Starting phenix.real_space_refine on Fri Mar 6 01:48:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k8y_22735/03_2026/7k8y_22735.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k8y_22735/03_2026/7k8y_22735.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7k8y_22735/03_2026/7k8y_22735.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k8y_22735/03_2026/7k8y_22735.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7k8y_22735/03_2026/7k8y_22735.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k8y_22735/03_2026/7k8y_22735.map" } resolution = 4.4 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 Anisotropic ADP refinement not supported. Converting 1619 atoms to isotropic. 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 116 5.16 5 C 16284 2.51 5 N 4219 2.21 5 O 4941 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 160 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: 25560 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 7823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7823 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 49, 'TRANS': 952} Chain breaks: 7 Chain: "D" Number of atoms: 7823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7823 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 49, 'TRANS': 952} Chain breaks: 7 Chain: "E" Number of atoms: 7823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7823 Classifications: {'peptide': 1002} Link IDs: {'CIS': 2, 'PTRANS': 49, 'TRANS': 950} Chain breaks: 7 Chain: "G" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 991 Classifications: {'peptide': 128} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 121} Chain: "I" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 778 Classifications: {'peptide': 108} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 101} Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "D" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "E" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 5.73, per 1000 atoms: 0.22 Number of scatterers: 25560 At special positions: 0 Unit cell: (141.284, 144.628, 204.82, 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 116 16.00 O 4941 8.00 N 4219 7.00 C 16284 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.04 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.04 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.04 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.03 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.03 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.03 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=2.03 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 301 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 538 " - pdb=" SG CYS E 590 " distance=2.03 Simple disulfide: pdb=" SG CYS E 617 " - pdb=" SG CYS E 649 " distance=2.03 Simple disulfide: pdb=" SG CYS E 662 " - pdb=" SG CYS E 671 " distance=2.03 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 760 " distance=2.03 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.03 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.03 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 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=3, symmetry=0 Links applied NAG-ASN " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 709 " " NAG B1304 " - " ASN B 717 " " NAG B1305 " - " ASN B 801 " " NAG B1306 " - " ASN B1074 " " NAG B1307 " - " ASN B1134 " " NAG D1301 " - " ASN D 282 " " NAG D1302 " - " ASN D 331 " " NAG D1303 " - " ASN D 603 " " NAG D1304 " - " ASN D 616 " " NAG D1305 " - " ASN D 709 " " NAG D1306 " - " ASN D 717 " " NAG D1307 " - " ASN D 801 " " NAG D1308 " - " ASN D1134 " " NAG E1301 " - " ASN E 122 " " NAG E1302 " - " ASN E 282 " " NAG E1303 " - " ASN E 331 " " NAG E1304 " - " ASN E 616 " " NAG E1305 " - " ASN E 709 " " NAG E1306 " - " ASN E 717 " " NAG E1307 " - " ASN E 801 " " NAG E1308 " - " ASN E1074 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.59 Conformation dependent library (CDL) restraints added in 954.7 milliseconds 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6048 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 50 sheets defined 24.3% alpha, 26.