Starting phenix.real_space_refine on Mon Oct 26 22:36:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6m39_30071/10_2026/6m39_30071.cif Found real_map, /net/cci-nas-00/data/ceres_data/6m39_30071/10_2026/6m39_30071.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6m39_30071/10_2026/6m39_30071.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6m39_30071/10_2026/6m39_30071.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6m39_30071/10_2026/6m39_30071.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6m39_30071/10_2026/6m39_30071.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6m39_30071/10_2026/6m39_30071.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6m39_30071/10_2026/6m39_30071.map" } resolution = 3.55 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 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 14415 2.51 5 N 3771 2.21 5 O 4395 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22716 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 937, 7320 Classifications: {'peptide': 937} Link IDs: {'PTRANS': 39, 'TRANS': 897} Chain breaks: 4 Chain: "A" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 252 Unusual residues: {'NAG': 18} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen chiralities: 18 Restraints were copied for chains: B, C Time building chain proxies: 9.09, per 1000 atoms: 0.40 Number of scatterers: 22716 At special positions: 0 Unit cell: (118.56, 119.6, 158.08, 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 4395 8.00 N 3771 7.00 C 14415 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 58 " distance=2.03 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 246 " distance=2.01 Simple disulfide: pdb=" SG CYS A 279 " - pdb=" SG CYS A 302 " distance=2.01 Simple disulfide: pdb=" SG CYS A 287 " - pdb=" SG CYS A 292 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 371 " distance=2.02 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 399 " distance=2.04 Simple disulfide: pdb=" SG CYS A 592 " - pdb=" SG CYS A 614 " distance=2.02 Simple disulfide: pdb=" SG CYS A 597 " - pdb=" SG CYS A 603 " distance=2.01 Simple disulfide: pdb=" SG CYS A 698 " - pdb=" SG CYS A 708 " distance=2.02 Simple disulfide: pdb=" SG CYS A 886 " - pdb=" SG CYS A 897 " distance=2.02 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 58 " distance=2.03 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 246 " distance=2.01 Simple disulfide: pdb=" SG CYS B 279 " - pdb=" SG CYS B 302 " distance=2.01 Simple disulfide: pdb=" SG CYS B 287 " - pdb=" SG CYS B 292 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 371 " distance=2.02 Simple disulfide: pdb=" SG CYS B 343 " - pdb=" SG CYS B 399 " distance=2.04 Simple disulfide: pdb=" SG CYS B 592 " - pdb=" SG CYS B 614 " distance=2.02 Simple disulfide: pdb=" SG CYS B 597 " - pdb=" SG CYS B 603 " distance=2.01 Simple disulfide: pdb=" SG CYS B 698 " - pdb=" SG CYS B 708 " distance=2.02 Simple disulfide: pdb=" SG CYS B 886 " - pdb=" SG CYS B 897 " distance=2.02 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 58 " distance=2.03 Simple disulfide: pdb=" SG CYS C 236 " - pdb=" SG CYS C 246 " distance=2.01 Simple disulfide: pdb=" SG CYS C 279 " - pdb=" SG CYS C 302 " distance=2.01 Simple disulfide: pdb=" SG CYS C 287 " - pdb=" SG CYS C 292 " distance=2.03 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 371 " distance=2.02 Simple disulfide: pdb=" SG CYS C 343 " - pdb=" SG CYS C 399 " distance=2.04 Simple disulfide: pdb=" SG CYS C 592 " - pdb=" SG CYS C 614 " distance=2.03 Simple disulfide: pdb=" SG CYS C 597 " - pdb=" SG CYS C 603 " distance=2.01 Simple disulfide: pdb=" SG CYS C 698 " - pdb=" SG CYS C 708 " distance=2.02 Simple disulfide: pdb=" SG CYS C 886 " - pdb=" SG CYS C 897 " distance=2.02 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 Links applied NAG-ASN " NAG A1001 " - " ASN A 654 " " NAG A1002 " - " ASN A 924 " " NAG A1003 " - " ASN A 957 " " NAG A1004 " - " ASN A 973 " " NAG A1005 " - " ASN A 987 " " NAG A1006 " - " ASN A 52 " " NAG A1007 " - " ASN A 992 " " NAG A1008 " - " ASN A 154 " " NAG A1009 " - " ASN A 358 " " NAG A1010 " - " ASN A 520 " " NAG A1011 " - " ASN A 305 " " NAG A1012 " - " ASN A 275 " " NAG A1013 " - " ASN A 39 " " NAG A1014 " - " ASN A 472 " " NAG A1015 " - " ASN A 514 " " NAG A1016 " - " ASN A 503 " " NAG A1017 " - " ASN A 104 " " NAG A1018 " - " ASN A 525 " " NAG B1001 " - " ASN B 654 " " NAG B1002 " - " ASN B 924 " " NAG B1003 " - " ASN B 957 " " NAG B1004 " - " ASN B 973 " " NAG B1005 " - " ASN B 987 " " NAG B1006 " - " ASN B 52 " " NAG B1007 " - " ASN B 992 " " NAG B1008 " - " ASN B 154 " " NAG B1009 " - " ASN B 358 " " NAG B1010 " - " ASN B 520 " " NAG B1011 " - " ASN B 305 " " NAG B1012 " - " ASN B 275 " " NAG B1013 " - " ASN B 39 " " NAG B1014 " - " ASN B 472 " " NAG B1015 " - " ASN B 514 " " NAG B1016 " - " ASN B 503 " " NAG B1017 " - " ASN B 104 " " NAG B1018 " - " ASN B 525 " " NAG C1001 " - " ASN C 654 " " NAG C1002 " - " ASN C 924 " " NAG C1003 " - " ASN C 957 " " NAG C1004 " - " ASN C 973 " " NAG C1005 " - " ASN C 987 " " NAG C1006 " - " ASN C 52 " " NAG C1007 " - " ASN C 992 " " NAG C1008 " - " ASN C 154 " " NAG C1009 " - " ASN C 358 " " NAG C1010 " - " ASN C 520 " " NAG C1011 " - " ASN C 305 " " NAG C1012 " - " ASN C 275 " " NAG C1013 " - " ASN C 39 " " NAG C1014 " - " ASN C 472 " " NAG C1015 " - " ASN C 514 " " NAG C1016 " - " ASN C 503 " " NAG C1017 " - " ASN C 104 " " NAG C1018 " - " ASN C 525 " Time building additional restraints: 1.88 Conformation dependent library (CDL) restraints added in 869.2 milliseconds 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5220 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 33 sheets defined 21.6% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 24 through 28 removed outlier: 3.518A pdb=" N PHE A 27 " --> pdb=" O PHE A 24 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASN A 28 " --> pdb=" O ASN A 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 24 through 28' Processing helix chain 'A' and resid 171 through 173 No H-bonds generated for 'chain 'A' and resid 171 through 173' Processing helix chain 'A' and resid 240 through 248 removed outlier: 3.637A pdb=" N LEU A 244 " --> pdb=" O PHE A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 490 removed outlier: 3.751A pdb=" N LYS A 490 " --> pdb=" O GLN A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 503 removed outlier: 3.551A pdb=" N HIS A 502 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASN A 503 " --> pdb=" O PRO A 500 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 499 through 503' Processing helix chain 'A' and resid 591 through 596 Processing helix chain 'A' and resid 600 through 608 removed outlier: 4.260A pdb=" N LYS A 604 " --> pdb=" O SER A 600 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU A 606 " --> pdb=" O ALA A 602 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N PHE A 608 " --> pdb=" O LYS A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 638 Processing helix chain 'A' and resid 676 through 682 Processing helix chain 'A' and resid 690 through 702 removed outlier: 3.743A pdb=" N ASN A 701 " --> pdb=" O ASN A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 763 Processing helix chain 'A' and resid 770 through 786 Processing helix chain 'A' and resid 787 through 789 No H-bonds generated for 'chain 'A' and resid 787 through 789' Processing helix chain 'A' and resid 798 through 822 removed outlier: 3.553A pdb=" N ILE A 802 " --> pdb=" O ALA A 798 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ILE A 820 " --> pdb=" O LEU A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 836 Processing helix chain 'A' and resid 841 through 887 removed outlier: 3.773A pdb=" N ARG A 849 " --> pdb=" O VAL A 845 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU A 850 " --> pdb=" O GLN A 846 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ASN A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY A 853 " --> pdb=" O ARG A 849 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASN A 856 " --> pdb=" O ASN A 852 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLU A 885 " --> pdb=" O SER A 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 28 removed outlier: 3.518A pdb=" N PHE B 27 " --> pdb=" O PHE B 24 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASN B 28 " --> pdb=" O ASN B 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 24 through 28' Processing helix chain 'B' and resid 171 through 173 No H-bonds generated for 'chain 'B' and resid 171 through 173' Processing helix chain 'B' and resid 240 through 248 removed outlier: 3.637A pdb=" N LEU B 244 " --> pdb=" O PHE B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 490 removed outlier: 3.751A pdb=" N LYS B 490 " --> pdb=" O GLN B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 503 removed outlier: 3.552A pdb=" N HIS B 502 " --> pdb=" O LEU B 499 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASN B 503 " --> pdb=" O PRO B 500 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 499 through 503' Processing helix chain 'B' and resid 591 through 596 Processing helix chain 'B' and resid 600 through 608 removed outlier: 4.260A pdb=" N LYS B 604 " --> pdb=" O SER B 600 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU B 606 " --> pdb=" O ALA B 602 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N PHE B 608 " --> pdb=" O LYS B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 638 Processing helix chain 'B' and resid 676 through 682 Processing helix chain 'B' and resid 690 through 702 removed outlier: 3.743A pdb=" N ASN B 701 " --> pdb=" O ASN B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 751 through 763 Processing helix chain 'B' and resid 770 through 786 Processing