Starting phenix.real_space_refine on Thu Jun 26 12:59:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bdc_15981/06_2025/8bdc_15981.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bdc_15981/06_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_15981/06_2025/8bdc_15981.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bdc_15981/06_2025/8bdc_15981.map" model { file = "/net/cci-nas-00/data/ceres_data/8bdc_15981/06_2025/8bdc_15981.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bdc_15981/06_2025/8bdc_15981.cif" } resolution = 2.65 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 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): 2.23s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 8, 'ARG:plan': 11, 'TYR:plan': 1, 'ASN:plan1': 8, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 26, 'ASP:plan': 14} 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: C, B, D Time building chain proxies: 23.18, per 1000 atoms: 0.77 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 C 54 " - pdb=" SG CYS C 68 " distance=2.04 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 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: 9.07 Conformation dependent library (CDL) restraints added in 5.5 seconds 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7328 Finding SS restraints... Secondary structure from input PDB file: 188 helices and 12 sheets defined 69.5% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.69 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: 12.00 Time building geometry restraints manager: 10.71 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: 0.23 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 6.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.310 Check model and map are aligned: 0.290 Set scattering table: 0.310 Process input model: 78.010 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.090 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: 0.020 Load rotamer database and sin/cos tables:13.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.780 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.012 0.001 TRP D 877 HIS 0.002 0.000 HIS A 500 PHE 0.013 0.001 PHE A 165 TYR 0.015 0.001 TYR D 621 ARG 0.001 0.000 ARG A 998 Details of bonding type rmsd hydrogen bonds : bond 0.10883 ( 1965) hydrogen bonds : angle 4.38402 ( 5811) SS BOND : bond 0.00560 ( 4) SS BOND : angle 1.58990 ( 8) covalent geometry : bond 0.00286 (30856) covalent geometry : angle 0.41042 (42016) *********************** 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 : 2.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7559 (mt-10) REVERT: A 219 MET cc_start: 0.8308 (mmm) cc_final: 0.8055 (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: 0.7277 (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: 0.8015 (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: 0.8022 (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: 0.8048 (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: 1.3122 time to fit residues: 1038.9379 Evaluate side-chains 547 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 495 time to evaluate : 6.357 ------------------------------------------------------------------------------- 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 324 optimal weight: 0.5980 chunk 291 optimal weight: 9.9990 chunk 161 optimal weight: 3.9990 chunk 99 optimal weight: 8.9990 chunk 196 optimal weight: 10.0000 chunk 155 optimal weight: 1.9990 chunk 300 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 chunk 183 optimal weight: 0.5980 chunk 224 optimal weight: 6.9990 chunk 348 optimal weight: 0.2980 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 ASN B 294 ASN B 317 ASN B 437 ASN ** B 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 222 ASN C 294 ASN C 317 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.136325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.104778 restraints weight = 47098.216| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.73 r_work: 0.3171 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 30860 Z= 0.194 Angle : 0.515 6.855 42024 Z= 0.269 Chirality : 0.041 0.143 4856 Planarity : 0.004 0.054 5164 Dihedral : 7.931 78.926 4894 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 5.85 % Allowed : 21.96 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.14), residues: 3780 helix: 2.15 (0.10), residues: 2548 sheet: -1.64 (0.34), residues: 220 loop : -0.50 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 426 HIS 0.003 0.001 HIS B 667 PHE 0.017 0.002 PHE D 629 TYR 0.019 0.002 TYR B 621 ARG 0.003 0.000 ARG B 167 Details of bonding type rmsd hydrogen bonds : bond 0.03982 ( 1965) hydrogen bonds : angle 3.95163 ( 5811) SS BOND : bond 0.00990 ( 4) SS BOND : angle 2.75900 ( 8) covalent geometry : bond 0.00464 (30856) covalent geometry : angle 0.51372 (42016) *********************** 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 693 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 522 time to evaluate : 3.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 ASP cc_start: 0.7983 (p0) cc_final: 0.7698 (p0) REVERT: A 219 MET cc_start: 0.8662 (mmm) cc_final: 0.8410 (mmt) REVERT: A 378 ILE cc_start: 0.8281 (mm) cc_final: 0.7860 (mt) REVERT: A 383 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8199 (tp30) REVERT: A 655 ASN cc_start: 0.8350 (t0) cc_final: 0.7903 (t0) REVERT: A 851 ARG cc_start: 0.8919 (OUTLIER) cc_final: 0.8490 (ttt-90) REVERT: B 101 ASP cc_start: 0.8097 (p0) cc_final: 0.7805 (p0) REVERT: B 219 MET cc_start: 0.8678 (mmm) cc_final: 0.8424 (mmt) REVERT: B 378 ILE cc_start: 0.8251 (mm) cc_final: 0.7819 (mt) REVERT: B 655 ASN cc_start: 0.8334 (t0) cc_final: 0.7893 (t0) REVERT: B 851 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.8494 (ttt-90) REVERT: C 98 PHE cc_start: 0.7965 (m-80) cc_final: 0.7643 (m-80) REVERT: C 101 ASP cc_start: 0.8090 (p0) cc_final: 0.7808 (p0) REVERT: C 219 MET cc_start: 0.8670 (mmm) cc_final: 0.8422 (mmt) REVERT: C 378 ILE cc_start: 0.8223 (mm) cc_final: 0.7795 (mt) REVERT: C 655 ASN cc_start: 0.8320 (t0) cc_final: 0.7853 (t0) REVERT: C 851 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.8501 (ttt-90) REVERT: D 101 ASP cc_start: 0.7943 (p0) cc_final: 0.7670 (p0) REVERT: D 219 MET cc_start: 0.8664 (mmm) cc_final: 0.8412 (mmt) REVERT: D 330 GLU cc_start: 0.8083 (tt0) cc_final: 0.7760 (tt0) REVERT: D 378 ILE cc_start: 0.8295 (mm) cc_final: 0.7871 (mt) REVERT: D 383 GLU cc_start: 0.8506 (mt-10) cc_final: 0.8158 (tp30) REVERT: D 435 GLU cc_start: 0.8284 (tm-30) cc_final: 0.7864 (tp30) REVERT: D 655 ASN cc_start: 0.8341 (t0) cc_final: 0.7875 (t0) REVERT: D 851 ARG cc_start: 0.8907 (OUTLIER) cc_final: 0.8468 (ttt-90) outliers start: 171 outliers final: 61 residues processed: 628 average time/residue: 1.2325 time to fit residues: 931.9151 Evaluate side-chains 558 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 493 time to evaluate : 3.