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 366 through 371 Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.962A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.522A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.522A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 760 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.627A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 941 removed outlier: 4.353A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 966 removed outlier: 4.314A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.996A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.618A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'D' and resid 294 through 304 Processing helix chain 'D' and resid 337 through 343 Processing helix chain 'D' and resid 366 through 371 Processing helix chain 'D' and resid 384 through 388 removed outlier: 3.859A pdb=" N LEU D 387 " --> pdb=" O PRO D 384 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ASN D 388 " --> pdb=" O THR D 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 384 through 388' Processing helix chain 'D' and resid 405 through 410 removed outlier: 3.848A pdb=" N ARG D 408 " --> pdb=" O ASP D 405 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE D 410 " --> pdb=" O VAL D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 422 Processing helix chain 'D' and resid 502 through 506 removed outlier: 3.822A pdb=" N GLN D 506 " --> pdb=" O VAL D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 737 through 744 removed outlier: 3.563A pdb=" N GLY D 744 " --> pdb=" O MET D 740 " (cutoff:3.500A) Processing helix chain 'D' and resid 746 through 754 Processing helix chain 'D' and resid 755 through 757 No H-bonds generated for 'chain 'D' and resid 755 through 757' Processing helix chain 'D' and resid 758 through 783 removed outlier: 3.988A pdb=" N LEU D 763 " --> pdb=" O PHE D 759 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP D 775 " --> pdb=" O ALA D 771 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 826 Processing helix chain 'D' and resid 866 through 884 Processing helix chain 'D' and resid 886 through 891 removed outlier: 3.733A pdb=" N ALA D 890 " --> pdb=" O TRP D 886 " (cutoff:3.500A) Processing helix chain 'D' and resid 897 through 909 Processing helix chain 'D' and resid 912 through 941 removed outlier: 4.351A pdb=" N LEU D 916 " --> pdb=" O THR D 912 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LYS D 921 " --> pdb=" O TYR D 917 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU D 922 " --> pdb=" O GLU D 918 " (cutoff:3.500A) Processing helix chain 'D' and resid 942 through 944 No H-bonds generated for 'chain 'D' and resid 942 through 944' Processing helix chain 'D' and resid 945 through 966 removed outlier: 4.344A pdb=" N VAL D 951 " --> pdb=" O LYS D 947 " (cutoff:3.500A) Processing helix chain 'D' and resid 976 through 984 removed outlier: 4.134A pdb=" N ILE D 980 " --> pdb=" O VAL D 976 " (cutoff:3.500A) Processing helix chain 'D' and resid 985 through 1033 removed outlier: 4.856A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) Processing helix chain 'D' and resid 1116 through 1118 No H-bonds generated for 'chain 'D' and resid 1116 through 1118' Processing helix chain 'D' and resid 1140 through 1147 removed outlier: 3.976A pdb=" N GLU D1144 " --> pdb=" O PRO D1140 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 304 Processing helix chain 'E' and resid 337 through 342 Processing helix chain 'E' and resid 365 through 371 Processing helix chain 'E' and resid 405 through 410 removed outlier: 4.312A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE E 410 " --> pdb=" O VAL E 407 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'E' and resid 502 through 505 Processing helix chain 'E' and resid 737 through 743 Processing helix chain 'E' and resid 747 through 754 Processing helix chain 