helix chain 'B' and resid 787 through 789 No H-bonds generated for 'chain 'B' and resid 787 through 789' Processing helix chain 'B' and resid 798 through 822 removed outlier: 3.553A pdb=" N ILE B 802 " --> pdb=" O ALA B 798 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ILE B 820 " --> pdb=" O LEU B 816 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 836 Processing helix chain 'B' and resid 841 through 887 removed outlier: 3.774A pdb=" N ARG B 849 " --> pdb=" O VAL B 845 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU B 850 " --> pdb=" O GLN B 846 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ASN B 852 " --> pdb=" O ASP B 848 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY B 853 " --> pdb=" O ARG B 849 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASN B 856 " --> pdb=" O ASN B 852 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU B 885 " --> pdb=" O SER B 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 28 removed outlier: 3.518A pdb=" N PHE C 27 " --> pdb=" O PHE C 24 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASN C 28 " --> pdb=" O ASN C 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 24 through 28' Processing helix chain 'C' and resid 171 through 173 No H-bonds generated for 'chain 'C' and resid 171 through 173' Processing helix chain 'C' and resid 240 through 248 removed outlier: 3.637A pdb=" N LEU C 244 " --> pdb=" O PHE C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 490 removed outlier: 3.751A pdb=" N LYS C 490 " --> pdb=" O GLN C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 503 removed outlier: 3.551A pdb=" N HIS C 502 " --> pdb=" O LEU C 499 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASN C 503 " --> pdb=" O PRO C 500 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 499 through 503' Processing helix chain 'C' and resid 591 through 596 Processing helix chain 'C' and resid 600 through 608 removed outlier: 4.260A pdb=" N LYS C 604 " --> pdb=" O SER C 600 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU C 606 " --> pdb=" O ALA C 602 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N PHE C 608 " --> pdb=" O LYS C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 638 Processing helix chain 'C' and resid 676 through 682 Processing helix chain 'C' and resid 690 through 702 removed outlier: 3.743A pdb=" N ASN C 701 " --> pdb=" O ASN C 697 " (cutoff:3.500A) Processing helix chain 'C' and resid 751 through 763 Processing helix chain 'C' and resid 770 through 786 Processing helix chain 'C' and resid 787 through 789 No H-bonds generated for 'chain 'C' and resid 787 through 789' Processing helix chain 'C' and resid 798 through 822 removed outlier: 3.553A pdb=" N ILE C 802 " --> pdb=" O ALA C 798 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ILE C 820 " --> pdb=" O LEU C 816 " (cutoff:3.500A) Processing helix chain 'C' and resid 830 through 836 Processing helix chain 'C' and resid 841 through 887 removed outlier: 3.774A pdb=" N ARG C 849 " --> pdb=" O VAL C 845 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU C 850 " --> pdb=" O GLN C 846 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ASN C 852 " --> pdb=" O ASP C 848 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY C 853 " --> pdb=" O ARG C 849 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASN C 856 " --> pdb=" O ASN C 852 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLU C 885 " --> pdb=" O SER C 881 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.242A pdb=" N ARG A 232 " --> pdb=" O GLU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 67 through 70 removed outlier: 7.261A pdb=" N TRP A 110 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N VAL A 123 " --> pdb=" O TRP A 110 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N HIS A 112 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL A 121 " --> pdb=" O HIS A 112 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 186 through 188 removed outlier: 3.600A pdb=" N GLY A 168 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N TYR A 165 " --> pdb=" O THR A 78 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLN A 77 " --> pdb=" O ARG A 210 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ARG A 210 " --> pdb=" O GLN A 77 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 256 through 262 removed outlier: 5.643A pdb=" N VAL A 257 " --> pdb=" O TYR A 469 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N TYR A 469 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N SER A 259 " --> pdb=" O VAL A 467 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL A 467 " --> pdb=" O SER A 259 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A 512 " --> pdb=" O THR A 505 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR A 505 " --> pdb=" O LEU A 512 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 297 through 299 Processing sheet with id=AA6, first strand: chain 'A' and resid 413 through 415 removed outlier: 3.597A pdb=" N LYS A 453 " --> pdb=" O ILE A 450 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ARG A 446 " --> pdb=" O VAL A 457 " (cutoff:3.500A) removed outlier: 10.538A pdb=" N SER A 459 " --> pdb=" O GLN A 444 " (cutoff:3.500A) removed outlier: 13.181A pdb=" N GLN A 444 " --> pdb=" O SER A 459 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N LEU A 445 " --> pdb=" O VAL A 441 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL A 441 " --> pdb=" O LEU A 445 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TYR A 447 " --> pdb=" O LEU A 439 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 522 through 523 removed outlier: 3.636A pdb=" N ALA A 543 " --> pdb=" O ASP A 537 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N PHE A 534 " --> pdb=" O LEU A 530 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 567 through 582 removed outlier: 6.942A pdb=" N ASN A 925 " --> pdb=" O LEU A 570 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N HIS A 572 " --> pdb=" O PRO A 923 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU A 574 " --> pdb=" O LEU A 921 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU A 921 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LEU A 576 " --> pdb=" O TYR A 919 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N TYR A 919 " --> pdb=" O LEU A 576 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLU A 578 " --> pdb=" O PHE A 917 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N PHE A 917 " --> pdb=" O GLU A 578 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N PHE A 580 " --> pdb=" O MET A 915 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N MET A 915 " --> pdb=" O PHE A 580 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLN A 582 " --> pdb=" O GLY A 913 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N GLY A 913 " --> pdb=" O GLN A 582 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY A 913 " --> pdb=" O ALA A 910 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU A 921 " --> pdb=" O HIS A 902 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N HIS A 902 " --> pdb=" O LEU A 921 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 587 through 590 Processing sheet with id=AB1, first strand: chain 'A' and resid 979 through 981 Processing sheet with id=AB2, first strand: chain 'A' and resid 952 through 954 Processing sheet with id=AB3, first strand: chain 'B' and resid 42 through 43 removed outlier: 4.242A pdb=" N ARG B 232 " --> pdb=" O GLU B 223 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 67 through 70 removed outlier: 7.261A pdb=" N TRP B 110 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N VAL B 123 " --> pdb=" O TRP B 110 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N HIS B 112 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL B 121 " --> pdb=" O HIS B 112 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 186 through 188 removed outlier: 3.601A pdb=" N GLY B 168 " --> pdb=" O VAL B 179 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N TYR B 165 " --> pdb=" O THR B 78 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLN B 77 " --> pdb=" O ARG B 210 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ARG B 210 " --> pdb=" O GLN B 77 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 256 through 262 removed outlier: 5.643A pdb=" N VAL B 257 " --> pdb=" O TYR B 469 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N TYR B 469 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N SER B 259 " --> pdb=" O VAL B 467 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL B 467 " --> pdb=" O SER B 259 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU B 512 " --> pdb=" O THR B 505 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR B 505 " --> pdb=" O LEU B 512 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 297 through 299 Processing sheet with id=AB8, first strand: chain 'B' and resid 413 through 415 removed outlier: 3.597A pdb=" N LYS B 453 " --> pdb=" O ILE B 450 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ARG B 446 " --> pdb=" O VAL B 457 " (cutoff:3.500A) removed outlier: 10.538A pdb=" N SER B 459 " --> pdb=" O GLN B 444 " (cutoff:3.500A) removed outlier: 13.181A pdb=" N GLN B 444 " --> pdb=" O SER B 459 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N LEU B 445 " --> pdb=" O VAL B 441 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL B 441 " --> pdb=" O LEU B 445 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TYR B 447 " --> pdb=" O LEU B 439 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 522 through 523 removed outlier: 3.638A pdb=" N ALA B 543 " --> pdb=" O ASP B 537 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N PHE B 534 " --> pdb=" O LEU B 530 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 