Starting phenix.real_space_refine on Mon Aug 25 20:32:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bdc_15981/08_2025/8bdc_15981.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bdc_15981/08_2025/8bdc_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8bdc_15981/08_2025/8bdc_15981.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bdc_15981/08_2025/8bdc_15981.map" model { file = "/net/cci-nas-00/data/ceres_data/8bdc_15981/08_2025/8bdc_15981.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bdc_15981/08_2025/8bdc_15981.cif" } 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-2.0-5787/lib/python3.9/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: 16 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: B, C, D Time building chain proxies: 7.83, per 1000 atoms: 0.26 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: 2.45 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.68 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: 5.72 Time building geometry restraints manager: 3.22 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: 15982 17.97 - 35.93: 1627 35.93 - 53.90: 526 53.90 - 71.87: 97 71.87 - 89.84: 36 Dihedral angle restraints: 18268 sinusoidal: 6972 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 18265 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: 0.05 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: 6.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 26.080 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 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:8.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.010 Internal consistency checks: 0.000 Total: 42.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 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 : 16.761 89.835 10928 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 aren 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 covalent geometry : bond 0.00286 (30856) covalent geometry : angle 0.41042 (42016) SS BOND : bond 0.00560 ( 4) SS BOND : angle 1.58990 ( 8) hydrogen bonds : bond 0.10883 ( 1965) hydrogen bonds : angle 4.38402 ( 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 : 0.925 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: 0.5304 time to fit residues: 419.2602 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 : 0.737 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3912 r_free = 0.3912 target = 0.139356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.107769 restraints weight = 47443.932| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.73 r_work: 0.3204 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1019 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= 0.125 Angle : 0.457 6.794 42024 Z= 0.241 Chirality : 0.038 0.164 4856 Planarity : 0.004 0.053 5164 Dihedral : 7.707 77.641 4894 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 5.44 % Allowed : 22.54 % Favored : 72.02 % 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 aren not related in a simple way. whole: 2.14 (0.14), residues: 3780 helix: 2.39 (0.10), residues: 2544 sheet: -1.41 (0.36), residues: 212 loop : -0.44 (0.19), residues: 1024 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 B 629 TRP 0.014 0.001 TRP C 426 HIS 0.002 0.001 HIS B 500 Details of bonding type rmsd covalent geometry : bond 0.00284 (30856) covalent geometry : angle 0.45558 (42016) SS BOND : bond 0.00857 ( 4) SS BOND : angle 2.41393 ( 8) hydrogen bonds : bond 0.03494 ( 1965) hydrogen bonds : angle 3.78564 ( 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 673 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 514 time to evaluate : 0.857 Fit side-chains REVERT: A 101 ASP cc_start: 0.7945 (p0) cc_final: 0.7656 (p0) REVERT: A 131 GLU cc_start: 0.8272 (tp30) cc_final: 0.7457 (tp30) REVERT: A 219 MET cc_start: 0.8635 (mmm) cc_final: 0.8379 (mmt) REVERT: A 378 ILE cc_start: 0.8239 (mm) cc_final: 0.7789 (mt) REVERT: A 383 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8210 (tp30) REVERT: A 655 ASN cc_start: 0.8097 (t0) cc_final: 0.7809 (t0) REVERT: A 851 ARG cc_start: 0.8918 (OUTLIER) cc_final: 0.6864 (tpt-90) REVERT: B 98 PHE cc_start: 0.7925 (m-80) cc_final: 0.7721 (m-80) REVERT: B 101 ASP cc_start: 0.8063 (p0) cc_final: 0.7770 (p0) REVERT: B 219 MET cc_start: 0.8619 (mmm) cc_final: 0.8357 (mmt) REVERT: B 378 ILE cc_start: 0.8181 (mm) cc_final: 0.7760 (mp) REVERT: B 655 ASN cc_start: 0.8071 (t0) cc_final: 0.7717 (t0) REVERT: B 851 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.6922 (tpt-90) REVERT: C 101 ASP cc_start: 0.8067 (p0) cc_final: 0.7759 (p0) REVERT: C 189 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.8199 (mtm) REVERT: C 219 MET cc_start: 0.8611 (mmm) cc_final: 0.8369 (mmt) REVERT: C 378 ILE cc_start: 0.8204 (mm) cc_final: 0.7779 (mp) REVERT: C 655 ASN cc_start: 0.8059 (t0) cc_final: 0.7730 (t0) REVERT: C 851 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.6858 (tpt-90) REVERT: D 101 ASP cc_start: 0.7900 (p0) cc_final: 0.7638 (p0) REVERT: D 219 MET cc_start: 0.8648 (mmm) cc_final: 0.8402 (mmt) REVERT: D 378 ILE cc_start: 0.8232 (mm) cc_final: 0.7801 (mt) REVERT: D 655 ASN cc_start: 0.8080 (t0) cc_final: 0.7808 (t0) REVERT: D 851 ARG cc_start: 0.8907 (OUTLIER) cc_final: 0.6841 (tpt-90) outliers start: 159 outliers final: 45 residues processed: 624 average time/residue: 0.5215 time to fit residues: 390.3894 Evaluate side-chains 546 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 496 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER 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 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 1024 VAL Chi-restraints excluded: chain B residue 121 SER 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 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 189 MET 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 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 769 LEU Chi-restraints excluded: chain D residue 825 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: 0.6980 chunk 4 optimal weight: 20.0000 chunk 285 optimal weight: 0.7980 chunk 242 optimal weight: 0.7980 chunk 203 optimal weight: 9.9990 chunk 142 optimal weight: 0.9990 chunk 153 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 51 optimal weight: 0.5980 chunk 105 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3904 