'E' and resid 755 through 757 No H-bonds generated for 'chain 'E' and resid 755 through 757' Processing helix chain 'E' and resid 758 through 783 Processing helix chain 'E' and resid 816 through 825 Processing helix chain 'E' and resid 866 through 884 Processing helix chain 'E' and resid 886 through 891 removed outlier: 3.830A pdb=" N ALA E 890 " --> pdb=" O TRP E 886 " (cutoff:3.500A) Processing helix chain 'E' and resid 897 through 909 Processing helix chain 'E' and resid 913 through 919 Processing helix chain 'E' and resid 919 through 941 Processing helix chain 'E' and resid 942 through 944 No H-bonds generated for 'chain 'E' and resid 942 through 944' Processing helix chain 'E' and resid 945 through 966 removed outlier: 4.152A pdb=" N VAL E 951 " --> pdb=" O LYS E 947 " (cutoff:3.500A) Processing helix chain 'E' and resid 976 through 984 removed outlier: 3.726A pdb=" N ILE E 980 " --> pdb=" O VAL E 976 " (cutoff:3.500A) Processing helix chain 'E' and resid 985 through 1033 removed outlier: 4.529A pdb=" N VAL E 991 " --> pdb=" O PRO E 987 " (cutoff:3.500A) Processing helix chain 'E' and resid 1140 through 1147 removed outlier: 3.874A pdb=" N GLU E1144 " --> pdb=" O PRO E1140 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.598A pdb=" N TYR G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'I' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'B' and resid 28 through 29 removed outlier: 6.758A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 42 through 43 removed outlier: 3.623A pdb=" N ALA E 575 " --> pdb=" O GLY E 566 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ASP E 574 " --> pdb=" O ILE E 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.925A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'B' and resid 141 through 142 removed outlier: 6.306A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.731A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.334A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.690A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.961A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.689A pdb=" N ALA B 701 " --> pdb=" O ILE D 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.472A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.472A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.368A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE B1081 " --> pdb=" O HIS B1088 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 28 through 29 removed outlier: 6.519A pdb=" N SER D 205 " --> pdb=" O PRO D 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 47 through 55 removed outlier: 3.994A pdb=" N ASP D 287 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 84 through 85 Processing sheet with id=AC2, first strand: chain 'D' and resid 141 through 142 removed outlier: 6.392A pdb=" N LEU D 141 " --> pdb=" O LEU D 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'D' and resid 311 through 313 Processing sheet with id=AC4, first strand: chain 'D' and resid 325 through 328 removed outlier: 5.356A pdb=" N ASP D 574 " --> pdb=" O ILE D 587 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA D 575 " --> pdb=" O GLY D 566 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N PHE D 565 " --> pdb=" O PHE E 43 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 354 through 358 Processing sheet with id=AC6, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'D' and resid 473 through 474 removed outlier: 3.644A pdb=" N TYR D 473 " --> pdb=" O TYR D 489 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TYR D 489 " --> pdb=" O TYR D 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'D' and resid 654 through 655 removed outlier: 5.921A pdb=" N GLU D 654 " --> pdb=" O ALA D 694 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N THR D 696 " --> pdb=" O GLU D 654 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ALA D 672 " --> pdb=" O PRO D 665 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 701 through 702 removed outlier: 7.081A pdb=" N ALA D 701 " --> pdb=" O ILE