567 through 582 removed outlier: 6.943A pdb=" N ASN B 925 " --> pdb=" O LEU B 570 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N HIS B 572 " --> pdb=" O PRO B 923 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU B 574 " --> pdb=" O LEU B 921 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU B 921 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LEU B 576 " --> pdb=" O TYR B 919 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N TYR B 919 " --> pdb=" O LEU B 576 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N GLU B 578 " --> pdb=" O PHE B 917 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N PHE B 917 " --> pdb=" O GLU B 578 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N PHE B 580 " --> pdb=" O MET B 915 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N MET B 915 " --> pdb=" O PHE B 580 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLN B 582 " --> pdb=" O GLY B 913 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N GLY B 913 " --> pdb=" O GLN B 582 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY B 913 " --> pdb=" O ALA B 910 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU B 921 " --> pdb=" O HIS B 902 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N HIS B 902 " --> pdb=" O LEU B 921 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 587 through 590 Processing sheet with id=AC3, first strand: chain 'B' and resid 979 through 981 Processing sheet with id=AC4, first strand: chain 'B' and resid 952 through 954 Processing sheet with id=AC5, first strand: chain 'C' and resid 42 through 43 removed outlier: 4.243A pdb=" N ARG C 232 " --> pdb=" O GLU C 223 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 67 through 70 removed outlier: 7.260A pdb=" N TRP C 110 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N VAL C 123 " --> pdb=" O TRP C 110 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N HIS C 112 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL C 121 " --> pdb=" O HIS C 112 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 186 through 188 removed outlier: 3.600A pdb=" N GLY C 168 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N TYR C 165 " --> pdb=" O THR C 78 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLN C 77 " --> pdb=" O ARG C 210 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ARG C 210 " --> pdb=" O GLN C 77 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 256 through 262 removed outlier: 5.643A pdb=" N VAL C 257 " --> pdb=" O TYR C 469 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N TYR C 469 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N SER C 259 " --> pdb=" O VAL C 467 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N VAL C 467 " --> pdb=" O SER C 259 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU C 512 " --> pdb=" O THR C 505 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR C 505 " --> pdb=" O LEU C 512 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 297 through 299 Processing sheet with id=AD1, first strand: chain 'C' and resid 413 through 415 removed outlier: 3.598A pdb=" N LYS C 453 " --> pdb=" O ILE C 450 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ARG C 446 " --> pdb=" O VAL C 457 " (cutoff:3.500A) removed outlier: 10.538A pdb=" N SER C 459 " --> pdb=" O GLN C 444 " (cutoff:3.500A) removed outlier: 13.181A pdb=" N GLN C 444 " --> pdb=" O SER C 459 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N LEU C 445 " --> pdb=" O VAL C 441 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL C 441 " --> pdb=" O LEU C 445 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TYR C 447 " --> pdb=" O LEU C 439 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 522 through 523 removed outlier: 3.637A pdb=" N ALA C 543 " --> pdb=" O ASP C 537 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N PHE C 534 " --> pdb=" O LEU C 530 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 567 through 582 removed outlier: 6.943A pdb=" N ASN C 925 " --> pdb=" O LEU C 570 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N HIS C 572 " --> pdb=" O PRO C 923 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU C 574 " --> pdb=" O LEU C 921 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU C 921 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LEU C 576 " --> pdb=" O TYR C 919 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N TYR C 919 " --> pdb=" O LEU C 576 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLU C 578 " --> pdb=" O PHE C 917 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N PHE C 917 " --> pdb=" O GLU C 578 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N PHE C 580 " --> pdb=" O MET C 915 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N MET C 915 " --> pdb=" O PHE C 580 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N GLN C 582 " --> pdb=" O GLY C 913 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N GLY C 913 " --> pdb=" O GLN C 582 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY C 913 " --> pdb=" O ALA C 910 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU C 921 " --> pdb=" O HIS C 902 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N HIS C 902 " --> pdb=" O LEU C 921 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 587 through 590 Processing sheet with id=AD5, first strand: chain 'C' and resid 979 through 981 Processing sheet with id=AD6, first strand: chain 'C' and resid 952 through 954 687 hydrogen bonds defined for protein. 1890 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.81 Time building geometry restraints manager: 2.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6987 1.34 - 1.46: 5940 1.46 - 1.58: 10122 1.58 - 1.71: 0 1.71 - 1.83: 180 Bond restraints: 23229 Sorted by residual: bond pdb=" CB ILE A 802 " pdb=" CG2 ILE A 802 " ideal model delta sigma weight residual 1.521 1.428 0.093 3.30e-02 9.18e+02 7.93e+00 bond pdb=" CB ILE B 802 " pdb=" CG2 ILE B 802 " ideal model delta sigma weight residual 1.521 1.429 0.092 3.30e-02 9.18e+02 7.79e+00 bond pdb=" CB ILE C 802 " pdb=" CG2 ILE C 802 " ideal model delta sigma weight residual 1.521 1.429 0.092 3.30e-02 9.18e+02 7.79e+00 bond pdb=" C1 NAG A1006 " pdb=" O5 NAG A1006 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.23e+00 bond pdb=" C1 NAG C1006 " pdb=" O5 NAG C1006 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.17e+00 ... (remaining 23224 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.32: 30867 3.32 - 6.63: 622 6.63 - 9.95: 107 9.95 - 13.26: 15 13.26 - 16.58: 9 Bond angle restraints: 31620 Sorted by residual: angle pdb=" N VAL A 392 " pdb=" CA VAL A 392 " pdb=" C VAL A 392 " ideal model delta sigma weight residual 106.21 113.15 -6.94 1.07e+00 8.73e-01 4.20e+01 angle pdb=" N VAL B 392 " pdb=" CA VAL B 392 " pdb=" C VAL B 392 " ideal model delta sigma weight residual 106.21 113.14 -6.93 1.07e+00 8.73e-01 4.19e+01 angle pdb=" N VAL C 392 " pdb=" CA VAL C 392 " pdb=" C VAL C 392 " ideal model delta sigma weight residual 106.21 113.10 -6.89 1.07e+00 8.73e-01 4.15e+01 angle pdb=" C HIS C 712 " pdb=" N ASN C 713 " pdb=" CA ASN C 713 " ideal model delta sigma weight residual 121.54 130.67 -9.13 1.91e+00 2.74e-01 2.29e+01 angle pdb=" C HIS A 712 " pdb=" N ASN A 713 " pdb=" CA ASN A 713 " ideal model delta sigma weight residual 121.54 130.65 -9.11 1.91e+00 2.74e-01 2.27e+01 ... (remaining 31615 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.31: 12069 15.31 - 30.63: 955 30.63 - 45.94: 200 45.94 - 61.26: 30 61.26 - 76.57: 15 Dihedral angle restraints: 13269 sinusoidal: 5121 harmonic: 8148 Sorted by residual: dihedral pdb=" CB CYS C 287 " pdb=" SG CYS C 287 " pdb=" SG CYS C 292 " pdb=" CB CYS C 292 " ideal model delta sinusoidal sigma weight residual 93.00 153.40 -60.40 1 1.00e+01 1.00e-02 4.86e+01 dihedral pdb=" CB CYS B 287 " pdb=" SG CYS B 287 " pdb=" SG CYS B 292 " pdb=" CB CYS B 292 " ideal model delta sinusoidal sigma weight residual 93.00 153.39 -60.39 1 1.00e+01 1.00e-02 4.86e+01 dihedral pdb=" CB CYS A 287 " pdb=" SG CYS A 287 " pdb=" SG CYS A 292 " pdb=" CB CYS A 292 " ideal model delta sinusoidal sigma weight residual 93.00 153.35 -60.35 1 1.00e+01 1.00e-02 4.85e+01 ... (remaining 13266 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 3069 0.090 - 0.181: 599 0.181 - 0.271: 43 0.271 - 0.361: 6 0.361 - 0.452: 9 Chirality restraints: 3726 Sorted by residual: chirality pdb=" C1 NAG B1007 " pdb=" ND2 ASN B 992 " pdb=" C2 NAG B1007 " pdb=" O5 NAG B1007 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.10e+00 chirality pdb=" C1 NAG C1007 " pdb=" ND2 ASN C 992 " pdb=" C2 NAG C1007 " pdb=" O5 NAG C1007 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.08e+00 chirality pdb=" C1 NAG A1007 " pdb=" ND2 ASN A 992 " pdb=" C2 NAG A1007 " pdb=" O5 NAG A1007 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.04e+00 ... (remaining 3723 not shown) Planarity restraints: 4044 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1018 " 0.044 2.00e-02 2.50e+03 3.64e-02 1.65e+01 pdb=" C7 NAG B1018 " -0.012 2.00e-02 2.50e+03 pdb=" C8 NAG B1018 " 0.033 2.00e-02 2.50e+03 pdb=" N2 NAG B1018 " -0.058 2.00e-02 2.50e+03 pdb=" O7 NAG B1018 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1018 " 0.044 2.00e-02 2.50e+03 3.63e-02 1.65e+01 pdb=" C7 NAG A1018 " -0.012 2.00e-02 2.50e+03 pdb=" C8 NAG A1018 " 0.033 2.00e-02 2.50e+03 pdb=" N2 NAG A1018 " -0.058 2.00e-02 2.50e+03 pdb=" O7 NAG A1018 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1018 " -0.044 2.00e-02 2.50e+03 3.61e-02 1.63e+01 pdb=" C7 NAG C1018 " 0.012 2.00e-02 2.50e+03 pdb=" C8 NAG C1018 " -0.033 2.00e-02 2.50e+03 pdb=" N2 NAG C1018 " 0.057 2.00e-02 2.50e+03 pdb=" O7 NAG C1018 " 0.008 2.00e-02 2.50e+03 ... (remaining 4041 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 6094 2.80 - 3.32: 20894 3.32 - 3.85: 37722 3.85 - 4.37: 42393 4.37 - 4.90: 72504 Nonbonded interactions: 179607 Sorted by model distance: nonbonded pdb=" O THR C 584 " pdb=" OG SER C 912 " model vdw 2.271 3.040 nonbonded pdb=" O THR A 584 " pdb=" OG SER A 912 " model vdw 2.272 3.040 nonbonded pdb=" O THR B 584 " pdb=" OG SER B 912 " model vdw 2.273 3.040 nonbonded pdb=" O ALA A 47 " pdb=" OH TYR A 75 " model vdw 2.297 3.040 nonbonded pdb=" O ALA B 47 " pdb=" OH TYR B 75 " model vdw 2.297 3.040 ... (remaining 179602 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' 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: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 25.030 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 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 : 0.010 0.093 23313 Z= 0.421 Angle : 1.303 16.578 31842 Z= 0.675 Chirality : 0.071 0.452 3726 Planarity : 0.007 0.062 3990 Dihedral : 11.665 76.569 7959 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.74 % Favored : 90.26 % Rotamer: Outliers : 1.23 % Allowed : 7.39 % Favored : 91.