Starting phenix.real_space_refine on Wed Nov 19 14:45:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6acd_9589/11_2025/6acd_9589.cif Found real_map, /net/cci-nas-00/data/ceres_data/6acd_9589/11_2025/6acd_9589.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6acd_9589/11_2025/6acd_9589.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6acd_9589/11_2025/6acd_9589.map" model { file = "/net/cci-nas-00/data/ceres_data/6acd_9589/11_2025/6acd_9589.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6acd_9589/11_2025/6acd_9589.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.873 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 135 5.16 5 C 15872 2.51 5 N 4112 2.21 5 O 4726 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24845 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1065, 8302 Classifications: {'peptide': 1065} Link IDs: {'PCIS': 1, 'PTRANS': 50, 'TRANS': 1013} Chain breaks: 3 Chain: "B" Number of atoms: 8302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1065, 8302 Classifications: {'peptide': 1065} Link IDs: {'PCIS': 1, 'PTRANS': 50, 'TRANS': 1013} Chain breaks: 3 Chain: "C" Number of atoms: 8241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1057, 8241 Classifications: {'peptide': 1057} Link IDs: {'PCIS': 1, 'PTRANS': 49, 'TRANS': 1006} Chain breaks: 5 Time building chain proxies: 5.94, per 1000 atoms: 0.24 Number of scatterers: 24845 At special positions: 0 Unit cell: (146.52, 146.52, 179.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 135 16.00 O 4726 8.00 N 4112 7.00 C 15872 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 288 " distance=2.03 Simple disulfide: pdb=" SG CYS A 323 " - pdb=" SG CYS A 348 " distance=2.03 Simple disulfide: pdb=" SG CYS A 366 " - pdb=" SG CYS A 419 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 511 " distance=2.03 Simple disulfide: pdb=" SG CYS A 467 " - pdb=" SG CYS A 474 " distance=2.03 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 576 " distance=2.03 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 635 " distance=2.02 Simple disulfide: pdb=" SG CYS A 648 " - pdb=" SG CYS A 657 " distance=2.04 Simple disulfide: pdb=" SG CYS A 720 " - pdb=" SG CYS A 742 " distance=2.03 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 731 " distance=2.01 Simple disulfide: pdb=" SG CYS A1014 " - pdb=" SG CYS A1025 " distance=2.03 Simple disulfide: pdb=" SG CYS A1064 " - pdb=" SG CYS A1108 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 288 " distance=2.03 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 348 " distance=2.02 Simple disulfide: pdb=" SG CYS B 366 " - pdb=" SG CYS B 419 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 511 " distance=2.03 Simple disulfide: pdb=" SG CYS B 467 " - pdb=" SG CYS B 474 " distance=2.03 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 576 " distance=2.04 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 635 " distance=2.02 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B 657 " distance=2.04 Simple disulfide: pdb=" SG CYS B 720 " - pdb=" SG CYS B 742 " distance=2.03 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 731 " distance=2.02 Simple disulfide: pdb=" SG CYS B1014 " - pdb=" SG CYS B1025 " distance=2.04 Simple disulfide: pdb=" SG CYS B1064 " - pdb=" SG CYS B1108 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 288 " distance=2.03 Simple disulfide: pdb=" SG CYS C 323 " - pdb=" SG CYS C 348 " distance=2.02 Simple disulfide: pdb=" SG CYS C 366 " - pdb=" SG CYS C 419 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 511 " distance=2.03 Simple disulfide: pdb=" SG CYS C 467 " - pdb=" SG CYS C 474 " distance=2.03 Simple disulfide: pdb=" SG CYS C 524 " - pdb=" SG CYS C 576 " distance=2.03 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 635 " distance=2.02 Simple disulfide: pdb=" SG CYS C 648 " - pdb=" SG CYS C 657 " distance=2.04 Simple disulfide: pdb=" SG CYS C 720 " - pdb=" SG CYS C 742 " distance=2.03 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 731 " distance=2.01 Simple disulfide: pdb=" SG CYS C1014 " - pdb=" SG CYS C1025 " distance=2.03 Simple disulfide: pdb=" SG CYS C1064 " - pdb=" SG CYS C1108 " 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: 1.83 Conformation dependent library (CDL) restraints added in 1.2 seconds 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5972 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 44 sheets defined 20.2% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 324 through 329 Processing helix chain 'A' and resid 371 through 377 removed outlier: 3.513A pdb=" N LEU A 374 " --> pdb=" O ALA A 371 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ASN A 375 " --> pdb=" O THR A 372 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP A 376 " --> pdb=" O LYS A 373 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU A 377 " --> pdb=" O LEU A 374 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 371 through 377' Processing helix chain 'A' and resid 404 through 409 Processing helix chain 'A' and resid 488 through 492 Processing helix chain 'A' and resid 604 through 612 Processing helix chain 'A' and resid 730 through 737 Processing helix chain 'A' and resid 740 through 765 removed outlier: 3.555A pdb=" N GLN A 744 " --> pdb=" O SER A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 808 Processing helix chain 'A' and resid 848 through 865 Processing helix chain 'A' and resid 880 through 888 removed outlier: 3.580A pdb=" N MET A 884 " --> pdb=" O PHE A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 900 removed outlier: 3.884A pdb=" N TYR A 899 " --> pdb=" O GLN A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 922 removed outlier: 3.906A pdb=" N THR A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 950 removed outlier: 4.312A pdb=" N GLN A 931 " --> pdb=" O LEU A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 1017 removed outlier: 3.753A pdb=" N VAL A1015 " --> pdb=" O MET A1011 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A1016 " --> pdb=" O SER A1012 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY A1017 " --> pdb=" O GLU A1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 324 through 330 Processing helix chain 'B' and resid 373 through 377 removed outlier: 3.898A pdb=" N ASP B 376 " --> pdb=" O LYS B 373 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU B 377 " --> pdb=" O LEU B 374 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 373 through 377' Processing helix chain 'B' and resid 404 through 409 Processing helix chain 'B' and resid 488 through 492 Processing helix chain 'B' and resid 604 through 611 removed outlier: 3.706A pdb=" N THR B 608 " --> pdb=" O THR B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 730 through 737 Processing helix chain 'B' and resid 740 through 765 Processing helix chain 'B' and resid 798 through 808 Processing helix chain 'B' and resid 848 through 865 Processing helix chain 'B' and resid 880 through 887 removed outlier: 3.545A pdb=" N MET B 884 " --> pdb=" O PHE B 880 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 900 removed outlier: 3.877A pdb=" N TYR B 899 " --> pdb=" O GLN B 895 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 922 removed outlier: 4.151A pdb=" N THR B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 927 through 950 removed outlier: 4.083A pdb=" N GLN B 931 " --> pdb=" O LEU B 927 " (cutoff:3.500A) Processing helix chain 'B' and resid 968 through 1014 Processing helix chain 'C' and resid 281 through 291 Processing helix chain 'C' and resid 325 through 330 Processing helix chain 'C' and resid 371 through 375 removed outlier: 3.546A pdb=" N LEU C 374 " --> pdb=" O ALA C 371 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ASN C 375 " --> pdb=" O THR C 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 371 through 375' Processing helix chain 'C' and resid 390 through 397 removed outlier: 4.513A pdb=" N ARG C 395 " --> pdb=" O ASP C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 409 removed outlier: 3.547A pdb=" N TYR C 408 " --> pdb=" O VAL C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 603 through 612 Processing helix chain 'C' and resid 730 through 737 Processing helix chain 'C' and resid 740 through 764 Processing helix chain 'C' and resid 798 through 808 Processing helix chain 'C' and resid 848 through 865 Processing helix chain 'C' and resid 880 through 888 removed outlier: 3.687A pdb=" N MET C 884 " --> pdb=" O PHE C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 900 Processing helix chain 'C' and resid 901 through 922 removed outlier: 4.010A pdb=" N THR C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 927 through 950 removed outlier: 4.142A pdb=" N GLN C 931 " --> pdb=" O LEU C 927 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER C 949 " --> pdb=" O VAL C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 969 through 1014 removed outlier: 4.000A pdb=" N GLN C 974 " --> pdb=" O GLU C 970 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34 removed outlier: 7.627A pdb=" N ASN A 65 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N TYR A 256 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N LYS A 198 " --> pdb=" O PRO A 218 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 59 removed outlier: 3.781A pdb=" N THR A 260 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP A 274 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 81 through 82 removed outlier: 6.939A pdb=" N ASN A 129 " --> pdb=" O CYS A 159 