E 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'D' and resid 711 through 715 Processing sheet with id=AD2, first strand: chain 'D' and resid 718 through 728 removed outlier: 6.839A pdb=" N GLY D1059 " --> pdb=" O SER D1055 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N SER D1055 " --> pdb=" O GLY D1059 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL D1061 " --> pdb=" O PRO D1053 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU D1063 " --> pdb=" O SER D1051 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N SER D1051 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL D1065 " --> pdb=" O LEU D1049 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 734 through 735 Processing sheet with id=AD4, first strand: chain 'D' and resid 1120 through 1125 removed outlier: 4.377A pdb=" N ALA D1087 " --> pdb=" O SER D1123 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N HIS D1088 " --> pdb=" O ILE D1081 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE D1081 " --> pdb=" O HIS D1088 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 28 through 31 removed outlier: 3.723A pdb=" N SER E 60 " --> pdb=" O SER E 31 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N ASN E 61 " --> pdb=" O TYR E 269 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N TYR E 269 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N SER E 205 " --> pdb=" O PRO E 225 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 47 through 55 removed outlier: 4.049A pdb=" N ASP E 287 " --> pdb=" O LYS E 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 84 through 85 removed outlier: 6.021A pdb=" N LEU E 141 " --> pdb=" O LEU E 244 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 84 through 85 removed outlier: 5.784A pdb=" N ALA E 243 " --> pdb=" O ILE E 101 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE E 101 " --> pdb=" O ALA E 243 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ARG E 102 " --> pdb=" O ASN E 121 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 311 through 319 removed outlier: 5.475A pdb=" N ILE E 312 " --> pdb=" O THR E 599 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N THR E 599 " --> pdb=" O ILE E 312 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N GLN E 314 " --> pdb=" O VAL E 597 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL E 597 " --> pdb=" O GLN E 314 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N GLY E 594 " --> pdb=" O GLN E 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 354 through 358 Processing sheet with id=AE2, first strand: chain 'E' and resid 391 through 392 Processing sheet with id=AE3, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'E' and resid 654 through 655 removed outlier: 6.079A pdb=" N GLU E 654 " --> pdb=" O ALA E 694 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N THR E 696 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ALA E 672 " --> pdb=" O PRO E 665 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 712 through 728 removed outlier: 6.837A pdb=" N ALA E 713 " --> pdb=" O ASN E1074 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ASN E1074 " --> pdb=" O ALA E 713 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N GLU E1072 " --> pdb=" O PRO E 715 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ASN E 717 " --> pdb=" O ALA E1070 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N TYR E1067 " --> pdb=" O HIS E1048 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N HIS E1048 " --> pdb=" O TYR E1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 734 through 736 Processing sheet with id=AE8, first strand: chain 'E' and resid 1120 through 1122 Processing sheet with id=AE9, first strand: chain 'E' and resid 1094 through 1097 Processing sheet with id=AF1, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AF2, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.315A pdb=" N MET G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N TRP G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 10 through 12 Processing sheet with id=AF4, first strand: chain 'I' and resid 9 through 13 removed outlier: 6.490A pdb=" N TRP I 35 " --> pdb=" O MET I 47 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 19 through 24 1096 hydrogen bonds defined for protein. 