050 5164 Dihedral : 6.676 76.984 4374 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 5.03 % Allowed : 23.67 % Favored : 71.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 2.10 (0.14), residues: 3780 helix: 2.42 (0.10), residues: 2544 sheet: -1.58 (0.35), residues: 220 loop : -0.59 (0.18), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 167 TYR 0.015 0.001 TYR D 621 PHE 0.013 0.001 PHE A 629 TRP 0.015 0.001 TRP D 426 HIS 0.002 0.001 HIS C 500 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (30856) covalent geometry : angle 0.43601 / 0.23 (42016) SS BOND : bond 0.00703 / 0.35 ( 4) SS BOND : angle 1.95145 / 0.84 ( 8) hydrogen bonds : bond 0.03240 / 2.18 ( 1965) hydrogen bonds : angle 3.68833 / 2.61 ( 5811) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 523 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8483 (tp) REVERT: A 135 GLN cc_start: 0.7530 (mp10) cc_final: 0.7117 (mp10) REVERT: A 140 LYS cc_start: 0.8967 (OUTLIER) cc_final: 0.8697 (mtmm) REVERT: A 219 MET cc_start: 0.8665 (mmm) cc_final: 0.8409 (mmt) REVERT: A 378 ILE cc_start: 0.8190 (mm) cc_final: 0.7778 (mp) REVERT: A 383 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8168 (tp30) REVERT: A 851 ARG cc_start: 0.8883 (OUTLIER) cc_final: 0.6953 (tpt-90) REVERT: A 900 PHE cc_start: 0.7761 (OUTLIER) cc_final: 0.7536 (m-80) REVERT: A 1009 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7723 (mp) REVERT: B 98 PHE cc_start: 0.7957 (m-80) cc_final: 0.7756 (m-80) REVERT: B 101 ASP cc_start: 0.7887 (p0) cc_final: 0.7646 (p0) REVERT: B 131 GLU cc_start: 0.8273 (tp30) cc_final: 0.7248 (tp30) REVERT: B 219 MET cc_start: 0.8645 (mmm) cc_final: 0.8383 (mmt) REVERT: B 378 ILE cc_start: 0.8153 (mm) cc_final: 0.7741 (mp) REVERT: B 435 GLU cc_start: 0.8283 (tm-30) cc_final: 0.7871 (tp30) REVERT: B 851 ARG cc_start: 0.8868 (OUTLIER) cc_final: 0.6950 (tpt-90) REVERT: B 900 PHE cc_start: 0.7735 (OUTLIER) cc_final: 0.7497 (m-80) REVERT: B 1009 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7733 (mp) REVERT: C 101 ASP cc_start: 0.7908 (p0) cc_final: 0.7658 (p0) REVERT: C 131 GLU cc_start: 0.8262 (tp30) cc_final: 0.7880 (tp30) REVERT: C 186 TYR cc_start: 0.8694 (m-80) cc_final: 0.8011 (m-80) REVERT: C 219 MET cc_start: 0.8655 (mmm) cc_final: 0.8397 (mmt) REVERT: C 378 ILE cc_start: 0.8183 (mm) cc_final: 0.7735 (mt) REVERT: C 655 ASN cc_start: 0.8060 (t0) cc_final: 0.7766 (t0) REVERT: C 851 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.6942 (tpt-90) REVERT: C 900 PHE cc_start: 0.7688 (OUTLIER) cc_final: 0.7447 (m-80) REVERT: C 1009 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7889 (mp) REVERT: D 167 ARG cc_start: 0.7956 (mmm160) cc_final: 0.7569 (tpm-80) REVERT: D 219 MET cc_start: 0.8660 (mmm) cc_final: 0.8414 (mmt) REVERT: D 378 ILE cc_start: 0.8201 (mm) cc_final: 0.7762 (mt) REVERT: D 851 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.7042 (tpt-90) REVERT: D 1009 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7890 (mp) outliers start: 147 outliers final: 64 residues processed: 617 average time/residue: 0.5644 time to fit residues: 422.5980 Evaluate side-chains 579 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 502 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 140 LYS Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 785 GLN Chi-restraints excluded: chain A residue 851 ARG Chi-restraints excluded: chain A residue 898 TRP Chi-restraints excluded: chain A residue 900 PHE Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 676 ASN Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 785 GLN Chi-restraints excluded: chain B residue 808 TYR Chi-restraints excluded: chain B residue 851 ARG Chi-restraints excluded: chain B residue 898 TRP Chi-restraints excluded: chain B residue 900 PHE Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 1009 LEU Chi-restraints excluded: chain B residue 1024 VAL Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 491 ASP Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 656 CYS Chi-restraints excluded: chain C residue 676 ASN Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 808 TYR Chi-restraints excluded: chain C residue 851 ARG Chi-restraints excluded: chain C residue 898 TRP Chi-restraints excluded: chain C residue 900 PHE Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 1009 LEU Chi-restraints excluded: chain D residue 122 CYS Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 255 ASN Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 491 ASP Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 656 CYS Chi-restraints excluded: chain D residue 676 ASN Chi-restraints excluded: chain D residue 769 LEU Chi-restraints excluded: chain D residue 785 GLN Chi-restraints excluded: chain D residue 808 TYR Chi-restraints excluded: chain D residue 851 ARG Chi-restraints excluded: chain D residue 898 TRP Chi-restraints excluded: chain D residue 955 ILE Chi-restraints excluded: chain D residue 1009 LEU Chi-restraints excluded: chain D residue 1024 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 44 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 369 optimal weight: 5.9990 chunk 354 optimal weight: 0.9980 chunk 239 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 324 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 225 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 306 GLN ** A 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 GLN ** B 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 306 GLN ** C 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 306 GLN D 510 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.135034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.103040 restraints weight = 47230.805| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.74 r_work: 0.3163 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 30860 Z= 0.178 Angle : 0.505 7.866 42024 Z= 0.263 Chirality : 0.040 0.193 4856 Planarity : 0.004 0.047 5164 Dihedral : 6.846 78.767 4372 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 5.78 % Allowed : 23.94 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.83 (0.14), residues: 3780 helix: 2.19 (0.10), residues: 2552 sheet: -1.70 (0.34), residues: 220 loop : -0.64 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 167 TYR 0.019 0.002 TYR D 621 PHE 0.021 0.002 PHE B1013 TRP 0.019 0.002 TRP D 426 HIS 0.004 0.001 HIS A 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 (30856) covalent geometry : angle 0.50431 / 0.26 (42016) SS BOND : bond 0.00848 / 0.43 ( 4) SS BOND : angle 2.33173 / 0.99 ( 8) hydrogen bonds : bond 0.03800 / 2.55 ( 1965) hydrogen bonds : angle 3.86970 / 2.74 ( 5811) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 503 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 LYS cc_start: 0.8687 (tppp) cc_final: 0.8475 (tppp) REVERT: A 