Starting phenix.real_space_refine on Thu Mar 5 13:25:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6m39_30071/03_2026/6m39_30071.cif Found real_map, /net/cci-nas-00/data/ceres_data/6m39_30071/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6m39_30071/03_2026/6m39_30071.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6m39_30071/03_2026/6m39_30071.map" model { file = "/net/cci-nas-00/data/ceres_data/6m39_30071/03_2026/6m39_30071.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6m39_30071/03_2026/6m39_30071.cif" } 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-dev-5986/lib/python3.9/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 dihedrals: 54 Unresolved non-hydrogen chiralities: 18 Restraints were copied for chains: B, C Time building chain proxies: 7.95, per 1000 atoms: 0.35 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 C 19 " - pdb=" SG CYS C 58 " distance=2.03 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 246 " distance=2.01 Simple disulfide: pdb=" SG CYS C 236 " - pdb=" SG CYS C 246 " distance=2.01 Simple disulfide: pdb=" SG CYS B 279 " - pdb=" SG CYS B 302 " distance=2.01 Simple disulfide: pdb=" SG CYS C 279 " - pdb=" SG CYS C 302 " distance=2.01 Simple disulfide: pdb=" SG CYS B 287 " - pdb=" SG CYS B 292 " distance=2.03 Simple disulfide: pdb=" SG CYS C 287 " - pdb=" SG CYS C 292 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 371 " distance=2.02 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 371 " distance=2.02 Simple disulfide: pdb=" SG CYS B 343 " - pdb=" SG CYS B 399 " distance=2.04 Simple disulfide: pdb=" SG CYS C 343 " - pdb=" SG CYS C 399 " distance=2.04 Simple disulfide: pdb=" SG CYS B 592 " - pdb=" SG CYS B 614 " distance=2.02 Simple disulfide: pdb=" SG CYS C 592 " - pdb=" SG CYS C 614 " distance=2.03 Simple disulfide: pdb=" SG CYS B 597 " - pdb=" SG CYS B 603 " distance=2.01 Simple disulfide: pdb=" SG CYS C 597 " - pdb=" SG CYS C 603 " distance=2.01 Simple disulfide: pdb=" SG CYS B 698 " - pdb=" SG CYS B 708 " distance=2.02 Simple disulfide: pdb=" SG CYS C 698 " - pdb=" SG CYS C 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 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: 1.66 Conformation dependent library (CDL) restraints added in 813.1 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: 0.89 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: 4.78 Time building geometry restraints manager: 2.33 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 - 20.99: 13625 20.99 - 41.98: 641 41.98 - 62.98: 101 62.98 - 83.97: 12 83.97 - 104.96: 24 Dihedral angle restraints: 14403 sinusoidal: 6255 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 14400 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: 0.05 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: 1.580 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: 0.070 Set scattering table: 0.060 Process input model: 23.910 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 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 : 13.057 104.958 9093 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 covalent geometry : bond 0.00953 (23229) covalent geometry : angle 1.26292 (31620) SS BOND : bond 0.01186 ( 30) SS BOND : angle 3.14176 ( 60) hydrogen bonds : bond 0.22433 ( 687) hydrogen bonds : angle 9.41211 ( 1890) link_NAG-ASN : bond 0.00848 ( 54) link_NAG-ASN : angle 4.33096 ( 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 : 0.803 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: 0.1577 time to fit residues: 144.0753 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 : 0.846 ------------------------------------------------------------------------------- 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: 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... Flipped N/Q/H residues before XYZ refinement: A 101 HIS A 112 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: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.134938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.110284 restraints weight = 39139.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.113072 restraints weight = 21743.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.114912 restraints weight = 14584.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.115842 restraints weight = 11387.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.116645 restraints weight = 9883.395| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2576 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= 0.151 Angle : 0.804 11.810 31842 Z= 0.397 Chirality : 0.049 0.354 3726 Planarity : 0.005 0.047 3990 Dihedral : 9.737 73.855 4191 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 4.15 % Allowed : 13.92 % Favored : 81.94 % 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: -3.63 (0.14), residues: 2781 helix: -2.23 (0.17), residues: 645 sheet: -1.57 (0.22), residues: 519 loop : -2.88 (0.13), residues: 1617 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 0.005 0.001 HIS B 902 Details of bonding type rmsd covalent geometry : bond 0.00327 (23229) covalent geometry : angle 0.77844 (31620) SS BOND : bond 0.00623 ( 30) SS BOND : angle 1.51201 ( 60) hydrogen bonds : bond 0.05226 ( 687) hydrogen bonds : angle 6.54155 ( 1890) link_NAG-ASN : bond 0.00506 ( 54) link_NAG-ASN : angle 2.79882 ( 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 477 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 376 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 ARG cc_start: 0.5787 (pmm-80) cc_final: 0.5275 (ptp90) REVERT: A 478 LEU cc_start: 0.9605 (tp) cc_final: 0.9394 (tp) REVERT: A 620 ASP cc_start: 0.8259 (t70) cc_final: 0.7952 (t0) REVERT: A 633 SER cc_start: 0.8895 (t) cc_final: 0.8567 (p) REVERT: A 770 LEU cc_start: 0.8243 (mm) cc_final: 0.7998 (mt) REVERT: B 301 ASN cc_start: 0.8359 (m-40) cc_final: 0.8029 (m-40) REVERT: B 370 GLU cc_start: 0.7392 (pt0) cc_final: 