2979 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: 6.41 Time building geometry restraints manager: 2.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 8199 1.35 - 1.47: 6559 1.47 - 1.59: 11225 1.59 - 1.72: 1 1.72 - 1.84: 146 Bond restraints: 26130 Sorted by residual: bond pdb=" CA PHE I 98 " pdb=" C PHE I 98 " ideal model delta sigma weight residual 1.525 1.595 -0.070 1.25e-02 6.40e+03 3.14e+01 bond pdb=" CA VAL I 97 " pdb=" C VAL I 97 " ideal model delta sigma weight residual 1.523 1.592 -0.069 1.27e-02 6.20e+03 2.93e+01 bond pdb=" N PHE I 98 " pdb=" CA PHE I 98 " ideal model delta sigma weight residual 1.458 1.521 -0.063 1.42e-02 4.96e+03 1.96e+01 bond pdb=" N VAL I 97 " pdb=" CA VAL I 97 " ideal model delta sigma weight residual 1.459 1.506 -0.047 1.25e-02 6.40e+03 1.41e+01 bond pdb=" C1 NAG E1307 " pdb=" O5 NAG E1307 " ideal model delta sigma weight residual 1.406 1.478 -0.072 2.00e-02 2.50e+03 1.29e+01 ... (remaining 26125 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.53: 35482 3.53 - 7.06: 65 7.06 - 10.59: 3 10.59 - 14.12: 0 14.12 - 17.65: 1 Bond angle restraints: 35551 Sorted by residual: angle pdb=" N PHE I 98 " pdb=" CA PHE I 98 " pdb=" C PHE I 98 " ideal model delta sigma weight residual 108.24 125.89 -17.65 1.32e+00 5.74e-01 1.79e+02 angle pdb=" C PHE I 98 " pdb=" N GLY I 99 " pdb=" CA GLY I 99 " ideal model delta sigma weight residual 121.96 130.85 -8.89 1.38e+00 5.25e-01 4.15e+01 angle pdb=" N THR G 104 " pdb=" CA THR G 104 " pdb=" C THR G 104 " ideal model delta sigma weight residual 113.17 106.20 6.97 1.26e+00 6.30e-01 3.06e+01 angle pdb=" N TYR G 115 " pdb=" CA TYR G 115 " pdb=" C TYR G 115 " ideal model delta sigma weight residual 108.38 114.73 -6.35 1.35e+00 5.49e-01 2.22e+01 angle pdb=" N THR E 124 " pdb=" CA THR E 124 " pdb=" C THR E 124 " ideal model delta sigma weight residual 114.75 109.06 5.69 1.26e+00 6.30e-01 2.04e+01 ... (remaining 35546 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.70: 15334 24.70 - 49.40: 437 49.40 - 74.10: 52 74.10 - 98.80: 20 98.80 - 123.49: 1 Dihedral angle restraints: 15844 sinusoidal: 6434 harmonic: 9410 Sorted by residual: dihedral pdb=" CB CYS E 738 " pdb=" SG CYS E 738 " pdb=" SG CYS E 760 " pdb=" CB CYS E 760 " ideal model delta sinusoidal sigma weight residual 93.00 4.25 88.75 1 1.00e+01 1.00e-02 9.39e+01 dihedral pdb=" CB CYS B 738 " pdb=" SG CYS B 738 " pdb=" SG CYS B 760 " pdb=" CB CYS B 760 " ideal model delta sinusoidal sigma weight residual 93.00 5.04 87.96 1 1.00e+01 1.00e-02 9.26e+01 dihedral pdb=" CB CYS D 662 " pdb=" SG CYS D 662 " pdb=" SG CYS D 671 " pdb=" CB CYS D 671 " ideal model delta sinusoidal sigma weight residual -86.00 -173.52 87.52 1 1.00e+01 1.00e-02 9.18e+01 ... (remaining 15841 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 4077 0.123 - 0.246: 23 0.246 - 0.369: 7 0.369 - 0.491: 2 0.491 - 0.614: 2 Chirality restraints: 4111 Sorted by residual: chirality pdb=" C1 NAG E1305 " pdb=" ND2 ASN E 709 " pdb=" C2 NAG E1305 " pdb=" O5 NAG E1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.43e+00 chirality pdb=" C1 NAG D1302 " pdb=" ND2 ASN D 331 " pdb=" C2 NAG D1302 " pdb=" O5 NAG D1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.19e+00 chirality pdb=" C1 NAG E1306 " pdb=" ND2 ASN E 717 " pdb=" C2 NAG E1306 " pdb=" O5 NAG E1306 " both_signs ideal model delta sigma weight residual False -2.40 -2.86 0.46 2.00e-01 2.50e+01 5.36e+00 ... (remaining 4108 not shown) Planarity restraints: 4594 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 717 " -0.034 2.00e-02 2.50e+03 8.07e-02 8.14e+01 pdb=" CG ASN E 717 " -0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN E 717 " 0.081 2.00e-02 2.50e+03 pdb=" ND2 ASN E 717 " -0.124 2.00e-02 2.50e+03 pdb=" C1 NAG E1306 " 0.096 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 