131 GLU cc_start: 0.8180 (tp30) cc_final: 0.7827 (tp30) REVERT: A 135 GLN cc_start: 0.7596 (mp10) cc_final: 0.7354 (mp10) REVERT: A 219 MET cc_start: 0.8648 (mmm) cc_final: 0.8394 (mmt) REVERT: A 383 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8204 (tp30) REVERT: A 458 LEU cc_start: 0.7580 (pp) cc_final: 0.7357 (pp) REVERT: A 482 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7431 (tp) REVERT: A 655 ASN cc_start: 0.8371 (t0) cc_final: 0.8059 (t0) REVERT: A 851 ARG cc_start: 0.8896 (OUTLIER) cc_final: 0.8493 (ttt-90) REVERT: A 1009 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7892 (mp) REVERT: B 98 PHE cc_start: 0.7941 (m-10) cc_final: 0.7721 (m-80) REVERT: B 101 ASP cc_start: 0.7903 (p0) cc_final: 0.7662 (p0) REVERT: B 219 MET cc_start: 0.8680 (mmm) cc_final: 0.8435 (mmt) REVERT: B 378 ILE cc_start: 0.8256 (mm) cc_final: 0.7822 (mp) REVERT: B 458 LEU cc_start: 0.7558 (pp) cc_final: 0.7339 (pp) REVERT: B 482 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7459 (tp) REVERT: B 655 ASN cc_start: 0.8344 (t0) cc_final: 0.8053 (t0) REVERT: B 851 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.8480 (ttt-90) REVERT: B 900 PHE cc_start: 0.7766 (OUTLIER) cc_final: 0.7529 (m-80) REVERT: B 992 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.8177 (pt0) REVERT: B 1009 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7857 (mp) REVERT: C 96 LYS cc_start: 0.8682 (tppp) cc_final: 0.8436 (tppp) REVERT: C 101 ASP cc_start: 0.7965 (p0) cc_final: 0.7729 (p0) REVERT: C 131 GLU cc_start: 0.8084 (tp30) cc_final: 0.7749 (tp30) REVERT: C 132 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8480 (tp) REVERT: C 186 TYR cc_start: 0.8784 (m-80) cc_final: 0.8107 (m-80) REVERT: C 219 MET cc_start: 0.8680 (mmm) cc_final: 0.8438 (mmt) REVERT: C 228 ARG cc_start: 0.7594 (OUTLIER) cc_final: 0.7206 (mmm-85) REVERT: C 458 LEU cc_start: 0.7608 (pp) cc_final: 0.7391 (pp) REVERT: C 479 GLU cc_start: 0.8372 (pt0) cc_final: 0.8143 (pt0) REVERT: C 482 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7473 (tp) REVERT: C 655 ASN cc_start: 0.8289 (t0) cc_final: 0.7892 (t0) REVERT: C 851 ARG cc_start: 0.8891 (OUTLIER) cc_final: 0.8481 (ttt-90) REVERT: C 900 PHE cc_start: 0.7767 (OUTLIER) cc_final: 0.7532 (m-80) REVERT: C 1009 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7997 (mp) REVERT: D 101 ASP cc_start: 0.7850 (p0) cc_final: 0.7644 (p0) REVERT: D 131 GLU cc_start: 0.8307 (tp30) cc_final: 0.8016 (tp30) REVERT: D 132 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8492 (tp) REVERT: D 186 TYR cc_start: 0.8756 (m-80) cc_final: 0.8136 (m-80) REVERT: D 219 MET cc_start: 0.8668 (mmm) cc_final: 0.8423 (mmt) REVERT: D 378 ILE cc_start: 0.8261 (mm) cc_final: 0.7820 (mp) REVERT: D 655 ASN cc_start: 0.8365 (t0) cc_final: 0.8019 (t0) REVERT: D 851 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.8489 (ttt-90) outliers start: 169 outliers final: 56 residues processed: 618 average time/residue: 0.5856 time to fit residues: 436.2680 Evaluate side-chains 559 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 487 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 656 CYS Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain A residue 785 GLN Chi-restraints excluded: chain A residue 808 TYR Chi-restraints excluded: chain A residue 851 ARG Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 676 ASN Chi-restraints excluded: chain B residue 785 GLN Chi-restraints excluded: chain B residue 808 TYR Chi-restraints excluded: chain B residue 851 ARG Chi-restraints excluded: chain B residue 900 PHE Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 992 GLN Chi-restraints excluded: chain B residue 1009 LEU Chi-restraints excluded: chain B residue 1024 VAL Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 228 ARG Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 280 GLN Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 491 ASP Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 656 CYS Chi-restraints excluded: chain C residue 676 ASN Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 808 TYR Chi-restraints excluded: chain C residue 851 ARG Chi-restraints excluded: chain C residue 900 PHE Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 1009 LEU Chi-restraints excluded: chain D residue 122 CYS Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 280 GLN Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 491 ASP Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 656 CYS Chi-restraints excluded: chain D residue 676 ASN Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 808 TYR Chi-restraints excluded: chain D residue 851 ARG Chi-restraints excluded: chain D residue 955 ILE Chi-restraints excluded: chain D residue 1024 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 361 optimal weight: 4.9990 chunk 271 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 chunk 365 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 278 optimal weight: 1.9990 chunk 317 optimal weight: 2.9990 chunk 370 optimal weight: 0.9980 chunk 284 optimal weight: 0.9980 chunk 242 optimal weight: 0.0980 chunk 261 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1003 GLN ** B 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1003 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.137079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.105376 restraints weight = 47548.817| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.72 r_work: 0.3180 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 30860 Z= 0.141 Angle : 0.482 7.284 42024 Z= 0.251 Chirality : 0.039 0.204 4856 Planarity : 0.004 0.047 5164 Dihedral : 6.749 77.852 4368 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 5.54 % Allowed : 24.18 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.84 (0.14), residues: 3780 helix: 2.21 (0.10), residues: 2552 sheet: -1.76 (0.34), residues: 220 loop : -0.67 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 167 TYR 0.021 0.002 TYR C 117 PHE 0.020 0.001 PHE A 44 TRP 0.020 0.001 TRP C 426 HIS 0.003 0.001 HIS A 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (30856) covalent geometry : angle 0.48073 / 0.25 (42016) SS BOND : bond 0.00786 / 0.39 ( 4) SS BOND : angle 2.07630 / 0.88 ( 8) hydrogen bonds : bond 0.03494 / 2.35 ( 1965) hydrogen bonds : angle 3.80072 / 2.69 ( 5811) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 499 time to evaluate : 1.120 Fit side-chains revert: symmetry clash REVERT: A 101 ASP cc_start: 0.7764 (p0) cc_final: 0.7564 (p0) REVERT: A 131 GLU cc_start: 0.8186 (tp30) cc_final: 0.7777 (tp30) REVERT: A 132 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8421 (tp) REVERT: A 167 ARG cc_start: 0.8002 (mmm160) cc_final: 0.7678 (tpm-80) REVERT: A 186 TYR cc_start: 0.8785 (m-80) cc_final: 0.8112 (m-80) REVERT: A 219 MET cc_start: 0.8650 (mmm) cc_final: 