0.7130 (pt0) REVERT: B 620 ASP cc_start: 0.8416 (t70) cc_final: 0.8007 (t0) REVERT: B 633 SER cc_start: 0.8789 (t) cc_final: 0.8425 (p) REVERT: C 259 SER cc_start: 0.8835 (m) cc_final: 0.8600 (p) REVERT: C 348 VAL cc_start: 0.8464 (p) cc_final: 0.8240 (m) REVERT: C 370 GLU cc_start: 0.7350 (pt0) cc_final: 0.6779 (pt0) REVERT: C 620 ASP cc_start: 0.8293 (t70) cc_final: 0.7978 (t0) REVERT: C 633 SER cc_start: 0.8833 (t) cc_final: 0.8446 (p) REVERT: C 874 ASN cc_start: 0.8700 (OUTLIER) cc_final: 0.8110 (t160) REVERT: C 893 ARG cc_start: 0.8668 (mtp180) cc_final: 0.8278 (mtp180) outliers start: 101 outliers final: 38 residues processed: 452 average time/residue: 0.1371 time to fit residues: 100.6080 Evaluate side-chains 322 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 283 time to evaluate : 0.818 ------------------------------------------------------------------------------- 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 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 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 34 HIS 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 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 645 SER 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: chunk 164 optimal weight: 9.9990 chunk 229 optimal weight: 0.0270 chunk 180 optimal weight: 6.9990 chunk 130 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 121 optimal weight: 0.9980 chunk 46 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 overall best weight: 1.2042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN C 101 HIS ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 488 HIS ** C 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 615 GLN C 783 GLN C 808 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.134222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.109949 restraints weight = 39486.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.112661 restraints weight = 21580.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.114427 restraints weight = 14534.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.115302 restraints weight = 11366.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.116170 restraints weight = 9881.229| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23313 Z= 0.147 Angle : 0.748 12.051 31842 Z= 0.367 Chirality : 0.047 0.335 3726 Planarity : 0.004 0.040 3990 Dihedral : 8.030 55.457 4189 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 4.56 % Allowed : 14.82 % Favored : 80.62 % 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: -3.08 (0.14), residues: 2781 helix: -1.64 (0.18), residues: 642 sheet: -1.34 (0.23), residues: 501 loop : -2.53 (0.14), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 497 TYR 0.016 0.002 TYR B 465 PHE 0.022 0.001 PHE B 317 TRP 0.015 0.001 TRP B 110 HIS 0.009 0.001 HIS A 112 Details of bonding type rmsd covalent geometry : bond 0.00320 (23229) covalent geometry : angle 0.72498 (31620) SS BOND : bond 0.00679 ( 30) SS BOND : angle 1.54213 ( 60) hydrogen bonds : bond 0.04700 ( 687) hydrogen bonds : angle 6.08119 ( 1890) link_NAG-ASN : bond 0.00449 ( 54) link_NAG-ASN : angle 2.55509 ( 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 423 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 312 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8323 (tp) REVERT: A 315 ARG cc_start: 0.6245 (mmm160) cc_final: 0.6017 (mmm160) REVERT: A 620 ASP cc_start: 0.8299 (t70) cc_final: 0.7969 (t0) REVERT: A 633 SER cc_start: 0.8886 (t) cc_final: 0.8583 (p) REVERT: A 770 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8036 (mt) REVERT: B 269 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8228 (tp) REVERT: B 301 ASN cc_start: 0.8528 (m-40) cc_final: 0.7994 (m-40) REVERT: B 303 ILE cc_start: 0.8433 (mm) cc_final: 0.8232 (mm) REVERT: B 633 SER cc_start: 0.8747 (t) cc_final: 0.8445 (p) REVERT: C 269 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8132 (tp) REVERT: C 874 ASN cc_start: 0.8593 (OUTLIER) cc_final: 0.8041 (t0) REVERT: C 950 ASP cc_start: 0.7622 (t0) cc_final: 0.7411 (t0) outliers start: 111 outliers final: 63 residues processed: 395 average time/residue: 0.1275 time to fit residues: 84.0996 Evaluate side-chains 337 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 269 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 523 MET 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 A residue 931 THR 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 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 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 499 LEU Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 881 SER 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 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 467 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 599 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 214 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 180 optimal weight: 8.9990 chunk 245 optimal weight: 6.9990 chunk 55 optimal weight: 7.9990 chunk 152 optimal weight: 10.0000 chunk 193 optimal weight: 6.9990 chunk 117 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 202 optimal weight: 9.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 852 ASN ** A 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 528 ASN B 573 GLN B 710 GLN ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 488 HIS C 528 ASN ** C 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.131657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.107209 restraints weight = 39742.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.109963 restraints weight = 21776.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.111804 restraints weight = 14536.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.112661 restraints weight = 11277.