r_free = 0.3904 target = 0.136823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.105169 restraints weight = 47693.453| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.72 r_work: 0.3200 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1247 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= 0.125 Angle : 0.450 7.700 42024 Z= 0.237 Chirality : 0.038 0.204 4856 Planarity : 0.004 0.050 5164 Dihedral : 7.054 78.052 4842 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 5.03 % Allowed : 23.87 % Favored : 71.10 % 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 aren not related in a simple way. whole: 2.05 (0.14), residues: 3780 helix: 2.37 (0.10), residues: 2544 sheet: -1.59 (0.35), residues: 220 loop : -0.59 (0.18), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 167 TYR 0.016 0.001 TYR A 621 PHE 0.014 0.001 PHE A 629 TRP 0.015 0.001 TRP C 426 HIS 0.003 0.001 HIS C 500 Details of bonding type rmsd covalent geometry : bond 0.00286 (30856) covalent geometry : angle 0.44878 (42016) SS BOND : bond 0.00735 ( 4) SS BOND : angle 2.07063 ( 8) hydrogen bonds : bond 0.03376 ( 1965) hydrogen bonds : angle 3.73693 ( 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 673 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 526 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8478 (tp) REVERT: A 135 GLN cc_start: 0.7529 (mp10) cc_final: 0.7039 (mp10) REVERT: A 140 LYS cc_start: 0.8982 (OUTLIER) cc_final: 0.8698 (mtmm) REVERT: A 219 MET cc_start: 0.8680 (mmm) cc_final: 0.8427 (mmt) REVERT: A 378 ILE cc_start: 0.8221 (mm) cc_final: 0.7768 (mt) REVERT: A 383 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8185 (tp30) REVERT: A 655 ASN cc_start: 0.8096 (t0) cc_final: 0.7855 (t0) REVERT: A 851 ARG cc_start: 0.8877 (OUTLIER) cc_final: 0.7202 (tpt-90) REVERT: A 1009 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7750 (mp) REVERT: B 101 ASP cc_start: 0.7905 (p0) cc_final: 0.7658 (p0) REVERT: B 131 GLU cc_start: 0.8295 (tp30) cc_final: 0.7243 (tp30) REVERT: B 219 MET cc_start: 0.8681 (mmm) cc_final: 0.8424 (mmt) REVERT: B 378 ILE cc_start: 0.8197 (mm) cc_final: 0.7789 (mp) REVERT: B 655 ASN cc_start: 0.8047 (t0) cc_final: 0.7814 (t0) REVERT: B 851 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.7122 (tpt-90) REVERT: B 900 PHE cc_start: 0.7732 (OUTLIER) cc_final: 0.7495 (m-80) REVERT: B 1009 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7758 (mp) REVERT: C 101 ASP cc_start: 0.7924 (p0) cc_final: 0.7689 (p0) REVERT: C 131 GLU cc_start: 0.8253 (tp30) cc_final: 0.7215 (tp30) REVERT: C 219 MET cc_start: 0.8672 (mmm) cc_final: 0.8419 (mmt) REVERT: C 378 ILE cc_start: 0.8213 (mm) cc_final: 0.7766 (mt) REVERT: C 655 ASN cc_start: 0.8036 (t0) cc_final: 0.7788 (t0) REVERT: C 851 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.7106 (tpt-90) REVERT: C 900 PHE cc_start: 0.7709 (OUTLIER) cc_final: 0.7476 (m-80) REVERT: C 1009 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7948 (mp) REVERT: D 131 GLU cc_start: 0.8259 (tp30) cc_final: 0.6717 (tp30) REVERT: D 219 MET cc_start: 0.8672 (mmm) cc_final: 0.8426 (mmt) REVERT: D 378 ILE cc_start: 0.8238 (mm) cc_final: 0.7799 (mt) REVERT: D 655 ASN cc_start: 0.8084 (t0) cc_final: 0.7786 (t0) REVERT: D 851 ARG cc_start: 0.8874 (OUTLIER) cc_final: 0.7210 (tpt-90) REVERT: D 1009 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7967 (mp) outliers start: 147 outliers final: 63 residues processed: 617 average time/residue: 0.4981 time to fit residues: 370.9896 Evaluate side-chains 569 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 494 time to evaluate : 1.144 ------------------------------------------------------------------------------- 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 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 676 ASN Chi-restraints excluded: chain A residue 769 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 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 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 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 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: 0.0270 chunk 141 optimal weight: 0.5980 chunk 369 optimal weight: 5.9990 chunk 354 optimal weight: 1.9990 chunk 239 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 324 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 225 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 overall best weight: 1.1042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN A 510 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.136235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.104589 restraints weight = 47211.024| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.75 r_work: 0.3179 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 30860 Z= 0.155 Angle : 0.482 7.716 42024 Z= 0.252 Chirality : 0.039 0.194 4856 Planarity : 0.004 0.047 5164 Dihedral : 7.073 78.700 4836 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 5.78 % Allowed : 24.01 % Favored : 70.21 % 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 aren not related in a simple way. whole: 1.90 (0.14), residues: 3780 helix: 2.25 (0.10), residues: 2552 sheet: -1.67 (0.34), residues: 220 loop : -0.63 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 167 TYR 0.018 0.002 TYR D 621 PHE 0.019 0.001 PHE B1013 TRP 0.018 0.001 TRP D 426 HIS 0.003 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00366 (30856) covalent geometry : angle 0.48088 (42016) SS BOND : bond 0.00792 ( 4) SS BOND : angle 2.14632 ( 8) hydrogen bonds : bond 0.03589 ( 1965) hydrogen bonds : angle 3.81385 ( 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 674 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 505 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 LYS cc_start: 0.8681 (tppp) cc_final: 0.8442 (tppp) REVERT: A 131 GLU cc_start: 0.8144 (tp30) cc_final: 0.7764 (tp30) REVERT: A 219 MET cc_start: 0.8676 (mmm) cc_final: 0.8433 (mmt) REVERT: A 378 ILE cc_start: 0.8250 (mm) cc_final: 0.7815 (mp) REVERT: A 383 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8205 (tp30) REVERT: A 458 LEU cc_start: 0.7594 (pp) cc_final: 0.7383 (pp) REVERT: A 482 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7426 (tp) REVERT: A 655 ASN cc_start: 0.8206 (t0) cc_final: 0.7842 (t0) REVERT: A 851 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.8469 (ttt-90) REVERT: A 1009 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7793 (mp) REVERT: B 101 ASP cc_start: 0.7886 (p0) cc_final: 0.7646 (p0) REVERT: B 132 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8423 (tp) REVERT: B 167 ARG cc_start: 0.8048 (mmm160) cc_final: 0.7816 (ttm-80) REVERT: B 219 MET cc_start: 0.8695 (mmm) cc_final: 0.8440 (mmt) REVERT: B 378 ILE cc_start: 0.8241 (mm) cc_final: 0.7813 (mp) REVERT: B 458 LEU cc_start: 0.7571 (pp) cc_final: 0.7370 (pp) REVERT: B 482 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7428 (tp) REVERT: B 655 ASN cc_start: 0.8163 (t0) cc_final: 0.7778 (t0) REVERT: B 851 ARG cc_start: 0.8895 (OUTLIER) cc_final: 0.8502 (ttt-90) REVERT: B 900 PHE cc_start: 0.7772 (OUTLIER) cc_final: 0.7538 (m-80) REVERT: B 1009 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7820 (mp) REVERT: C 96 LYS cc_start: 0.8674 (tppp) cc_final: 0.8451 (tppp) REVERT: C 101 ASP cc_start: 0.7913 (p0) cc_final: 0.7703 (p0) REVERT: C 131 GLU cc_start: 0.8059 (tp30) cc_final: 0.7800 (tp30) REVERT: C 132 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8465 (tp) REVERT: C 186 TYR cc_start: 0.8780 (m-80) cc_final: 0.8105 (m-80) REVERT: C 219 MET cc_start: 0.8683 (mmm) cc_final: 0.8435 (mmt) REVERT: C 378 ILE cc_start: 0.8245 (mm) cc_final: 0.7817 (mp) REVERT: C 458 LEU cc_start: 0.7568 (pp) cc_final: 0.7356 (pp) REVERT: C 482 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7429 (tp) REVERT: C 655 ASN cc_start: 0.8160 (t0) cc_final: 0.7786 (t0) REVERT: C 851 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.8504 (ttt-90) REVERT: C 900 PHE cc_start: 0.7786 (OUTLIER) cc_final: 0.7554 (m-80) REVERT: D 131 GLU cc_start: 0.8121 (tp30) cc_final: 0.7803 (tp30) REVERT: D 132 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8405 (tp) REVERT: D 219 MET cc_start: 0.8681 (mmm) cc_final: 0.8441 (mmt) REVERT: D 383 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8196 (tp30) REVERT: D 655 ASN cc_start: 0.8202 (t0) cc_final: 0.7831 (t0) REVERT: D 851 ARG cc_start: 0.8896 (OUTLIER) cc_final: 0.8463 (ttt-90) outliers start: 169 outliers final: 68 residues processed: 621 average time/residue: 0.5250 time to fit residues: 392.3568 Evaluate side-chains 571 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 489 time to evaluate : 1.011 ------------------------------------------------------------------------------- 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 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 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 769 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 132 LEU 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 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 656 CYS 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 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 164 ILE Chi-restraints excluded: chain C residue 184 THR 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 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 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 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 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 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: 3.9990 chunk 271 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 365 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 278 optimal weight: 1.9990 chunk 317 optimal weight: 0.8980 chunk 370 optimal weight: 4.9990 chunk 284 optimal weight: 0.7980 chunk 242 optimal weight: 1.9990 chunk 261 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 510 GLN ** A 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3887 r_free = 0.3887 target = 0.135376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.102965 restraints weight = 47570.954| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.74 r_work: 0.3186 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 30860 Z= 0.150 Angle : 0.481 7.326 42024 Z= 0.251 Chirality : 0.039 0.205 4856 Planarity : 0.004 0.047 5164 Dihedral : 7.053 78.222 4832 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 5.51 % Allowed : 24.18 % Favored : 70.31 % 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 aren not related in a simple way. whole: 1.85 (0.14), residues: 3780 helix: 2.21 (0.10), residues: 2552 sheet: -1.76 (0.34), residues: 220 loop : -0.64 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 167 TYR 0.021 0.002 TYR C 117 PHE 0.018 0.001 PHE B1013 TRP 0.020 0.001 TRP D 426 HIS 0.003 0.001 HIS B 667 Details of bonding type rmsd covalent geometry : bond 0.00351 (30856) covalent geometry : angle 0.47993 (42016) SS BOND : bond 0.00788 ( 4) SS BOND : angle 2.08083 ( 8) hydrogen bonds : bond 0.03539 ( 1965) hydrogen bonds : angle 3.80597 ( 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 659 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 498 time to evaluate : 1.116 Fit side-chains revert: symmetry clash REVERT: A 131 GLU cc_start: 0.8118 (tp30) cc_final: 0.7761 (tp30) REVERT: A 186 TYR cc_start: 0.8785 (m-80) cc_final: 0.8112 (m-80) REVERT: A 219 MET cc_start: 0.8621 (mmm) cc_final: 0.8372 (mmt) REVERT: A 383 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8195 (tp30) REVERT: A 396 MET cc_start: 0.7959 (mtp) cc_final: 0.7651 (mpp) REVERT: A 458 LEU cc_start: 0.7609 (pp) cc_final: 0.7405 (pp) REVERT: A 482 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7441 (tp) REVERT: A 655 ASN cc_start: 0.8192 (t0) cc_final: 0.7854 (t0) REVERT: A 851 ARG cc_start: 0.8892 (OUTLIER) cc_final: 0.8464 (ttt-90) REVERT: A 1009 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7872 (mp) REVERT: B 96 LYS cc_start: 0.8706 (tppp) cc_final: 0.8469 (tppp) REVERT: B 101 ASP cc_start: 0.7908 (p0) cc_final: 0.7686 (p0) REVERT: B 131 GLU cc_start: 0.8095 (tp30) cc_final: 0.7797 (tp30) REVERT: B 132 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8400 (tp) REVERT: B 167 ARG cc_start: 0.7993 (mmm160) cc_final: 0.7781 (tpm-80) REVERT: B 186 TYR cc_start: 0.8765 (m-80) cc_final: 0.8063 (m-80) REVERT: B 219 MET cc_start: 0.8650 (mmm) cc_final: 0.8394 (mmt) REVERT: B 228 ARG cc_start: 0.7594 (OUTLIER) cc_final: 0.7201 (mmm-85) REVERT: B 378 ILE cc_start: 0.8212 (mm) cc_final: 0.7768 (mp) REVERT: B 482 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7484 (tp) REVERT: B 655 ASN cc_start: 0.8138 (t0) cc_final: 0.7801 (t0) REVERT: B 851 ARG cc_start: 0.8883 (OUTLIER) cc_final: 0.8444 (ttt-90) REVERT: B 900 PHE cc_start: 0.7772 (OUTLIER) cc_final: 0.7533 (m-80) REVERT: B 1009 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7878 (mp) REVERT: C 131 GLU cc_start: 0.8166 (tp30) cc_final: 0.7845 (tp30) REVERT: C 186 TYR cc_start: 0.8784 (m-80) cc_final: 0.8073 (m-80) REVERT: C 219 MET cc_start: 0.8647 (mmm) cc_final: 0.8390 (mmt) REVERT: C 458 LEU cc_start: 0.7576 (pp) cc_final: 0.7370 (pp) REVERT: C 482 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7448 (tp) REVERT: C 655 ASN cc_start: 0.8130 (t0) cc_final: 0.7819 (t0) REVERT: C 851 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.8452 (ttt-90) REVERT: C 900 PHE cc_start: 0.7738 (OUTLIER) cc_final: 0.7499 (m-80) REVERT: D 131 GLU cc_start: 0.8191 (tp30) cc_final: 0.7880 (tp30) REVERT: D 132 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8339 (tp) REVERT: D 167 ARG cc_start: 0.8016 (mmm160) cc_final: 0.7701 (tpm-80) REVERT: D 186 TYR cc_start: 0.8768 (m-80) cc_final: 0.8099 (m-80) REVERT: D 219 MET cc_start: 0.8640 (mmm) cc_final: 0.8398 (mmt) REVERT: D 383 GLU cc_start: 0.8497 (mt-10) cc_final: 0.8195 (tp30) REVERT: D 482 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7410 (tp) REVERT: D 655 ASN cc_start: 0.8186 (t0) cc_final: 0.7834 (t0) REVERT: D 851 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.8461 (ttt-90) outliers start: 161 outliers final: 78 residues processed: 607 average time/residue: 0.5307 time to fit residues: 387.6262 Evaluate side-chains 580 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 487 time to evaluate : 1.134 ------------------------------------------------------------------------------- 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 184 THR 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 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 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 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 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 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 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 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 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 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 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 785 GLN 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: 0.6980 chunk 323 optimal weight: 7.9990 chunk 120 optimal weight: 0.4980 chunk 135 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 307 optimal weight: 6.9990 chunk 185 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 359 optimal weight: 2.9990 chunk 82 optimal weight: 7.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN A 294 ASN A 437 ASN A 510 GLN ** A 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 ASN B 437 ASN ** B 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 294 ASN C 306 GLN C 437 ASN ** C 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.134348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.101741 restraints weight = 47244.743| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.65 r_work: 0.3151 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 30860 Z= 0.251 Angle : 0.572 7.093 42024 Z= 0.298 Chirality : 0.044 0.200 4856 Planarity : 0.004 0.048 5164 Dihedral : 7.557 79.354 4832 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 5.88 % Allowed : 24.18 % Favored : 69.94 % 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 aren not related in a simple way. whole: 1.47 (0.14), residues: 3780 helix: 1.90 (0.10), residues: 2556 sheet: -1.96 (0.33), residues: 220 loop : -0.71 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 167 TYR 0.025 0.002 TYR C 117 PHE 0.020 0.002 PHE B 165 TRP 0.025 0.002 TRP D 426 HIS 0.006 0.001 HIS D 185 Details of bonding type rmsd covalent geometry : bond 0.00605 (30856) covalent geometry : angle 0.57083 (42016) SS BOND : bond 0.00948 ( 4) SS BOND : angle 2.66159 ( 8) hydrogen bonds : bond 0.04329 ( 1965) hydrogen bonds : angle 4.07577 ( 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 671 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 499 time to evaluate : 0.836 Fit side-chains REVERT: A 131 GLU cc_start: 0.8117 (tp30) cc_final: 0.7859 (tp30) REVERT: A 167 ARG cc_start: 0.8020 (mmm160) cc_final: 0.7709 (tpm-80) REVERT: A 186 TYR cc_start: 0.8805 (m-80) cc_final: 0.8243 (m-80) REVERT: A 219 MET cc_start: 0.8681 (mmm) cc_final: 0.8441 (mmt) REVERT: A 222 ASN cc_start: 0.7505 (m-40) cc_final: 0.7204 (m110) REVERT: A 383 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8167 (tp30) REVERT: A 479 GLU cc_start: 0.8402 (pt0) cc_final: 0.8196 (pt0) REVERT: A 482 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7851 (tt) REVERT: A 507 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.7919 (tpm170) REVERT: A 655 ASN cc_start: 0.8456 (t0) cc_final: 0.7998 (t0) REVERT: A 851 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.8553 (ttt-90) REVERT: A 911 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.7464 (mtm) REVERT: A 992 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.7983 (pp30) REVERT: A 1009 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7979 (mp) REVERT: B 131 GLU cc_start: 0.8084 (tp30) cc_final: 0.7879 (tp30) REVERT: B 167 ARG cc_start: 0.8046 (mmm160) cc_final: 0.7830 (ttm-80) REVERT: B 186 TYR cc_start: 0.8798 (m-80) cc_final: 0.8211 (m-80) REVERT: B 219 MET cc_start: 0.8700 (mmm) cc_final: 0.8455 (mmt) REVERT: B 222 ASN cc_start: 0.7447 (m-40) cc_final: 0.7143 (m110) REVERT: B 382 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8618 (mtpt) REVERT: B 482 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7961 (tt) REVERT: B 507 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.7924 (tpm170) REVERT: B 655 ASN cc_start: 0.8446 (t0) cc_final: 0.7991 (t0) REVERT: B 851 ARG cc_start: 0.8907 (OUTLIER) cc_final: 0.8540 (ttt-90) REVERT: B 992 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.7986 (pp30) REVERT: B 1009 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.8003 (mp) REVERT: C 186 TYR cc_start: 0.8824 (m-80) cc_final: 0.8220 (m-80) REVERT: C 219 MET cc_start: 0.8689 (mmm) cc_final: 0.8450 (mmt) REVERT: C 222 ASN cc_start: 0.7502 (m-40) cc_final: 0.7196 (m110) REVERT: C 482 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7853 (tt) REVERT: C 507 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.7915 (tpm170) REVERT: C 655 ASN cc_start: 0.8457 (t0) cc_final: 0.7996 (t0) REVERT: C 851 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.8544 (ttt-90) REVERT: C 992 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.7979 (pp30) REVERT: D 131 GLU cc_start: 0.8182 (tp30) cc_final: 0.7923 (tp30) REVERT: D 135 GLN cc_start: 0.7272 (mp10) cc_final: 0.7064 (mp10) REVERT: D 186 TYR cc_start: 0.8796 (m-80) cc_final: 0.8239 (m-80) REVERT: D 219 MET cc_start: 0.8702 (mmm) cc_final: 0.8452 (mmt) REVERT: D 222 ASN cc_start: 0.7481 (m-40) cc_final: 0.7188 (m110) REVERT: D 383 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8172 (tp30) REVERT: D 458 LEU cc_start: 0.7755 (pp) cc_final: 0.7471 (pp) REVERT: D 482 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7829 (tt) REVERT: D 507 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.7921 (tpm170) REVERT: D 655 ASN cc_start: 0.8475 (t0) cc_final: 0.7995 (t0) REVERT: D 851 ARG cc_start: 0.8907 (OUTLIER) cc_final: 0.8549 (ttt-90) REVERT: D 911 MET cc_start: 0.7941 (OUTLIER) cc_final: 0.7488 (mtm) REVERT: D 992 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.7960 (pp30) outliers start: 172 outliers final: 81 residues processed: 607 average time/residue: 0.5395 time to fit residues: 392.6088 Evaluate side-chains 578 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 476 time to evaluate : 1.149 ------------------------------------------------------------------------------- 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 181 THR 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 448 THR 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 507 ARG 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 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 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 405 SER Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 448 THR 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 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 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 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 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 482 LEU 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 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 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 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 448 THR 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 507 ARG 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 353 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 352 optimal weight: 0.9990 chunk 359 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 154 optimal weight: 0.5980 chunk 347 optimal weight: 0.8980 chunk 342 optimal weight: 2.9990 chunk 210 optimal weight: 0.5980 chunk 132 optimal weight: 4.9990 chunk 275 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1003 GLN B 306 GLN ** B 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.136708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.105105 restraints weight = 47247.356| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.68 r_work: 0.3181 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 30860 Z= 0.134 Angle : 0.492 7.796 42024 Z= 0.257 Chirality : 0.039 0.222 4856 Planarity : 0.004 0.046 5164 Dihedral : 7.193 77.384 4832 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.75 % Allowed : 25.41 % 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 aren not related in a simple way. whole: 1.70 (0.14), residues: 3780 helix: 2.12 (0.10), residues: 2556 sheet: -1.94 (0.33), residues: 220 loop : -0.73 (0.18), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 167 TYR 0.026 0.002 TYR B 117 PHE 0.021 0.001 PHE D1013 TRP 0.025 0.001 TRP D 426 HIS 0.003 0.001 HIS D 185 Details of bonding type rmsd covalent geometry : bond 0.00308 (30856) covalent geometry : angle 0.49101 (42016) SS BOND : bond 0.00832 ( 4) SS BOND : angle 2.08617 ( 8) hydrogen bonds : bond 0.03492 ( 1965) hydrogen bonds : angle 3.84181 ( 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 640 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 501 time to evaluate : 1.042 Fit side-chains REVERT: A 96 LYS cc_start: 0.8693 (tppp) cc_final: 0.8284 (tttm) REVERT: A 167 ARG cc_start: 0.8011 (mmm160) cc_final: 0.7696 (tpm-80) REVERT: A 186 TYR cc_start: 0.8821 (m-80) cc_final: 0.8226 (m-80) REVERT: A 219 MET cc_start: 0.8683 (mmm) cc_final: 0.8436 (mmt) REVERT: A 383 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8152 (tp30) REVERT: A 655 ASN cc_start: 0.8147 (t0) cc_final: 0.7822 (t0) REVERT: A 851 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.7077 (tpt-90) REVERT: A 1009 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7920 (mp) REVERT: B 96 LYS cc_start: 0.8711 (tppp) cc_final: 0.8275 (tttm) REVERT: B 186 TYR cc_start: 0.8792 (m-80) cc_final: 0.8153 (m-80) REVERT: B 219 MET cc_start: 0.8692 (mmm) cc_final: 0.8437 (mmt) REVERT: B 655 ASN cc_start: 0.8123 (t0) cc_final: 0.7834 (t0) REVERT: B 851 ARG cc_start: 0.8863 (OUTLIER) cc_final: 0.7160 (tpt-90) REVERT: B 900 PHE cc_start: 0.7736 (OUTLIER) cc_final: 0.7491 (m-80) REVERT: B 1009 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7940 (mp) REVERT: C 186 TYR cc_start: 0.8823 (m-80) cc_final: 0.8177 (m-80) REVERT: C 219 MET cc_start: 0.8692 (mmm) cc_final: 0.8445 (mmt) REVERT: C 655 ASN cc_start: 0.8133 (t0) cc_final: 0.7839 (t0) REVERT: C 851 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.7149 (tpt-90) REVERT: D 96 LYS cc_start: 0.8705 (tppp) cc_final: 0.8279 (tttm) REVERT: D 131 GLU cc_start: 0.8168 (tp30) cc_final: 0.7957 (tp30) REVERT: D 132 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8306 (tp) REVERT: D 186 TYR cc_start: 0.8799 (m-80) cc_final: 0.8210 (m-80) REVERT: D 219 MET cc_start: 0.8694 (mmm) cc_final: 0.8439 (mmt) REVERT: D 383 GLU cc_start: 0.8464 (mt-10) cc_final: 0.8142 (tp30) REVERT: D 394 ILE cc_start: 0.8401 (mt) cc_final: 0.8097 (mt) REVERT: D 655 ASN cc_start: 0.8157 (t0) cc_final: 0.7848 (t0) REVERT: D 851 ARG cc_start: 0.8868 (OUTLIER) cc_final: 0.7163 (tpt-90) outliers start: 139 outliers final: 77 residues processed: 597 average time/residue: 0.5263 time to fit residues: 378.5964 Evaluate side-chains 564 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 