0.8394 (mmt) REVERT: A 383 GLU cc_start: 0.8474 (mt-10) cc_final: 0.8191 (tp30) REVERT: A 482 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7418 (tp) REVERT: A 655 ASN cc_start: 0.8224 (t0) cc_final: 0.7897 (t0) REVERT: A 851 ARG cc_start: 0.8874 (OUTLIER) cc_final: 0.8444 (ttt-90) REVERT: A 1009 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7876 (mp) REVERT: B 98 PHE cc_start: 0.7956 (m-10) cc_final: 0.7737 (m-80) REVERT: B 101 ASP cc_start: 0.7874 (p0) cc_final: 0.7658 (p0) REVERT: B 131 GLU cc_start: 0.8063 (tp30) cc_final: 0.7774 (tp30) REVERT: B 132 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8386 (tp) REVERT: B 167 ARG cc_start: 0.8005 (mmm160) cc_final: 0.7676 (tpm-80) REVERT: B 219 MET cc_start: 0.8668 (mmm) cc_final: 0.8421 (mmt) REVERT: B 228 ARG cc_start: 0.7610 (OUTLIER) cc_final: 0.7206 (mmm-85) REVERT: B 378 ILE cc_start: 0.8270 (mm) cc_final: 0.7832 (mp) REVERT: B 482 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7477 (tp) REVERT: B 655 ASN cc_start: 0.8222 (t0) cc_final: 0.7905 (t0) REVERT: B 851 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.8429 (ttt-90) REVERT: B 900 PHE cc_start: 0.7745 (OUTLIER) cc_final: 0.7508 (m-80) REVERT: B 1009 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7910 (mp) REVERT: C 101 ASP cc_start: 0.7921 (p0) cc_final: 0.7717 (p0) REVERT: C 131 GLU cc_start: 0.8119 (tp30) cc_final: 0.7793 (tp30) REVERT: C 132 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8435 (tp) REVERT: C 186 TYR cc_start: 0.8804 (m-80) cc_final: 0.8129 (m-80) REVERT: C 219 MET cc_start: 0.8686 (mmm) cc_final: 0.8444 (mmt) REVERT: C 228 ARG cc_start: 0.7624 (OUTLIER) cc_final: 0.7259 (mmm-85) REVERT: C 458 LEU cc_start: 0.7543 (pp) cc_final: 0.7337 (pp) REVERT: C 482 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7430 (tp) REVERT: C 655 ASN cc_start: 0.8156 (t0) cc_final: 0.7873 (t0) REVERT: C 851 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.8435 (ttt-90) REVERT: C 900 PHE cc_start: 0.7764 (OUTLIER) cc_final: 0.7528 (m-80) REVERT: C 1009 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7975 (mp) REVERT: D 96 LYS cc_start: 0.8689 (tppp) cc_final: 0.8376 (tmmt) REVERT: D 131 GLU cc_start: 0.8075 (tp30) cc_final: 0.7833 (tp30) REVERT: D 132 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8437 (tp) REVERT: D 186 TYR cc_start: 0.8772 (m-80) cc_final: 0.8148 (m-80) REVERT: D 219 MET cc_start: 0.8666 (mmm) cc_final: 0.8422 (mmt) REVERT: D 383 GLU cc_start: 0.8464 (mt-10) cc_final: 0.8198 (tp30) REVERT: D 482 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7393 (tp) REVERT: D 655 ASN cc_start: 0.8216 (t0) cc_final: 0.7924 (t0) REVERT: D 851 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.8448 (ttt-90) outliers start: 162 outliers final: 76 residues processed: 609 average time/residue: 0.5773 time to fit residues: 423.8488 Evaluate side-chains 567 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 472 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 656 CYS Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 785 GLN Chi-restraints excluded: chain A residue 808 TYR Chi-restraints excluded: chain A residue 851 ARG Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ARG Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 255 ASN Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 656 CYS Chi-restraints excluded: chain B residue 676 ASN Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 785 GLN Chi-restraints excluded: chain B residue 808 TYR Chi-restraints excluded: chain B residue 851 ARG Chi-restraints excluded: chain B residue 900 PHE Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 1009 LEU Chi-restraints excluded: chain B residue 1024 VAL Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 228 ARG Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 255 ASN Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 280 GLN Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 491 ASP Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 656 CYS Chi-restraints excluded: chain C residue 676 ASN Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 808 TYR Chi-restraints excluded: chain C residue 851 ARG Chi-restraints excluded: chain C residue 900 PHE Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 1009 LEU Chi-restraints excluded: chain D residue 122 CYS Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 255 ASN Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 280 GLN Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 491 ASP Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 656 CYS Chi-restraints excluded: chain D residue 676 ASN Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 808 TYR Chi-restraints excluded: chain D residue 851 ARG Chi-restraints excluded: chain D residue 955 ILE Chi-restraints excluded: chain D residue 1024 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 51 optimal weight: 0.9980 chunk 323 optimal weight: 6.9990 chunk 120 optimal weight: 0.9990 chunk 135 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 307 optimal weight: 0.2980 chunk 185 optimal weight: 0.9980 chunk 11 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 359 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 46 GLN A 294 ASN A 437 ASN ** A 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 ASN ** B 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 294 ASN C 437 ASN ** C 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.134476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.102406 restraints weight = 47303.996| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.78 r_work: 0.3163 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 30860 Z= 0.170 Angle : 0.503 7.119 42024 Z= 0.263 Chirality : 0.040 0.201 4856 Planarity : 0.004 0.048 5164 Dihedral : 6.821 78.233 4368 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 5.10 % Allowed : 25.00 % Favored : 69.