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N CYS A 159 " --> pdb=" O ASN A 129 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 138 through 141 removed outlier: 5.472A pdb=" N ALA A 237 " --> pdb=" O VAL A 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 298 through 306 removed outlier: 4.107A pdb=" N THR A 585 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR A 302 " --> pdb=" O VAL A 581 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N VAL A 581 " --> pdb=" O THR A 302 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ASN A 304 " --> pdb=" O GLY A 579 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N GLY A 579 " --> pdb=" O ASN A 304 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL A 628 " --> pdb=" O LEU A 636 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 314 removed outlier: 3.538A pdb=" N ASN A 526 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY A 534 " --> pdb=" O PHE A 527 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR A 539 " --> pdb=" O LEU A 571 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N SER A 568 " --> pdb=" O ASP A 564 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 341 through 345 Processing sheet with id=AA8, first strand: chain 'A' and resid 348 through 349 removed outlier: 6.385A pdb=" N CYS A 348 " --> pdb=" O CYS A 511 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 439 through 441 Processing sheet with id=AB1, first strand: chain 'A' and resid 640 through 642 removed outlier: 5.557A pdb=" N GLU A 640 " --> pdb=" O ALA A 676 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE A 650 " --> pdb=" O ALA A 658 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 683 through 684 removed outlier: 6.015A pdb=" N ALA A 683 " --> pdb=" O MET C 770 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 700 through 701 removed outlier: 3.603A pdb=" N VAL A1050 " --> pdb=" O SER A 701 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 704 through 710 removed outlier: 3.626A pdb=" N GLU A 707 " --> pdb=" O PHE A1044 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 716 through 718 Processing sheet with id=AB6, first strand: chain 'A' and resid 769 through 770 removed outlier: 6.158A pdb=" N ALA B 683 " --> pdb=" O MET A 770 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 778 through 779 Processing sheet with id=AB8, first strand: chain 'A' and resid 1069 through 1071 removed outlier: 3.689A pdb=" N PHE A1071 " --> pdb=" O PHE A1103 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1078 through 1079 Processing sheet with id=AC1, first strand: chain 'B' and resid 31 through 34 removed outlier: 4.191A pdb=" N THR B 31 " --> pdb=" O GLY B 68 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ASN B 65 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N TYR B 256 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR B 252 " --> pdb=" O PHE B 69 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N HIS B 181 " --> pdb=" O GLU B 93 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU B 184 " --> pdb=" O GLY B 199 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LYS B 198 " --> pdb=" O PRO B 218 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 52 through 59 removed outlier: 3.908A pdb=" N ASP B 274 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 81 through 82 removed outlier: 7.020A pdb=" N ASN B 129 " --> pdb=" O CYS B 159 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N CYS B 159 " --> pdb=" O ASN B 129 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 139 through 141 removed outlier: 6.433A pdb=" N VAL B 140 " --> pdb=" O SER B 239 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 300 through 306 removed outlier: 5.838A pdb=" N GLN B 301 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N VAL B 583 " --> pdb=" O GLN B 301 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N SER B 303 " --> pdb=" O VAL B 581 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 341 through 345 Processing sheet with id=AC7, first strand: chain 'B' and resid 440 through 441 Processing sheet with id=AC8, first strand: chain 'B' and resid 525 through 528 removed outlier: 4.093A pdb=" N GLY B 534 " --> pdb=" O PHE B 527 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR B 539 " --> pdb=" O LEU B 571 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N SER B 568 " --> pdb=" O ASP B 564 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 650 through 651 removed outlier: 3.999A pdb=" N ILE B 650 " --> pdb=" O ALA B 658 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA B 658 " --> pdb=" O ILE B 650 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 700 through 701 Processing sheet with id=AD2, first strand: chain 'B' and resid 704 through 710 Processing sheet with id=AD3, first strand: chain 'B' and resid 716 through 718 Processing sheet with id=AD4, first strand: chain 'B' and resid 1078 through 1079 removed outlier: 3.527A pdb=" N GLN B1095 " --> pdb=" O ILE B1086 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 31 through 34 removed outlier: 3.507A pdb=" N THR C 31 " --> pdb=" O GLY C 68 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N ASN C 65 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N TYR C 256 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR C 252 " --> pdb=" O PHE C 69 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR C 71 " --> pdb=" O ALA C 250 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA C 250 " --> pdb=" O THR C 71 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA C 251 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N LYS C 198 " --> pdb=" O PRO C 218 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 51 through 59 removed outlier: 4.157A pdb=" N ASP C 274 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 81 through 82 removed outlier: 7.168A pdb=" N ASN C 129 " --> pdb=" O CYS C 159 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N CYS C 159 " --> pdb=" O ASN C 129 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 139 through 141 removed outlier: 5.453A pdb=" N ALA C 237 " --> pdb=" O VAL C 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'C' and resid 300 through 306 removed outlier: 4.471A pdb=" N VAL C 581 " --> pdb=" O THR C 302 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ASN C 304 " --> pdb=" O GLY C 579 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N GLY C 579 " --> pdb=" O ASN C 304 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 314 removed outlier: 3.629A pdb=" N GLY C 534 " --> pdb=" O PHE C 527 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASP C 560 " --> pdb=" O ASP C 572 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 341 through 345 Processing sheet with id=AE3, first strand: chain 'C' and resid 439 through 441 Processing sheet with id=AE4, first strand: chain 'C' and resid 650 through 652 removed outlier: 3.555A pdb=" N ILE C 656 " --> pdb=" O ILE C 652 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 704 through 710 removed outlier: 3.668A pdb=" N ALA C1038 " --> pdb=" O GLY C1041 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 716 through 718 Processing sheet with id=AE7, first strand: chain 'C' and resid 1069 through 1071 removed outlier: 3.665A pdb=" N ALA C1069 " --> pdb=" O SER C1105 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N PHE C1071 " --> pdb=" O PHE C1103 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE C1103 " --> pdb=" O PHE C1071 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1078 through 1079 844 hydrogen bonds defined for protein. 2310 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.32 Time building geometry restraints manager: 2.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7362 1.33 - 1.46: 6117 1.46 - 1.58: 11771 1.58 - 1.71: 0 1.71 - 1.83: 183 Bond restraints: 25433 Sorted by residual: bond pdb=" C PHE C 316 " pdb=" N PRO C 317 " ideal model delta sigma weight residual 1.331 1.368 -0.036 1.21e-02 6.83e+03 8.96e+00 bond pdb=" CA THR C 517 " pdb=" C THR C 517 " ideal model delta sigma weight residual 1.525 1.466 0.059 2.10e-02 2.27e+03 7.79e+00 bond pdb=" CB CYS B 725 " pdb=" SG CYS B 725 " ideal model delta sigma weight residual 1.808 1.740 0.068 3.30e-02 9.18e+02 4.29e+00 bond pdb=" C LYS C 142 " pdb=" N PRO C 143 " ideal model delta sigma weight residual 1.334 1.380 -0.046 2.34e-02 1.83e+03 3.94e+00 bond pdb=" C LYS B 142 " pdb=" N PRO B 143 " ideal model delta sigma weight residual 1.332 1.349 -0.017 8.90e-03 1.26e+04 3.55e+00 ... (remaining 25428 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.05: 34303 4.05 - 8.10: 283 8.10 - 12.14: 23 12.14 - 16.19: 3 16.19 - 20.24: 1 Bond angle restraints: 34613 Sorted by residual: angle pdb=" N THR C 517 " pdb=" CA THR C 517 " pdb=" C THR C 517 " ideal model delta sigma weight residual 111.00 131.24 -20.24 2.80e+00 1.28e-01 5.22e+01 angle pdb=" N ILE C 891 " pdb=" CA ILE C 891 " pdb=" C ILE C 891 " ideal model delta sigma weight residual 113.71 107.02 6.69 9.50e-01 1.11e+00 4.96e+01 angle pdb=" C THR C 517 " pdb=" N ASP C 518 " pdb=" CA ASP C 518 " ideal model delta sigma weight residual 121.54 108.48 13.06 1.91e+00 2.74e-01 4.67e+01 angle pdb=" N GLY A 634 " pdb=" CA GLY A 634 " pdb=" C GLY A 634 " ideal model delta sigma weight residual 111.63 117.99 -6.36 1.15e+00 7.56e-01 3.06e+01 angle pdb=" C LYS B 968 " pdb=" N VAL B 969 " pdb=" CA VAL B 969 " ideal model delta sigma weight residual 120.62 129.43 -8.81 1.64e+00 3.72e-01 2.89e+01 ... (remaining 