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 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 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 955 ILE Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 225 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 405 SER 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 851 ARG Chi-restraints excluded: chain C residue 121 SER 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 676 ASN Chi-restraints excluded: chain C residue 697 LEU 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 D residue 121 SER Chi-restraints excluded: chain D residue 122 CYS Chi-restraints excluded: chain D residue 184 THR 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 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 851 ARG Chi-restraints excluded: chain D residue 955 ILE 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 186 optimal weight: 7.9990 chunk 251 optimal weight: 0.3980 chunk 118 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 246 optimal weight: 3.9990 chunk 249 optimal weight: 0.9980 chunk 200 optimal weight: 0.0670 chunk 220 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 378 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 overall best weight: 0.8922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 671 GLN A1003 GLN B 671 GLN B1003 GLN ** C 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1003 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.136222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.104301 restraints weight = 47567.626| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.79 r_work: 0.3185 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1368 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 : 0.462 6.368 42024 Z= 0.244 Chirality : 0.038 0.137 4856 Planarity : 0.004 0.049 5164 Dihedral : 7.322 78.325 4850 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 5.44 % Allowed : 23.29 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.14), residues: 3780 helix: 2.24 (0.10), residues: 2544 sheet: -1.71 (0.34), residues: 220 loop : -0.66 (0.18), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 426 HIS 0.003 0.001 HIS B 500 PHE 0.022 0.001 PHE C 44 TYR 0.016 0.001 TYR D 621 ARG 0.003 0.000 ARG B 167 Details of bonding type rmsd hydrogen bonds : bond 0.03503 ( 1965) hydrogen bonds : angle 3.80729 ( 5811) SS BOND : bond 0.00733 ( 4) SS BOND : angle 2.14341 ( 8) covalent geometry : bond 0.00312 (30856) covalent geometry : angle 0.46124 (42016) *********************** 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 676 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 517 time to evaluate : 3.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 GLU cc_start: 0.8270 (tp30) cc_final: 0.7356 (tp30) REVERT: A 132 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8444 (tp) REVERT: A 161 MET cc_start: 0.8287 (tpp) cc_final: 0.7704 (mmm) REVERT: A 219 MET cc_start: 0.8686 (mmm) cc_final: 0.8444 (mmt) REVERT: A 222 ASN cc_start: 0.7474 (m-40) cc_final: 0.7162 (m110) REVERT: A 378 ILE cc_start: 0.8239 (mm) cc_final: 0.7798 (mt) REVERT: A 383 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8191 (tp30) REVERT: A 655 ASN cc_start: 0.8157 (t0) cc_final: 0.7820 (t0) REVERT: A 851 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.7246 (tpt-90) REVERT: A 1009 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7844 (mp) REVERT: B 101 ASP cc_start: 0.7942 (p0) cc_final: 0.7715 (p0) REVERT: B 131 GLU cc_start: 0.8283 (tp30) cc_final: 0.7368 (tp30) REVERT: B 132 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8399 (tp) REVERT: B 161 MET cc_start: 0.8285 (tpp) cc_final: 0.7704 (mmm) REVERT: B 219 MET cc_start: 0.8680 (mmm) cc_final: 0.8425 (mmt) REVERT: B 222 ASN cc_start: 0.7469 (m-40) cc_final: 0.7157 (m110) REVERT: B 378 ILE cc_start: 0.8240 (mm) cc_final: 0.7797 (mt) REVERT: B 655 ASN cc_start: 0.8160 (t0) cc_final: 0.7821 (t0) REVERT: B 851 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.7234 (tpt-90) REVERT: B 900 PHE cc_start: 0.7721 (OUTLIER) cc_final: 0.7489 (m-80) REVERT: B 1009 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7903 (mp) REVERT: C 96 LYS cc_start: 0.8700 (tppp) cc_final: 0.8480 (tppp) REVERT: C 98 PHE cc_start: 0.7973 (m-10) cc_final: 0.7613 (m-80) REVERT: C 101 ASP cc_start: 0.7965 (p0) cc_final: 0.7744 (p0) REVERT: C 131 GLU cc_start: 0.8273 (tp30) cc_final: 0.7385 (tp30) REVERT: C 132 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8461 (tp) REVERT: C 161 MET cc_start: 0.8309 (tpp) cc_final: 0.7716 (mmm) REVERT: C 186 TYR cc_start: 0.8767 (m-80) cc_final: 0.8102 (m-80) REVERT: C 219 MET cc_start: 0.8697 (mmm) cc_final: 0.8447 (mmt) REVERT: C 222 ASN cc_start: 0.7476 (m-40) cc_final: 0.7179 (m110) REVERT: C 378 ILE cc_start: 0.8245 (mm) cc_final: 0.7797 (mt) REVERT: C 655 ASN cc_start: 0.8133 (t0) cc_final: 0.7772 (t0) REVERT: C 851 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.7251 (tpt-90) REVERT: C 900 PHE cc_start: 0.7678 (OUTLIER) cc_final: 0.7447 (m-80) REVERT: D 96 LYS cc_start: 0.8663 (tppp) cc_final: 0.8424 (tmmt) REVERT: D 131 GLU cc_start: 0.8267 (tp30) cc_final: 0.7334 (tp30) REVERT: D 132 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8430 (tp) REVERT: D 161 MET cc_start: 0.8301 (tpp) cc_final: 0.7702 (mmm) REVERT: D 219 MET cc_start: 0.8705 (mmm) cc_final: 0.8451 (mmt) REVERT: D 222 ASN cc_start: 0.7381 (m-40) cc_final: 0.7096 (m110) REVERT: D 330 GLU cc_start: 0.7961 (tt0) cc_final: 0.7739 (tt0) REVERT: D 378 ILE cc_start: 0.8255 (mm) cc_final: 0.7808 (mt) REVERT: D 396 MET cc_start: 0.7888 (mtp) cc_final: 0.7610 (mtp) REVERT: D 458 LEU cc_start: 0.7572 (pp) cc_final: 0.7354 (pp) REVERT: D 482 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7294 (tp) REVERT: D 655 ASN cc_start: 0.8127 (t0) cc_final: 0.7787 (t0) REVERT: D 851 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.7250 (tpt-90) outliers start: 159 outliers final: 74 residues processed: 624 average time/residue: 1.2120 time to fit residues: 911.5602 Evaluate side-chains 577 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 490 time to evaluate : 3.205 ------------------------------------------------------------------------------- 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 164 ILE Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 785 GLN Chi-restraints excluded: chain A residue 808 TYR Chi-restraints excluded: chain A residue 851 ARG 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 184 THR Chi-restraints excluded: chain B residue 255 ASN 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 448 THR Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 676 ASN Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 785 GLN Chi-restraints excluded: chain B residue 808 TYR Chi-restraints excluded: chain B residue 851 ARG Chi-restraints excluded: chain B residue 900 PHE Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 1009 LEU Chi-restraints excluded: chain B residue 1024 VAL Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 255 ASN 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 448 THR Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 491 ASP Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 656 CYS Chi-restraints excluded: chain C residue 676 ASN Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 808 TYR Chi-restraints excluded: chain C residue 851 ARG Chi-restraints excluded: chain C residue 900 PHE Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain 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 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 17 optimal weight: 0.1980 chunk 238 optimal weight: 0.8980 chunk 213 optimal weight: 2.9990 chunk 195 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 chunk 132 optimal weight: 6.9990 chunk 90 optimal weight: 8.9990 chunk 233 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 377 optimal weight: 0.7980 