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.113377 restraints weight = 9798.069| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3443 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= 0.167 Angle : 0.732 9.891 31842 Z= 0.360 Chirality : 0.047 0.299 3726 Planarity : 0.004 0.040 3990 Dihedral : 7.081 55.566 4189 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 5.75 % Allowed : 16.01 % Favored : 78.24 % 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: -2.77 (0.14), residues: 2781 helix: -1.30 (0.19), residues: 651 sheet: -1.39 (0.23), residues: 483 loop : -2.28 (0.14), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 497 TYR 0.019 0.002 TYR B 306 PHE 0.026 0.002 PHE A 199 TRP 0.017 0.001 TRP C 110 HIS 0.005 0.001 HIS B 552 Details of bonding type rmsd covalent geometry : bond 0.00383 (23229) covalent geometry : angle 0.71252 (31620) SS BOND : bond 0.00827 ( 30) SS BOND : angle 1.57976 ( 60) hydrogen bonds : bond 0.04512 ( 687) hydrogen bonds : angle 5.81710 ( 1890) link_NAG-ASN : bond 0.00405 ( 54) link_NAG-ASN : angle 2.33141 ( 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 441 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 301 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8880 (tp) REVERT: A 253 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.8308 (pt) REVERT: A 315 ARG cc_start: 0.6408 (mmm160) cc_final: 0.6194 (mmm160) REVERT: A 370 GLU cc_start: 0.7289 (pt0) cc_final: 0.6981 (pt0) REVERT: A 599 VAL cc_start: 0.8607 (m) cc_final: 0.8402 (p) REVERT: A 620 ASP cc_start: 0.8332 (t70) cc_final: 0.8008 (t0) REVERT: A 633 SER cc_start: 0.8871 (t) cc_final: 0.8536 (p) REVERT: A 651 ASP cc_start: 0.6528 (p0) cc_final: 0.5925 (t0) REVERT: A 770 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8182 (mt) REVERT: B 107 TRP cc_start: 0.8039 (m-90) cc_final: 0.7544 (m-90) REVERT: B 244 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8861 (tt) REVERT: B 253 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.8031 (pt) REVERT: B 269 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8225 (tp) REVERT: B 301 ASN cc_start: 0.8537 (m-40) cc_final: 0.8170 (m-40) REVERT: B 303 ILE cc_start: 0.8498 (mm) cc_final: 0.8241 (mm) REVERT: B 370 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7361 (pt0) REVERT: C 251 PHE cc_start: 0.8873 (OUTLIER) cc_final: 0.8434 (m-80) REVERT: C 269 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8231 (tp) REVERT: C 361 ILE cc_start: 0.7349 (pt) cc_final: 0.7088 (pt) REVERT: C 367 LYS cc_start: 0.8748 (mtmt) cc_final: 0.8311 (mtmt) REVERT: C 370 GLU cc_start: 0.7063 (pt0) cc_final: 0.6781 (pt0) REVERT: C 651 ASP cc_start: 0.6342 (p0) cc_final: 0.5607 (t0) REVERT: C 874 ASN cc_start: 0.8575 (OUTLIER) cc_final: 0.8009 (t0) outliers start: 140 outliers final: 77 residues processed: 404 average time/residue: 0.1285 time to fit residues: 87.1563 Evaluate side-chains 342 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 255 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR 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 253 ILE 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 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 922 ILE Chi-restraints excluded: chain B residue 51 THR 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 244 LEU Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 370 GLU 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 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 881 SER 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 76 VAL Chi-restraints excluded: chain C residue 101 HIS 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 222 VAL Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 251 PHE 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 498 LEU 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 599 VAL 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: chunk 163 optimal weight: 6.9990 chunk 240 optimal weight: 3.9990 chunk 244 optimal weight: 0.6980 chunk 39 optimal weight: 5.9990 chunk 66 optimal weight: 0.0970 chunk 59 optimal weight: 4.9990 chunk 145 optimal weight: 1.9990 chunk 268 optimal weight: 4.9990 chunk 231 optimal weight: 9.9990 chunk 99 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 528 ASN ** C 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.131845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.107536 restraints weight = 39286.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.110304 restraints weight = 21605.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.112134 restraints weight = 14497.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.113102 restraints weight = 11200.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.113775 restraints weight = 9646.096| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23313 Z= 0.147 Angle : 0.703 9.551 31842 Z= 0.347 Chirality : 0.046 0.248 3726 Planarity : 0.004 0.039 3990 Dihedral : 6.592 55.637 4188 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 5.62 % Allowed : 17.08 % Favored : 77.30 % 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: -2.53 (0.15), residues: 2781 helix: -0.97 (0.20), residues: 639 sheet: -1.33 (0.23), residues: 492 loop : -2.16 (0.14), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 849 TYR 0.015 0.001 TYR B 306 PHE 0.022 0.002 PHE A 513 TRP 0.027 0.001 TRP C 110 HIS 0.005 0.001 HIS B 552 Details of bonding type rmsd covalent geometry : bond 0.00333 (23229) covalent geometry : angle 0.68695 (31620) SS BOND : bond 0.00540 ( 30) SS BOND : angle 1.45943 ( 60) hydrogen bonds : bond 0.04309 ( 687) hydrogen bonds : angle 5.68766 ( 1890) link_NAG-ASN : bond 0.00359 ( 54) link_NAG-ASN : angle 2.06384 ( 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 418 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 281 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8928 (tp) REVERT: A 253 ILE cc_start: 0.8758 (OUTLIER) cc_final: 0.8299 (pt) REVERT: A 276 MET cc_start: 0.8222 (mmt) cc_final: 0.7684 (mmt) REVERT: A 620 