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.52 (0.12), residues: 2781 helix: -3.53 (0.13), residues: 636 sheet: -2.24 (0.19), residues: 564 loop : -3.16 (0.13), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.002 ARG C 673 TYR 0.037 0.004 TYR C 436 PHE 0.040 0.004 PHE A 588 TRP 0.023 0.004 TRP C 110 HIS 0.013 0.004 HIS C 902 Details of bonding type rmsd/Z covalent geometry : bond 0.00953 / 0.42 (23229) covalent geometry : angle 1.26292 / 0.67 (31620) SS BOND : bond 0.01186 / 0.81 ( 30) SS BOND : angle 3.14176 / 1.99 ( 60) hydrogen bonds : bond 0.22433 / 15.00 ( 687) hydrogen bonds : angle 9.41211 / 6.59 ( 1890) link_NAG-ASN : bond 0.00848 / 0.59 ( 54) link_NAG-ASN : angle 4.33096 / 3.05 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 582 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 620 ASP cc_start: 0.8282 (t70) cc_final: 0.7826 (t0) REVERT: A 770 LEU cc_start: 0.8247 (mm) cc_final: 0.8037 (mt) REVERT: B 28 ASN cc_start: 0.8758 (p0) cc_final: 0.8318 (p0) REVERT: B 186 GLU cc_start: 0.6015 (tm-30) cc_final: 0.5749 (tm-30) REVERT: B 210 ARG cc_start: 0.5843 (pmm-80) cc_final: 0.5636 (ptp-170) REVERT: B 468 LEU cc_start: 0.9429 (OUTLIER) cc_final: 0.9208 (pp) REVERT: B 620 ASP cc_start: 0.8513 (t70) cc_final: 0.7901 (t0) REVERT: B 808 GLN cc_start: 0.7890 (tp-100) cc_final: 0.7654 (tt0) REVERT: C 210 ARG cc_start: 0.5725 (pmm-80) cc_final: 0.5485 (ptp-170) REVERT: C 259 SER cc_start: 0.8825 (m) cc_final: 0.8599 (p) REVERT: C 848 ASP cc_start: 0.7669 (t0) cc_final: 0.7286 (t0) outliers start: 30 outliers final: 5 residues processed: 598 average time/residue: 0.1585 time to fit residues: 146.1225 Evaluate side-chains 298 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 292 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 253 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 111] chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.4980 chunk 111 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 HIS ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 318 GLN A 319 HIS A 444 GLN A 488 HIS A 528 ASN A 710 GLN A 809 ASN A 852 ASN B 101 HIS B 112 HIS ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 301 ASN B 318 GLN B 319 HIS ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 528 ASN B 809 ASN C 101 HIS C 112 HIS ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 318 GLN C 319 HIS C 334 ASN C 488 HIS C 528 ASN C 615 GLN C 710 GLN C 809 ASN C 823 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.135062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.110449 restraints weight = 39145.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.113212 restraints weight = 21635.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.115046 restraints weight = 14656.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.116002 restraints weight = 11409.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.116776 restraints weight = 9872.330| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23313 Z= 0.150 Angle : 0.793 12.010 31842 Z= 0.394 Chirality : 0.049 0.364 3726 Planarity : 0.005 0.047 3990 Dihedral : 6.919 53.929 3057 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 4.11 % Allowed : 13.88 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.60 (0.14), residues: 2781 helix: -2.22 (0.17), residues: 645 sheet: -1.55 (0.22), residues: 516 loop : -2.86 (0.13), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 113 TYR 0.019 0.002 TYR B 286 PHE 0.028 0.002 PHE C 608 TRP 0.020 0.002 TRP C 376 HIS 0.004 0.001 HIS B 902 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (23229) covalent geometry : angle 0.76916 / 0.39 (31620) SS BOND : bond 0.00618 / 0.41 ( 30) SS BOND : angle 1.50144 / 0.98 ( 60) hydrogen bonds : bond 0.05180 / 3.50 ( 687) hydrogen bonds : angle 6.53164 / 4.55 ( 1890) link_NAG-ASN : bond 0.00502 / 0.35 ( 54) link_NAG-ASN : angle 2.68232 / 1.89 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 376 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 ARG cc_start: 0.5784 (pmm-80) cc_final: 0.5289 (ptp90) REVERT: A 478 LEU cc_start: 0.9593 (tp) cc_final: 0.9378 (tp) REVERT: A 620 ASP cc_start: 0.8256 (t70) cc_final: 0.7951 (t0) REVERT: A 633 SER cc_start: 0.8896 (t) cc_final: 0.8556 (p) REVERT: A 770 LEU cc_start: 0.8242 (mm) cc_final: 0.7989 (mt) REVERT: B 301 ASN cc_start: 0.8359 (m-40) cc_final: 0.8054 (m-40) REVERT: B 370 GLU cc_start: 0.7422 (pt0) cc_final: 0.7108 (pt0) REVERT: B 494 PHE cc_start: 0.7825 (OUTLIER) cc_final: 0.7620 (t80) REVERT: B 620 ASP cc_start: 0.8414 (t70) cc_final: 0.8004 (t0) REVERT: B 633 SER cc_start: 0.8787 (t) cc_final: 0.8409 (p) REVERT: C 37 LEU cc_start: 0.8669 (mt) cc_final: 0.8413 (mt) REVERT: C 259 SER cc_start: 0.8832 (m) cc_final: 0.8596 (p) REVERT: C 348 VAL cc_start: 0.8463 (p) cc_final: 0.8221 (m) REVERT: C 366 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.8078 (pp) REVERT: C 370 GLU cc_start: 0.7343 (pt0) cc_final: 0.6943 (pt0) REVERT: C 620 ASP cc_start: 0.8285 (t70) cc_final: 0.7980 (t0) REVERT: C 633 SER cc_start: 0.8833 (t) cc_final: 0.8447 (p) REVERT: C 874 ASN cc_start: 0.8699 (OUTLIER) cc_final: 0.8102 (t160) REVERT: C 893 ARG cc_start: 0.8656 (mtp180) cc_final: 0.8275 (mtp180) outliers start: 100 outliers final: 38 residues processed: 452 average time/residue: 0.1398 time to fit residues: 103.0792 Evaluate side-chains 321 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 280 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 528 ASN Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 852 ASN Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 528 ASN Chi-restraints excluded: chain B residue 874 ASN Chi-restraints excluded: chain B residue 881 SER Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 528 ASN Chi-restraints excluded: chain C residue 874 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: [164, 229, 180, 130, 49, 31, 62, 121, 46, 33, 140] chunk 164 optimal weight: 9.9990 chunk 229 optimal weight: 3.9990 chunk 180 optimal weight: 8.9990 chunk 130 optimal weight: 0.7980 chunk 49 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 62 optimal weight: 0.3980 chunk 121 optimal weight: 0.1980 chunk 46 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 140 optimal weight: 5.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 488 HIS A 783 GLN A 852 ASN ** A 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN C 101 HIS C 193 GLN ** C 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 488 HIS C 615 GLN C 783 GLN C 808 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.135128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.110914 restraints weight = 39445.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.113614 restraints weight = 21611.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.115449 restraints weight = 14536.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.116475 restraints weight = 11284.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.117112 restraints weight = 9710.859| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 23313 Z= 0.137 Angle : 0.736 12.496 31842 Z= 0.362 Chirality : 0.047 0.327 3726 Planarity : 0.004 0.040 3990 Dihedral : 6.405 53.460 3055 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 4.15 % Allowed : 14.98 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.09 (0.14), residues: 2781 helix: -1.62 (0.18), residues: 639 sheet: -1.39 (0.23), residues: 501 loop : -2.55 (0.14), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 210 TYR 0.015 0.002 TYR B 465 PHE 0.023 0.001 PHE B 317 TRP 0.015 0.001 TRP A 110 HIS 0.006 0.001 HIS B 552 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (23229) covalent geometry : angle 0.71525 / 0.36 (31620) SS BOND : bond 0.00556 / 0.37 ( 30) SS BOND : angle 1.46323 / 0.93 ( 60) hydrogen bonds : bond 0.04676 / 3.17 ( 687) hydrogen bonds : angle 6.11576 / 4.24 ( 1890) link_NAG-ASN : bond 0.00428 / 0.30 ( 54) link_NAG-ASN : angle 2.39871 / 1.69 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 324 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8309 (tp) REVERT: A 315 ARG cc_start: 0.6258 (mmm160) cc_final: 0.6016 (mmm160) REVERT: A 608 PHE cc_start: 0.7035 (p90) cc_final: 0.6720 (p90) REVERT: A 620 ASP cc_start: 0.8276 (t70) cc_final: 0.7949 (t0) REVERT: A 633 SER cc_start: 0.8866 (t) cc_final: 0.8570 (p) REVERT: A 770 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.8027 (mt) REVERT: B 269 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8220 (tp) REVERT: B 301 ASN cc_start: 0.8518 (m-40) cc_final: 0.7978 (m-40) REVERT: B 303 ILE cc_start: 0.8414 (mm) cc_final: 0.8204 (mm) REVERT: B 494 PHE cc_start: 