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 GLN ** C 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.135960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.103480 restraints weight = 47710.209| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.69 r_work: 0.3158 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 30860 Z= 0.201 Angle : 0.522 7.714 42024 Z= 0.272 Chirality : 0.041 0.149 4856 Planarity : 0.004 0.047 5164 Dihedral : 7.519 79.014 4848 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 6.26 % Allowed : 22.91 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.14), residues: 3780 helix: 2.02 (0.10), residues: 2552 sheet: -1.80 (0.34), residues: 220 loop : -0.67 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 426 HIS 0.004 0.001 HIS C 185 PHE 0.019 0.002 PHE A1013 TYR 0.020 0.002 TYR B 621 ARG 0.004 0.000 ARG C 167 Details of bonding type rmsd hydrogen bonds : bond 0.03982 ( 1965) hydrogen bonds : angle 3.95854 ( 5811) SS BOND : bond 0.00878 ( 4) SS BOND : angle 2.42997 ( 8) covalent geometry : bond 0.00483 (30856) covalent geometry : angle 0.52122 (42016) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 489 time to evaluate : 2.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 GLU cc_start: 0.8077 (tp30) cc_final: 0.7838 (tp30) REVERT: A 219 MET cc_start: 0.8647 (mmm) cc_final: 0.8393 (mmt) REVERT: A 222 ASN cc_start: 0.7536 (m-40) cc_final: 0.7231 (m110) REVERT: A 228 ARG cc_start: 0.7514 (OUTLIER) cc_final: 0.7311 (mmm-85) REVERT: A 378 ILE cc_start: 0.8205 (mm) cc_final: 0.7757 (mp) REVERT: A 383 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8157 (tp30) REVERT: A 479 GLU cc_start: 0.8417 (pt0) cc_final: 0.8203 (pt0) REVERT: A 482 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7544 (tp) REVERT: A 655 ASN cc_start: 0.8398 (t0) cc_final: 0.7972 (t0) REVERT: A 851 ARG cc_start: 0.8905 (OUTLIER) cc_final: 0.8527 (ttt-90) REVERT: A 911 MET cc_start: 0.7959 (OUTLIER) cc_final: 0.7666 (mtm) REVERT: A 992 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.8187 (pt0) REVERT: A 1009 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7965 (mp) REVERT: B 131 GLU cc_start: 0.8089 (tp30) cc_final: 0.7850 (tp30) REVERT: B 135 GLN cc_start: 0.7119 (mp10) cc_final: 0.6889 (mp10) REVERT: B 219 MET cc_start: 0.8664 (mmm) cc_final: 0.8414 (mmt) REVERT: B 222 ASN cc_start: 0.7523 (m-40) cc_final: 0.7240 (m110) REVERT: B 228 ARG cc_start: 0.7567 (OUTLIER) cc_final: 0.7362 (mmm-85) REVERT: B 382 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8602 (mtpt) REVERT: B 458 LEU cc_start: 0.7689 (pp) cc_final: 0.7486 (pp) REVERT: B 482 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7543 (tp) REVERT: B 655 ASN cc_start: 0.8397 (t0) cc_final: 0.7962 (t0) REVERT: B 851 ARG cc_start: 0.8898 (OUTLIER) cc_final: 0.8513 (ttt-90) REVERT: B 992 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.8186 (pt0) REVERT: B 1009 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7981 (mp) REVERT: C 101 ASP cc_start: 0.7970 (p0) cc_final: 0.7769 (p0) REVERT: C 131 GLU cc_start: 0.8059 (tp30) cc_final: 0.7811 (tp30) REVERT: C 219 MET cc_start: 0.8681 (mmm) cc_final: 0.8429 (mmt) REVERT: C 222 ASN cc_start: 0.7549 (m-40) cc_final: 0.7261 (m110) REVERT: C 382 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8609 (mtpt) REVERT: C 482 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7568 (tp) REVERT: C 655 ASN cc_start: 0.8378 (t0) cc_final: 0.7931 (t0) REVERT: C 851 ARG cc_start: 0.8895 (OUTLIER) cc_final: 0.8510 (ttt-90) REVERT: C 992 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.8201 (pt0) REVERT: D 219 MET cc_start: 0.8660 (mmm) cc_final: 0.8399 (mmt) REVERT: D 222 ASN cc_start: 0.7521 (m-40) cc_final: 0.7224 (m110) REVERT: D 330 GLU cc_start: 0.7922 (tt0) cc_final: 0.7557 (tt0) REVERT: D 383 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8151 (tp30) REVERT: D 396 MET cc_start: 0.7853 (mtp) cc_final: 0.7544 (mtp) REVERT: D 435 GLU cc_start: 0.8309 (tm-30) cc_final: 0.7847 (tp30) REVERT: D 482 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7492 (tp) REVERT: D 655 ASN cc_start: 0.8390 (t0) cc_final: 0.7938 (t0) REVERT: D 851 ARG cc_start: 0.8903 (OUTLIER) cc_final: 0.8525 (ttt-90) REVERT: D 911 MET cc_start: 0.7970 (OUTLIER) cc_final: 0.7628 (mtm) REVERT: D 992 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.8188 (pt0) outliers start: 183 outliers final: 80 residues processed: 611 average time/residue: 1.1928 time to fit residues: 881.6945 Evaluate side-chains 576 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 476 time to evaluate : 3.251 ------------------------------------------------------------------------------- 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 228 ARG 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 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 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 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 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 328 VAL 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 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 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 328 VAL Chi-restraints excluded: chain C residue 382 LYS 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 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 122 CYS Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 280 GLN Chi-restraints excluded: chain D residue 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 482 LEU Chi-restraints excluded: chain D residue 491 ASP Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 656 CYS Chi-restraints excluded: chain D residue 676 ASN Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 808 TYR Chi-restraints excluded: chain D residue 851 ARG Chi-restraints excluded: chain D residue 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 59 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 137 optimal weight: 2.9990 chunk 243 optimal weight: 0.6980 chunk 353 optimal weight: 1.9990 chunk 200 optimal weight: 0.5980 chunk 173 optimal weight: 0.9990 chunk 168 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 291 optimal weight: 9.9990 chunk 193 optimal weight: 10.0000 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN ** A 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 ASN ** B 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 294 ASN C 671 GLN D 294 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.135206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.103194 restraints weight = 47503.749| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.76 r_work: 0.3168 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 30860 Z= 0.147 Angle : 0.488 7.136 42024 Z= 0.254 Chirality : 0.039 0.160 4856 Planarity : 0.004 0.047 5164 Dihedral : 7.354 77.938 4848 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 5.40 % Allowed : 23.87 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.14), residues: 3780 helix: 2.13 (0.10), residues: 2552 sheet: -1.80 (0.33), residues: 220 loop : -0.71 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 426 HIS 0.003 0.001 HIS B 185 PHE 0.015 0.001 PHE A1013 TYR 0.021 0.002 TYR D 117 ARG 0.004 0.000 ARG D 167 Details of bonding type rmsd hydrogen bonds : bond 0.03585 ( 1965) hydrogen bonds : angle 3.85313 ( 5811) SS BOND : bond 0.00845 ( 4) SS BOND : angle 2.20758 ( 8) covalent geometry : bond 0.00346 (30856) covalent geometry : angle 0.48709 (42016) *********************** 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 655 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 497 time to evaluate : 3.