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.71 (0.14), residues: 3780 helix: 2.11 (0.10), residues: 2556 sheet: -1.88 (0.34), residues: 220 loop : -0.69 (0.18), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 167 TYR 0.024 0.002 TYR C 117 PHE 0.020 0.001 PHE C1013 TRP 0.023 0.002 TRP D 426 HIS 0.004 0.001 HIS A 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 (30856) covalent geometry : angle 0.50253 / 0.26 (42016) SS BOND : bond 0.00839 / 0.42 ( 4) SS BOND : angle 2.22561 / 0.94 ( 8) hydrogen bonds : bond 0.03708 / 2.49 ( 1965) hydrogen bonds : angle 3.85996 / 2.73 ( 5811) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 492 time to evaluate : 1.071 Fit side-chains REVERT: A 131 GLU cc_start: 0.8120 (tp30) cc_final: 0.7787 (tp30) REVERT: A 161 MET cc_start: 0.8556 (tpp) cc_final: 0.8352 (mmm) REVERT: A 186 TYR cc_start: 0.8805 (m-80) cc_final: 0.8201 (m-80) REVERT: A 219 MET cc_start: 0.8648 (mmm) cc_final: 0.8406 (mmt) REVERT: A 383 GLU cc_start: 0.8506 (mt-10) cc_final: 0.8204 (tp30) REVERT: A 482 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7577 (tp) REVERT: A 655 ASN cc_start: 0.8257 (t0) cc_final: 0.7942 (t0) REVERT: A 851 ARG cc_start: 0.8896 (OUTLIER) cc_final: 0.8492 (ttt-90) REVERT: A 992 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.7888 (pp30) REVERT: A 1009 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7928 (mp) REVERT: B 98 PHE cc_start: 0.7915 (m-10) cc_final: 0.7711 (m-80) REVERT: B 101 ASP cc_start: 0.7916 (p0) cc_final: 0.7711 (p0) REVERT: B 131 GLU cc_start: 0.8080 (tp30) cc_final: 0.7849 (tp30) REVERT: B 219 MET cc_start: 0.8670 (mmm) cc_final: 0.8424 (mmt) REVERT: B 382 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8609 (mtpt) REVERT: B 482 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7807 (tp) REVERT: B 655 ASN cc_start: 0.8271 (t0) cc_final: 0.7927 (t0) REVERT: B 851 ARG cc_start: 0.8891 (OUTLIER) cc_final: 0.8483 (ttt-90) REVERT: B 900 PHE cc_start: 0.7769 (OUTLIER) cc_final: 0.7561 (m-80) REVERT: B 992 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.8189 (pt0) REVERT: B 1009 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7940 (mp) REVERT: C 96 LYS cc_start: 0.8694 (tppp) cc_final: 0.8492 (tppp) REVERT: C 101 ASP cc_start: 0.7947 (p0) cc_final: 0.7745 (p0) REVERT: C 167 ARG cc_start: 0.8028 (mmm160) cc_final: 0.7730 (tpm-80) REVERT: C 186 TYR cc_start: 0.8816 (m-80) cc_final: 0.8168 (m-80) REVERT: C 219 MET cc_start: 0.8688 (mmm) cc_final: 0.8447 (mmt) REVERT: C 228 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.7176 (mmm-85) REVERT: C 655 ASN cc_start: 0.8233 (t0) cc_final: 0.7910 (t0) REVERT: C 851 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.8471 (ttt-90) REVERT: C 900 PHE cc_start: 0.7787 (OUTLIER) cc_final: 0.7577 (m-80) REVERT: C 992 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.7888 (pp30) REVERT: C 1009 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7995 (mp) REVERT: D 131 GLU cc_start: 0.8126 (tp30) cc_final: 0.7841 (tp30) REVERT: D 132 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8402 (tp) REVERT: D 161 MET cc_start: 0.8583 (tpp) cc_final: 0.8377 (mmm) REVERT: D 167 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7873 (tpm-80) REVERT: D 186 TYR cc_start: 0.8781 (m-80) cc_final: 0.8136 (m-80) REVERT: D 219 MET cc_start: 0.8681 (mmm) cc_final: 0.8428 (mmt) REVERT: D 383 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8201 (tp30) REVERT: D 655 ASN cc_start: 0.8299 (t0) cc_final: 0.7931 (t0) REVERT: D 851 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.8481 (ttt-90) REVERT: D 992 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.7882 (pp30) outliers start: 149 outliers final: 76 residues processed: 593 average time/residue: 0.5163 time to fit residues: 371.7254 Evaluate side-chains 571 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 476 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 656 CYS Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain A residue 785 GLN Chi-restraints excluded: chain A residue 808 TYR Chi-restraints excluded: chain A residue 851 ARG Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 992 GLN Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 255 ASN Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 382 LYS Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 656 CYS Chi-restraints excluded: chain B residue 676 ASN Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 785 GLN Chi-restraints excluded: chain B residue 808 TYR Chi-restraints excluded: chain B residue 851 ARG Chi-restraints excluded: chain B residue 900 PHE Chi-restraints excluded: chain B residue 911 MET Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 992 GLN Chi-restraints excluded: chain B residue 1009 LEU Chi-restraints excluded: chain B residue 1024 VAL Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 228 ARG Chi-restraints excluded: chain C residue 255 ASN Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 280 GLN Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 491 ASP Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 656 CYS Chi-restraints excluded: chain C residue 676 ASN Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 808 TYR Chi-restraints excluded: chain C residue 851 ARG Chi-restraints excluded: chain C residue 900 PHE Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 992 GLN Chi-restraints excluded: chain C residue 1009 LEU Chi-restraints excluded: chain D residue 122 CYS Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 167 ARG Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 280 GLN Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 491 ASP Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 656 CYS Chi-restraints excluded: chain D residue 676 ASN Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 808 TYR Chi-restraints excluded: chain D residue 851 ARG Chi-restraints excluded: chain D residue 955 ILE Chi-restraints excluded: chain D residue 992 GLN Chi-restraints excluded: chain D residue 1024 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 353 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 352 optimal weight: 0.5980 chunk 359 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 154 optimal weight: 0.9980 chunk 347 optimal weight: 0.9990 chunk 342 optimal weight: 4.9990 chunk 210 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 275 optimal weight: 0.0010 overall best weight: 0.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN ** B 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.135569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.103703 restraints weight = 47201.596| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.76 r_work: 0.3178 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 30860 Z= 0.139 Angle : 0.491 7.131 42024 Z= 0.255 Chirality : 0.039 0.218 4856 Planarity : 0.004 0.046 5164 Dihedral : 6.740 77.421 4368 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 5.16 % Allowed : 25.00 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.77 (0.14), residues: 3780 helix: 2.17 (0.10), residues: 2556 sheet: -1.88 (0.33), residues: 228 loop : -0.69 (0.18), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 360 TYR 0.026 0.002 TYR A 117 PHE 0.020 0.001 PHE D1013 TRP 0.025 0.001 TRP D 426 HIS 0.004 0.001 HIS A 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (30856) covalent geometry : angle 0.49022 / 0.25 (42016) SS BOND : bond 0.00808 / 0.40 ( 4) SS BOND : angle 2.05497 / 0.86 ( 8) hydrogen bonds : bond 0.03479 / 2.34 ( 1965) hydrogen bonds : angle 3.79699 / 2.68 ( 5811) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 499 time to evaluate : 1.186 Fit side-chains REVERT: A 96 LYS cc_start: 0.8697 (tppp) cc_final: 