ASP cc_start: 0.8306 (t70) cc_final: 0.8074 (t0) REVERT: A 633 SER cc_start: 0.8877 (t) cc_final: 0.8573 (p) REVERT: A 770 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8258 (mt) REVERT: B 276 MET cc_start: 0.8218 (mmt) cc_final: 0.7825 (mmt) REVERT: B 301 ASN cc_start: 0.8662 (m-40) cc_final: 0.8153 (m-40) REVERT: B 303 ILE cc_start: 0.8526 (mm) cc_final: 0.8278 (mm) REVERT: B 651 ASP cc_start: 0.6476 (p0) cc_final: 0.6050 (t0) REVERT: C 174 ASP cc_start: 0.7362 (m-30) cc_final: 0.7125 (m-30) REVERT: C 361 ILE cc_start: 0.7496 (pt) cc_final: 0.7150 (pt) REVERT: C 367 LYS cc_start: 0.8703 (mtmt) cc_final: 0.8353 (mtmt) REVERT: C 370 GLU cc_start: 0.6953 (pt0) cc_final: 0.6663 (pt0) REVERT: C 599 VAL cc_start: 0.8498 (OUTLIER) cc_final: 0.8258 (p) REVERT: C 874 ASN cc_start: 0.8541 (OUTLIER) cc_final: 0.7954 (t0) outliers start: 137 outliers final: 94 residues processed: 387 average time/residue: 0.1280 time to fit residues: 83.6613 Evaluate side-chains 340 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 241 time to evaluate : 0.723 ------------------------------------------------------------------------------- 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 244 LEU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 349 LEU 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 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 34 HIS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 76 VAL 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 363 THR 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 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 788 VAL 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 922 ILE Chi-restraints excluded: chain B residue 931 THR Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain C residue 34 HIS Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 76 VAL 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 224 THR 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 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 508 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 528 ASN 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 660 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 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: chunk 131 optimal weight: 8.9990 chunk 195 optimal weight: 20.0000 chunk 17 optimal weight: 0.9980 chunk 133 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 164 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 24 optimal weight: 8.9990 chunk 86 optimal weight: 1.9990 chunk 201 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 874 ASN ** A 894 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 528 ASN ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 502 HIS C 528 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.130178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.106472 restraints weight = 39402.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.109062 restraints weight = 21655.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.110786 restraints weight = 14666.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.111668 restraints weight = 11466.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.112216 restraints weight = 9928.234| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 23313 Z= 0.167 Angle : 0.704 10.764 31842 Z= 0.349 Chirality : 0.046 0.242 3726 Planarity : 0.004 0.039 3990 Dihedral : 6.428 55.431 4183 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 5.83 % Allowed : 18.43 % Favored : 75.74 % 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: -2.38 (0.15), residues: 2781 helix: -0.76 (0.20), residues: 621 sheet: -1.30 (0.23), residues: 498 loop : -2.06 (0.14), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 849 TYR 0.015 0.002 TYR B 306 PHE 0.026 0.002 PHE A 513 TRP 0.024 0.001 TRP C 110 HIS 0.005 0.001 HIS A 712 Details of bonding type rmsd covalent geometry : bond 0.00381 (23229) covalent geometry : angle 0.68838 (31620) SS BOND : bond 0.00781 ( 30) SS BOND : angle 1.54484 ( 60) hydrogen bonds : bond 0.04320 ( 687) hydrogen bonds : angle 5.59936 ( 1890) link_NAG-ASN : bond 0.00330 ( 54) link_NAG-ASN : angle 2.02844 ( 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 403 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 261 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.8250 (mmt) cc_final: 0.7732 (mmt) REVERT: A 367 LYS cc_start: 0.8672 (mtmt) cc_final: 0.8261 (mtmm) REVERT: A 564 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.8322 (ptt90) REVERT: A 620 ASP cc_start: 0.8312 (t70) cc_final: 0.8072 (t0) REVERT: A 770 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8281 (mt) REVERT: A 950 ASP cc_start: 0.7620 (t70) cc_final: 0.7377 (t0) REVERT: B 107 TRP cc_start: 0.8022 (m-90) cc_final: 0.7585 (m-90) REVERT: B 244 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8899 (tt) REVERT: B 253 ILE cc_start: 0.8501 (OUTLIER) cc_final: 0.7943 (pt) REVERT: B 276 MET cc_start: 0.8248 (mmt) cc_final: 0.7924 (mmt) REVERT: B 301 ASN cc_start: 0.8678 (m-40) cc_final: 0.8198 (m-40) REVERT: B 303 ILE cc_start: 0.8578 (mm) cc_final: 0.8332 (mm) REVERT: C 269 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8254 (tp) REVERT: C 361 ILE cc_start: 0.7538 (pt) cc_final: 0.7224 (pt) REVERT: C 367 LYS cc_start: 0.8713 (mtmt) cc_final: 0.8398 (mtmt) REVERT: C 370 GLU cc_start: 0.6919 (pt0) cc_final: 0.6550 (pt0) REVERT: C 582 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.8267 (tm-30) REVERT: C 599 VAL cc_start: 0.8551 (OUTLIER) cc_final: 0.8317 (p) REVERT: C 874 ASN cc_start: 0.8569 (OUTLIER) cc_final: 0.7959 (t0) outliers start: 142 outliers final: 101 residues processed: 371 average time/residue: 0.1250 time to fit residues: 78.0028 Evaluate side-chains 346 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 237 time to evaluate : 0.792 ------------------------------------------------------------------------------- 