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 LYS cc_start: 0.8709 (tppp) cc_final: 0.8350 (tttm) REVERT: A 135 GLN cc_start: 0.7131 (mp10) cc_final: 0.6902 (mp10) REVERT: A 186 TYR cc_start: 0.8827 (m-80) cc_final: 0.8189 (m-80) REVERT: A 219 MET cc_start: 0.8666 (mmm) cc_final: 0.8424 (mmt) REVERT: A 222 ASN cc_start: 0.7555 (m-40) cc_final: 0.7252 (m110) REVERT: A 383 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8189 (tp30) REVERT: A 655 ASN cc_start: 0.8251 (t0) cc_final: 0.7905 (t0) REVERT: A 851 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.7245 (tpt-90) REVERT: A 992 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.8178 (pt0) REVERT: A 1009 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7937 (mp) REVERT: B 96 LYS cc_start: 0.8691 (tppp) cc_final: 0.8318 (tttm) REVERT: B 131 GLU cc_start: 0.8136 (tp30) cc_final: 0.7867 (tp30) REVERT: B 132 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8369 (tp) REVERT: B 135 GLN cc_start: 0.7228 (mp10) cc_final: 0.6981 (mp10) REVERT: B 219 MET cc_start: 0.8688 (mmm) cc_final: 0.8441 (mmt) REVERT: B 222 ASN cc_start: 0.7552 (m-40) cc_final: 0.7265 (m110) REVERT: B 378 ILE cc_start: 0.8287 (mm) cc_final: 0.7842 (mp) REVERT: B 655 ASN cc_start: 0.8241 (t0) cc_final: 0.7897 (t0) REVERT: B 851 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.7230 (tpt-90) REVERT: B 900 PHE cc_start: 0.7706 (OUTLIER) cc_final: 0.7466 (m-80) REVERT: B 992 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.8164 (pt0) REVERT: B 1009 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7949 (mp) REVERT: C 135 GLN cc_start: 0.7081 (mp10) cc_final: 0.6847 (mp10) REVERT: C 186 TYR cc_start: 0.8816 (m-80) cc_final: 0.8161 (m-80) REVERT: C 219 MET cc_start: 0.8689 (mmm) cc_final: 0.8435 (mmt) REVERT: C 222 ASN cc_start: 0.7526 (m-40) cc_final: 0.7238 (m110) REVERT: C 655 ASN cc_start: 0.8200 (t0) cc_final: 0.7864 (t0) REVERT: C 851 ARG cc_start: 0.8877 (OUTLIER) cc_final: 0.8484 (ttt-90) REVERT: C 900 PHE cc_start: 0.7714 (OUTLIER) cc_final: 0.7473 (m-80) REVERT: C 992 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.8175 (pt0) REVERT: D 131 GLU cc_start: 0.8099 (tp30) cc_final: 0.7784 (tp30) REVERT: D 132 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8377 (tp) REVERT: D 186 TYR cc_start: 0.8803 (m-80) cc_final: 0.8204 (m-80) REVERT: D 219 MET cc_start: 0.8707 (mmm) cc_final: 0.8449 (mmt) REVERT: D 222 ASN cc_start: 0.7520 (m-40) cc_final: 0.7221 (m110) REVERT: D 330 GLU cc_start: 0.8009 (tt0) cc_final: 0.7610 (pt0) REVERT: D 378 ILE cc_start: 0.8243 (mm) cc_final: 0.7806 (mp) REVERT: D 383 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8160 (tp30) REVERT: D 435 GLU cc_start: 0.8307 (tm-30) cc_final: 0.7935 (tp30) REVERT: D 655 ASN cc_start: 0.8218 (t0) cc_final: 0.7870 (t0) REVERT: D 851 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.8494 (ttt-90) REVERT: D 900 PHE cc_start: 0.7795 (OUTLIER) cc_final: 0.7566 (m-80) REVERT: D 992 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.8172 (pt0) outliers start: 158 outliers final: 81 residues processed: 598 average time/residue: 1.1858 time to fit residues: 861.1991 Evaluate side-chains 571 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 475 time to evaluate : 4.014 ------------------------------------------------------------------------------- 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 280 GLN Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 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 808 TYR Chi-restraints excluded: chain A residue 851 ARG Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 992 GLN Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 255 ASN Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 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 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 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 226 LEU 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 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 504 LEU Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 656 CYS Chi-restraints excluded: chain C residue 676 ASN Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 808 TYR Chi-restraints excluded: chain C residue 851 ARG Chi-restraints excluded: chain C residue 900 PHE Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 992 GLN Chi-restraints excluded: chain C residue 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 184 THR Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 255 ASN Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 280 GLN Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 491 ASP Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 656 CYS Chi-restraints excluded: chain D residue 676 ASN Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 808 TYR Chi-restraints excluded: chain D residue 851 ARG Chi-restraints excluded: chain D residue 900 PHE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 49 optimal weight: 2.9990 chunk 320 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 256 optimal weight: 0.3980 chunk 163 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 329 optimal weight: 1.9990 chunk 40 optimal weight: 0.0040 chunk 23 optimal weight: 4.9990 chunk 134 optimal weight: 0.5980 overall best weight: 0.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN A 306 GLN A 437 ASN ** A 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN B 671 GLN C 306 GLN C 437 ASN ** C 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 ASN D 306 GLN D1003 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.134446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.102259 restraints weight = 47601.906| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.66 r_work: 0.3188 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 30860 Z= 0.146 Angle : 0.486 6.682 42024 Z= 0.253 Chirality : 0.039 0.160 4856 Planarity : 0.004 0.048 5164 Dihedral : 7.301 77.712 4844 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 5.34 % Allowed : 24.32 % Favored : 70.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.14), residues: 3780 helix: 2.14 (0.10), residues: 2552 sheet: -1.80 (0.34), residues: 220 loop : -0.73 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 426 HIS 0.003 0.001 HIS C 185 PHE 0.016 0.001 PHE D 44 TYR 0.025 0.002 TYR A 117 ARG 0.004 0.000 ARG D 167 Details of bonding type rmsd hydrogen bonds : bond 0.03550 ( 1965) hydrogen bonds : angle 3.83996 ( 5811) SS BOND : bond 0.00842 ( 4) SS BOND : angle 2.14541 ( 8) covalent geometry : bond 0.00342 (30856) covalent geometry : angle 0.48492 (42016) *********************** 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 661 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 505 time to evaluate : 3.