34608 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 14522 17.87 - 35.74: 469 35.74 - 53.60: 96 53.60 - 71.47: 24 71.47 - 89.34: 8 Dihedral angle restraints: 15119 sinusoidal: 5833 harmonic: 9286 Sorted by residual: dihedral pdb=" CA GLU A1074 " pdb=" C GLU A1074 " pdb=" N GLY A1075 " pdb=" CA GLY A1075 " ideal model delta harmonic sigma weight residual -180.00 -109.21 -70.79 0 5.00e+00 4.00e-02 2.00e+02 dihedral pdb=" CA GLU C1074 " pdb=" C GLU C1074 " pdb=" N GLY C1075 " pdb=" CA GLY C1075 " ideal model delta harmonic sigma weight residual -180.00 -113.59 -66.41 0 5.00e+00 4.00e-02 1.76e+02 dihedral pdb=" CB CYS B 725 " pdb=" SG CYS B 725 " pdb=" SG CYS B 731 " pdb=" CB CYS B 731 " ideal model delta sinusoidal sigma weight residual -86.00 -175.34 89.34 1 1.00e+01 1.00e-02 9.49e+01 ... (remaining 15116 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.140: 3818 0.140 - 0.280: 99 0.280 - 0.420: 0 0.420 - 0.560: 0 0.560 - 0.700: 1 Chirality restraints: 3918 Sorted by residual: chirality pdb=" CA THR C 517 " pdb=" N THR C 517 " pdb=" C THR C 517 " pdb=" CB THR C 517 " both_signs ideal model delta sigma weight residual False 2.53 1.83 0.70 2.00e-01 2.50e+01 1.23e+01 chirality pdb=" CG LEU A 745 " pdb=" CB LEU A 745 " pdb=" CD1 LEU A 745 " pdb=" CD2 LEU A 745 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CB THR A 71 " pdb=" CA THR A 71 " pdb=" OG1 THR A 71 " pdb=" CG2 THR A 71 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 3915 not shown) Planarity restraints: 4485 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 678 " -0.016 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C THR A 678 " 0.058 2.00e-02 2.50e+03 pdb=" O THR A 678 " -0.022 2.00e-02 2.50e+03 pdb=" N MET A 679 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 678 " 0.016 2.00e-02 2.50e+03 3.31e-02 1.09e+01 pdb=" C THR B 678 " -0.057 2.00e-02 2.50e+03 pdb=" O THR B 678 " 0.021 2.00e-02 2.50e+03 pdb=" N MET B 679 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 517 " -0.016 2.00e-02 2.50e+03 3.22e-02 1.04e+01 pdb=" C THR C 517 " 0.056 2.00e-02 2.50e+03 pdb=" O THR C 517 " -0.022 2.00e-02 2.50e+03 pdb=" N ASP C 518 " -0.018 2.00e-02 2.50e+03 ... (remaining 4482 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.28: 5 2.28 - 2.94: 11203 2.94 - 3.59: 34304 3.59 - 4.25: 56511 4.25 - 4.90: 92829 Nonbonded interactions: 194852 Sorted by model distance: nonbonded pdb=" O VAL C 314 " pdb=" CG2 THR C 517 " model vdw 1.629 3.460 nonbonded pdb=" OG SER A 95 " pdb=" O SER A 173 " model vdw 2.242 3.040 nonbonded pdb=" O GLN C 939 " pdb=" OG1 THR C 943 " model vdw 2.246 3.040 nonbonded pdb=" OG SER C 95 " pdb=" O SER C 173 " model vdw 2.262 3.040 nonbonded pdb=" OG SER B 95 " pdb=" O SER B 173 " model vdw 2.281 3.040 ... (remaining 194847 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 18 through 318 or resid 323 through 512 or resid 517 throu \ gh 1119)) selection = (chain 'B' and (resid 18 through 318 or resid 323 through 512 or resid 517 throu \ gh 1119)) selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.510 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: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 23.750 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 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 : 0.007 0.080 25472 Z= 0.314 Angle : 1.047 20.239 34691 Z= 0.586 Chirality : 0.060 0.700 3918 Planarity : 0.008 0.073 4485 Dihedral : 9.719 83.092 9030 Min Nonbonded Distance : 1.629 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.54 % Allowed : 14.34 % Favored : 85.12 % Rotamer: Outliers : 0.25 % Allowed : 2.14 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.50 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.47 (0.12), residues: 3159 helix: -1.53 (0.17), residues: 635 sheet: -2.07 (0.20), residues: 567 loop : -4.01 (0.11), residues: 1957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 797 TYR 0.028 0.003 TYR B 300 PHE 0.034 0.004 PHE B 837 TRP 0.025 0.003 TRP C 868 HIS 0.013 0.002 HIS C1046 Details of bonding type rmsd covalent geometry : bond 0.00666 (25433) covalent geometry : angle 1.04427 (34613) SS BOND : bond 0.00690 ( 39) SS BOND : angle 1.86016 ( 78) hydrogen bonds : bond 0.13826 ( 844) hydrogen bonds : angle 7.86680 ( 2310) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 2758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 571 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 ILE cc_start: 0.9361 (mt) cc_final: 0.9129 (tp) REVERT: A 215 THR cc_start: 0.8560 (m) cc_final: 0.8288 (p) REVERT: A 245 TRP cc_start: 0.4032 (p-90) cc_final: 0.2769 (p-90) REVERT: A 360 PHE cc_start: 0.8056 (t80) cc_final: 0.7754 (m-10) REVERT: A 480 ASP cc_start: 0.8697 (m-30) cc_final: 0.8308 (t70) REVERT: A 491 TYR cc_start: 0.8606 (m-10) cc_final: 0.8281 (m-80) REVERT: A 502 GLU cc_start: 0.6107 (tt0) cc_final: 0.5901 (tt0) REVERT: A 519 LEU cc_start: 0.8854 (mp) cc_final: 0.8339 (tt) REVERT: A 687 ILE cc_start: 0.8659 (OUTLIER) cc_final: 0.8030 (tp) REVERT: A 752 ILE cc_start: 0.9011 (mt) cc_final: 0.8456 (mm) REVERT: B 96 ASN cc_start: 0.8145 (m-40) cc_final: 0.7516 (m-40) REVERT: B 300 TYR cc_start: 0.8878 (m-10) cc_final: 0.8536 (m-10) REVERT: B 571 LEU cc_start: 0.8937 (mt) cc_final: 0.8715 (tp) REVERT: B 738 TYR cc_start: 0.8281 (m-10) cc_final: 0.6685 (m-10) REVERT: B 1091 PHE cc_start: 0.8548 (t80) cc_final: 0.8347 (t80) REVERT: B 1101 ASN cc_start: 0.7982 (m-40) cc_final: 0.7663 (t0) REVERT: C 220 PHE cc_start: 0.7994 (m-10) cc_final: 0.7752 (m-80) REVERT: C 274 ASP cc_start: 0.7856 (t0) cc_final: 0.7560 (t0) REVERT: C 287 LYS cc_start: 0.9276 (mttt) cc_final: 0.9020 (mtpt) REVERT: C 289 SER cc_start: 0.8033 (m) cc_final: 0.7671 (p) REVERT: C 300 TYR cc_start: 0.8989 (m-10) cc_final: 0.8729 (m-10) REVERT: C 417 MET cc_start: -0.2484 (tpt) cc_final: -0.2733 (mmp) REVERT: C 528 ASN cc_start: 0.8590 (t0) cc_final: 0.8094 (t0) REVERT: C 738 TYR cc_start: 0.9017 (m-10) cc_final: 0.8563 (m-80) outliers start: 7 outliers final: 1 residues processed: 577 average time/residue: 0.1935 time to fit residues: 169.2029 Evaluate side-chains 297 residues out of total 2758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 295 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain C residue 510 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 0.0170 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 2.9990 overall best weight: 2.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN A 181 HIS A 505 ASN A 699 ASN A 733 ASN A 769 GLN A 931 GLN A 993 GLN A1005 ASN ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 GLN B 56 GLN B 129 ASN B 181 HIS ** B 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 ASN B 445 HIS B 699 ASN ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 759 ASN B1088 GLN B1101 ASN C 147 GLN C 181 HIS C 744 GLN C 759 ASN C 766 GLN ** C 937 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 947 GLN C 984 GLN C 987 GLN C 993 GLN C1005 ASN ** C1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.109077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.079625 restraints weight = 83022.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.083501 restraints weight = 47869.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.084540 restraints weight = 27081.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.085415 restraints weight = 19933.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.085761 restraints weight = 17356.046| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 25472 Z= 0.199 Angle : 0.773 13.321 34691 Z= 0.408 Chirality : 0.048 0.281 3918 Planarity : 0.006 0.063 4485 Dihedral : 7.097 64.946 3425 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.32 % Allowed : 12.85 % Favored : 86.83 % Rotamer: Outliers : 2.14 % Allowed : 9.28 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.62 (0.13), residues: 3159 helix: 0.04 (0.20), residues: 618 sheet: -1.78 (0.21), residues: 566 loop : -3.67 (0.11), residues: 1975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 620 TYR 0.022 0.001 TYR C 723 PHE 0.027 0.002 PHE B1077 TRP 0.025 0.001 TRP A 423 HIS 0.010 0.001 HIS C1030 Details of bonding type rmsd covalent geometry : bond 0.00440 (25433) covalent geometry : angle 0.76415 (34613) SS BOND : bond 0.00505 ( 39) SS BOND : angle 2.57194 ( 78) hydrogen bonds : bond 0.04550 ( 844) hydrogen bonds : angle 6.66551 ( 2310) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 328 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.8323 (mmm) cc_final: 0.7953 (mmt) REVERT: A 245 TRP cc_start: 0.4471 (p-90) cc_final: 0.3188 (p-90) REVERT: A 253 PHE cc_start: 0.9002 (m-10) cc_final: 0.8602 (m-10) REVERT: A 361 PHE cc_start: 0.7288 (m-10) cc_final: 0.6982 (m-10) REVERT: A 439 LYS cc_start: 0.7523 (pttt) cc_final: 0.7211 (ptpt) REVERT: A 491 TYR cc_start: 0.8562 (m-10) cc_final: 0.8158 (m-80) REVERT: A 519 LEU cc_start: 0.9001 (mp) cc_final: 0.8326 (tt) REVERT: A 687 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8060 (tp) REVERT: A 733 ASN cc_start: 0.8879 (m110) cc_final: 0.8575 (t0) REVERT: A 882 MET cc_start: 0.8268 (mtp) cc_final: 0.7843 (mtp) REVERT: A 1032 MET cc_start: 0.7531 (tpp) cc_final: 0.7240 (tpp) REVERT: B 107 MET cc_start: 0.2844 (mmp) cc_final: -0.0262 (mtt) REVERT: B 379 PHE cc_start: 0.7384 (m-10) cc_final: 0.7062 (m-80) REVERT: B 563 ARG cc_start: 0.8315 (ttt-90) cc_final: 0.8080 (tpt170) REVERT: B 571 LEU cc_start: 0.9031 (mt) cc_final: 0.8804 (tp) REVERT: B 762 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7888 (mt-10) REVERT: B 918 GLU cc_start: 0.8901 (mt-10) cc_final: 0.8522 (tp30) REVERT: B 1101 ASN cc_start: 0.7940 (m110) cc_final: 0.7483 (t0) REVERT: C 184 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.6878 (pt0) REVERT: C 220 PHE cc_start: 0.8081 (m-10) cc_final: 0.7863 (m-80) REVERT: C 274 ASP cc_start: 0.7923 (t0) cc_final: 0.7594 (t0) REVERT: C 287 LYS cc_start: 0.9409 (mttt) cc_final: 0.9053 (mtpt) REVERT: C 300 TYR cc_start: 0.9025 (m-10) cc_final: 0.8729 (m-10) REVERT: C 528 ASN cc_start: 0.8676 (t0) cc_final: 0.8087 (t0) REVERT: C 532 LEU cc_start: 0.8811 (tp) cc_final: 0.8592 (tt) REVERT: C 947 GLN cc_start: 0.8831 (mm110) cc_final: 0.8278 (mp10) REVERT: C 1089 ARG cc_start: 0.7977 (ttt180) cc_final: 0.7340 (mmm160) outliers start: 59 outliers final: 27 residues processed: 371 average time/residue: 0.1664 time to fit residues: 98.8452 Evaluate side-chains 267 residues out of total 2758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 238 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 945 VAL Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain B residue 848 THR Chi-restraints excluded: chain B residue 902 GLN Chi-restraints excluded: chain B residue 921 THR Chi-restraints excluded: chain B residue 972 GLU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 560 ASP Chi-restraints excluded: chain C residue 927 LEU Chi-restraints excluded: chain C residue 967 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 313 optimal weight: 0.0010 chunk 149 optimal weight: 9.9990 chunk 307 optimal weight: 5.9990 chunk 271 optimal weight: 8.9990 chunk 198 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 264 optimal weight: 5.9990 chunk 170 optimal weight: 5.9990 chunk 184 optimal weight: 3.9990 chunk 192 optimal weight: 2.9990 chunk 273 optimal weight: 0.8980 overall best weight: 1.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 HIS A 505 ASN A 947 GLN A 984 GLN ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 GLN B 135 ASN ** B 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 381 ASN B 409 ASN B 984 GLN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 877 GLN ** C1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.108374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.078803 restraints weight = 82974.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.082416 restraints weight = 49336.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.083391 restraints weight = 28722.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.084336 restraints weight = 21116.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.084686 restraints weight = 17980.851| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 25472 Z= 0.186 Angle : 0.729 11.050 34691 Z= 0.383 Chirality : 0.047 0.230 3918 Planarity : 0.005 0.062 4485 Dihedral : 6.695 65.617 3424 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.28 % Allowed : 12.69 % Favored : 87.02 % Rotamer: Outliers : 2.57 % Allowed : 10.80 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.28 (0.14), residues: 3159 helix: 0.59 (0.21), residues: 613 sheet: -1.65 (0.22), residues: 562 loop : -3.50 (0.12), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 620 TYR 0.029 0.001 TYR B 689 PHE 0.021 0.002 PHE B 837 TRP 0.013 0.001 TRP A 476 HIS 0.009 0.001 HIS C1030 Details of bonding type rmsd covalent geometry : bond 0.00412 (25433) covalent geometry : angle 0.72300 (34613) SS BOND : bond 0.00449 ( 39) SS BOND : angle 2.03750 ( 78) hydrogen bonds : bond 0.04208 ( 844) hydrogen bonds : angle 6.33682 ( 2310) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 261 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.9061 (tt) REVERT: A 245 TRP cc_start: 0.4614 (p-90) cc_final: 0.3324 (p-90) REVERT: A 289 SER cc_start: 0.8953 (OUTLIER) cc_final: 0.8497 (p) REVERT: A 393 ASP cc_start: 0.8693 (m-30) cc_final: 0.8356 (m-30) REVERT: A 491 TYR cc_start: 0.8627 (m-10) cc_final: 0.8221 (m-80) REVERT: A 502 GLU cc_start: 0.7019 (tt0) cc_final: 0.6471 (mt-10) REVERT: A 687 ILE cc_start: 0.8786 (OUTLIER) cc_final: 0.8310 (tp) REVERT: A 733 ASN cc_start: 0.8850 (m110) cc_final: 0.8620 (t0) REVERT: A 801 GLU cc_start: 0.8993 (mt-10) cc_final: 0.8672 (mm-30) REVERT: A 882 MET cc_start: 0.8436 (mtp) cc_final: 0.7990 (mtp) REVERT: A 918 GLU cc_start: 0.8562 (mt-10) cc_final: 0.7939 (mp0) REVERT: A 946 LYS cc_start: 0.9377 (tmtt) cc_final: 0.9070 (tptp) REVERT: B 107 MET cc_start: 0.3063 (mmp) cc_final: -0.0070 (mtt) REVERT: B 299 ILE cc_start: 0.9229 (OUTLIER) cc_final: 0.8960 (tp) REVERT: B 379 PHE cc_start: 0.7193 (m-10) cc_final: 0.6891 (m-80) REVERT: B 527 PHE cc_start: 0.7256 (m-10) cc_final: 0.6949 (m-10) REVERT: B 657 CYS cc_start: 0.3092 (m) cc_final: 0.2419 (m) REVERT: B 677 TYR cc_start: 0.7814 (p90) cc_final: 0.7209 (p90) REVERT: B 679 MET cc_start: 0.8556 (tpp) cc_final: 0.8132 (tpp) REVERT: B 721 ASN cc_start: 0.9168 (m-40) cc_final: 0.8562 (t0) REVERT: B 746 ASN cc_start: 0.8768 (m110) cc_final: 0.8564 (m110) REVERT: B 801 GLU cc_start: 0.7327 (mt-10) cc_final: 0.7125 (mt-10) REVERT: B 918 GLU cc_start: 0.8917 (mt-10) cc_final: 0.8556 (tp30) REVERT: B 1013 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7900 (mt-10) REVERT: B 1101 ASN cc_start: 0.7715 (m110) cc_final: 0.7288 (t0) REVERT: C 184 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.6831 (pt0) REVERT: C 220 PHE cc_start: 0.8294 (m-10) cc_final: 0.7957 (m-80) REVERT: C 274 ASP cc_start: 0.8029 (t0) cc_final: 0.7717 (t0) REVERT: C 287 LYS cc_start: 0.9253 (mttt) cc_final: 0.8877 (mtpt) REVERT: C 300 TYR cc_start: 0.9040 (m-10) cc_final: 0.8714 (m-10) REVERT: C 528 ASN cc_start: 0.8526 (t0) cc_final: 0.7965 (t0) REVERT: C 1079 PHE cc_start: 0.7260 (t80) cc_final: 0.6988 (t80) REVERT: C 1089 ARG cc_start: 0.8048 (ttt90) cc_final: 0.7615 (mmm160) outliers start: 71 outliers final: 43 residues processed: 315 average time/residue: 0.1614 time to fit residues: 82.9244 Evaluate side-chains 280 residues out of total 2758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 231 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 859 LEU Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 914 SER Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 1011 MET Chi-restraints excluded: chain A residue 1082 THR Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 620 ARG Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain B residue 939 GLN Chi-restraints excluded: chain B residue 972 GLU Chi-restraints excluded: chain B residue 1013 GLU Chi-restraints excluded: chain B residue 1033 SER Chi-restraints excluded: chain B residue 1082 THR Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 560 ASP Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 652 ILE Chi-restraints excluded: chain C residue 840 LEU Chi-restraints excluded: chain C residue 927 LEU Chi-restraints excluded: chain C residue 1082 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 91 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 chunk 170 optimal weight: 0.9980 chunk 41 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 chunk 223 optimal weight: 20.0000 chunk 209 optimal weight: 3.9990 chunk 16 optimal weight: 9.9990 chunk 255 optimal weight: 30.0000 chunk 215 optimal weight: 8.9990 chunk 242 optimal weight: 1.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 ASN ** A 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1018 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 ASN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 766 GLN ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 883 GLN C 917 GLN ** C1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.105793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.077331 restraints weight = 83666.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.079485 restraints weight = 53532.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.080698 restraints weight = 34266.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.081543 restraints weight = 25977.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.081641 restraints weight = 22525.939| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 25472 Z= 0.273 Angle : 0.786 10.643 34691 Z= 0.412 Chirality : 0.048 0.271 3918 Planarity : 0.005 0.075 4485 Dihedral : 6.798 66.145 3424 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.28 % Allowed : 14.50 % Favored : 85.22 % Rotamer: Outliers : 3.59 % Allowed : 10.95 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.27 (0.14), residues: 3159 helix: 0.44 (0.20), residues: 634 sheet: -1.70 (0.22), residues: 568 loop : -3.46 (0.12), residues: 1957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 620 TYR 0.026 0.002 TYR B 689 PHE 0.039 0.002 PHE B 837 TRP 0.013 0.002 TRP C 423 HIS 0.010 0.002 HIS C1030 Details of bonding type rmsd covalent geometry : bond 0.00591 (25433) covalent geometry : angle 0.78349 (34613) SS BOND : bond 0.00545 ( 39) SS BOND : angle 1.64858 ( 78) hydrogen bonds : bond 0.04500 ( 844) hydrogen bonds : angle 6.39657 ( 2310) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 232 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.9121 (tt) REVERT: A 80 VAL cc_start: 0.8611 (OUTLIER) cc_final: 0.8406 (p) REVERT: A 245 TRP cc_start: 0.4784 (p-90) cc_final: 0.3805 (p-90) REVERT: A 393 ASP cc_start: 0.8694 (m-30) cc_final: 0.8401 (m-30) REVERT: A 491 TYR cc_start: 0.8630 (m-10) cc_final: 0.8267 (m-80) REVERT: A 498 VAL cc_start: 0.9465 (t) cc_final: 0.9230 (p) REVERT: A 502 GLU cc_start: 0.7214 (tt0) cc_final: 0.6693 (mt-10) REVERT: A 649 ASP cc_start: 0.8573 (t0) cc_final: 0.8266 (m-30) REVERT: A 687 ILE cc_start: 0.8850 (OUTLIER) cc_final: 0.8303 (tp) REVERT: A 755 GLU cc_start: 0.8135 (tp30) cc_final: 0.7852 (tp30) REVERT: A 801 GLU cc_start: 0.8992 (mt-10) cc_final: 0.8657 (mm-30) REVERT: A 838 ASN cc_start: 0.8249 (OUTLIER) cc_final: 0.7767 (p0) REVERT: A 946 LYS cc_start: 0.9363 (tmtt) cc_final: 0.8913 (tptp) REVERT: A 966 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7564 (pp) REVERT: B 285 GLU cc_start: 0.8773 (tp30) cc_final: 0.8392 (tp30) REVERT: B 299 ILE cc_start: 0.9121 (OUTLIER) cc_final: 0.8880 (tp) REVERT: B 379 PHE cc_start: 0.7718 (m-10) cc_final: 0.7303 (m-80) REVERT: B 585 THR cc_start: 0.9322 (OUTLIER) cc_final: 0.9099 (m) REVERT: B 721 ASN cc_start: 0.8839 (m-40) cc_final: 0.8477 (t0) REVERT: B 918 GLU cc_start: 0.8980 (mt-10) cc_final: 0.8739 (tm-30) REVERT: B 1013 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7887 (mt-10) REVERT: C 184 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.6899 (pt0) REVERT: C 220 PHE cc_start: 0.8360 (m-10) cc_final: 0.8009 (m-80) REVERT: C 274 ASP cc_start: 0.8152 (t0) cc_final: 0.7805 (t0) REVERT: C 287 LYS cc_start: 0.9366 (mttt) cc_final: 0.8976 (mtpt) REVERT: C 528 ASN cc_start: 0.8414 (t0) cc_final: 0.7896 (t0) REVERT: C 851 MET cc_start: 0.9285 (ptm) cc_final: 0.9064 (ptp) REVERT: C 1089 ARG cc_start: 0.8053 (ttt90) cc_final: 0.7711 (mmm160) outliers start: 99 outliers final: 57 residues processed: 310 average time/residue: 0.1568 time to fit residues: 80.1460 Evaluate side-chains 272 residues out of total 2758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 206 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 838 ASN Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 851 MET Chi-restraints excluded: chain A residue 859 LEU Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1082 THR Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain B residue 841 THR Chi-restraints excluded: chain B residue 848 THR Chi-restraints excluded: chain B residue 916 ILE Chi-restraints excluded: chain B residue 921 THR Chi-restraints excluded: chain B residue 939 GLN Chi-restraints excluded: chain B residue 972 GLU Chi-restraints excluded: chain B residue 1013 GLU Chi-restraints excluded: chain B residue 1033 SER Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 560 ASP Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 652 ILE Chi-restraints excluded: chain C residue 841 THR Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain C residue 927 LEU Chi-restraints excluded: chain C residue 967 ASP Chi-restraints excluded: chain C residue 1082 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 3 optimal weight: 0.6980 chunk 238 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 228 optimal weight: 10.0000 chunk 270 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 chunk 33 optimal weight: 10.0000 chunk 102 optimal weight: 8.9990 chunk 113 optimal weight: 10.0000 chunk 194 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN A 877 GLN A 984 GLN ** A1018 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 505 ASN B 984 GLN C 96 ASN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 304 ASN ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 896 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.107898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.079107 restraints weight = 82794.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.082117 restraints weight = 51513.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.083147 restraints weight = 31912.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.084149 restraints weight = 23344.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.084343 restraints weight = 19878.322| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 25472 Z= 0.163 Angle : 0.694 9.826 34691 Z= 0.365 Chirality : 0.047 0.277 3918 Planarity : 0.005 0.061 4485 Dihedral : 6.451 62.672 3424 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.28 % Allowed : 12.41 % Favored : 87.31 % Rotamer: Outliers : 2.86 % Allowed : 11.89 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.98 (0.14), residues: 3159 helix: 0.82 (0.21), residues: 634 sheet: -1.47 (0.22), residues: 559 loop : -3.33 (0.12), residues: 1966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 620 TYR 0.015 0.001 TYR B 689 PHE 0.037 0.001 PHE B 837 TRP 0.016 0.001 TRP C 423 HIS 0.008 0.001 HIS C1030 Details of bonding type rmsd covalent geometry : bond 0.00361 (25433) covalent geometry : angle 0.68996 (34613) SS BOND : bond 0.00490 ( 39) SS BOND : angle 1.72780 ( 78) hydrogen bonds : bond 0.04066 ( 844) hydrogen bonds : angle 6.08315 ( 2310) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 248 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.8433 (mmm) cc_final: 0.8200 (mmt) REVERT: A 54 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.9126 (tt) REVERT: A 80 VAL cc_start: 0.8551 (OUTLIER) cc_final: 0.8256 (p) REVERT: A 245 TRP cc_start: 0.4827 (p-90) cc_final: 0.4312 (p-90) REVERT: A 253 PHE cc_start: 0.8877 (m-10) cc_final: 0.8555 (m-10) REVERT: A 263 MET cc_start: 0.7298 (tmm) cc_final: 0.7045 (tmm) REVERT: A 393 ASP cc_start: 0.8708 (m-30) cc_final: 0.8415 (m-30) REVERT: A 491 TYR cc_start: 0.8690 (m-10) cc_final: 0.8234 (m-80) REVERT: A 502 GLU cc_start: 0.7031 (tt0) cc_final: 0.6618 (mt-10) REVERT: A 755 GLU cc_start: 0.8093 (tp30) cc_final: 0.7761 (tp30) REVERT: A 801 GLU cc_start: 0.8869 (mt-10) cc_final: 0.8632 (mm-30) REVERT: A 838 ASN cc_start: 0.8255 (OUTLIER) cc_final: 0.7492 (p0) REVERT: A 946 LYS cc_start: 0.9330 (tmtt) cc_final: 0.8854 (tptp) REVERT: B 87 ILE cc_start: 0.8521 (OUTLIER) cc_final: 0.8227 (mt) REVERT: B 299 ILE cc_start: 0.9066 (OUTLIER) cc_final: 0.8834 (tp) REVERT: B 379 PHE cc_start: 0.7455 (m-10) cc_final: 0.7061 (m-80) REVERT: B 679 MET cc_start: 0.8200 (tpp) cc_final: 0.7771 (tpp) REVERT: B 746 ASN cc_start: 0.8874 (m110) cc_final: 0.8667 (m110) REVERT: B 755 GLU cc_start: 0.9062 (tt0) cc_final: 0.8738 (tt0) REVERT: B 918 GLU cc_start: 0.8909 (mt-10) cc_final: 0.8535 (tp30) REVERT: B 1013 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7790 (mt-10) REVERT: B 1101 ASN cc_start: 0.7761 (m110) cc_final: 0.7547 (t0) REVERT: C 184 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.6888 (pt0) REVERT: C 220 PHE cc_start: 0.8341 (m-10) cc_final: 0.8001 (m-80) REVERT: C 231 PHE cc_start: 0.8750 (p90) cc_final: 0.7911 (p90) REVERT: C 274 ASP cc_start: 0.8012 (t0) cc_final: 0.7677 (t0) REVERT: C 287 LYS cc_start: 0.9319 (mttt) cc_final: 0.8932 (mtpt) REVERT: C 528 ASN cc_start: 0.8351 (t0) cc_final: 0.7783 (t0) REVERT: C 948 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.9004 (mt) REVERT: C 972 GLU cc_start: 0.8727 (mp0) cc_final: 0.8109 (mp0) REVERT: C 1089 ARG cc_start: 0.8095 (ttt90) cc_final: 0.7714 (ttm-80) outliers start: 79 outliers final: 54 residues processed: 312 average time/residue: 0.1548 time to fit residues: 79.6572 Evaluate side-chains 277 residues out of total 2758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 215 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 838 ASN Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 851 MET Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1082 THR Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain B residue 848 THR Chi-restraints excluded: chain B residue 921 THR Chi-restraints excluded: chain B residue 939 GLN Chi-restraints excluded: chain B residue 972 GLU Chi-restraints excluded: chain B residue 984 GLN Chi-restraints excluded: chain B residue 1013 GLU Chi-restraints excluded: chain B residue 1033 SER Chi-restraints excluded: chain B residue 1082 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 304 ASN Chi-restraints excluded: chain C residue 560 ASP Chi-restraints excluded: chain C residue 570 ILE Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 652 ILE Chi-restraints excluded: chain C residue 687 ILE Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain C residue 927 LEU Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 967 ASP Chi-restraints excluded: chain C residue 1082 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 30 optimal weight: 9.9990 chunk 86 optimal weight: 0.6980 chunk 223 optimal weight: 10.0000 chunk 158 optimal weight: 4.9990 chunk 316 optimal weight: 8.9990 chunk 298 optimal weight: 0.0870 chunk 45 optimal weight: 10.0000 chunk 302 optimal weight: 3.9990 chunk 227 optimal weight: 7.9990 chunk 281 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 overall best weight: 2.5564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 GLN A 523 GLN A 550 GLN A 721 ASN ** A 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1018 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 721 ASN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 993 GLN C 96 ASN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 632 GLN ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 883 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.112908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.086502 restraints weight = 89801.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.086944 restraints weight = 51845.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.088140 restraints weight = 37045.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.088251 restraints weight = 28832.