0.7867 (OUTLIER) cc_final: 0.7626 (t80) REVERT: B 620 ASP cc_start: 0.8196 (t70) cc_final: 0.7929 (t0) REVERT: B 633 SER cc_start: 0.8744 (t) cc_final: 0.8448 (p) REVERT: C 37 LEU cc_start: 0.8552 (mt) cc_final: 0.8348 (mt) REVERT: C 269 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8126 (tp) REVERT: C 874 ASN cc_start: 0.8571 (OUTLIER) cc_final: 0.8363 (t0) REVERT: C 950 ASP cc_start: 0.7518 (t0) cc_final: 0.7290 (t0) outliers start: 101 outliers final: 59 residues processed: 400 average time/residue: 0.1334 time to fit residues: 89.1296 Evaluate side-chains 340 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 275 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 319 HIS Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 881 SER Chi-restraints excluded: chain B residue 922 ILE Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 319 HIS Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 371 CYS Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 578 GLU Chi-restraints excluded: chain C residue 645 SER Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 874 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: [214, 53, 180, 245, 55, 152, 193, 117, 153, 54, 202] chunk 214 optimal weight: 0.0270 chunk 53 optimal weight: 0.9990 chunk 180 optimal weight: 5.9990 chunk 245 optimal weight: 3.9990 chunk 55 optimal weight: 8.9990 chunk 152 optimal weight: 9.9990 chunk 193 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 153 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 202 optimal weight: 10.0000 overall best weight: 1.1642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 528 ASN C 488 HIS ** C 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.134001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.109333 restraints weight = 39508.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.112111 restraints weight = 21751.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.113915 restraints weight = 14739.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.114864 restraints weight = 11489.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.115594 restraints weight = 9964.855| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23313 Z= 0.136 Angle : 0.702 11.970 31842 Z= 0.345 Chirality : 0.047 0.291 3726 Planarity : 0.004 0.040 3990 Dihedral : 6.076 53.819 3055 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 5.42 % Allowed : 15.80 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.71 (0.15), residues: 2781 helix: -1.19 (0.19), residues: 642 sheet: -1.30 (0.22), residues: 531 loop : -2.31 (0.14), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 177 TYR 0.017 0.001 TYR B 306 PHE 0.023 0.002 PHE C 513 TRP 0.017 0.001 TRP C 110 HIS 0.006 0.001 HIS B 552 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (23229) covalent geometry : angle 0.68504 / 0.34 (31620) SS BOND : bond 0.00571 / 0.39 ( 30) SS BOND : angle 1.43623 / 0.91 ( 60) hydrogen bonds : bond 0.04332 / 2.94 ( 687) hydrogen bonds : angle 5.83073 / 4.02 ( 1890) link_NAG-ASN : bond 0.00387 / 0.27 ( 54) link_NAG-ASN : angle 2.11598 / 1.50 ( 162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 303 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8257 (tp) REVERT: A 315 ARG cc_start: 0.6280 (mmm160) cc_final: 0.6068 (mmm160) REVERT: A 370 GLU cc_start: 0.6919 (pt0) cc_final: 0.6297 (pt0) REVERT: A 599 VAL cc_start: 0.8497 (m) cc_final: 0.8296 (p) REVERT: A 620 ASP cc_start: 0.8295 (t70) cc_final: 0.7990 (t0) REVERT: A 633 SER cc_start: 0.8830 (t) cc_final: 0.8545 (p) REVERT: A 651 ASP cc_start: 0.6297 (p0) cc_final: 0.5813 (t0) REVERT: A 770 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8092 (mt) REVERT: A 950 ASP cc_start: 0.7605 (t70) cc_final: 0.7342 (t0) REVERT: B 244 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8747 (tt) REVERT: B 253 ILE cc_start: 0.8465 (OUTLIER) cc_final: 0.7800 (pt) REVERT: B 301 ASN cc_start: 0.8496 (m-40) cc_final: 0.8130 (m-40) REVERT: B 303 ILE cc_start: 0.8422 (mm) cc_final: 0.8169 (mm) REVERT: B 315 ARG cc_start: 0.6236 (mmm160) cc_final: 0.6023 (mmm160) REVERT: B 366 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7677 (pp) REVERT: B 494 PHE cc_start: 0.7877 (OUTLIER) cc_final: 0.7230 (m-80) REVERT: B 615 GLN cc_start: 0.7328 (mm-40) cc_final: 0.7104 (mm-40) REVERT: B 633 SER cc_start: 0.8718 (t) cc_final: 0.8438 (p) REVERT: B 874 ASN cc_start: 0.8659 (OUTLIER) cc_final: 0.8266 (t160) REVERT: C 37 LEU cc_start: 0.8541 (mt) cc_final: 0.8306 (mt) REVERT: C 269 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8173 (tp) REVERT: C 361 ILE cc_start: 0.7300 (pt) cc_final: 0.7096 (pt) REVERT: C 367 LYS cc_start: 0.8867 (mtmt) cc_final: 0.8482 (mtmt) REVERT: C 370 GLU cc_start: 0.6995 (pt0) cc_final: 0.6565 (pt0) REVERT: C 874 ASN cc_start: 0.8510 (OUTLIER) cc_final: 0.7967 (t0) REVERT: C 950 ASP cc_start: 0.7597 (t0) cc_final: 0.7390 (t0) outliers start: 132 outliers final: 77 residues processed: 397 average time/residue: 0.1237 time to fit residues: 83.3459 Evaluate side-chains 346 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 260 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 658 PHE Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 852 ASN Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 874 ASN Chi-restraints excluded: chain B residue 881 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 319 HIS Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 371 CYS Chi-restraints excluded: chain C residue 390 ASP Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 467 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 527 THR Chi-restraints excluded: chain C residue 578 GLU Chi-restraints excluded: chain C residue 645 SER Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 874 ASN Chi-restraints excluded: chain C residue 931 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: [163, 240, 244, 39, 66, 59, 145, 268, 231, 99, 61] chunk 163 optimal weight: 6.9990 chunk 240 optimal weight: 0.9990 chunk 244 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 145 optimal weight: 0.9990 chunk 268 optimal weight: 5.9990 chunk 231 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 61 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 ASN ** A 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 ASN B 334 ASN B 528 ASN B 710 GLN C 488 HIS C 528 ASN ** C 552 HIS ** 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 = 0.3688 r_free = 0.3688 target = 0.131072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.106528 restraints weight = 39459.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.109290 restraints weight = 21760.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.111088 restraints weight = 14637.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.112046 restraints weight = 11441.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.112411 restraints weight = 9882.642| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23313 Z= 0.175 Angle : 0.718 9.722 31842 Z= 0.355 Chirality : 0.047 0.261 3726 Planarity : 0.004 0.040 3990 Dihedral : 5.770 39.146 3053 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 5.67 % Allowed : 17.16 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.48 (0.15), residues: 2781 helix: -0.90 (0.20), residues: 630 sheet: -1.30 (0.23), residues: 492 loop : -2.14 (0.14), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 849 TYR 0.018 0.002 TYR A 711 PHE 0.026 0.002 PHE A 608 TRP 0.026 0.002 TRP C 110 HIS 0.005 0.001 HIS B 502 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 (23229) covalent geometry : angle 0.70260 / 0.35 (31620) SS BOND : bond 0.00847 / 0.58 ( 30) SS BOND : angle 1.56942 / 1.01 ( 60) hydrogen bonds : bond 0.04389 / 2.97 ( 687) hydrogen bonds : angle 5.68188 / 3.90 ( 1890) link_NAG-ASN : bond 0.00364 / 0.26 ( 54) link_NAG-ASN : angle 2.04652 / 1.46 ( 162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 269 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8921 (tp) REVERT: A 253 ILE cc_start: 0.8717 (OUTLIER) cc_final: 0.8247 (pt) REVERT: A 269 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8323 (tp) REVERT: A 276 MET cc_start: 0.8234 (mmt) cc_final: 0.7689 (mmt) REVERT: A 315 ARG cc_start: 0.6500 (mmm160) cc_final: 0.6271 (mmm160) REVERT: A 620 ASP cc_start: 0.8312 (t70) cc_final: 0.8042 (t0) REVERT: A 633 SER cc_start: 0.8872 (t) cc_final: 0.8573 (p) REVERT: A 770 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8267 (mt) REVERT: A 950 ASP cc_start: 0.7645 (t70) cc_final: 0.7375 (t0) REVERT: B 107 TRP cc_start: 0.8042 (m-90) cc_final: 0.7569 (m-90) REVERT: B 269 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8150 (tp) REVERT: B 276 MET cc_start: 0.8305 (mmt) cc_final: 0.7895 (mmt) REVERT: B 301 ASN cc_start: 0.8672 (m-40) cc_final: 0.8141 (m-40) REVERT: B 303 ILE cc_start: 0.8507 (mm) cc_final: 0.8266 (mm) REVERT: B 315 ARG cc_start: 0.6615 (mmm160) cc_final: 0.6385 (mmm160) REVERT: B 370 GLU cc_start: 0.7221 (pt0) cc_final: 0.6607 (pt0) REVERT: B 494 PHE cc_start: 0.7960 (OUTLIER) cc_final: 0.7285 (m-80) REVERT: C 37 LEU cc_start: 0.8562 (mt) cc_final: 0.8299 (mt) REVERT: C 251 PHE cc_start: 0.8859 (OUTLIER) cc_final: 0.8413 (m-80) REVERT: C 269 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8228 (tp) REVERT: C 361 ILE cc_start: 0.7454 (pt) cc_final: 0.7093 (pt) REVERT: C 367 LYS cc_start: 0.8728 (mtmt) cc_final: 0.8326 (mtmt) REVERT: C 370 GLU cc_start: 0.6970 (pt0) cc_final: 0.6636 (pt0) REVERT: C 651 ASP cc_start: 0.6467 (p0) cc_final: 0.5664 (t0) REVERT: C 874 ASN cc_start: 0.8562 (OUTLIER) cc_final: 0.8034 (t0) REVERT: C 950 ASP cc_start: 0.7711 (t0) cc_final: 0.7466 (t0) outliers start: 138 outliers final: 91 residues processed: 378 average time/residue: 0.1224 time to fit