0.8269 (tttm) REVERT: A 131 GLU cc_start: 0.8123 (tp30) cc_final: 0.7860 (tp30) REVERT: A 186 TYR cc_start: 0.8802 (m-80) cc_final: 0.8194 (m-80) REVERT: A 219 MET cc_start: 0.8659 (mmm) cc_final: 0.8431 (mmt) REVERT: A 383 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8191 (tp30) REVERT: A 655 ASN cc_start: 0.8124 (t0) cc_final: 0.7870 (t0) REVERT: A 851 ARG cc_start: 0.8874 (OUTLIER) cc_final: 0.7235 (tpt-90) REVERT: A 911 MET cc_start: 0.7948 (OUTLIER) cc_final: 0.7409 (mtm) REVERT: A 992 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.7898 (pp30) REVERT: A 1009 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7906 (mp) REVERT: B 98 PHE cc_start: 0.7920 (m-10) cc_final: 0.7715 (m-80) REVERT: B 101 ASP cc_start: 0.7903 (p0) cc_final: 0.7684 (p0) REVERT: B 186 TYR cc_start: 0.8801 (m-80) cc_final: 0.8190 (m-80) REVERT: B 219 MET cc_start: 0.8666 (mmm) cc_final: 0.8432 (mmt) REVERT: B 378 ILE cc_start: 0.8259 (mm) cc_final: 0.7809 (mp) REVERT: B 507 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.7910 (tpm170) REVERT: B 655 ASN cc_start: 0.8150 (t0) cc_final: 0.7868 (t0) REVERT: B 851 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.7230 (tpt-90) REVERT: B 900 PHE cc_start: 0.7754 (OUTLIER) cc_final: 0.7544 (m-80) REVERT: B 1009 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7912 (mp) REVERT: C 96 LYS cc_start: 0.8684 (tppp) cc_final: 0.8462 (tppp) REVERT: C 101 ASP cc_start: 0.7905 (p0) cc_final: 0.7704 (p0) REVERT: C 131 GLU cc_start: 0.8141 (tp30) cc_final: 0.7740 (tp30) REVERT: C 186 TYR cc_start: 0.8816 (m-80) cc_final: 0.8193 (m-80) REVERT: C 219 MET cc_start: 0.8686 (mmm) cc_final: 0.8442 (mmt) REVERT: C 228 ARG cc_start: 0.7586 (OUTLIER) cc_final: 0.7208 (mmm-85) REVERT: C 458 LEU cc_start: 0.7584 (pp) cc_final: 0.7382 (pp) REVERT: C 507 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.7924 (tpm170) REVERT: C 655 ASN cc_start: 0.8086 (t0) cc_final: 0.7848 (t0) REVERT: C 851 ARG cc_start: 0.8868 (OUTLIER) cc_final: 0.7222 (tpt-90) REVERT: C 900 PHE cc_start: 0.7792 (OUTLIER) cc_final: 0.7576 (m-80) REVERT: C 992 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.7906 (pp30) REVERT: C 1009 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7976 (mp) REVERT: D 131 GLU cc_start: 0.8113 (tp30) cc_final: 0.7859 (tp30) REVERT: D 167 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7856 (tpm-80) REVERT: D 186 TYR cc_start: 0.8793 (m-80) cc_final: 0.8116 (m-80) REVERT: D 219 MET cc_start: 0.8692 (mmm) cc_final: 0.8437 (mmt) REVERT: D 383 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8192 (tp30) REVERT: D 655 ASN cc_start: 0.8152 (t0) cc_final: 0.7864 (t0) REVERT: D 851 ARG cc_start: 0.8874 (OUTLIER) cc_final: 0.7232 (tpt-90) REVERT: D 911 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.7499 (mtm) REVERT: D 992 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.7897 (pp30) outliers start: 151 outliers final: 76 residues processed: 597 average time/residue: 0.5456 time to fit residues: 392.3075 Evaluate side-chains 581 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 487 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 785 GLN Chi-restraints excluded: chain A residue 808 TYR Chi-restraints excluded: chain A residue 851 ARG Chi-restraints excluded: chain A residue 911 MET Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 992 GLN Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 255 ASN Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 507 ARG Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 656 CYS Chi-restraints excluded: chain B residue 676 ASN Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 785 GLN Chi-restraints excluded: chain B residue 808 TYR Chi-restraints excluded: chain B residue 851 ARG Chi-restraints excluded: chain B residue 900 PHE Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 1009 LEU Chi-restraints excluded: chain B residue 1024 VAL Chi-restraints excluded: chain B residue 1052 THR Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 228 ARG Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 280 GLN Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 491 ASP Chi-restraints excluded: chain C residue 507 ARG Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 676 ASN Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 808 TYR Chi-restraints excluded: chain C residue 851 ARG Chi-restraints excluded: chain C residue 900 PHE Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 992 GLN Chi-restraints excluded: chain C residue 1009 LEU Chi-restraints excluded: chain C residue 1052 THR Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 122 CYS Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 167 ARG Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 280 GLN Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 491 ASP Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 656 CYS Chi-restraints excluded: chain D residue 676 ASN Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 808 TYR Chi-restraints excluded: chain D residue 851 ARG Chi-restraints excluded: chain D residue 911 MET Chi-restraints excluded: chain D residue 955 ILE Chi-restraints excluded: chain D residue 992 GLN Chi-restraints excluded: chain D residue 1024 VAL Chi-restraints excluded: chain D residue 1052 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 217 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 chunk 309 optimal weight: 2.9990 chunk 185 optimal weight: 3.9990 chunk 381 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 358 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 142 optimal weight: 0.9990 chunk 137 optimal weight: 0.0670 overall best weight: 1.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 46 GLN A 437 ASN ** A 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN ** B 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN ** C 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.134353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.102016 restraints weight = 47522.494| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.69 r_work: 0.3168 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 30860 Z= 0.202 Angle : 0.545 8.450 42024 Z= 0.284 Chirality : 0.042 0.217 4856 Planarity : 0.004 0.046 5164 Dihedral : 6.964 78.114 4368 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 4.58 % Allowed : 26.13 % Favored : 69.