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 220 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 244 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 392 VAL Chi-restraints excluded: chain A residue 413 THR 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 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 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 852 ASN Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 922 ILE Chi-restraints excluded: chain A residue 931 THR Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain B residue 51 THR 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 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 253 ILE 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 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 467 VAL 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 706 LEU Chi-restraints excluded: chain B residue 722 MET 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 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 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 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 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 660 LEU Chi-restraints excluded: chain C residue 676 ILE 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 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: chunk 151 optimal weight: 0.8980 chunk 224 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 209 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 186 optimal weight: 20.0000 chunk 211 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 247 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 169 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 ASN ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 894 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 ASN ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 ASN ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 528 ASN ** B 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 ASN ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.132335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.108265 restraints weight = 39155.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.111021 restraints weight = 21340.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.112841 restraints weight = 14277.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.113823 restraints weight = 11052.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.114537 restraints weight = 9495.853| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23313 Z= 0.131 Angle : 0.692 11.490 31842 Z= 0.339 Chirality : 0.046 0.240 3726 Planarity : 0.004 0.040 3990 Dihedral : 6.172 55.749 4182 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 5.25 % Allowed : 19.46 % Favored : 75.29 % 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: -2.25 (0.15), residues: 2781 helix: -0.60 (0.20), residues: 615 sheet: -1.26 (0.23), residues: 489 loop : -1.98 (0.14), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 849 TYR 0.022 0.001 TYR B 306 PHE 0.029 0.001 PHE A 513 TRP 0.034 0.001 TRP C 110 HIS 0.004 0.001 HIS B 552 Details of bonding type rmsd covalent geometry : bond 0.00292 (23229) covalent geometry : angle 0.67793 (31620) SS BOND : bond 0.00620 ( 30) SS BOND : angle 1.41531 ( 60) hydrogen bonds : bond 0.04130 ( 687) hydrogen bonds : angle 5.51150 ( 1890) link_NAG-ASN : bond 0.00297 ( 54) link_NAG-ASN : angle 1.90140 ( 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 391 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 263 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.8226 (mmt) cc_final: 0.7685 (mmt) REVERT: A 367 LYS cc_start: 0.8749 (mtmt) cc_final: 0.8496 (mtmm) REVERT: A 370 GLU cc_start: 0.7099 (pt0) cc_final: 0.6651 (pt0) REVERT: A 564 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.8312 (ptt90) REVERT: A 582 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.8614 (tt0) REVERT: A 620 ASP cc_start: 0.8274 (t70) cc_final: 0.8043 (t0) REVERT: A 770 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8291 (mt) REVERT: A 950 ASP cc_start: 0.7695 (t70) cc_final: 0.7422 (t0) REVERT: B 276 MET cc_start: 0.8214 (mmt) cc_final: 0.7877 (mmt) REVERT: B 301 ASN cc_start: 0.8549 (m-40) cc_final: 0.8124 (m-40) REVERT: B 303 ILE cc_start: 0.8444 (mm) cc_final: 0.8097 (mt) REVERT: B 311 ASN cc_start: 0.8233 (t0) cc_final: 0.7865 (p0) REVERT: B 370 GLU cc_start: 0.7259 (pt0) cc_final: 0.6703 (pt0) REVERT: B 582 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.8408 (tt0) REVERT: C 361 ILE cc_start: 0.7481 (pt) cc_final: 0.7150 (pt) REVERT: C 367 LYS cc_start: 0.8664 (mtmt) cc_final: 0.8442 (mtmt) REVERT: C 370 GLU cc_start: 0.6875 (pt0) cc_final: 0.6668 (pt0) REVERT: C 564 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.8416 (ptt90) REVERT: C 599 VAL cc_start: 0.8430 (OUTLIER) cc_final: 0.8207 (p) REVERT: C 874 ASN cc_start: 0.8508 (OUTLIER) cc_final: 0.7979 (t0) outliers start: 128 outliers final: 95 residues processed: 359 average time/residue: 0.1317 time to fit residues: 78.8552 Evaluate side-chains 348 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 246 time to evaluate : 0.792 ------------------------------------------------------------------------------- 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 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 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 527 THR Chi-restraints excluded: chain A residue 564 ARG Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain A residue 582 GLN 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 686 THR 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 922 ILE Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain B residue 51 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 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 467 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain B residue 582 GLN 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 722 MET 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 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 95 ILE 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 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 424 VAL Chi-restraints excluded: chain C residue 441 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 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 686 THR 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 974 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 51 optimal weight: 0.9980 chunk 148 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 136 optimal weight: 0.8980 chunk 187 optimal weight: 8.9990 chunk 81 optimal weight: 2.9990 chunk 180 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 184 optimal weight: 0.0980 chunk 151 optimal weight: 4.9990 chunk 104 optimal weight: 10.0000 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 894 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 ASN B 528 ASN ** B 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 488 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.131594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.108533 restraints weight = 38947.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.111374 restraints weight = 22380.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.112053 restraints weight = 13725.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.112320 restraints weight = 12542.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.112467 restraints weight = 11248.128| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23313 Z= 0.134 Angle : 0.694 11.821 31842 Z= 0.339 Chirality : 0.046 0.241 3726 Planarity : 0.004 0.041 3990 Dihedral : 6.064 55.586 4182 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 5.46 % Allowed : 20.53 % Favored : 74.01 % 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: -2.22 (0.15), residues: 2781 helix: -0.69 (0.20), residues: 636 sheet: -1.21 (0.22), residues: 534 loop : -1.94 (0.15), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 849 TYR 0.014 0.001 TYR A 711 PHE 0.027 0.001 PHE C 513 TRP 0.030 0.001 TRP C 110 HIS 0.004 0.001 HIS A 712 Details of bonding type rmsd covalent geometry : bond 0.00303 (23229) covalent geometry : angle 0.68084 (31620) SS BOND : bond 0.00704 ( 30) SS BOND : angle 1.47930 ( 60) hydrogen bonds : bond 0.04106 ( 687) hydrogen bonds : angle 5.45915 ( 1890) link_NAG-ASN : bond 0.00283 ( 54) link_NAG-ASN : angle 1.85154 ( 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 393 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 260 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 SER cc_start: 0.8770 (t) cc_final: 0.8203 (p) REVERT: A 276 MET cc_start: 0.8268 (mmt) cc_final: 0.7723 (mmt) REVERT: A 564 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.8310 (ptt90) REVERT: A 582 GLN cc_start: 0.8870 (OUTLIER) cc_final: 0.8623 (tt0) REVERT: A 620 ASP cc_start: 0.8214 (t70) cc_final: 0.7963 (t70) REVERT: A 770 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8264 (mt) REVERT: A 950 ASP cc_start: 0.7712 (t70) cc_final: 0.7441 (t0) REVERT: B 276 MET cc_start: 0.8335 (mmt) cc_final: 0.7925 (mmt) REVERT: B 301 ASN cc_start: 0.8506 (m-40) cc_final: 0.8083 (m-40) REVERT: B 303 ILE cc_start: 0.8499 (mm) cc_final: 0.8148 (mt) REVERT: B 311 ASN cc_start: 0.8301 (t0) cc_final: 0.7902 (p0) REVERT: B 370 GLU cc_start: 0.7247 (pt0) cc_final: 0.6742 (pt0) REVERT: B 582 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.8390 (tt0) REVERT: B 950 ASP cc_start: 0.7525 (t70) cc_final: 0.7241 (t0) REVERT: C 367 LYS cc_start: 0.8718 (mtmt) cc_final: 0.8488 (mtmt) REVERT: C 370 GLU cc_start: 0.6821 (pt0) cc_final: 0.6591 (pt0) REVERT: C 564 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.8381 (ptt90) REVERT: C 582 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.8250 (tt0) REVERT: C 599 VAL cc_start: 0.8405 (m) cc_final: 0.8187 (p) REVERT: C 725 GLU cc_start: 0.7944 (pm20) cc_final: 0.7603 (pt0) REVERT: C 874 ASN cc_start: 0.8485 (OUTLIER) cc_final: 0.7937 (t0) outliers start: 133 outliers final: 105 residues processed: 364 average time/residue: 0.1322 time to fit residues: 80.2326 Evaluate side-chains 357 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 245 time to evaluate : 0.602 ------------------------------------------------------------------------------- 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 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 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 413 THR 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 564 ARG Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain A residue 582 GLN 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 676 ILE 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 850 LEU Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 907 MET 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 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 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 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 467 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 582 GLN 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 722 MET 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 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 413 THR Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 441 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 547 MET Chi-restraints excluded: chain C residue 564 ARG Chi-restraints excluded: chain C residue 578 GLU 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 660 LEU 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 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 974 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 271 optimal weight: 0.8980 chunk 138 optimal weight: 5.9990 chunk 48 optimal weight: 8.9990 chunk 240 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 chunk 236 optimal weight: 6.9990 chunk 186 optimal weight: 20.0000 chunk 118 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 192 optimal weight: 6.