residues: 78.9933 Evaluate side-chains 341 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 241 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 658 PHE Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 852 ASN Chi-restraints excluded: chain A residue 922 ILE Chi-restraints excluded: chain A residue 931 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 328 ASN Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 881 SER Chi-restraints excluded: chain B residue 906 LEU Chi-restraints excluded: chain B residue 915 MET Chi-restraints excluded: chain B residue 922 ILE Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 251 PHE Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 319 HIS Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 371 CYS Chi-restraints excluded: chain C residue 390 ASP Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 467 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 578 GLU Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 606 LEU Chi-restraints excluded: chain C residue 645 SER Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 802 ILE Chi-restraints excluded: chain C residue 850 LEU Chi-restraints excluded: chain C residue 874 ASN Chi-restraints excluded: chain C residue 931 THR Chi-restraints excluded: chain C residue 974 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: [131, 195, 17, 133, 81, 164, 75, 24, 86, 201, 172] chunk 131 optimal weight: 3.9990 chunk 195 optimal weight: 20.0000 chunk 17 optimal weight: 0.8980 chunk 133 optimal weight: 8.9990 chunk 81 optimal weight: 3.9990 chunk 164 optimal weight: 4.9990 chunk 75 optimal weight: 0.4980 chunk 24 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 201 optimal weight: 8.9990 chunk 172 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 528 ASN B 573 GLN C 528 ASN ** C 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.132737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.108580 restraints weight = 39642.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.111324 restraints weight = 21653.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.113194 restraints weight = 14548.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.114219 restraints weight = 11171.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.114768 restraints weight = 9571.289| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23313 Z= 0.135 Angle : 0.685 11.143 31842 Z= 0.338 Chirality : 0.046 0.248 3726 Planarity : 0.004 0.041 3990 Dihedral : 5.544 32.526 3052 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer: Outliers : 5.62 % Allowed : 17.78 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.36 (0.15), residues: 2781 helix: -0.76 (0.20), residues: 639 sheet: -1.30 (0.23), residues: 498 loop : -2.06 (0.14), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 849 TYR 0.015 0.001 TYR A 711 PHE 0.024 0.002 PHE A 608 TRP 0.028 0.001 TRP B 110 HIS 0.005 0.001 HIS B 552 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (23229) covalent geometry : angle 0.67157 / 0.34 (31620) SS BOND : bond 0.00537 / 0.37 ( 30) SS BOND : angle 1.32108 / 0.82 ( 60) hydrogen bonds : bond 0.04177 / 2.83 ( 687) hydrogen bonds : angle 5.57748 / 3.81 ( 1890) link_NAG-ASN : bond 0.00336 / 0.23 ( 54) link_NAG-ASN : angle 1.89593 / 1.35 ( 162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 272 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8338 (tp) REVERT: A 276 MET cc_start: 0.8259 (mmt) cc_final: 0.7672 (mmt) REVERT: A 315 ARG cc_start: 0.6542 (mmm160) cc_final: 0.6294 (mmm160) REVERT: A 367 LYS cc_start: 0.8615 (mtmt) cc_final: 0.8244 (mtmm) REVERT: A 370 GLU cc_start: 0.6740 (pt0) cc_final: 0.6175 (pt0) REVERT: A 564 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.8300 (ptt90) REVERT: A 620 ASP cc_start: 0.8285 (t70) cc_final: 0.8055 (t0) REVERT: A 770 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8263 (mt) REVERT: A 950 ASP cc_start: 0.7654 (t70) cc_final: 0.7369 (t0) REVERT: B 276 MET cc_start: 0.8273 (mmt) cc_final: 0.7914 (mmt) REVERT: B 301 ASN cc_start: 0.8620 (m-40) cc_final: 0.8156 (m-40) REVERT: B 303 ILE cc_start: 0.8545 (mm) cc_final: 0.8293 (mm) REVERT: B 315 ARG cc_start: 0.6623 (mmm160) cc_final: 0.6396 (mmm160) REVERT: B 370 GLU cc_start: 0.7307 (pt0) cc_final: 0.6522 (pt0) REVERT: B 494 PHE cc_start: 0.8113 (OUTLIER) cc_final: 0.7372 (m-80) REVERT: C 37 LEU cc_start: 0.8508 (mt) cc_final: 0.8242 (mt) REVERT: C 174 ASP cc_start: 0.7289 (m-30) cc_final: 0.7055 (m-30) REVERT: C 367 LYS cc_start: 0.8673 (mtmt) cc_final: 0.8288 (mtmt) REVERT: C 370 GLU cc_start: 0.6938 (pt0) cc_final: 0.6496 (pt0) REVERT: C 494 PHE cc_start: 0.8233 (OUTLIER) cc_final: 0.7594 (m-80) REVERT: C 547 MET cc_start: 0.8039 (ttm) cc_final: 0.7755 (ttm) REVERT: C 599 VAL cc_start: 0.8453 (OUTLIER) cc_final: 0.8226 (p) REVERT: C 874 ASN cc_start: 0.8520 (OUTLIER) cc_final: 0.8009 (t0) REVERT: C 950 ASP cc_start: 0.7801 (t0) cc_final: 0.7542 (t0) outliers start: 137 outliers final: 92 residues processed: 374 average time/residue: 0.1282 time to fit residues: 80.4251 Evaluate side-chains 344 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 245 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 564 ARG Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain A residue 658 PHE Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 931 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 328 ASN Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 528 ASN Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain B residue 592 CYS Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 706 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 881 SER Chi-restraints excluded: chain B residue 906 LEU Chi-restraints excluded: chain B residue 915 MET Chi-restraints excluded: chain B residue 922 ILE Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 371 CYS Chi-restraints excluded: chain C residue 390 ASP Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 467 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 578 GLU Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 606 LEU Chi-restraints excluded: chain C residue 645 SER Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 802 ILE Chi-restraints excluded: chain C residue 850 LEU Chi-restraints excluded: chain C residue 869 ILE Chi-restraints excluded: chain C residue 874 ASN Chi-restraints excluded: chain C residue 931 THR Chi-restraints excluded: chain C residue 974 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: [151, 224, 55, 209, 37, 186, 211, 124, 247, 18, 169] chunk 151 optimal weight: 4.9990 chunk 224 optimal weight: 6.9990 chunk 55 optimal weight: 0.8980 chunk 209 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 186 optimal weight: 20.0000 chunk 211 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 247 optimal weight: 0.9980 chunk 18 optimal weight: 7.9990 chunk 169 optimal weight: 0.0040 overall best weight: 1.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 ASN ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 874 ASN B 118 ASN ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 328 ASN B 528 ASN ** B 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 ASN C 528 ASN ** C 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.131760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.107536 restraints weight = 39560.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.110334 restraints weight = 21804.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.112136 restraints weight = 14617.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.113121 restraints weight = 11346.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.113642 restraints weight = 9742.533| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.4037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23313 Z= 0.147 Angle : 0.690 9.558 31842 Z= 0.341 Chirality : 0.046 0.249 3726 Planarity : 0.004 0.043 3990 Dihedral : 5.443 28.265 3050 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 5.50 % Allowed : 18.80 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.15), residues: 2781 helix: -0.65 (0.20), residues: 627 sheet: -1.25 (0.23), residues: 489 loop : -1.92 (0.14), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 849 TYR 0.025 0.001 TYR B 306 PHE 0.026 0.002 PHE A 513 TRP 0.021 0.001 TRP B 110 HIS 0.004 0.001 HIS B 552 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (23229) covalent geometry : angle 0.67673 / 0.34 (31620) SS BOND : bond 0.00823 / 0.54 ( 30) SS BOND : angle 1.44360 / 0.91 ( 60) hydrogen bonds : bond 0.04189 / 2.84 ( 687) hydrogen bonds : angle 5.49239 / 3.76 ( 1890) link_NAG-ASN : bond 0.00299 / 0.21 ( 54) link_NAG-ASN : angle 1.84530 / 1.31 ( 162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 259 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.8278 (mmt) cc_final: 0.7689 (mmt) REVERT: A 315 ARG cc_start: 0.6533 (mmm160) cc_final: 0.6322 (mmm160) REVERT: A 367 LYS cc_start: 0.8571 (mtmt) cc_final: 0.8321 (mtmt) REVERT: A 370 GLU cc_start: 0.6831 (pt0) cc_final: 0.6248 (pt0) REVERT: A 564 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.8324 (ptt90) REVERT: A 620 ASP cc_start: 0.8283 (t70) cc_final: 0.8025 (t0) REVERT: A 770 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8283 (mt) REVERT: A 950 ASP cc_start: 0.7748 (t70) cc_final: 0.7480 (t0) REVERT: B 107 TRP cc_start: 0.8007 (m-90) cc_final: 0.7536 (m-90) REVERT: B 189 LEU cc_start: 0.7518 (OUTLIER) cc_final: 0.7186 (tt) REVERT: B 244 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8898 (tt) REVERT: B 253 ILE cc_start: 0.8292 (pp) cc_final: 0.7694 (pt) REVERT: B 276 MET cc_start: 0.8255 (mmt) cc_final: 0.7875 (mmt) REVERT: B 301 ASN cc_start: 0.8567 (m-40) cc_final: 0.8092 (m-40) REVERT: B 303 ILE cc_start: 