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.55 (0.14), residues: 3780 helix: 1.99 (0.10), residues: 2556 sheet: -2.02 (0.32), residues: 228 loop : -0.72 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D1008 TYR 0.026 0.002 TYR B 117 PHE 0.022 0.002 PHE C 44 TRP 0.029 0.002 TRP C 426 HIS 0.005 0.001 HIS A 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.20 (30856) covalent geometry : angle 0.54396 / 0.28 (42016) SS BOND : bond 0.00880 / 0.44 ( 4) SS BOND : angle 2.35645 / 0.98 ( 8) hydrogen bonds : bond 0.03967 / 2.66 ( 1965) hydrogen bonds : angle 3.96093 / 2.80 ( 5811) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 485 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 LYS cc_start: 0.8667 (tppp) cc_final: 0.8460 (tppp) REVERT: A 131 GLU cc_start: 0.8069 (tp30) cc_final: 0.7786 (tp30) REVERT: A 186 TYR cc_start: 0.8801 (m-80) cc_final: 0.8238 (m-80) REVERT: A 219 MET cc_start: 0.8710 (mmm) cc_final: 0.8463 (mmt) REVERT: A 383 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8177 (tp30) REVERT: A 507 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.7947 (tpm170) REVERT: A 655 ASN cc_start: 0.8288 (t0) cc_final: 0.7964 (t0) REVERT: A 851 ARG cc_start: 0.8903 (OUTLIER) cc_final: 0.8524 (ttt-90) REVERT: A 911 MET cc_start: 0.7977 (OUTLIER) cc_final: 0.7537 (mtm) REVERT: A 992 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.7956 (pp30) REVERT: B 186 TYR cc_start: 0.8790 (m-80) cc_final: 0.8239 (m-80) REVERT: B 219 MET cc_start: 0.8718 (mmm) cc_final: 0.8471 (mmt) REVERT: B 382 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8525 (mtmp) REVERT: B 507 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.7953 (tpm170) REVERT: B 655 ASN cc_start: 0.8294 (t0) cc_final: 0.7939 (t0) REVERT: B 851 ARG cc_start: 0.8898 (OUTLIER) cc_final: 0.8515 (ttt-90) REVERT: B 900 PHE cc_start: 0.7783 (OUTLIER) cc_final: 0.7575 (m-80) REVERT: C 186 TYR cc_start: 0.8796 (m-80) cc_final: 0.8246 (m-80) REVERT: C 219 MET cc_start: 0.8702 (mmm) cc_final: 0.8468 (mmt) REVERT: C 228 ARG cc_start: 0.7598 (OUTLIER) cc_final: 0.7169 (mmm-85) REVERT: C 458 LEU cc_start: 0.7758 (pp) cc_final: 0.7553 (pp) REVERT: C 507 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.7957 (tpm170) REVERT: C 655 ASN cc_start: 0.8281 (t0) cc_final: 0.7911 (t0) REVERT: C 851 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.8512 (ttt-90) REVERT: C 992 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.7976 (pp30) REVERT: D 114 LYS cc_start: 0.8348 (mmtt) cc_final: 0.8106 (mmtt) REVERT: D 167 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7913 (tpm-80) REVERT: D 186 TYR cc_start: 0.8786 (m-80) cc_final: 0.8199 (m-80) REVERT: D 219 MET cc_start: 0.8689 (mmm) cc_final: 0.8455 (mmt) REVERT: D 383 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8145 (tp30) REVERT: D 507 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.7957 (tpm170) REVERT: D 655 ASN cc_start: 0.8318 (t0) cc_final: 0.7956 (t0) REVERT: D 851 ARG cc_start: 0.8903 (OUTLIER) cc_final: 0.8524 (ttt-90) REVERT: D 911 MET cc_start: 0.8001 (OUTLIER) cc_final: 0.7606 (mtm) REVERT: D 992 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.7958 (pp30) outliers start: 134 outliers final: 71 residues processed: 575 average time/residue: 0.5550 time to fit residues: 384.3661 Evaluate side-chains 565 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 477 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 507 ARG Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 808 TYR Chi-restraints excluded: chain A residue 851 ARG Chi-restraints excluded: chain A residue 911 MET Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 992 GLN Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 382 LYS Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 507 ARG Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 676 ASN Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 785 GLN Chi-restraints excluded: chain B residue 808 TYR Chi-restraints excluded: chain B residue 851 ARG Chi-restraints excluded: chain B residue 900 PHE Chi-restraints excluded: chain B residue 911 MET Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 1024 VAL Chi-restraints excluded: chain B residue 1052 THR Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 228 ARG Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 280 GLN Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 491 ASP Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 507 ARG Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 676 ASN Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 808 TYR Chi-restraints excluded: chain C residue 851 ARG Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 992 GLN Chi-restraints excluded: chain C residue 1052 THR Chi-restraints excluded: chain D residue 122 CYS Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 167 ARG Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 280 GLN Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 491 ASP Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 507 ARG Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 676 ASN Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 808 TYR Chi-restraints excluded: chain D residue 851 ARG Chi-restraints excluded: chain D residue 911 MET Chi-restraints excluded: chain D residue 955 ILE Chi-restraints excluded: chain D residue 992 GLN Chi-restraints excluded: chain D residue 1024 VAL Chi-restraints excluded: chain D residue 1052 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 32 optimal weight: 5.9990 chunk 241 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 92 optimal weight: 0.8980 chunk 99 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 345 optimal weight: 0.6980 chunk 277 optimal weight: 2.9990 chunk 166 optimal weight: 3.9990 chunk 374 optimal weight: 2.9990 chunk 334 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 437 ASN ** A 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN ** B 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 306 GLN C 437 ASN ** C 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.135509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.103547 restraints weight = 47554.533| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.66 r_work: 0.3193 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 30860 Z= 0.137 Angle : 0.514 9.149 42024 Z= 0.266 Chirality : 0.040 0.243 4856 Planarity : 0.004 0.046 5164 Dihedral : 6.788 76.877 4368 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 4.07 % Allowed : 26.71 % Favored : 69.