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.088527 restraints weight = 27508.381| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 25472 Z= 0.214 Angle : 0.727 10.234 34691 Z= 0.380 Chirality : 0.047 0.205 3918 Planarity : 0.005 0.059 4485 Dihedral : 6.424 61.673 3422 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.25 % Allowed : 14.21 % Favored : 85.53 % Rotamer: Outliers : 3.30 % Allowed : 12.29 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.94 (0.14), residues: 3159 helix: 0.94 (0.21), residues: 621 sheet: -1.51 (0.22), residues: 563 loop : -3.30 (0.12), residues: 1975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 620 TYR 0.019 0.001 TYR B 689 PHE 0.042 0.002 PHE B 837 TRP 0.015 0.001 TRP C 868 HIS 0.012 0.001 HIS C1030 Details of bonding type rmsd covalent geometry : bond 0.00470 (25433) covalent geometry : angle 0.72308 (34613) SS BOND : bond 0.00517 ( 39) SS BOND : angle 1.77290 ( 78) hydrogen bonds : bond 0.04190 ( 844) hydrogen bonds : angle 6.13789 ( 2310) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 225 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.9457 (OUTLIER) cc_final: 0.9171 (tt) REVERT: A 80 VAL cc_start: 0.8662 (OUTLIER) cc_final: 0.8361 (p) REVERT: A 220 PHE cc_start: 0.8211 (m-10) cc_final: 0.7878 (m-10) REVERT: A 393 ASP cc_start: 0.8611 (m-30) cc_final: 0.8359 (m-30) REVERT: A 491 TYR cc_start: 0.8587 (m-10) cc_final: 0.8176 (m-80) REVERT: A 502 GLU cc_start: 0.7082 (tt0) cc_final: 0.6775 (mt-10) REVERT: A 649 ASP cc_start: 0.8602 (t0) cc_final: 0.8365 (m-30) REVERT: A 755 GLU cc_start: 0.8025 (tp30) cc_final: 0.7732 (tp30) REVERT: A 801 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8516 (mm-30) REVERT: A 838 ASN cc_start: 0.8236 (OUTLIER) cc_final: 0.7837 (p0) REVERT: A 946 LYS cc_start: 0.9261 (tmtt) cc_final: 0.8823 (tptp) REVERT: B 379 PHE cc_start: 0.7773 (m-10) cc_final: 0.7499 (m-80) REVERT: B 679 MET cc_start: 0.8338 (tpp) cc_final: 0.7784 (tpp) REVERT: B 721 ASN cc_start: 0.8239 (OUTLIER) cc_final: 0.7992 (t0) REVERT: B 762 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7766 (mp0) REVERT: B 918 GLU cc_start: 0.8935 (mt-10) cc_final: 0.8720 (tm-30) REVERT: B 1013 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7728 (mt-10) REVERT: C 184 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.6864 (pt0) REVERT: C 220 PHE cc_start: 0.8303 (m-10) cc_final: 0.7976 (m-80) REVERT: C 231 PHE cc_start: 0.8779 (p90) cc_final: 0.7932 (p90) REVERT: C 274 ASP cc_start: 0.7916 (t0) cc_final: 0.7591 (t0) REVERT: C 287 LYS cc_start: 0.9319 (mttt) cc_final: 0.8989 (mttm) REVERT: C 528 ASN cc_start: 0.8321 (t0) cc_final: 0.7802 (t0) REVERT: C 948 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.8973 (mt) REVERT: C 972 GLU cc_start: 0.8442 (mp0) cc_final: 0.8042 (mp0) REVERT: C 1089 ARG cc_start: 0.8058 (ttt90) cc_final: 0.7725 (mmm160) outliers start: 91 outliers final: 67 residues processed: 299 average time/residue: 0.1488 time to fit residues: 74.6509 Evaluate side-chains 281 residues out of total 2758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 207 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 768 LYS Chi-restraints excluded: chain A residue 838 ASN Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 851 MET Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1082 THR Chi-restraints excluded: chain A residue 1097 ILE Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 721 ASN Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain B residue 801 GLU Chi-restraints excluded: chain B residue 848 THR Chi-restraints excluded: chain B residue 916 ILE Chi-restraints excluded: chain B residue 921 THR Chi-restraints excluded: chain B residue 939 GLN Chi-restraints excluded: chain B residue 972 GLU Chi-restraints excluded: chain B residue 1013 GLU Chi-restraints excluded: chain B residue 1033 SER Chi-restraints excluded: chain B residue 1082 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 348 CYS Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 560 ASP Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 652 ILE Chi-restraints excluded: chain C residue 656 ILE Chi-restraints excluded: chain C residue 687 ILE Chi-restraints excluded: chain C residue 841 THR Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain C residue 927 LEU Chi-restraints excluded: chain C residue 930 LEU Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 967 ASP Chi-restraints excluded: chain C residue 1082 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 210 optimal weight: 0.7980 chunk 45 optimal weight: 20.0000 chunk 265 optimal weight: 10.0000 chunk 30 optimal weight: 8.9990 chunk 22 optimal weight: 20.0000 chunk 17 optimal weight: 5.9990 chunk 233 optimal weight: 7.9990 chunk 138 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 204 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1018 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 721 ASN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 984 GLN C 96 ASN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 883 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.104793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.075786 restraints weight = 84597.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.078331 restraints weight = 50175.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.079667 restraints weight = 29751.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.080040 restraints weight = 23220.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.080387 restraints weight = 20985.695| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.110 25472 Z= 0.253 Angle : 0.762 15.817 34691 Z= 0.399 Chirality : 0.048 0.246 3918 Planarity : 0.005 0.074 4485 Dihedral : 6.516 61.620 3422 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.28 % Allowed : 14.78 % Favored : 84.93 % Rotamer: Outliers : 3.66 % Allowed : 12.40 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.99 (0.14), residues: 3159 helix: 0.81 (0.21), residues: 629 sheet: -1.60 (0.22), residues: 559 loop : -3.29 (0.12), residues: 1971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 620 TYR 0.020 0.002 TYR B 689 PHE 0.041 0.002 PHE B 837 TRP 0.018 0.001 TRP C 868 HIS 0.011 0.002 HIS C1030 Details of bonding type rmsd covalent geometry : bond 0.00554 (25433) covalent geometry : angle 0.75736 (34613) SS BOND : bond 0.00601 ( 39) SS BOND : angle 1.90747 ( 78) hydrogen bonds : bond 0.04374 ( 844) hydrogen bonds : angle 6.27496 ( 2310) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 225 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.9133 (tt) REVERT: A 220 PHE cc_start: 0.8495 (m-10) cc_final: 0.8040 (m-10) REVERT: A 245 TRP cc_start: 0.4854 (p-90) cc_final: 0.4630 (p-90) REVERT: A 393 ASP cc_start: 0.8747 (m-30) cc_final: 0.8484 (m-30) REVERT: A 410 TYR cc_start: 0.5856 (t80) cc_final: 0.5363 (t80) REVERT: A 491 TYR cc_start: 0.8694 (m-10) cc_final: 0.8262 (m-80) REVERT: A 498 VAL cc_start: 0.9461 (t) cc_final: 0.9240 (m) REVERT: A 502 GLU cc_start: 0.7190 (tt0) cc_final: 0.6858 (mt-10) REVERT: A 755 GLU cc_start: 0.8370 (tp30) cc_final: 0.8056 (tp30) REVERT: A 801 GLU cc_start: 0.9008 (mt-10) cc_final: 0.8601 (mm-30) REVERT: A 838 ASN cc_start: 0.8307 (OUTLIER) cc_final: 0.7669 (p0) REVERT: A 1011 MET cc_start: 0.8322 (tpp) cc_final: 0.8044 (tpt) REVERT: B 285 GLU cc_start: 0.8735 (tp30) cc_final: 0.8446 (tp30) REVERT: B 379 PHE cc_start: 0.7939 (m-10) cc_final: 0.7639 (m-80) REVERT: B 679 MET cc_start: 0.8527 (tpp) cc_final: 0.7926 (tpp) REVERT: B 762 GLU cc_start: 0.8364 (mt-10) cc_final: 0.7754 (mp0) REVERT: B 918 GLU cc_start: 0.9066 (mt-10) cc_final: 0.8766 (tm-30) REVERT: B 1013 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7806 (mt-10) REVERT: C 184 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.6891 (pt0) REVERT: C 220 PHE cc_start: 0.8501 (m-10) cc_final: 0.8173 (m-80) REVERT: C 231 PHE cc_start: 0.8951 (p90) cc_final: 0.8114 (p90) REVERT: C 274 ASP cc_start: 0.7950 (t0) cc_final: 0.7627 (t0) REVERT: C 287 LYS cc_start: 0.9271 (mttt) cc_final: 0.8915 (mtpt) REVERT: C 528 ASN cc_start: 0.8547 (t0) cc_final: 0.8020 (t0) REVERT: C 948 LEU cc_start: 0.9425 (OUTLIER) cc_final: 0.9120 (mt) REVERT: C 972 GLU cc_start: 0.8575 (mp0) cc_final: 0.8125 (mp0) outliers start: 101 outliers final: 75 residues processed: 306 average time/residue: 0.1519 time to fit residues: 77.7407 Evaluate side-chains 294 residues out of total 2758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 214 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 366 CYS Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 768 LYS Chi-restraints excluded: chain A residue 838 ASN Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 851 MET Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1082 THR Chi-restraints excluded: chain A residue 1097 ILE Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain B residue 801 GLU Chi-restraints excluded: chain B residue 848 THR Chi-restraints excluded: chain B residue 883 GLN Chi-restraints excluded: chain B residue 916 ILE Chi-restraints excluded: chain B residue 921 THR Chi-restraints excluded: chain B residue 939 GLN Chi-restraints excluded: chain B residue 972 GLU Chi-restraints excluded: chain B residue 984 GLN Chi-restraints excluded: chain B residue 1013 GLU Chi-restraints excluded: chain B residue 1033 SER Chi-restraints excluded: chain B residue 1082 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 348 CYS Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 560 ASP Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 652 ILE Chi-restraints excluded: chain C residue 656 ILE Chi-restraints excluded: chain C residue 687 ILE Chi-restraints excluded: chain C residue 841 THR Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain C residue 927 LEU Chi-restraints excluded: chain C residue 930 LEU Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 967 ASP Chi-restraints excluded: chain C residue 1001 ARG Chi-restraints excluded: chain C residue 1082 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 251 optimal weight: 8.9990 chunk 281 optimal weight: 4.9990 chunk 286 optimal weight: 4.9990 chunk 213 optimal weight: 0.0670 chunk 66 optimal weight: 2.9990 chunk 243 optimal weight: 30.0000 chunk 28 optimal weight: 0.8980 chunk 100 optimal weight: 0.2980 chunk 47 optimal weight: 10.0000 chunk 85 optimal weight: 0.9980 chunk 56 optimal weight: 8.9990 overall best weight: 1.0520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 ASN A1018 GLN ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 721 ASN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 883 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.110178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.082718 restraints weight = 84994.