0.8446 (mm) cc_final: 0.8085 (mt) REVERT: B 370 GLU cc_start: 0.7210 (pt0) cc_final: 0.6548 (pt0) REVERT: B 494 PHE cc_start: 0.8251 (OUTLIER) cc_final: 0.7394 (m-80) REVERT: C 174 ASP cc_start: 0.7311 (m-30) cc_final: 0.7070 (m-30) REVERT: C 367 LYS cc_start: 0.8724 (mtmt) cc_final: 0.8337 (mtmt) REVERT: C 370 GLU cc_start: 0.6971 (pt0) cc_final: 0.6552 (pt0) REVERT: C 547 MET cc_start: 0.8023 (ttm) cc_final: 0.7760 (ttm) REVERT: C 582 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.8300 (tt0) REVERT: C 599 VAL cc_start: 0.8513 (OUTLIER) cc_final: 0.8284 (p) REVERT: C 874 ASN cc_start: 0.8495 (OUTLIER) cc_final: 0.7994 (t0) REVERT: C 950 ASP cc_start: 0.7715 (t0) cc_final: 0.7450 (t0) outliers start: 134 outliers final: 97 residues processed: 355 average time/residue: 0.1291 time to fit residues: 77.2100 Evaluate side-chains 343 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 238 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 564 ARG Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 922 ILE Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 328 ASN Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain B residue 592 CYS Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 706 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 881 SER Chi-restraints excluded: chain B residue 906 LEU Chi-restraints excluded: chain B residue 915 MET Chi-restraints excluded: chain B residue 922 ILE Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 371 CYS Chi-restraints excluded: chain C residue 390 ASP Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 467 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 578 GLU Chi-restraints excluded: chain C residue 582 GLN Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 606 LEU Chi-restraints excluded: chain C residue 645 SER Chi-restraints excluded: chain C residue 658 PHE Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain C residue 679 LEU Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 802 ILE Chi-restraints excluded: chain C residue 850 LEU Chi-restraints excluded: chain C residue 874 ASN Chi-restraints excluded: chain C residue 974 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: [51, 148, 33, 136, 187, 81, 180, 0, 184, 151, 104] chunk 51 optimal weight: 0.9990 chunk 148 optimal weight: 0.0870 chunk 33 optimal weight: 9.9990 chunk 136 optimal weight: 2.9990 chunk 187 optimal weight: 0.0670 chunk 81 optimal weight: 1.9990 chunk 180 optimal weight: 0.0870 chunk 0 optimal weight: 20.0000 chunk 184 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 193 GLN ** A 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 488 HIS C 528 ASN ** C 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.134998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.111094 restraints weight = 39327.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.113914 restraints weight = 21366.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.115771 restraints weight = 14244.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.116933 restraints weight = 10976.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.117271 restraints weight = 9313.923| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.4262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23313 Z= 0.116 Angle : 0.666 9.517 31842 Z= 0.328 Chirality : 0.045 0.252 3726 Planarity : 0.004 0.041 3990 Dihedral : 5.218 20.825 3048 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 4.64 % Allowed : 20.16 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.15), residues: 2781 helix: -0.60 (0.20), residues: 636 sheet: -1.14 (0.23), residues: 513 loop : -1.91 (0.14), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 849 TYR 0.014 0.001 TYR A 414 PHE 0.032 0.001 PHE A 513 TRP 0.024 0.001 TRP C 110 HIS 0.004 0.001 HIS B 552 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (23229) covalent geometry : angle 0.65490 / 0.33 (31620) SS BOND : bond 0.00564 / 0.37 ( 30) SS BOND : angle 1.24233 / 0.78 ( 60) hydrogen bonds : bond 0.03944 / 2.67 ( 687) hydrogen bonds : angle 5.41837 / 3.70 ( 1890) link_NAG-ASN : bond 0.00303 / 0.20 ( 54) link_NAG-ASN : angle 1.70149 / 1.20 ( 162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 284 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 SER cc_start: 0.8746 (t) cc_final: 0.8203 (p) REVERT: A 276 MET cc_start: 0.8213 (mmt) cc_final: 0.7689 (mmt) REVERT: A 530 LEU cc_start: 0.8309 (tt) cc_final: 0.8055 (tt) REVERT: A 620 ASP cc_start: 0.8177 (t70) cc_final: 0.7931 (t0) REVERT: A 770 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8201 (mt) REVERT: A 950 ASP cc_start: 0.7736 (t70) cc_final: 0.7484 (t0) REVERT: B 174 ASP cc_start: 0.7322 (m-30) cc_final: 0.7062 (t0) REVERT: B 244 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8777 (tt) REVERT: B 253 ILE cc_start: 0.8196 (OUTLIER) cc_final: 0.7604 (pt) REVERT: B 301 ASN cc_start: 0.8451 (m-40) cc_final: 0.8040 (m-40) REVERT: B 303 ILE cc_start: 0.8405 (mm) cc_final: 0.8043 (mt) REVERT: B 311 ASN cc_start: 0.8199 (t0) cc_final: 0.7856 (p0) REVERT: B 370 GLU cc_start: 0.7192 (pt0) cc_final: 0.6575 (pt0) REVERT: B 494 PHE cc_start: 0.8194 (OUTLIER) cc_final: 0.7595 (t80) REVERT: B 599 VAL cc_start: 0.8529 (m) cc_final: 0.8171 (p) REVERT: B 651 ASP cc_start: 0.6504 (p0) cc_final: 0.6084 (t0) REVERT: B 950 ASP cc_start: 0.7367 (t70) cc_final: 0.7104 (t0) REVERT: C 234 SER cc_start: 0.8854 (t) cc_final: 0.8330 (p) REVERT: C 367 LYS cc_start: 0.8635 (mtmt) cc_final: 0.8256 (mtmt) REVERT: C 370 GLU cc_start: 0.6872 (pt0) cc_final: 0.6470 (pt0) REVERT: C 564 ARG cc_start: 0.8496 (pmt100) cc_final: 0.8273 (ptt90) REVERT: C 582 GLN cc_start: 0.8892 (OUTLIER) cc_final: 0.8244 (tt0) REVERT: C 599 VAL cc_start: 0.8404 (m) cc_final: 0.8187 (p) REVERT: C 725 GLU cc_start: 0.7881 (pm20) cc_final: 0.7559 (pt0) REVERT: C 874 ASN cc_start: 0.8435 (OUTLIER) cc_final: 0.7899 (t0) REVERT: C 950 ASP cc_start: 0.7721 (t0) cc_final: 0.7453 (t0) outliers start: 113 outliers final: 89 residues processed: 368 average time/residue: 0.1292 time to fit residues: 79.5008 Evaluate side-chains 351 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 256 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 922 ILE Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain B residue 592 CYS Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 706 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 906 LEU Chi-restraints excluded: chain B residue 922 ILE Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 371 CYS Chi-restraints excluded: chain C residue 390 ASP Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 467 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 528 ASN Chi-restraints excluded: chain C residue 578 GLU Chi-restraints excluded: chain C residue 582 GLN Chi-restraints excluded: chain C residue 592 CYS Chi-restraints excluded: chain C residue 606 LEU Chi-restraints excluded: chain C residue 645 SER Chi-restraints excluded: chain C residue 658 PHE Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 869 ILE Chi-restraints excluded: chain C residue 874 ASN Chi-restraints excluded: chain C residue 974 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: [271, 138, 48, 240, 60, 248, 236, 186, 118, 46, 192] chunk 271 optimal weight: 5.9990 chunk 138 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 chunk 240 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 248 optimal weight: 5.9990 chunk 236 optimal weight: 3.9990 chunk 186 optimal weight: 20.0000 chunk 118 optimal weight: 0.9980 chunk 46 optimal weight: 8.9990 chunk 192 optimal weight: 10.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS A 488 HIS A 502 HIS ** A 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 502 HIS ** B 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 488 HIS C 502 HIS C 528 ASN ** C 552 HIS ** 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 = 0.3605 r_free = 0.3605 target = 0.125317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.101541 restraints weight = 39893.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.103401 restraints weight = 23944.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.104376 restraints weight = 15905.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.104574 restraints weight = 13811.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.104984 restraints weight = 12900.699| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.4245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 23313 Z= 0.291 Angle : 0.823 11.144 31842 Z= 0.411 Chirality : 0.050 0.249 3726 Planarity : 0.005 0.046 3990 Dihedral : 5.799 22.480 3048 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 5.13 % Allowed : 20.28 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.32 (0.15), residues: 2781 helix: -0.87 (0.20), residues: 657 sheet: -1.23 (0.22), residues: 537 loop : -1.98 (0.14), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 849 TYR 0.026 0.002 TYR C 369 PHE 0.029 0.003 PHE C 513 TRP 0.020 0.002 TRP C 110 HIS 0.007 0.002 HIS C 502 Details of bonding type rmsd/Z covalent geometry : bond 0.00679 / 0.29 (23229) covalent geometry : angle 0.80759 / 0.41 (31620) SS BOND : bond 0.01015 / 0.66 ( 30) SS BOND : angle 2.10514 / 1.37 ( 60) hydrogen bonds : bond 0.04855 / 3.26 ( 687) hydrogen bonds : angle 5.57808 / 3.84 ( 1890) link_NAG-ASN : bond 0.00387 / 0.27 ( 54) link_NAG-ASN : angle 2.06177 / 1.47 ( 162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 236 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASN cc_start: 0.9015 (OUTLIER) cc_final: 0.8604 (p0) REVERT: A 199 PHE cc_start: 0.7012 (t80) cc_final: 0.6789 (t80) REVERT: A 244 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9136 (tp) REVERT: A 253 ILE cc_start: 0.8547 (pp) cc_final: 