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.68 (0.14), residues: 3780 helix: 2.11 (0.10), residues: 2556 sheet: -1.98 (0.32), residues: 228 loop : -0.75 (0.18), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 360 TYR 0.026 0.002 TYR B 117 PHE 0.024 0.001 PHE B 44 TRP 0.032 0.002 TRP D 426 HIS 0.004 0.001 HIS A 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (30856) covalent geometry : angle 0.51296 / 0.27 (42016) SS BOND : bond 0.00807 / 0.40 ( 4) SS BOND : angle 1.99966 / 0.84 ( 8) hydrogen bonds : bond 0.03484 / 2.34 ( 1965) hydrogen bonds : angle 3.83554 / 2.71 ( 5811) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 480 time to evaluate : 1.158 Fit side-chains revert: symmetry clash REVERT: A 96 LYS cc_start: 0.8664 (tppp) cc_final: 0.8455 (tppp) REVERT: A 131 GLU cc_start: 0.8091 (tp30) cc_final: 0.7782 (tp30) REVERT: A 167 ARG cc_start: 0.8083 (tpm-80) cc_final: 0.7865 (tpm-80) REVERT: A 186 TYR cc_start: 0.8795 (m-80) cc_final: 0.8153 (m-80) REVERT: A 219 MET cc_start: 0.8674 (mmm) cc_final: 0.8423 (mmt) REVERT: A 383 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8151 (tp30) REVERT: A 507 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.7901 (tpm170) REVERT: A 655 ASN cc_start: 0.8058 (t0) cc_final: 0.7842 (t0) REVERT: A 851 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.7155 (tpt-90) REVERT: A 911 MET cc_start: 0.7946 (OUTLIER) cc_final: 0.7464 (mtm) REVERT: A 992 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.7895 (pp30) REVERT: B 96 LYS cc_start: 0.8707 (tppp) cc_final: 0.8343 (tppp) REVERT: B 167 ARG cc_start: 0.8072 (tpm-80) cc_final: 0.7856 (tpm-80) REVERT: B 186 TYR cc_start: 0.8780 (m-80) cc_final: 0.8140 (m-80) REVERT: B 219 MET cc_start: 0.8684 (mmm) cc_final: 0.8439 (mmt) REVERT: B 382 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8547 (mtmp) REVERT: B 507 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.7906 (tpm170) REVERT: B 655 ASN cc_start: 0.8078 (t0) cc_final: 0.7875 (t0) REVERT: B 851 ARG cc_start: 0.8857 (OUTLIER) cc_final: 0.7143 (tpt-90) REVERT: B 900 PHE cc_start: 0.7797 (OUTLIER) cc_final: 0.7557 (m-80) REVERT: B 992 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.7927 (pp30) REVERT: C 186 TYR cc_start: 0.8794 (m-80) cc_final: 0.8169 (m-80) REVERT: C 219 MET cc_start: 0.8694 (mmm) cc_final: 0.8444 (mmt) REVERT: C 507 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.7910 (tpm170) REVERT: C 851 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.7151 (tpt-90) REVERT: C 900 PHE cc_start: 0.7800 (OUTLIER) cc_final: 0.7589 (m-80) REVERT: C 992 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.7908 (pp30) REVERT: D 131 GLU cc_start: 0.8118 (tp30) cc_final: 0.7850 (tp30) REVERT: D 167 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7890 (tpm-80) REVERT: D 186 TYR cc_start: 0.8785 (m-80) cc_final: 0.8211 (m-80) REVERT: D 219 MET cc_start: 0.8678 (mmm) cc_final: 0.8424 (mmt) REVERT: D 383 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8161 (tp30) REVERT: D 507 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.7917 (tpm170) REVERT: D 655 ASN cc_start: 0.8088 (t0) cc_final: 0.7853 (t0) REVERT: D 851 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.7152 (tpt-90) REVERT: D 911 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.7496 (mtm) REVERT: D 992 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.7895 (pp30) outliers start: 119 outliers final: 72 residues processed: 559 average time/residue: 0.5615 time to fit residues: 377.8042 Evaluate side-chains 556 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 466 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 TYR Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 507 ARG Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 808 TYR Chi-restraints excluded: chain A residue 851 ARG Chi-restraints excluded: chain A residue 911 MET Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 992 GLN Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 255 ASN Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 382 LYS Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 491 ASP Chi-restraints excluded: chain B residue 507 ARG Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 676 ASN Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 785 GLN Chi-restraints excluded: chain B residue 808 TYR Chi-restraints excluded: chain B residue 851 ARG Chi-restraints excluded: chain B residue 900 PHE Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 992 GLN Chi-restraints excluded: chain B residue 1024 VAL Chi-restraints excluded: chain B residue 1052 THR Chi-restraints excluded: chain C residue 117 TYR Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 280 GLN Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 491 ASP Chi-restraints excluded: chain C residue 507 ARG Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 676 ASN Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 785 GLN Chi-restraints excluded: chain C residue 808 TYR Chi-restraints excluded: chain C residue 851 ARG Chi-restraints excluded: chain C residue 900 PHE Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 992 GLN Chi-restraints excluded: chain C residue 1052 THR Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 117 TYR Chi-restraints excluded: chain D residue 122 CYS Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 167 ARG Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 280 GLN Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 491 ASP Chi-restraints excluded: chain D residue 507 ARG Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 676 ASN Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 808 TYR Chi-restraints excluded: chain D residue 851 ARG Chi-restraints excluded: chain D residue 911 MET Chi-restraints excluded: chain D residue 955 ILE Chi-restraints excluded: chain D residue 992 GLN Chi-restraints excluded: chain D residue 1024 VAL Chi-restraints excluded: chain D residue 1052 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 256 optimal weight: 0.7980 chunk 261 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 177 optimal weight: 5.9990 chunk 374 optimal weight: 3.9990 chunk 100 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 129 optimal weight: 5.9990 chunk 343 optimal weight: 1.9990 chunk 182 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 306 GLN A 437 ASN ** A 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN ** B 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 306 GLN C 437 ASN ** C 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.133644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.101375 restraints weight = 47358.235| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.67 r_work: 0.3167 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 30860 Z= 0.221 Angle : 0.572 8.560 42024 Z= 0.296 Chirality : 0.043 0.224 4856 Planarity : 0.004 0.047 5164 Dihedral : 6.966 77.789 4368 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.52 % Allowed : 27.70 % Favored : 68.