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS A 502 HIS ** A 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 894 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 ASN B 488 HIS B 502 HIS B 528 ASN ** 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 488 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.125462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.101260 restraints weight = 39624.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.103916 restraints weight = 21797.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.105569 restraints weight = 14612.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.106767 restraints weight = 11447.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.107180 restraints weight = 9759.063| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 23313 Z= 0.244 Angle : 0.800 11.870 31842 Z= 0.397 Chirality : 0.049 0.248 3726 Planarity : 0.005 0.046 3990 Dihedral : 6.603 54.673 4182 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.25 % Favored : 89.75 % Rotamer: Outliers : 5.54 % Allowed : 20.69 % Favored : 73.77 % 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: -0.93 (0.20), residues: 657 sheet: -1.23 (0.22), residues: 537 loop : -2.01 (0.14), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 849 TYR 0.019 0.002 TYR C 369 PHE 0.030 0.002 PHE C 513 TRP 0.034 0.002 TRP C 110 HIS 0.006 0.001 HIS C 918 Details of bonding type rmsd covalent geometry : bond 0.00567 (23229) covalent geometry : angle 0.78341 (31620) SS BOND : bond 0.00891 ( 30) SS BOND : angle 2.07501 ( 60) hydrogen bonds : bond 0.04720 ( 687) hydrogen bonds : angle 5.58766 ( 1890) link_NAG-ASN : bond 0.00347 ( 54) link_NAG-ASN : angle 2.07489 ( 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 380 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 245 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7406 (tt) REVERT: A 244 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.9122 (tp) REVERT: A 253 ILE cc_start: 0.8615 (pp) cc_final: 0.8099 (pt) REVERT: A 276 MET cc_start: 0.8357 (mmt) cc_final: 0.7762 (mmt) REVERT: A 367 LYS cc_start: 0.8805 (mtmt) cc_final: 0.8296 (mtmm) REVERT: A 564 ARG cc_start: 0.8804 (OUTLIER) cc_final: 0.8511 (ptt90) REVERT: A 770 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8363 (mt) REVERT: A 822 GLU cc_start: 0.7888 (tp30) cc_final: 0.7660 (tp30) REVERT: A 950 ASP cc_start: 0.7754 (t70) cc_final: 0.7495 (t0) REVERT: B 107 TRP cc_start: 0.8067 (m-90) cc_final: 0.7716 (m-90) REVERT: B 253 ILE cc_start: 0.8526 (pp) cc_final: 0.8003 (pt) REVERT: B 301 ASN cc_start: 0.8542 (m-40) cc_final: 0.8093 (m-40) REVERT: B 370 GLU cc_start: 0.7220 (pt0) cc_final: 0.6723 (pt0) REVERT: B 582 GLN cc_start: 0.8925 (OUTLIER) cc_final: 0.8489 (tt0) REVERT: B 950 ASP cc_start: 0.7668 (t70) cc_final: 0.7415 (t0) REVERT: C 367 LYS cc_start: 0.8714 (mtmt) cc_final: 0.8439 (mtmt) REVERT: C 564 ARG cc_start: 0.8891 (OUTLIER) cc_final: 0.8480 (ptt90) REVERT: C 582 GLN cc_start: 0.8919 (OUTLIER) cc_final: 0.8326 (tt0) REVERT: C 599 VAL cc_start: 0.8588 (OUTLIER) cc_final: 0.8365 (p) REVERT: C 874 ASN cc_start: 0.8637 (OUTLIER) cc_final: 0.8053 (t0) outliers start: 135 outliers final: 94 residues processed: 358 average time/residue: 0.1269 time to fit residues: 75.6239 Evaluate side-chains 328 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 225 time to evaluate : 0.832 ------------------------------------------------------------------------------- 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 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 189 LEU 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 272 VAL 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 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 676 ILE 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 907 MET Chi-restraints excluded: chain A residue 922 ILE Chi-restraints excluded: chain A residue 931 THR Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain B residue 51 THR 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 214 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 241 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 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 467 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain B residue 582 GLN 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 676 ILE Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 763 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 222 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 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 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 660 LEU 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 802 ILE 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: chunk 114 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 105 optimal weight: 0.0370 chunk 226 optimal weight: 0.9990 chunk 36 optimal weight: 6.9990 chunk 137 optimal weight: 0.1980 chunk 276 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 overall best weight: 0.5660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 528 ASN ** 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.131177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.107735 restraints weight = 38889.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.110362 restraints weight = 21795.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.110924 restraints weight = 14008.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.111148 restraints weight = 12560.