0.8003 (pt) REVERT: A 269 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8385 (tp) REVERT: A 276 MET cc_start: 0.8354 (mmt) cc_final: 0.7746 (mmt) REVERT: A 367 LYS cc_start: 0.9184 (mtpp) cc_final: 0.8835 (mtmt) REVERT: A 564 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.8578 (ptt90) REVERT: A 770 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8361 (mt) REVERT: A 880 GLN cc_start: 0.7934 (mt0) cc_final: 0.7727 (mt0) REVERT: A 950 ASP cc_start: 0.7698 (t70) cc_final: 0.7430 (t0) REVERT: B 107 TRP cc_start: 0.8115 (m-90) cc_final: 0.7781 (m-90) REVERT: B 189 LEU cc_start: 0.7329 (OUTLIER) cc_final: 0.7111 (tt) REVERT: B 253 ILE cc_start: 0.8560 (OUTLIER) cc_final: 0.8044 (pt) REVERT: B 301 ASN cc_start: 0.8437 (m-40) cc_final: 0.8052 (m-40) REVERT: B 370 GLU cc_start: 0.7187 (pt0) cc_final: 0.6526 (pt0) REVERT: B 494 PHE cc_start: 0.8344 (OUTLIER) cc_final: 0.7632 (t80) REVERT: B 513 PHE cc_start: 0.8249 (t80) cc_final: 0.8020 (t80) REVERT: B 950 ASP cc_start: 0.7620 (t70) cc_final: 0.7352 (t0) REVERT: C 276 MET cc_start: 0.8207 (tpp) cc_final: 0.8005 (mmt) REVERT: C 564 ARG cc_start: 0.8907 (OUTLIER) cc_final: 0.8538 (ptt90) REVERT: C 582 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.8408 (tt0) REVERT: C 874 ASN cc_start: 0.8675 (OUTLIER) cc_final: 0.8036 (t0) REVERT: C 950 ASP cc_start: 0.7742 (t0) cc_final: 0.7482 (t0) outliers start: 125 outliers final: 83 residues processed: 339 average time/residue: 0.1396 time to fit residues: 78.4115 Evaluate side-chains 312 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 218 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 564 ARG Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 922 ILE Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 706 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 881 SER Chi-restraints excluded: chain B residue 922 ILE Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 371 CYS Chi-restraints excluded: chain C residue 390 ASP Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 467 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 564 ARG Chi-restraints excluded: chain C residue 582 GLN Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 606 LEU Chi-restraints excluded: chain C residue 645 SER Chi-restraints excluded: chain C residue 658 PHE Chi-restraints excluded: chain C residue 679 LEU Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain C residue 869 ILE Chi-restraints excluded: chain C residue 874 ASN Chi-restraints excluded: chain C residue 974 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: [114, 70, 90, 51, 105, 226, 36, 137, 276, 35, 23] chunk 114 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 226 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 137 optimal weight: 6.9990 chunk 276 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 488 HIS ** B 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 528 ASN ** C 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.129223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.105415 restraints weight = 39470.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.107989 restraints weight = 22264.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.109655 restraints weight = 15304.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.110576 restraints weight = 12009.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.110871 restraints weight = 10394.084| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.4374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 23313 Z= 0.156 Angle : 0.733 11.989 31842 Z= 0.359 Chirality : 0.047 0.248 3726 Planarity : 0.004 0.047 3990 Dihedral : 5.550 21.550 3048 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 3.86 % Allowed : 22.04 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.15), residues: 2781 helix: -0.79 (0.20), residues: 657 sheet: -1.18 (0.22), residues: 534 loop : -1.89 (0.15), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 849 TYR 0.016 0.002 TYR C 369 PHE 0.034 0.002 PHE C 513 TRP 0.021 0.001 TRP C 110 HIS 0.004 0.001 HIS C 918 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (23229) covalent geometry : angle 0.71871 / 0.36 (31620) SS BOND : bond 0.00758 / 0.49 ( 30) SS BOND : angle 1.75047 / 1.09 ( 60) hydrogen bonds : bond 0.04294 / 2.91 ( 687) hydrogen bonds : angle 5.49322 / 3.75 ( 1890) link_NAG-ASN : bond 0.00274 / 0.19 ( 54) link_NAG-ASN : angle 1.88495 / 1.33 ( 162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 249 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 ASN cc_start: 0.8884 (OUTLIER) cc_final: 0.8421 (p0) REVERT: A 244 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.9011 (tp) REVERT: A 253 ILE cc_start: 0.8417 (pp) cc_final: 0.7836 (pt) REVERT: A 276 MET cc_start: 0.8274 (mmt) cc_final: 0.7759 (mmt) REVERT: A 367 LYS cc_start: 0.9131 (mtpp) cc_final: 0.8728 (mtmm) REVERT: A 370 GLU cc_start: 0.6934 (pt0) cc_final: 0.6385 (pt0) REVERT: A 564 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.8393 (ptt90) REVERT: A 620 ASP cc_start: 0.8215 (t70) cc_final: 0.7990 (t70) REVERT: A 770 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8232 (mt) REVERT: A 822 GLU cc_start: 0.7811 (tp30) cc_final: 0.7555 (tp30) REVERT: A 950 ASP cc_start: 0.7675 (t70) cc_final: 0.7448 (t0) REVERT: B 107 TRP cc_start: 0.8064 (m-90) cc_final: 0.7728 (m-90) REVERT: B 189 LEU cc_start: 0.7106 (tt) cc_final: 0.6883 (tt) REVERT: B 301 ASN cc_start: 0.8312 (m-40) cc_final: 0.7996 (m-40) REVERT: B 303 ILE cc_start: 0.8562 (mm) cc_final: 0.8234 (mt) REVERT: B 311 ASN cc_start: 0.8125 (t0) cc_final: 0.7803 (p0) REVERT: B 370 GLU cc_start: 0.7174 (pt0) cc_final: 0.6477 (pt0) REVERT: B 494 PHE cc_start: 0.8269 (OUTLIER) cc_final: 0.7662 (t80) REVERT: B 513 PHE cc_start: 0.8133 (t80) cc_final: 0.7908 (t80) REVERT: B 822 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.7103 (tp30) REVERT: B 950 ASP cc_start: 0.7683 (t70) cc_final: 0.7377 (t0) REVERT: C 174 ASP cc_start: 0.7658 (m-30) cc_final: 0.7369 (t0) REVERT: C 564 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.8453 (ptt90) REVERT: C 582 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.8215 (tt0) REVERT: C 599 VAL cc_start: 0.8447 (m) cc_final: 0.8237 (p) REVERT: C 725 GLU cc_start: 0.7987 (pm20) cc_final: 0.7726 (pt0) REVERT: C 874 ASN cc_start: 0.8497 (OUTLIER) cc_final: 0.7905 (t0) REVERT: C 950 ASP cc_start: 0.7735 (t0) cc_final: 0.7509 (t0) outliers start: 94 outliers final: 81 residues processed: 324 average time/residue: 0.1334 time to fit residues: 71.9828 Evaluate side-chains 326 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 236 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 564 ARG Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 922 ILE Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 706 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 822 GLU Chi-restraints excluded: chain B residue 881 SER Chi-restraints excluded: chain B residue 922 ILE Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 371 CYS Chi-restraints excluded: chain C residue 390 ASP Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 467 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 528 ASN Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain C residue 564 ARG Chi-restraints excluded: chain C residue 582 GLN Chi-restraints excluded: chain C residue 606 LEU Chi-restraints excluded: chain C residue 645 SER Chi-restraints excluded: chain C residue 679 LEU Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain C residue 874 ASN Chi-restraints excluded: chain C residue 974 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: [275, 129, 226, 188, 246, 253, 166, 151, 214, 104, 185] chunk 275 optimal weight: 3.9990 chunk 129 optimal weight: 0.2980 chunk 226 optimal weight: 10.0000 chunk 188 optimal weight: 5.9990 chunk 246 optimal weight: 0.9980 chunk 253 optimal weight: 7.9990 chunk 166 optimal weight: 0.9990 chunk 151 optimal weight: 0.9990 chunk 214 optimal weight: 7.9990 chunk 104 optimal weight: 2.9990 chunk 185 optimal weight: 6.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 488 HIS ** B 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.129045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.105558 restraints weight = 39236.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.107848 restraints weight = 22067.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.108508 restraints weight = 14065.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.108793 restraints weight = 14029.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.108987 restraints weight = 11960.575| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.139 23313 Z= 0.175 Angle : 0.852 59.200 31842 Z= 0.449 Chirality : 0.048 0.867 3726 Planarity : 0.004 0.046 3990 Dihedral : 5.560 23.929 3048 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.92 % Favored : 91.05 % Rotamer: Outliers : 4.06 % Allowed : 21.96 % Favored : 73.97 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.15), residues: 2781 helix: -0.79 (0.20), residues: 657 sheet: -1.17 (0.22), residues: 534 loop : -1.90 (0.15), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 849 TYR 0.016 0.001 TYR C 369 PHE 0.032 0.002 PHE C 513 TRP 0.019 0.001 TRP C 110 HIS 0.004 0.001 HIS C 918 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (23229) covalent geometry : angle 0.84048 / 0.45 (31620) SS BOND : bond 0.00758 / 0.50 ( 30) SS BOND : angle 1.75954 / 1.10 ( 60) hydrogen bonds : bond 0.04292 / 2.91 ( 687) hydrogen bonds : angle 5.49474 / 3.76 ( 1890) link_NAG-ASN : bond 0.00273 / 0.19 ( 54) link_NAG-ASN : angle 1.88442 / 1.33 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3402.74 seconds wall clock time: 59 minutes 52.45 seconds (3592.45 seconds total)