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.085691 restraints weight = 49724.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.086657 restraints weight = 30364.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.087443 restraints weight = 24487.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.087498 restraints weight = 21686.222| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.4344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 25472 Z= 0.139 Angle : 0.698 12.527 34691 Z= 0.364 Chirality : 0.047 0.255 3918 Planarity : 0.004 0.065 4485 Dihedral : 6.159 58.170 3422 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.25 % Allowed : 12.76 % Favored : 86.99 % Rotamer: Outliers : 2.57 % Allowed : 13.71 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.70 (0.15), residues: 3159 helix: 1.29 (0.22), residues: 607 sheet: -1.42 (0.22), residues: 590 loop : -3.15 (0.13), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 761 TYR 0.020 0.001 TYR A 689 PHE 0.038 0.001 PHE B 837 TRP 0.014 0.001 TRP C 868 HIS 0.008 0.001 HIS C1030 Details of bonding type rmsd covalent geometry : bond 0.00312 (25433) covalent geometry : angle 0.69311 (34613) SS BOND : bond 0.00472 ( 39) SS BOND : angle 1.84652 ( 78) hydrogen bonds : bond 0.03997 ( 844) hydrogen bonds : angle 5.96184 ( 2310) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 250 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.9436 (OUTLIER) cc_final: 0.9178 (tt) REVERT: A 220 PHE cc_start: 0.8323 (m-10) cc_final: 0.7882 (m-10) REVERT: A 245 TRP cc_start: 0.4759 (p-90) cc_final: 0.4322 (p-90) REVERT: A 393 ASP cc_start: 0.8707 (m-30) cc_final: 0.8441 (m-30) REVERT: A 410 TYR cc_start: 0.5670 (t80) cc_final: 0.5452 (t80) REVERT: A 417 MET cc_start: 0.5667 (tpp) cc_final: 0.5409 (tpt) REVERT: A 491 TYR cc_start: 0.8673 (m-10) cc_final: 0.8239 (m-80) REVERT: A 502 GLU cc_start: 0.7024 (tt0) cc_final: 0.6727 (mt-10) REVERT: A 755 GLU cc_start: 0.8223 (tp30) cc_final: 0.7953 (tp30) REVERT: A 801 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8557 (mm-30) REVERT: A 838 ASN cc_start: 0.7823 (OUTLIER) cc_final: 0.7304 (p0) REVERT: A 841 THR cc_start: 0.9110 (t) cc_final: 0.8905 (m) REVERT: A 946 LYS cc_start: 0.9293 (tmtt) cc_final: 0.8962 (tptp) REVERT: B 235 LEU cc_start: 0.9075 (mp) cc_final: 0.8610 (pp) REVERT: B 285 GLU cc_start: 0.8723 (tp30) cc_final: 0.8437 (tp30) REVERT: B 379 PHE cc_start: 0.7415 (m-10) cc_final: 0.7145 (m-80) REVERT: B 601 VAL cc_start: 0.8655 (OUTLIER) cc_final: 0.8413 (t) REVERT: B 679 MET cc_start: 0.8829 (tpp) cc_final: 0.8385 (tpp) REVERT: B 720 CYS cc_start: 0.5532 (p) cc_final: 0.5302 (p) REVERT: B 755 GLU cc_start: 0.9037 (tt0) cc_final: 0.8566 (tp30) REVERT: B 762 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7686 (mp0) REVERT: B 884 MET cc_start: 0.8213 (mmt) cc_final: 0.7973 (mmp) REVERT: B 918 GLU cc_start: 0.8919 (mt-10) cc_final: 0.8546 (tp30) REVERT: B 1013 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7724 (mt-10) REVERT: B 1032 MET cc_start: 0.7157 (tpp) cc_final: 0.6949 (mmm) REVERT: B 1071 PHE cc_start: 0.8336 (m-10) cc_final: 0.8100 (m-10) REVERT: C 184 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.6976 (pt0) REVERT: C 231 PHE cc_start: 0.8934 (p90) cc_final: 0.8297 (p90) REVERT: C 274 ASP cc_start: 0.7999 (t0) cc_final: 0.7647 (t0) REVERT: C 287 LYS cc_start: 0.9265 (mttt) cc_final: 0.8992 (mttm) REVERT: C 528 ASN cc_start: 0.8302 (t0) cc_final: 0.7801 (t0) REVERT: C 948 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.8946 (mt) REVERT: C 972 GLU cc_start: 0.8513 (mp0) cc_final: 0.8046 (mp0) REVERT: C 1070 TYR cc_start: 0.9021 (OUTLIER) cc_final: 0.8562 (m-10) outliers start: 71 outliers final: 50 residues processed: 311 average time/residue: 0.1516 time to fit residues: 78.5117 Evaluate side-chains 279 residues out of total 2758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 222 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 366 CYS Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 768 LYS Chi-restraints excluded: chain A residue 838 ASN Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 965 ARG Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1082 THR Chi-restraints excluded: chain A residue 1097 ILE Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain B residue 801 GLU Chi-restraints excluded: chain B residue 883 GLN Chi-restraints excluded: chain B residue 921 THR Chi-restraints excluded: chain B residue 939 GLN Chi-restraints excluded: chain B residue 972 GLU Chi-restraints excluded: chain B residue 1013 GLU Chi-restraints excluded: chain B residue 1033 SER Chi-restraints excluded: chain B residue 1082 THR Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 348 CYS Chi-restraints excluded: chain C residue 560 ASP Chi-restraints excluded: chain C residue 652 ILE Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain C residue 927 LEU Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 1070 TYR Chi-restraints excluded: chain C residue 1082 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 306 optimal weight: 1.9990 chunk 283 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 35 optimal weight: 0.0980 chunk 237 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 304 optimal weight: 1.9990 chunk 279 optimal weight: 4.9990 chunk 280 optimal weight: 0.7980 chunk 81 optimal weight: 6.9990 chunk 158 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 ASN A 744 GLN ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 721 ASN B 744 GLN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 984 GLN C 96 ASN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.114320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.089736 restraints weight = 86018.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.091060 restraints weight = 51739.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.092442 restraints weight = 33852.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.092782 restraints weight = 27547.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.092918 restraints weight = 25155.191| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.4479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 25472 Z= 0.133 Angle : 0.705 18.181 34691 Z= 0.366 Chirality : 0.047 0.233 3918 Planarity : 0.004 0.060 4485 Dihedral : 6.042 58.305 3422 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.22 % Allowed : 12.60 % Favored : 87.18 % Rotamer: Outliers : 2.43 % Allowed : 14.14 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.61 (0.15), residues: 3159 helix: 1.26 (0.22), residues: 616 sheet: -1.31 (0.22), residues: 575 loop : -3.08 (0.13), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 563 TYR 0.024 0.001 TYR A 689 PHE 0.037 0.001 PHE B 220 TRP 0.013 0.001 TRP C 101 HIS 0.007 0.001 HIS C1030 Details of bonding type rmsd covalent geometry : bond 0.00300 (25433) covalent geometry : angle 0.69980 (34613) SS BOND : bond 0.00549 ( 39) SS BOND : angle 2.01027 ( 78) hydrogen bonds : bond 0.03953 ( 844) hydrogen bonds : angle 5.83705 ( 2310) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 249 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 PHE cc_start: 0.8255 (m-10) cc_final: 0.7811 (m-10) REVERT: A 285 GLU cc_start: 0.8420 (tm-30) cc_final: 0.8174 (tm-30) REVERT: A 393 ASP cc_start: 0.8663 (m-30) cc_final: 0.8097 (m-30) REVERT: A 410 TYR cc_start: 0.5674 (t80) cc_final: 0.5463 (t80) REVERT: A 491 TYR cc_start: 0.8607 (m-10) cc_final: 0.8180 (m-80) REVERT: A 502 GLU cc_start: 0.6995 (tt0) cc_final: 0.6713 (mt-10) REVERT: A 755 GLU cc_start: 0.8172 (tp30) cc_final: 0.7910 (tp30) REVERT: A 801 GLU cc_start: 0.8795 (mt-10) cc_final: 0.8485 (mm-30) REVERT: A 946 LYS cc_start: 0.9204 (tmtt) cc_final: 0.8894 (tptp) REVERT: B 235 LEU cc_start: 0.9068 (mp) cc_final: 0.8672 (pp) REVERT: B 285 GLU cc_start: 0.8842 (tp30) cc_final: 0.8513 (tp30) REVERT: B 679 MET cc_start: 0.8830 (tpp) cc_final: 0.8383 (tpp) REVERT: B 720 CYS cc_start: 0.5203 (p) cc_final: 0.4880 (p) REVERT: B 755 GLU cc_start: 0.8922 (tt0) cc_final: 0.8459 (tp30) REVERT: B 762 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7628 (mt-10) REVERT: B 884 MET cc_start: 0.8207 (mmt) cc_final: 0.7965 (mmp) REVERT: B 918 GLU cc_start: 0.8843 (mt-10) cc_final: 0.8511 (tp30) REVERT: B 1013 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7583 (mt-10) REVERT: C 181 HIS cc_start: 