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.111422 restraints weight = 12105.797| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23313 Z= 0.126 Angle : 0.726 12.652 31842 Z= 0.354 Chirality : 0.046 0.239 3726 Planarity : 0.004 0.047 3990 Dihedral : 6.197 56.225 4182 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 3.69 % Allowed : 22.66 % Favored : 73.65 % 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: -2.19 (0.15), residues: 2781 helix: -0.75 (0.20), residues: 642 sheet: -1.21 (0.22), residues: 534 loop : -1.88 (0.15), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 849 TYR 0.015 0.001 TYR B 865 PHE 0.037 0.002 PHE C 513 TRP 0.031 0.002 TRP C 110 HIS 0.004 0.001 HIS A 712 Details of bonding type rmsd covalent geometry : bond 0.00269 (23229) covalent geometry : angle 0.71368 (31620) SS BOND : bond 0.00706 ( 30) SS BOND : angle 1.48229 ( 60) hydrogen bonds : bond 0.04141 ( 687) hydrogen bonds : angle 5.53038 ( 1890) link_NAG-ASN : bond 0.00310 ( 54) link_NAG-ASN : angle 1.85820 ( 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 349 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 259 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 SER cc_start: 0.8705 (t) cc_final: 0.8168 (p) REVERT: A 276 MET cc_start: 0.8334 (mmt) cc_final: 0.7752 (mmt) REVERT: A 564 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.8333 (ptt90) REVERT: A 770 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8219 (mt) REVERT: A 822 GLU cc_start: 0.7802 (tp30) cc_final: 0.7522 (tp30) REVERT: A 839 ASP cc_start: 0.7184 (t0) cc_final: 0.6894 (t0) REVERT: A 950 ASP cc_start: 0.7785 (t70) cc_final: 0.7532 (t0) REVERT: B 107 TRP cc_start: 0.7999 (m-90) cc_final: 0.7581 (m-90) REVERT: B 174 ASP cc_start: 0.7512 (m-30) cc_final: 0.7265 (m-30) REVERT: B 301 ASN cc_start: 0.8295 (m-40) cc_final: 0.8000 (m-40) REVERT: B 303 ILE cc_start: 0.8563 (mm) cc_final: 0.8302 (mm) REVERT: B 311 ASN cc_start: 0.8235 (t0) cc_final: 0.7899 (p0) REVERT: B 370 GLU cc_start: 0.7201 (pt0) cc_final: 0.6672 (pt0) REVERT: B 725 GLU cc_start: 0.8034 (pm20) cc_final: 0.7785 (pt0) REVERT: B 950 ASP cc_start: 0.7761 (t70) cc_final: 0.7458 (t0) REVERT: C 174 ASP cc_start: 0.7489 (m-30) cc_final: 0.7092 (t0) REVERT: C 564 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.8391 (ptt90) REVERT: C 582 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.8139 (tm-30) REVERT: C 599 VAL cc_start: 0.8428 (m) cc_final: 0.8210 (p) REVERT: C 725 GLU cc_start: 0.7963 (pm20) cc_final: 0.7593 (pt0) REVERT: C 874 ASN cc_start: 0.8403 (OUTLIER) cc_final: 0.7839 (t0) outliers start: 90 outliers final: 74 residues processed: 330 average time/residue: 0.1314 time to fit residues: 72.1037 Evaluate side-chains 317 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 238 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 109 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 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 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 676 ILE 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 869 ILE Chi-restraints excluded: chain A residue 907 MET 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 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 214 VAL Chi-restraints excluded: chain B residue 220 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 524 VAL Chi-restraints excluded: chain B residue 528 ASN Chi-restraints excluded: chain B residue 578 GLU 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 763 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 101 HIS Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 214 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 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 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 606 LEU Chi-restraints excluded: chain C residue 645 SER 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: chunk 275 optimal weight: 8.9990 chunk 129 optimal weight: 0.8980 chunk 226 optimal weight: 5.9990 chunk 188 optimal weight: 10.0000 chunk 246 optimal weight: 0.9990 chunk 253 optimal weight: 6.9990 chunk 166 optimal weight: 8.9990 chunk 151 optimal weight: 3.9990 chunk 214 optimal weight: 1.9990 chunk 104 optimal weight: 10.0000 chunk 185 optimal weight: 10.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 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** ** C 899 GLN ** 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 = 0.3690 r_free = 0.3690 target = 0.131272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.107075 restraints weight = 38933.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.109843 restraints weight = 21126.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.111586 restraints weight = 14212.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.112518 restraints weight = 11061.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.113323 restraints weight = 9574.485| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.4479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.121 23313 Z= 0.165 Angle : 0.848 59.199 31842 Z= 0.443 Chirality : 0.049 0.971 3726 Planarity : 0.004 0.047 3990 Dihedral : 6.206 56.232 4182 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.09 % Favored : 91.87 % Rotamer: Outliers : 3.74 % Allowed : 22.50 % Favored : 73.77 % 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: -0.77 (0.20), residues: 642 sheet: -1.21 (0.22), residues: 534 loop : -1.89 (0.15), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 849 TYR 0.015 0.001 TYR B 865 PHE 0.035 0.002 PHE C 513 TRP 0.028 0.002 TRP C 110 HIS 0.004 0.001 HIS A 712 Details of bonding type rmsd covalent geometry : bond 0.00357 (23229) covalent geometry : angle 0.83781 (31620) SS BOND : bond 0.00686 ( 30) SS BOND : angle 1.51777 ( 60) hydrogen bonds : bond 0.04160 ( 687) hydrogen bonds : angle 5.52465 ( 1890) link_NAG-ASN : bond 0.00313 ( 54) link_NAG-ASN : angle 1.86233 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3307.63 seconds wall clock time: 58 minutes 18.39 seconds (3498.39 seconds total)