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 GLU cc_start: 0.8112 (tp30) cc_final: 0.7775 (tp30) REVERT: A 132 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8427 (tp) REVERT: A 167 ARG cc_start: 0.7981 (mmm160) cc_final: 0.7681 (tpm-80) REVERT: A 186 TYR cc_start: 0.8804 (m-80) cc_final: 0.8149 (m-80) REVERT: A 219 MET cc_start: 0.8677 (mmm) cc_final: 0.8421 (mmt) REVERT: A 222 ASN cc_start: 0.7479 (m-40) cc_final: 0.7196 (m110) REVERT: A 378 ILE cc_start: 0.8249 (mm) cc_final: 0.7810 (mp) REVERT: A 383 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8190 (tp30) REVERT: A 507 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.7890 (tpm170) REVERT: A 655 ASN cc_start: 0.8215 (t0) cc_final: 0.7900 (t0) REVERT: A 851 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.8449 (ttt-90) REVERT: A 911 MET cc_start: 0.7954 (OUTLIER) cc_final: 0.7641 (mtm) REVERT: A 992 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.8168 (pt0) REVERT: A 1009 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7961 (mp) REVERT: B 131 GLU cc_start: 0.8117 (tp30) cc_final: 0.7867 (tp30) REVERT: B 132 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8382 (tp) REVERT: B 135 GLN cc_start: 0.7231 (mp10) cc_final: 0.6940 (mp10) REVERT: B 161 MET cc_start: 0.8553 (tpp) cc_final: 0.8329 (mmm) REVERT: B 167 ARG cc_start: 0.8006 (mmm160) cc_final: 0.7694 (tpm-80) REVERT: B 219 MET cc_start: 0.8685 (mmm) cc_final: 0.8430 (mmt) REVERT: B 222 ASN cc_start: 0.7498 (m-40) cc_final: 0.7216 (m110) REVERT: B 507 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.7906 (tpm170) REVERT: B 655 ASN cc_start: 0.8199 (t0) cc_final: 0.7861 (t0) REVERT: B 851 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.8435 (ttt-90) REVERT: B 900 PHE cc_start: 0.7746 (OUTLIER) cc_final: 0.7503 (m-80) REVERT: B 992 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.8169 (pt0) REVERT: B 1009 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7963 (mp) REVERT: C 96 LYS cc_start: 0.8719 (tppp) cc_final: 0.8351 (tttm) REVERT: C 131 GLU cc_start: 0.8125 (tp30) cc_final: 0.7765 (tp30) REVERT: C 167 ARG cc_start: 0.7976 (mmm160) cc_final: 0.7668 (tpm-80) REVERT: C 186 TYR cc_start: 0.8800 (m-80) cc_final: 0.8133 (m-80) REVERT: C 219 MET cc_start: 0.8685 (mmm) cc_final: 0.8431 (mmt) REVERT: C 222 ASN cc_start: 0.7460 (m-40) cc_final: 0.7193 (m110) REVERT: C 507 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.7918 (tpm170) REVERT: C 655 ASN cc_start: 0.8155 (t0) cc_final: 0.7859 (t0) REVERT: C 851 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.8437 (ttt-90) REVERT: C 900 PHE cc_start: 0.7754 (OUTLIER) cc_final: 0.7514 (m-80) REVERT: C 992 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.8173 (pt0) REVERT: D 96 LYS cc_start: 0.8723 (tppp) cc_final: 0.8378 (tmmt) REVERT: D 131 GLU cc_start: 0.8067 (tp30) cc_final: 0.7774 (tp30) REVERT: D 161 MET cc_start: 0.8549 (tpp) cc_final: 0.8324 (mmm) REVERT: D 167 ARG cc_start: 0.8001 (mmm160) cc_final: 0.7691 (tpm-80) REVERT: D 186 TYR cc_start: 0.8794 (m-80) cc_final: 0.8179 (m-80) REVERT: D 219 MET cc_start: 0.8696 (mmm) cc_final: 0.8432 (mmt) REVERT: D 222 ASN cc_start: 0.7462 (m-40) cc_final: 0.7185 (m110) REVERT: D 378 ILE cc_start: 0.8224 (mm) cc_final: 0.7789 (mp) REVERT: D 383 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8186 (tp30) REVERT: D 435 GLU cc_start: 0.8248 (tm-30) cc_final: 0.7873 (tp30) REVERT: D 655 ASN cc_start: 0.8159 (t0) cc_final: 0.7863 (t0) REVERT: D 851 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.8443 (ttt-90) REVERT: D 911 MET cc_start: 0.7985 (OUTLIER) cc_final: 0.7742 (mtm) outliers start: 156 outliers final: 85 residues processed: 612 average time/residue: 1.4210 time to fit residues: 1061.9072 Evaluate side-chains 581 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 478 time to evaluate : 4.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 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 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 132 LEU Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 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 911 MET Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 992 GLN Chi-restraints excluded: chain B residue 1009 LEU Chi-restraints excluded: chain B residue 1024 VAL Chi-restraints excluded: chain 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 184 THR Chi-restraints excluded: chain C residue 226 LEU 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 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 900 PHE Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 992 GLN Chi-restraints excluded: chain C residue 1052 THR Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 122 CYS 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 403 ILE Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 491 ASP Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 656 CYS Chi-restraints excluded: chain D residue 676 ASN Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 808 TYR Chi-restraints excluded: chain D residue 851 ARG Chi-restraints excluded: chain D residue 911 MET Chi-restraints excluded: chain D residue 955 ILE Chi-restraints excluded: chain D residue 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 112 optimal weight: 6.9990 chunk 376 optimal weight: 2.9990 chunk 197 optimal weight: 6.9990 chunk 102 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 175 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 278 optimal weight: 2.9990 chunk 354 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 = 0.3858 r_free = 0.3858 target = 0.133936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.102011 restraints weight = 47542.596| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.70 r_work: 0.3132 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 30860 Z= 0.262 Angle : 0.587 7.869 42024 Z= 0.304 Chirality : 0.045 0.225 4856 Planarity : 0.005 0.048 5164 Dihedral : 7.817 79.364 4844 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 5.20 % Allowed : 24.52 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.14), residues: 3780 helix: 1.83 (0.10), residues: 2556 sheet: -1.65 (0.35), residues: 196 loop : -0.77 (0.19), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 426 HIS 0.006 0.001 HIS B 185 PHE 0.021 0.002 PHE B1013 TYR 0.026 0.002 TYR C 117 ARG 0.003 0.000 ARG D1008 Details of bonding type rmsd hydrogen bonds : bond 0.04429 ( 1965) hydrogen bonds : angle 4.11525 ( 5811) SS BOND : bond 0.00981 ( 4) SS BOND : angle 2.72147 ( 8) covalent geometry : bond 0.00633 (30856) covalent geometry : angle 0.58537 (42016) *********************** 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 636 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 484 time to evaluate : 3.343 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 LYS cc_start: 0.8731 (tppp) cc_final: 0.8305 (tttm) REVERT: A 131 GLU cc_start: 0.8102 (tp30) cc_final: 0.7779 (tp30) REVERT: A 186 TYR cc_start: 0.8861 (m-80) cc_final: 0.8299 (m-80) REVERT: A 219 MET cc_start: 0.8705 (mmm) cc_final: 0.8456 (mmt) REVERT: A 222 ASN cc_start: 0.7641 (m-40) cc_final: 0.7363 (m110) REVERT: A 383 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8170 (tp30) REVERT: A 458 LEU cc_start: 0.7806 (pp) cc_final: 0.7549 (pp) REVERT: A 507 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.7904 (tpm170) REVERT: A 655 ASN cc_start: 0.8494 (t0) cc_final: 0.8247 (t0) REVERT: A 707 CYS cc_start: 0.7156 (m) cc_final: 0.6602 (t) REVERT: A 851 ARG cc_start: 0.8919 (OUTLIER) cc_final: 0.8555 (ttt-90) REVERT: A 992 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.7992 (pp30) REVERT: B 96 LYS cc_start: 0.8712 (tppp) cc_final: 0.8295 (tttm) REVERT: B 135 GLN cc_start: 0.7217 (mp10) cc_final: 0.6868 (mp10) REVERT: B 219 MET cc_start: 0.8715 (mmm) cc_final: 0.8459 (mmt) REVERT: B 222 ASN cc_start: 0.7631 (m-40) cc_final: 0.7351 (m110) REVERT: B 248 ASP cc_start: 0.7569 (t0) cc_final: 0.7335 (t0) REVERT: B 507 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.7916 (tpm170) REVERT: B 655 ASN cc_start: 0.8489 (t0) cc_final: 0.8246 (t0) REVERT: B 707 CYS cc_start: 0.7186 (m) cc_final: 0.6628 (t) REVERT: B 851 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.8547 (ttt-90) REVERT: B 992 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.7996 (pp30) REVERT: C 131 GLU cc_start: 0.8126 (tp30) cc_final: 0.7799 (tp30) REVERT: C 167 ARG cc_start: 0.8034 (mmm160) cc_final: 0.7824 (tpm-80) REVERT: C 219 MET cc_start: 0.8709 (mmm) cc_final: 0.8463 (mmt) REVERT: C 222 ASN cc_start: 0.7629 (m-40) cc_final: 0.7345 (m110) REVERT: C 248 ASP cc_start: 0.7584 (t0) cc_final: 0.7278 (t70) REVERT: C 458 LEU cc_start: 0.7764 (pp) cc_final: 0.7560 (pp) REVERT: C 507 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.7921 (tpm170) REVERT: C 655 ASN cc_start: 0.8474 (t0) cc_final: 0.8207 (t0) REVERT: C 707 CYS cc_start: 0.7176 (m) cc_final: 0.6593 (t) REVERT: C 851 ARG cc_start: 0.8917 (OUTLIER) cc_final: 0.8552 (ttt-90) REVERT: C 992 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.8006 (pp30) REVERT: D 131 GLU cc_start: 0.8090 (tp30) cc_final: 0.7875 (tp30) REVERT: D 186 TYR cc_start: 0.8826 (m-80) cc_final: 0.8282 (m-80) REVERT: D 219 MET cc_start: 0.8724 (mmm) cc_final: 0.8478 (mmt) REVERT: D 222 ASN cc_start: 0.7620 (m-40) cc_final: 0.7346 (m110) REVERT: D 278 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7768 (ttt180) REVERT: D 383 GLU cc_start: 0.8497 (mt-10) cc_final: 0.8171 (tp30) REVERT: D 507 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.7927 (tpm170) REVERT: D 655 ASN cc_start: 0.8488 (t0) cc_final: 0.8215 (t0) REVERT: D 707 CYS cc_start: 0.7183 (m) cc_final: 0.6600 (t) REVERT: D 851 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.8557 (ttt-90) outliers start: 152 outliers final: 75 residues processed: 587 average time/residue: 1.2133 time to fit residues: 854.8307 Evaluate side-chains 557 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 470 time to evaluate : 2.955 ------------------------------------------------------------------------------- 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 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 676 ASN Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 808 TYR Chi-restraints excluded: chain A residue 851 ARG Chi-restraints excluded: chain A residue 911 MET Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 992 GLN Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 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 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 911 MET 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 164 ILE Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 491 ASP Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 507 ARG Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 676 ASN Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 808 TYR Chi-restraints excluded: chain C residue 851 ARG Chi-restraints excluded: chain C residue 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 278 ARG Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 491 ASP Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 507 ARG Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 676 ASN Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 808 TYR Chi-restraints excluded: chain D residue 851 ARG Chi-restraints excluded: chain D residue 911 MET Chi-restraints excluded: chain D residue 955 ILE Chi-restraints excluded: chain D residue 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 32 optimal weight: 6.9990 chunk 251 optimal weight: 0.9980 chunk 247 optimal weight: 0.8980 chunk 274 optimal weight: 0.0870 chunk 188 optimal weight: 0.9980 chunk 367 optimal weight: 2.9990 chunk 236 optimal weight: 1.9990 chunk 272 optimal weight: 0.7980 chunk 320 optimal weight: 5.9990 chunk 167 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 671 GLN ** B 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 671 GLN D 294 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.134977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.101667 restraints weight = 46177.278| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.68 r_work: 0.3190 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1838 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= 0.130 Angle : 0.496 8.505 42024 Z= 0.259 Chirality : 0.039 0.184 4856 Planarity : 0.004 0.046 5164 Dihedral : 7.377 77.050 4844 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 4.10 % Allowed : 26.27 % Favored : 69.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.14), residues: 3780 helix: 2.08 (0.10), residues: 2556 sheet: -1.64 (0.35), residues: 196 loop : -0.74 (0.19), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 426 HIS 0.004 0.001 HIS B 389 PHE 0.016 0.001 PHE A 44 TYR 0.025 0.002 TYR A 117 ARG 0.004 0.000 ARG B 167 Details of bonding type rmsd hydrogen bonds : bond 0.03461 ( 1965) hydrogen bonds : angle 3.85656 ( 5811) SS BOND : bond 0.00847 ( 4) SS BOND : angle 2.07864 ( 8) covalent geometry : bond 0.00301 (30856) covalent geometry : angle 0.49506 (42016) *********************** 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 606 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 486 time to evaluate : 3.014 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 LYS cc_start: 0.8698 (tppp) cc_final: 0.8475 (tppp) REVERT: A 186 TYR cc_start: 0.8814 (m-80) cc_final: 0.8228 (m-80) REVERT: A 219 MET cc_start: 0.8700 (mmm) cc_final: 0.8450 (mmt) REVERT: A 222 ASN cc_start: 0.7337 (m-40) cc_final: 0.7082 (m110) REVERT: A 248 ASP cc_start: 0.7507 (t0) cc_final: 0.7197 (t70) REVERT: A 378 ILE cc_start: 0.8297 (mm) cc_final: 0.7863 (mp) REVERT: A 383 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8130 (tp30) REVERT: A 507 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.7943 (tpm170) REVERT: A 655 ASN cc_start: 0.8106 (t0) cc_final: 0.7856 (t0) REVERT: A 707 CYS cc_start: 0.7116 (m) cc_final: 0.6608 (t) REVERT: A 851 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.6926 (tpt-90) REVERT: B 96 LYS cc_start: 0.8692 (tppp) cc_final: 0.8451 (tppp) REVERT: B 131 GLU cc_start: 0.8121 (tp30) cc_final: 0.7737 (tp30) REVERT: B 186 TYR cc_start: 0.8810 (m-80) cc_final: 0.8223 (m-80) REVERT: B 219 MET cc_start: 0.8698 (mmm) cc_final: 0.8446 (mmt) REVERT: B 222 ASN cc_start: 0.7378 (m-40) cc_final: 0.7127 (m110) REVERT: B 248 ASP cc_start: 0.7431 (t0) cc_final: 0.7181 (t70) REVERT: B 378 ILE cc_start: 0.8310 (mm) cc_final: 0.7873 (mp) REVERT: B 507 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.7939 (tpm170) REVERT: B 655 ASN cc_start: 0.8095 (t0) cc_final: 0.7824 (t0) REVERT: B 707 CYS cc_start: 0.7127 (m) cc_final: 0.6609 (t) REVERT: B 851 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.6884 (tpt-90) REVERT: C 219 MET cc_start: 0.8702 (mmm) cc_final: 0.8443 (mmt) REVERT: C 222 ASN cc_start: 0.7375 (m-40) cc_final: 0.7122 (m110) REVERT: C 248 ASP cc_start: 0.7526 (t0) cc_final: 0.7253 (t70) REVERT: C 378 ILE cc_start: 0.8307 (mm) cc_final: 0.7864 (mp) REVERT: C 507 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.7946 (tpm170) REVERT: C 655 ASN cc_start: 0.8056 (t0) cc_final: 0.7812 (t0) REVERT: C 707 CYS cc_start: 0.7117 (m) cc_final: 0.6582 (t) REVERT: C 851 ARG cc_start: 0.8843 (OUTLIER) cc_final: 0.6911 (tpt-90) REVERT: D 161 MET cc_start: 0.8616 (mmm) cc_final: 0.7752 (mmm) REVERT: D 186 TYR cc_start: 0.8798 (m-80) cc_final: 0.8185 (m-80) REVERT: D 219 MET cc_start: 0.8723 (mmm) cc_final: 0.8462 (mmt) REVERT: D 222 ASN cc_start: 0.7329 (m-40) cc_final: 0.7080 (m110) REVERT: D 383 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8127 (tp30) REVERT: D 507 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.7950 (tpm170) REVERT: D 655 ASN cc_start: 0.8014 (t0) cc_final: 0.7798 (t0) REVERT: D 707 CYS cc_start: 0.7143 (m) cc_final: 0.6605 (t) REVERT: D 851 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.6908 (tpt-90) REVERT: D 992 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.7938 (pp30) outliers start: 120 outliers final: 66 residues processed: 570 average time/residue: 1.2161 time to fit residues: 833.7270 Evaluate side-chains 551 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 476 time to evaluate : 3.102 ------------------------------------------------------------------------------- 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 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 507 ARG Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 656 CYS Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 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 164 ILE Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 491 ASP Chi-restraints excluded: chain B residue 507 ARG Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 656 CYS Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 808 TYR Chi-restraints excluded: chain B residue 851 ARG Chi-restraints excluded: chain B residue 911 MET Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 1024 VAL Chi-restraints excluded: chain 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 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 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 911 MET Chi-restraints excluded: chain C residue 955 ILE 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 252 ILE Chi-restraints excluded: chain D residue 255 ASN Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 491 ASP Chi-restraints excluded: chain D residue 507 ARG Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 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 992 GLN Chi-restraints excluded: chain D residue 1024 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 136 optimal weight: 1.9990 chunk 347 optimal weight: 0.7980 chunk 205 optimal weight: 4.9990 chunk 353 optimal weight: 1.9990 chunk 343 optimal weight: 0.9980 chunk 306 optimal weight: 5.9990 chunk 279 optimal weight: 0.0980 chunk 90 optimal weight: 8.9990 chunk 335 optimal weight: 2.9990 chunk 167 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 306 GLN 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.134526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.102525 restraints weight = 47417.368| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.73 r_work: 0.3184 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 30860 Z= 0.144 Angle : 0.515 9.162 42024 Z= 0.266 Chirality : 0.040 0.214 4856 Planarity : 0.004 0.045 5164 Dihedral : 7.283 77.227 4836 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.86 % Allowed : 26.68 % Favored : 69.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.14), residues: 3780 helix: 2.10 (0.10), residues: 2556 sheet: -1.66 (0.35), residues: 196 loop : -0.76 (0.19), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 426 HIS 0.004 0.001 HIS A 185 PHE 0.024 0.001 PHE B 44 TYR 0.018 0.002 TYR D 621 ARG 0.004 0.000 ARG A 167 Details of bonding type rmsd hydrogen bonds : bond 0.03568 ( 1965) hydrogen bonds : angle 3.85025 ( 5811) SS BOND : bond 0.00849 ( 4) SS BOND : angle 2.07171 ( 8) covalent geometry : bond 0.00337 (30856) covalent geometry : angle 0.51401 (42016) *********************** 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 594 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 481 time to evaluate : 3.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 LYS cc_start: 0.8674 (tppp) cc_final: 0.8453 (tppp) REVERT: A 186 TYR cc_start: 0.8808 (m-80) cc_final: 0.8200 (m-80) REVERT: A 219 MET cc_start: 0.8702 (mmm) cc_final: 0.8446 (mmt) REVERT: A 222 ASN cc_start: 0.7256 (m-40) cc_final: 0.6989 (m110) REVERT: A 383 GLU cc_start: 0.8448 (mt-10) cc_final: 0.8163 (tp30) REVERT: A 507 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.7905 (tpm170) REVERT: A 655 ASN cc_start: 0.8183 (t0) cc_final: 0.7890 (t0) REVERT: A 707 CYS cc_start: 0.7077 (m) cc_final: 0.6554 (t) REVERT: A 851 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.7237 (tpt-90) REVERT: B 96 LYS cc_start: 0.8663 (tppp) cc_final: 0.8435 (tppp) REVERT: B 186 TYR cc_start: 0.8813 (m-80) cc_final: 0.8194 (m-80) REVERT: B 219 MET cc_start: 0.8718 (mmm) cc_final: 0.8460 (mmt) REVERT: B 222 ASN cc_start: 0.7406 (m-40) cc_final: 0.7150 (m110) REVERT: B 248 ASP cc_start: 0.7431 (t0) cc_final: 0.7214 (t0) REVERT: B 507 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.7907 (tpm170) REVERT: B 655 ASN cc_start: 0.8130 (t0) cc_final: 0.7867 (t0) REVERT: B 707 CYS cc_start: 0.7094 (m) cc_final: 0.6563 (t) REVERT: B 851 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.7227 (tpt-90) REVERT: C 219 MET cc_start: 0.8714 (mmm) cc_final: 0.8453 (mmt) REVERT: C 222 ASN cc_start: 0.7397 (m-40) cc_final: 0.7152 (m110) REVERT: C 248 ASP cc_start: 0.7522 (t0) cc_final: 0.7279 (t70) REVERT: C 507 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.7916 (tpm170) REVERT: C 655 ASN cc_start: 0.8089 (t0) cc_final: 0.7845 (t0) REVERT: C 707 CYS cc_start: 0.7086 (m) cc_final: 0.6539 (t) REVERT: C 851 ARG cc_start: 0.8877 (OUTLIER) cc_final: 0.8447 (ttt-90) REVERT: D 132 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8273 (tp) REVERT: D 186 TYR cc_start: 0.8795 (m-80) cc_final: 0.8219 (m-80) REVERT: D 219 MET cc_start: 0.8723 (mmm) cc_final: 0.8457 (mmt) REVERT: D 222 ASN cc_start: 0.7250 (m-40) cc_final: 0.6984 (m110) REVERT: D 378 ILE cc_start: 0.8277 (mm) cc_final: 0.7831 (mp) REVERT: D 383 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8130 (tp30) REVERT: D 507 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.7927 (tpm170) REVERT: D 655 ASN cc_start: 0.8077 (t0) cc_final: 0.7833 (t0) REVERT: D 851 ARG cc_start: 0.8875 (OUTLIER) cc_final: 0.8445 (ttt-90) REVERT: D 992 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.7940 (pp30) outliers start: 113 outliers final: 75 residues processed: 560 average time/residue: 1.2219 time to fit residues: 823.4030 Evaluate side-chains 552 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 467 time to evaluate : 3.261 ------------------------------------------------------------------------------- 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 252 ILE 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 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 164 ILE Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 396 MET 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 507 ARG Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 676 ASN Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 785 GLN Chi-restraints excluded: chain B residue 808 TYR Chi-restraints excluded: chain B residue 851 ARG Chi-restraints excluded: chain B residue 911 MET Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 1024 VAL Chi-restraints excluded: chain B residue 1052 THR Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 272 THR 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 