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.49 (0.14), residues: 3780 helix: 1.96 (0.10), residues: 2556 sheet: -2.06 (0.32), residues: 236 loop : -0.77 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 119 TYR 0.031 0.002 TYR C 117 PHE 0.028 0.002 PHE A 44 TRP 0.037 0.002 TRP D 426 HIS 0.005 0.001 HIS A 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.22 (30856) covalent geometry : angle 0.57135 / 0.30 (42016) SS BOND : bond 0.00878 / 0.44 ( 4) SS BOND : angle 2.34882 / 0.97 ( 8) hydrogen bonds : bond 0.04049 / 2.72 ( 1965) hydrogen bonds : angle 3.97872 / 2.82 ( 5811) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 479 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 LYS cc_start: 0.8670 (tppp) cc_final: 0.8466 (tppp) REVERT: A 131 GLU cc_start: 0.8073 (tp30) cc_final: 0.7817 (tp30) REVERT: A 161 MET cc_start: 0.8717 (mmm) cc_final: 0.7813 (mmm) REVERT: A 186 TYR cc_start: 0.8795 (m-80) cc_final: 0.8195 (m-80) REVERT: A 219 MET cc_start: 0.8694 (mmm) cc_final: 0.8442 (mmt) REVERT: A 383 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8143 (tp30) REVERT: A 507 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.7901 (tpm170) REVERT: A 655 ASN cc_start: 0.8274 (t0) cc_final: 0.7937 (t0) REVERT: A 707 CYS cc_start: 0.7124 (m) cc_final: 0.6548 (t) REVERT: A 851 ARG cc_start: 0.8892 (OUTLIER) cc_final: 0.8464 (ttt-90) REVERT: A 911 MET cc_start: 0.7907 (OUTLIER) cc_final: 0.7506 (mtm) REVERT: A 992 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.7940 (pp30) REVERT: B 96 LYS cc_start: 0.8712 (tppp) cc_final: 0.8347 (tppp) REVERT: B 131 GLU cc_start: 0.8517 (mm-30) cc_final: 0.8062 (mm-30) REVERT: B 161 MET cc_start: 0.8573 (tpp) cc_final: 0.8357 (mmm) REVERT: B 186 TYR cc_start: 0.8796 (m-80) cc_final: 0.8180 (m-80) REVERT: B 219 MET cc_start: 0.8697 (mmm) cc_final: 0.8451 (mmt) REVERT: B 382 LYS cc_start: 0.8829 (OUTLIER) cc_final: 0.8519 (mtmp) REVERT: B 507 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.7908 (tpm170) REVERT: B 655 ASN cc_start: 0.8313 (t0) cc_final: 0.7936 (t0) REVERT: B 707 CYS cc_start: 0.7114 (m) cc_final: 0.6551 (t) REVERT: B 851 ARG cc_start: 0.8885 (OUTLIER) cc_final: 0.8452 (ttt-90) REVERT: C 96 LYS cc_start: 0.8678 (tppp) cc_final: 0.8357 (tppt) REVERT: C 186 TYR cc_start: 0.8804 (m-80) cc_final: 0.8211 (m-80) REVERT: C 219 MET cc_start: 0.8698 (mmm) cc_final: 0.8450 (mmt) REVERT: C 507 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.7909 (tpm170) REVERT: C 851 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.8450 (ttt-90) REVERT: C 992 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.7961 (pp30) REVERT: D 96 LYS cc_start: 0.8681 (tppp) cc_final: 0.8345 (tppt) REVERT: D 167 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7898 (tpm-80) REVERT: D 186 TYR cc_start: 0.8798 (m-80) cc_final: 0.8183 (m-80) REVERT: D 219 MET cc_start: 0.8699 (mmm) cc_final: 0.8446 (mmt) REVERT: D 383 GLU cc_start: 0.8492 (mt-10) cc_final: 0.8140 (tp30) REVERT: D 507 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.7915 (tpm170) REVERT: D 655 ASN cc_start: 0.8331 (t0) cc_final: 0.7925 (t0) REVERT: D 851 ARG cc_start: 0.8895 (OUTLIER) cc_final: 0.8468 (ttt-90) REVERT: D 911 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.7605 (mtm) REVERT: D 992 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.7938 (pp30) outliers start: 103 outliers final: 68 residues processed: 549 average time/residue: 0.5645 time to fit residues: 371.7688 Evaluate side-chains 551 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 468 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 507 ARG Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 808 TYR Chi-restraints excluded: chain A residue 851 ARG Chi-restraints excluded: chain A residue 911 MET Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 992 GLN Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 382 LYS Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 491 ASP Chi-restraints excluded: chain B residue 507 ARG Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 676 ASN Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 785 GLN Chi-restraints excluded: chain B residue 808 TYR Chi-restraints excluded: chain B residue 851 ARG Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 1024 VAL Chi-restraints excluded: chain B residue 1052 THR Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 280 GLN Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 491 ASP Chi-restraints excluded: chain C residue 507 ARG Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 676 ASN Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 808 TYR Chi-restraints excluded: chain C residue 851 ARG Chi-restraints excluded: chain C residue 911 MET Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 992 GLN Chi-restraints excluded: chain C residue 1052 THR Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 122 CYS Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 167 ARG Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 280 GLN Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 491 ASP Chi-restraints excluded: chain D residue 507 ARG Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 676 ASN Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 808 TYR Chi-restraints excluded: chain D residue 851 ARG Chi-restraints excluded: chain D residue 911 MET Chi-restraints excluded: chain D residue 955 ILE Chi-restraints excluded: chain D residue 992 GLN Chi-restraints excluded: chain D residue 1052 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 240 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 chunk 120 optimal weight: 0.0670 chunk 209 optimal weight: 0.9980 chunk 304 optimal weight: 0.1980 chunk 124 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 300 optimal weight: 0.9990 chunk 324 optimal weight: 5.9990 chunk 157 optimal weight: 0.9980 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 437 ASN ** A 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN ** B 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 306 GLN C 437 ASN C 655 ASN ** C 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 ASN D1003 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.136218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.104027 restraints weight = 47565.326| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.67 r_work: 0.3200 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 30860 Z= 0.124 Angle : 0.523 8.860 42024 Z= 0.272 Chirality : 0.040 0.234 4856 Planarity : 0.004 0.047 5164 Dihedral : 6.817 76.781 4368 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.32 % Allowed : 27.67 % Favored : 69.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.67 (0.14), residues: 3780 helix: 2.13 (0.10), residues: 2556 sheet: -2.07 (0.31), residues: 240 loop : -0.77 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 360 TYR 0.028 0.001 TYR B 117 PHE 0.023 0.001 PHE C1013 TRP 0.038 0.002 TRP D 426 HIS 0.004 0.001 HIS A 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (30856) covalent geometry : angle 0.52232 / 0.27 (42016) SS BOND : bond 0.00847 / 0.42 ( 4) SS BOND : angle 2.01947 / 0.84 ( 8) hydrogen bonds : bond 0.03469 / 2.33 ( 1965) hydrogen bonds : angle 3.83842 / 2.71 ( 5811) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13423.19 seconds wall clock time: 228 minutes 29.90 seconds (13709.90 seconds total)