0.7544 (m90) cc_final: 0.7342 (m90) REVERT: C 184 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.6914 (pt0) REVERT: C 220 PHE cc_start: 0.7951 (m-80) cc_final: 0.7179 (m-80) REVERT: C 231 PHE cc_start: 0.8881 (p90) cc_final: 0.8317 (p90) REVERT: C 274 ASP cc_start: 0.7862 (t0) cc_final: 0.7561 (t0) REVERT: C 287 LYS cc_start: 0.9133 (mttt) cc_final: 0.8811 (mtpt) REVERT: C 528 ASN cc_start: 0.8125 (t0) cc_final: 0.7637 (t0) REVERT: C 948 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8924 (mt) REVERT: C 972 GLU cc_start: 0.8430 (mp0) cc_final: 0.8017 (mp0) REVERT: C 1070 TYR cc_start: 0.9007 (OUTLIER) cc_final: 0.8605 (m-10) outliers start: 67 outliers final: 49 residues processed: 304 average time/residue: 0.1514 time to fit residues: 76.5934 Evaluate side-chains 273 residues out of total 2758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 220 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 366 CYS Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 768 LYS Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 965 ARG Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1082 THR Chi-restraints excluded: chain A residue 1097 ILE Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 801 GLU Chi-restraints excluded: chain B residue 848 THR Chi-restraints excluded: chain B residue 883 GLN Chi-restraints excluded: chain B residue 921 THR Chi-restraints excluded: chain B residue 972 GLU Chi-restraints excluded: chain B residue 1013 GLU Chi-restraints excluded: chain B residue 1033 SER Chi-restraints excluded: chain B residue 1082 THR Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 348 CYS Chi-restraints excluded: chain C residue 560 ASP Chi-restraints excluded: chain C residue 652 ILE Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain C residue 687 ILE Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain C residue 927 LEU Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 1070 TYR Chi-restraints excluded: chain C residue 1082 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 204 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 196 optimal weight: 5.9990 chunk 306 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 chunk 235 optimal weight: 7.9990 chunk 75 optimal weight: 9.9990 chunk 109 optimal weight: 5.9990 chunk 92 optimal weight: 0.8980 chunk 218 optimal weight: 0.0770 overall best weight: 1.5340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 744 GLN A 759 ASN B 135 ASN ** B 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 984 GLN C 96 ASN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.113273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.088666 restraints weight = 86293.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.089844 restraints weight = 53178.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.091201 restraints weight = 34289.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.091438 restraints weight = 28589.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.091658 restraints weight = 25548.202| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.4605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 25472 Z= 0.159 Angle : 0.717 13.090 34691 Z= 0.373 Chirality : 0.047 0.212 3918 Planarity : 0.005 0.059 4485 Dihedral : 6.018 57.802 3422 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.25 % Allowed : 12.69 % Favored : 87.05 % Rotamer: Outliers : 2.28 % Allowed : 14.47 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.62 (0.15), residues: 3159 helix: 1.23 (0.22), residues: 606 sheet: -1.33 (0.22), residues: 591 loop : -3.06 (0.13), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 183 TYR 0.020 0.001 TYR A 689 PHE 0.028 0.001 PHE B 837 TRP 0.047 0.002 TRP A 245 HIS 0.009 0.001 HIS C1030 Details of bonding type rmsd covalent geometry : bond 0.00356 (25433) covalent geometry : angle 0.71250 (34613) SS BOND : bond 0.00480 ( 39) SS BOND : angle 1.87907 ( 78) hydrogen bonds : bond 0.03997 ( 844) hydrogen bonds : angle 5.84333 ( 2310) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 231 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 PHE cc_start: 0.8176 (m-10) cc_final: 0.7744 (m-10) REVERT: A 285 GLU cc_start: 0.8382 (tm-30) cc_final: 0.8010 (tm-30) REVERT: A 367 TYR cc_start: 0.8141 (m-10) cc_final: 0.7936 (m-10) REVERT: A 393 ASP cc_start: 0.8330 (m-30) cc_final: 0.8049 (m-30) REVERT: A 410 TYR cc_start: 0.5844 (t80) cc_final: 0.5642 (t80) REVERT: A 491 TYR cc_start: 0.8604 (m-10) cc_final: 0.8185 (m-80) REVERT: A 502 GLU cc_start: 0.7054 (tt0) cc_final: 0.6736 (mt-10) REVERT: A 755 GLU cc_start: 0.8132 (tp30) cc_final: 0.7880 (tp30) REVERT: A 801 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8480 (mm-30) REVERT: A 946 LYS cc_start: 0.9213 (tmtt) cc_final: 0.8861 (tptp) REVERT: B 235 LEU cc_start: 0.9074 (mp) cc_final: 0.8682 (pp) REVERT: B 285 GLU cc_start: 0.8847 (tp30) cc_final: 0.8516 (tp30) REVERT: B 679 MET cc_start: 0.8826 (tpp) cc_final: 0.8411 (tpp) REVERT: B 720 CYS cc_start: 0.5259 (p) cc_final: 0.5031 (p) REVERT: B 755 GLU cc_start: 0.8887 (tt0) cc_final: 0.8480 (tp30) REVERT: B 762 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7613 (mt-10) REVERT: B 918 GLU cc_start: 0.8852 (mt-10) cc_final: 0.8501 (tp30) REVERT: B 1013 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7555 (mt-10) REVERT: C 184 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7081 (pt0) REVERT: C 220 PHE cc_start: 0.7916 (m-80) cc_final: 0.7116 (m-80) REVERT: C 231 PHE cc_start: 0.8912 (p90) cc_final: 0.8354 (p90) REVERT: C 274 ASP cc_start: 0.7856 (t0) cc_final: 0.7562 (t0) REVERT: C 287 LYS cc_start: 0.9159 (mttt) cc_final: 0.8835 (mtpt) REVERT: C 528 ASN cc_start: 0.8161 (t0) cc_final: 0.7720 (t0) REVERT: C 722 MET cc_start: 0.8454 (ttm) cc_final: 0.8220 (ttm) REVERT: C 948 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8898 (mt) REVERT: C 972 GLU cc_start: 0.8413 (mp0) cc_final: 0.8038 (mp0) REVERT: C 1070 TYR cc_start: 0.8986 (OUTLIER) cc_final: 0.8592 (m-10) outliers start: 63 outliers final: 52 residues processed: 283 average time/residue: 0.1521 time to fit residues: 71.4596 Evaluate side-chains 273 residues out of total 2758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 217 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 366 CYS Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 768 LYS Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 965 ARG Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1082 THR Chi-restraints excluded: chain A residue 1097 ILE Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 848 THR Chi-restraints excluded: chain B residue 883 GLN Chi-restraints excluded: chain B residue 921 THR Chi-restraints excluded: chain B residue 972 GLU Chi-restraints excluded: chain B residue 1013 GLU Chi-restraints excluded: chain B residue 1033 SER Chi-restraints excluded: chain B residue 1082 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 348 CYS Chi-restraints excluded: chain C residue 560 ASP Chi-restraints excluded: chain C residue 652 ILE Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain C residue 687 ILE Chi-restraints excluded: chain C residue 841 THR Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain C residue 927 LEU Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 1001 ARG Chi-restraints excluded: chain C residue 1070 TYR Chi-restraints excluded: chain C residue 1082 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 40 optimal weight: 20.0000 chunk 68 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 230 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 127 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 287 optimal weight: 6.9990 chunk 69 optimal weight: 0.3980 chunk 21 optimal weight: 5.9990 chunk 194 optimal weight: 3.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN B 135 ASN ** B 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 721 ASN ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.108933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.081512 restraints weight = 85084.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.083692 restraints weight = 53489.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.085181 restraints weight = 34323.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.086124 restraints weight = 25730.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.086172 restraints weight = 22319.350| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.4717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 25472 Z= 0.184 Angle : 0.726 12.400 34691 Z= 0.379 Chirality : 0.047 0.187 3918 Planarity : 0.005 0.058 4485 Dihedral : 6.049 57.844 3422 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.22 % Allowed : 13.71 % Favored : 86.07 % Rotamer: Outliers : 2.39 % Allowed : 14.43 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.65 (0.15), residues: 3159 helix: 1.07 (0.22), residues: 622 sheet: -1.33 (0.22), residues: 567 loop : -3.06 (0.13), residues: 1970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 797 TYR 0.020 0.001 TYR A 689 PHE 0.048 0.002 PHE B 220 TRP 0.031 0.002 TRP A 245 HIS 0.009 0.001 HIS C1030 Details of bonding type rmsd covalent geometry : bond 0.00408 (25433) covalent geometry : angle 0.72153 (34613) SS BOND : bond 0.00463 ( 39) SS BOND : angle 1.81856 ( 78) hydrogen bonds : bond 0.04221 ( 844) hydrogen bonds : angle 5.89604 ( 2310) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4348.86 seconds wall clock time: 76 minutes 4.49 seconds (4564.49 seconds total)