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 911 MET Chi-restraints excluded: chain C residue 955 ILE 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 132 LEU Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 255 ASN Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 491 ASP Chi-restraints excluded: chain D residue 507 ARG Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 676 ASN Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 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 992 GLN Chi-restraints excluded: chain D residue 1024 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 174 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 271 optimal weight: 3.9990 chunk 224 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 141 optimal weight: 0.5980 chunk 131 optimal weight: 6.9990 chunk 256 optimal weight: 0.0980 chunk 149 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 312 optimal weight: 0.0970 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 294 ASN B 306 GLN 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.136964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.104986 restraints weight = 47556.037| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.67 r_work: 0.3213 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 30860 Z= 0.111 Angle : 0.492 9.869 42024 Z= 0.255 Chirality : 0.039 0.226 4856 Planarity : 0.004 0.045 5164 Dihedral : 7.068 77.231 4836 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.18 % Allowed : 27.50 % Favored : 69.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.14), residues: 3780 helix: 2.21 (0.10), residues: 2552 sheet: -1.94 (0.32), residues: 228 loop : -0.77 (0.18), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP D 426 HIS 0.003 0.001 HIS C 185 PHE 0.026 0.001 PHE A 44 TYR 0.027 0.001 TYR B 117 ARG 0.003 0.000 ARG A 167 Details of bonding type rmsd hydrogen bonds : bond 0.03239 ( 1965) hydrogen bonds : angle 3.73683 ( 5811) SS BOND : bond 0.00785 ( 4) SS BOND : angle 1.77674 ( 8) covalent geometry : bond 0.00250 (30856) covalent geometry : angle 0.49166 (42016) ********************** 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 583 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 490 time to evaluate : 2.949 Fit side-chains REVERT: A 131 GLU cc_start: 0.8418 (mm-30) cc_final: 0.7890 (mm-30) REVERT: A 186 TYR cc_start: 0.8790 (m-80) cc_final: 0.8152 (m-80) REVERT: A 219 MET cc_start: 0.8657 (mmm) cc_final: 0.8397 (mmt) REVERT: A 248 ASP cc_start: 0.7380 (t0) cc_final: 0.7169 (t70) REVERT: A 383 GLU cc_start: 0.8425 (mt-10) cc_final: 0.8165 (tp30) REVERT: A 851 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.6696 (tpt-90) REVERT: B 131 GLU cc_start: 0.8434 (mm-30) cc_final: 0.7920 (mm-30) REVERT: B 186 TYR cc_start: 0.8776 (m-80) cc_final: 0.8150 (m-80) REVERT: B 219 MET cc_start: 0.8661 (mmm) cc_final: 0.8394 (mmt) REVERT: B 222 ASN cc_start: 0.7211 (m-40) cc_final: 0.6886 (t0) REVERT: B 507 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.7917 (tpm170) REVERT: B 851 ARG cc_start: 0.8838 (OUTLIER) cc_final: 0.6694 (tpt-90) REVERT: C 131 GLU cc_start: 0.8412 (mm-30) cc_final: 0.7901 (mm-30) REVERT: C 186 TYR cc_start: 0.8743 (m-80) cc_final: 0.8135 (m-80) REVERT: C 219 MET cc_start: 0.8668 (mmm) cc_final: 0.8397 (mmt) REVERT: C 222 ASN cc_start: 0.7158 (m-40) cc_final: 0.6838 (t0) REVERT: C 507 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.7916 (tpm170) REVERT: C 851 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.6697 (tpt-90) REVERT: D 131 GLU cc_start: 0.8437 (mm-30) cc_final: 0.7968 (mm-30) REVERT: D 161 MET cc_start: 0.8692 (mmm) cc_final: 0.8489 (tpt) REVERT: D 186 TYR cc_start: 0.8769 (m-80) cc_final: 0.8162 (m-80) REVERT: D 219 MET cc_start: 0.8658 (mmm) cc_final: 0.8387 (mmt) REVERT: D 248 ASP cc_start: 0.7368 (t0) cc_final: 0.7167 (t70) REVERT: D 378 ILE cc_start: 0.8237 (mm) cc_final: 0.7806 (mp) REVERT: D 383 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8173 (tp30) REVERT: D 507 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.7926 (tpm170) REVERT: D 851 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.6700 (tpt-90) REVERT: D 885 ARG cc_start: 0.8123 (mtp85) cc_final: 0.6600 (tpt170) REVERT: D 992 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.7968 (pt0) outliers start: 93 outliers final: 57 residues processed: 560 average time/residue: 1.1929 time to fit residues: 804.1900 Evaluate side-chains 531 residues out of total 3432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 466 time to evaluate : 3.233 ------------------------------------------------------------------------------- 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 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 697 LEU 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 B residue 117 TYR Chi-restraints excluded: chain B residue 122 CYS 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 491 ASP Chi-restraints excluded: chain B residue 507 ARG Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 851 ARG Chi-restraints excluded: chain B residue 911 MET 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 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 697 LEU Chi-restraints excluded: chain C residue 851 ARG Chi-restraints excluded: chain C residue 911 MET Chi-restraints excluded: chain C residue 1052 THR Chi-restraints excluded: chain D residue 117 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 403 ILE Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 491 ASP Chi-restraints excluded: chain D residue 507 ARG Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 851 ARG Chi-restraints excluded: chain D residue 992 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 220 optimal weight: 4.9990 chunk 263 optimal weight: 3.9990 chunk 296 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 291 optimal weight: 8.9990 chunk 344 optimal weight: 0.9980 chunk 170 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 243 optimal weight: 1.9990 chunk 348 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN A 294 ASN A 437 ASN ** 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 437 ASN ** C 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 ASN D 294 ASN D 306 GLN D 437 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.134802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.102501 restraints weight = 47293.130| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.69 r_work: 0.3173 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 30860 Z= 0.199 Angle : 0.561 9.945 42024 Z= 0.291 Chirality : 0.043 0.216 4856 Planarity : 0.004 0.045 5164 Dihedral : 7.195 77.698 4832 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.04 % Allowed : 27.94 % Favored : 69.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.14), residues: 3780 helix: 2.04 (0.10), residues: 2556 sheet: -2.05 (0.31), residues: 240 loop : -0.80 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP D 426 HIS 0.004 0.001 HIS B 185 PHE 0.028 0.002 PHE D 44 TYR 0.036 0.002 TYR A 117 ARG 0.007 0.000 ARG D 360 Details of bonding type rmsd hydrogen bonds : bond 0.03856 ( 1965) hydrogen bonds : angle 3.88976 ( 5811) SS BOND : bond 0.00858 ( 4) SS BOND : angle 2.20042 ( 8) covalent geometry : bond 0.00477 (30856) covalent geometry : angle 0.55995 (42016) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 31170.07 seconds wall clock time: 535 minutes 52.92 seconds (32152.92 seconds total)