479 time to evaluate : 0.939 ------------------------------------------------------------------------------- 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 403 ILE Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 491 ASP 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 164 ILE Chi-restraints excluded: chain B residue 255 ASN Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 306 GLN Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 448 THR 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 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 122 CYS Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 164 ILE 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 448 THR 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 785 GLN 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 1052 THR 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 255 ASN 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 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 785 GLN 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 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: 1.9990 chunk 49 optimal weight: 2.9990 chunk 19 optimal weight: 0.4980 chunk 309 optimal weight: 3.9990 chunk 185 optimal weight: 0.8980 chunk 381 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 358 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 142 optimal weight: 0.8980 chunk 137 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 294 ASN D 437 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.137344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.105724 restraints weight = 47480.656| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.70 r_work: 0.3178 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 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 : 0.004 0.035 30860 Z= 0.154 Angle : 0.519 7.383 42024 Z= 0.269 Chirality : 0.040 0.214 4856 Planarity : 0.004 0.046 5164 Dihedral : 7.197 77.668 4832 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 4.45 % Allowed : 26.33 % 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 aren not related in a simple way. whole: 1.69 (0.14), residues: 3780 helix: 2.11 (0.10), residues: 2556 sheet: -1.95 (0.33), residues: 220 loop : -0.74 (0.18), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 360 TYR 0.025 0.002 TYR B 117 PHE 0.022 0.001 PHE B 44 TRP 0.028 0.002 TRP D 426 HIS 0.004 0.001 HIS A 389 Details of bonding type rmsd covalent geometry : bond 0.00364 (30856) covalent geometry : angle 0.51792 (42016) SS BOND : bond 0.00840 ( 4) SS BOND : angle 2.11944 ( 8) hydrogen bonds : bond 0.03618 ( 1965) hydrogen bonds : angle 3.84982 ( 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 614 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 484 time to evaluate : 0.960 Fit side-chains REVERT: A 96 LYS cc_start: 0.8675 (tppp) cc_final: 0.8468 (tppp) REVERT: A 186 TYR cc_start: 0.8828 (m-80) cc_final: 0.8232 (m-80) REVERT: A 219 MET cc_start: 0.8690 (mmm) cc_final: 0.8440 (mmt) REVERT: A 383 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8165 (tp30) REVERT: A 507 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.7921 (tpm170) REVERT: A 655 ASN cc_start: 0.8168 (t0) cc_final: 0.7873 (t0) REVERT: A 851 ARG cc_start: 0.8875 (OUTLIER) cc_final: 0.8437 (ttt-90) REVERT: A 911 MET cc_start: 0.7942 (OUTLIER) cc_final: 0.7481 (mtm) REVERT: A 1009 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7934 (mp) REVERT: B 96 LYS cc_start: 0.8676 (tppp) cc_final: 0.8455 (tppp) REVERT: B 131 GLU cc_start: 0.8476 (mm-30) cc_final: 0.7880 (mm-30) REVERT: B 161 MET cc_start: 0.8558 (tpp) cc_final: 0.8358 (mmm) REVERT: B 186 TYR cc_start: 0.8795 (m-80) cc_final: 0.8209 (m-80) REVERT: B 219 MET cc_start: 0.8707 (mmm) cc_final: 0.8452 (mmt) REVERT: B 382 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8545 (mtmp) REVERT: B 655 ASN cc_start: 0.8203 (t0) cc_final: 0.7863 (t0) REVERT: B 851 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.8427 (ttt-90) REVERT: B 900 PHE cc_start: 0.7716 (OUTLIER) cc_final: 0.7512 (m-80) REVERT: C 186 TYR cc_start: 0.8829 (m-80) cc_final: 0.8199 (m-80) REVERT: C 219 MET cc_start: 0.8702 (mmm) cc_final: 0.8450 (mmt) REVERT: C 507 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.7932 (tpm170) REVERT: C 655 ASN cc_start: 0.8199 (t0) cc_final: 0.7865 (t0) REVERT: C 851 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.8430 (ttt-90) REVERT: D 131 GLU cc_start: 0.8154 (tp30) cc_final: 0.7315 (tp30) REVERT: D 132 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8217 (tp) REVERT: D 161 MET cc_start: 0.8552 (tpp) cc_final: 0.8349 (mmm) REVERT: D 186 TYR cc_start: 0.8799 (m-80) cc_final: 0.8204 (m-80) REVERT: D 219 MET cc_start: 0.8697 (mmm) cc_final: 0.8450 (mmt) REVERT: D 383 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8152 (tp30) REVERT: D 655 ASN cc_start: 0.8227 (t0) cc_final: 0.7885 (t0) REVERT: D 851 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.8437 (ttt-90) outliers start: 130 outliers final: 76 residues processed: 574 average time/residue: 0.5402 time to fit residues: 372.2444 Evaluate side-chains 562 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 475 time to evaluate : 0.685 ------------------------------------------------------------------------------- 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 403 ILE Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 448 THR 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 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 911 MET 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 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 382 LYS Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 491 ASP 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 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 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 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 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 955 ILE 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 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 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 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 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: 4.9990 chunk 241 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 92 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 chunk 45 optimal weight: 0.3980 chunk 345 optimal weight: 0.9990 chunk 277 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 chunk 374 optimal weight: 2.9990 chunk 334 optimal weight: 1.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN A 294 ASN 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 294 ASN C 437 ASN ** C 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 ASN D 437 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.136513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.104884 restraints weight = 47501.965| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.76 r_work: 0.3172 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1836 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= 0.154 Angle : 0.527 8.885 42024 Z= 0.273 Chirality : 0.041 0.243 4856 Planarity : 0.004 0.045 5164 Dihedral : 7.182 77.526 4832 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.34 % Allowed : 26.71 % Favored : 68.95 % 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 aren not related in a simple way. whole: 1.66 (0.14), residues: 3780 helix: 2.10 (0.10), residues: 2556 sheet: -1.93 (0.33), residues: 220 loop : -0.78 (0.18), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 167 TYR 0.026 0.002 TYR B 117 PHE 0.024 0.001 PHE A 44 TRP 0.032 0.002 TRP D 426 HIS 0.004 0.001 HIS B 389 Details of bonding type rmsd covalent geometry : bond 0.00362 (30856) covalent geometry : angle 0.52598 (42016) SS BOND : bond 0.00847 ( 4) SS BOND : angle 2.11559 ( 8) hydrogen bonds : bond 0.03628 ( 1965) hydrogen bonds : angle 3.84885 ( 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 611 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 484 time to evaluate : 0.875 Fit side-chains REVERT: A 96 LYS cc_start: 0.8671 (tppp) cc_final: 0.8447 (tppp) REVERT: A 161 MET cc_start: 0.8551 (tpp) cc_final: 0.8343 (mmm) REVERT: A 186 TYR cc_start: 0.8811 (m-80) cc_final: 0.8194 (m-80) REVERT: A 219 MET cc_start: 0.8693 (mmm) cc_final: 0.8445 (mmt) REVERT: A 383 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8164 (tp30) REVERT: A 507 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.7922 (tpm170) REVERT: A 655 ASN cc_start: 0.8162 (t0) cc_final: 0.7843 (t0) REVERT: A 851 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.8448 (ttt-90) REVERT: A 992 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.7902 (pp30) REVERT: A 1009 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7918 (mp) REVERT: B 96 LYS cc_start: 0.8682 (tppp) cc_final: 0.8454 (tppp) REVERT: B 186 TYR cc_start: 0.8790 (m-80) cc_final: 0.8155 (m-80) REVERT: B 219 MET cc_start: 0.8713 (mmm) cc_final: 0.8458 (mmt) REVERT: B 382 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8535 (mtmp) REVERT: B 507 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.7920 (tpm170) REVERT: B 655 ASN cc_start: 0.8198 (t0) cc_final: 0.7856 (t0) REVERT: B 851 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.8439 (ttt-90) REVERT: B 900 PHE cc_start: 0.7714 (OUTLIER) cc_final: 0.7508 (m-80) REVERT: B 992 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.7889 (pp30) REVERT: C 132 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8335 (tp) REVERT: C 167 ARG cc_start: 0.8078 (tpm-80) cc_final: 0.7867 (tpm-80) REVERT: C 186 TYR cc_start: 0.8830 (m-80) cc_final: 0.8179 (m-80) REVERT: C 219 MET cc_start: 0.8703 (mmm) cc_final: 0.8456 (mmt) REVERT: C 655 ASN cc_start: 0.8197 (t0) cc_final: 0.7863 (t0) REVERT: C 851 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.8444 (ttt-90) REVERT: C 992 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.7914 (pp30) REVERT: D 186 TYR cc_start: 0.8787 (m-80) cc_final: 0.8177 (m-80) REVERT: D 219 MET cc_start: 0.8712 (mmm) cc_final: 0.8460 (mmt) REVERT: D 383 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8138 (tp30) REVERT: D 507 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.7938 (tpm170) REVERT: D 655 ASN cc_start: 0.8223 (t0) cc_final: 0.7883 (t0) REVERT: D 851 ARG cc_start: 0.8889 (OUTLIER) cc_final: 0.8454 (ttt-90) REVERT: D 911 MET cc_start: 0.7904 (OUTLIER) cc_final: 0.7435 (mtm) REVERT: D 992 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.7897 (pp30) outliers start: 127 outliers final: 84 residues processed: 568 average time/residue: 0.5198 time to fit residues: 354.7262 Evaluate side-chains 571 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 471 time to evaluate : 0.893 ------------------------------------------------------------------------------- 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 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 448 THR 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 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 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 117 TYR Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 128 ILE 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 382 LYS Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 491 ASP 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 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 992 GLN 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 132 LEU Chi-restraints excluded: chain C residue 164 ILE 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 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 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 128 ILE 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 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 504 LEU Chi-restraints excluded: chain D residue 507 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 256 optimal weight: 0.0770 chunk 261 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 177 optimal weight: 4.9990 chunk 374 optimal weight: 3.9990 chunk 100 optimal weight: 8.9990 chunk 107 optimal weight: 9.9990 chunk 129 optimal weight: 4.9990 chunk 343 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 overall best weight: 1.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN 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 294 ASN C 306 GLN C 437 ASN ** C 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 ASN D 437 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.134135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.102499 restraints weight = 47369.625| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.67 r_work: 0.3168 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 30860 Z= 0.185 Angle : 0.556 8.679 42024 Z= 0.288 Chirality : 0.042 0.223 4856 Planarity : 0.004 0.045 5164 Dihedral : 7.281 77.771 4832 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.97 % Allowed : 27.33 % Favored : 68.71 % 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 aren not related in a simple way. whole: 1.56 (0.14), residues: 3780 helix: 2.02 (0.10), residues: 2556 sheet: -1.97 (0.33), residues: 220 loop : -0.80 (0.18), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 119 TYR 0.036 0.002 TYR B 117 PHE 0.027 0.002 PHE B 44 TRP 0.036 0.002 TRP B 426 HIS 0.004 0.001 HIS C 185 Details of bonding type rmsd covalent geometry : bond 0.00443 (30856) covalent geometry : angle 0.55505 (42016) SS BOND : bond 0.00858 ( 4) SS BOND : angle 2.21705 ( 8) hydrogen bonds : bond 0.03861 ( 1965) hydrogen bonds : angle 3.91445 ( 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 599 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 483 time to evaluate : 1.325 Fit side-chains REVERT: A 131 GLU cc_start: 0.8472 (mm-30) cc_final: 0.8073 (mm-30) REVERT: A 186 TYR cc_start: 0.8806 (m-80) cc_final: 0.8184 (m-80) REVERT: A 219 MET cc_start: 0.8691 (mmm) cc_final: 0.8443 (mmt) REVERT: A 383 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8154 (tp30) REVERT: A 507 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.7920 (tpm170) REVERT: A 655 ASN cc_start: 0.8215 (t0) cc_final: 0.7896 (t0) REVERT: A 851 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.8470 (ttt-90) REVERT: B 167 ARG cc_start: 0.8072 (tpm-80) cc_final: 0.7855 (tpm-80) REVERT: B 186 TYR cc_start: 0.8788 (m-80) cc_final: 0.8148 (m-80) REVERT: B 219 MET cc_start: 0.8704 (mmm) cc_final: 0.8459 (mmt) REVERT: B 382 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8548 (mtmp) REVERT: B 507 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.7916 (tpm170) REVERT: B 655 ASN cc_start: 0.8281 (t0) cc_final: 0.7885 (t0) REVERT: B 851 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.8478 (ttt-90) REVERT: C 96 LYS cc_start: 0.8674 (tppp) cc_final: 0.8373 (tppt) REVERT: C 131 GLU cc_start: 0.8451 (mm-30) cc_final: 0.7925 (mm-30) REVERT: C 186 TYR cc_start: 0.8805 (m-80) cc_final: 0.8226 (m-80) REVERT: C 219 MET cc_start: 0.8699 (mmm) cc_final: 0.8447 (mmt) REVERT: C 507 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.7926 (tpm170) REVERT: C 655 ASN cc_start: 0.8282 (t0) cc_final: 0.7882 (t0) REVERT: C 851 ARG cc_start: 0.8883 (OUTLIER) cc_final: 0.8473 (ttt-90) REVERT: D 186 TYR cc_start: 0.8775 (m-80) cc_final: 0.8163 (m-80) REVERT: D 219 MET cc_start: 0.8701 (mmm) cc_final: 0.8447 (mmt) REVERT: D 383 GLU cc_start: 0.8479 (mt-10) cc_final: 0.8146 (tp30) REVERT: D 507 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.7932 (tpm170) REVERT: D 655 ASN cc_start: 0.8314 (t0) cc_final: 0.7935 (t0) REVERT: D 851 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.8487 (ttt-90) outliers start: 116 outliers final: 86 residues processed: 566 average time/residue: 0.5397 time to fit residues: 365.5699 Evaluate side-chains 561 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 466 time to evaluate : 1.231 ------------------------------------------------------------------------------- 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 272 THR Chi-restraints excluded: chain A residue 280 GLN 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 448 THR 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 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 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 128 ILE 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 448 THR Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 491 ASP 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 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 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 117 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 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 504 LEU Chi-restraints excluded: chain C residue 507 ARG 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 911 MET Chi-restraints excluded: chain C residue 955 ILE 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 128 ILE Chi-restraints excluded: chain D residue 164 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 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 504 LEU Chi-restraints excluded: chain D residue 507 ARG 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 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: 5.9990 chunk 120 optimal weight: 5.9990 chunk 209 optimal weight: 0.3980 chunk 304 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 300 optimal weight: 3.9990 chunk 324 optimal weight: 0.8980 chunk 157 optimal weight: 0.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN 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 294 ASN ** C 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN ** C 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 ASN D 437 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.134038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.102236 restraints weight = 47664.604| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.68 r_work: 0.3161 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.342 30860 Z= 0.270 Angle : 0.845 59.199 42024 Z= 0.494 Chirality : 0.044 0.555 4856 Planarity : 0.004 0.089 5164 Dihedral : 7.306 77.812 4832 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.07 % Allowed : 27.09 % Favored : 68.84 % Cbeta Deviations : 0.03 % 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 aren not related in a simple way. whole: 1.53 (0.14), residues: 3780 helix: 2.00 (0.10), residues: 2556 sheet: -1.97 (0.33), residues: 224 loop : -0.81 (0.18), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 167 TYR 0.202 0.003 TYR C 117 PHE 0.022 0.002 PHE C1013 TRP 0.032 0.002 TRP D 426 HIS 0.004 0.001 HIS C 185 Details of bonding type rmsd covalent geometry : bond 0.00668 (30856) covalent geometry : angle 0.84474 (42016) SS BOND : bond 0.00836 ( 4) SS BOND : angle 2.25947 ( 8) hydrogen bonds : bond 0.03954 ( 1965) hydrogen bonds : angle 3.92396 ( 5811) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12731.86 seconds wall clock time: 216 minutes 26.37 seconds (12986.37 seconds total)