122 " 0.046 2.00e-02 2.50e+03 5.41e-02 3.66e+01 pdb=" CG ASN E 122 " -0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN E 122 " -0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN E 122 " -0.086 2.00e-02 2.50e+03 pdb=" C1 NAG E1301 " 0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 282 " -0.045 2.00e-02 2.50e+03 5.15e-02 3.31e+01 pdb=" CG ASN D 282 " 0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN D 282 " 0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN D 282 " 0.086 2.00e-02 2.50e+03 pdb=" C1 NAG D1301 " -0.060 2.00e-02 2.50e+03 ... (remaining 4591 not shown) Histogram of nonbonded interaction distances: 1.14 - 1.89: 20 1.89 - 2.64: 517 2.64 - 3.39: 33948 3.39 - 4.15: 61462 4.15 - 4.90: 108946 Nonbonded interactions: 204893 Sorted by model distance: nonbonded pdb=" O ALA D 713 " pdb=" CG LEU E 894 " model vdw 1.137 3.470 nonbonded pdb=" O ALA D 713 " pdb=" CD1 LEU E 894 " model vdw 1.340 3.460 nonbonded pdb=" OE2 GLU B 516 " pdb=" OH TYR D 200 " model vdw 1.368 3.040 nonbonded pdb=" CE1 PHE D 559 " pdb=" CD2 PHE E 43 " model vdw 1.370 3.640 nonbonded pdb=" CH2 TRP G 47 " pdb=" OG SER I 95 " model vdw 1.387 3.340 ... (remaining 204888 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = (chain 'D' and resid 27 through 1307) selection = (chain 'E' and resid 27 through 1307) } 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: 5.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.020 Extract box with map and model: 0.530 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.820 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 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 : 0.005 0.395 26195 Z= 0.368 Angle : 0.616 17.652 35698 Z= 0.328 Chirality : 0.046 0.614 4111 Planarity : 0.004 0.048 4571 Dihedral : 10.962 123.494 9679 Min Nonbonded Distance : 1.137 Molprobity Statistics. All-atom Clashscore : 21.70 Ramachandran Plot: Outliers : 0.25 % Allowed : 2.79 % Favored : 96.96 % Rotamer: Outliers : 0.04 % Allowed : 3.30 % Favored : 96.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.11 (0.13), residues: 3190 helix: -0.03 (0.19), residues: 641 sheet: -0.91 (0.17), residues: 767 loop : -2.22 (0.12), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 98 TYR 0.023 0.001 TYR G 115 PHE 0.008 0.001 PHE B 192 TRP 0.015 0.001 TRP G 120 HIS 0.003 0.000 HIS E1048 Details of bonding type rmsd covalent geometry : bond 0.00277 (26130) covalent geometry : angle 0.54643 (35551) SS BOND : bond 0.00260 ( 39) SS BOND : angle 1.01172 ( 78) hydrogen bonds : bond 0.12459 ( 1076) hydrogen bonds : angle 6.33819 ( 2979) Misc. bond : bond 0.28798 ( 3) link_NAG-ASN : bond 0.08500 ( 23) link_NAG-ASN : angle 6.44105 ( 69) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 273 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 406 GLU cc_start: 0.9437 (mm-30) cc_final: 0.9223 (mp0) REVERT: B 902 MET cc_start: 0.9817 (mmm) cc_final: 0.9419 (mmp) REVERT: B 964 LYS cc_start: 0.9843 (tppt) cc_final: 0.9639 (mmmt) REVERT: B 966 LEU cc_start: 0.9554 (mt) cc_final: 0.9352 (mp) REVERT: B 1018 ILE cc_start: 0.9715 (mm) cc_final: 0.9490 (tp) REVERT: B 1062 PHE cc_start: 0.9722 (m-80) cc_final: 0.9318 (m-80) REVERT: D 552 LEU cc_start: 0.9277 (mt) cc_final: 0.9027 (mm) REVERT: D 902 MET cc_start: 0.9751 (mmm) cc_final: 0.9487 (mmp) REVERT: D 936 ASP cc_start: 0.9111 (m-30) cc_final: 0.8832 (t0) REVERT: D 960 ASN cc_start: 0.9189 (m-40) cc_final: 0.8750 (m110) REVERT: D 1029 MET cc_start: 0.9615 (tpp) cc_final: 0.9376 (tpp) REVERT: D 1063 LEU cc_start: 0.9806 (mt) cc_final: 0.9507 (pp) REVERT: E 203 ILE cc_start: 0.9702 (mt) cc_final: 0.9257 (mt) REVERT: E 227 VAL cc_start: 0.8783 (t) cc_final: 0.8535 (t) REVERT: E 270 LEU cc_start: 0.9024 (mt) cc_final: 0.8799 (mt) REVERT: E 495 TYR cc_start: 0.4989 (m-10) cc_final: 0.4338 (m-80) REVERT: E 606 ASN cc_start: 0.8857 (p0) cc_final: 0.8638 (p0) REVERT: E 773 GLU cc_start: 0.9214 (pt0) cc_final: 0.8970 (pp20) REVERT: E 782 PHE cc_start: 0.9182 (m-80) cc_final: 0.8571 (m-80) REVERT: E 802 PHE cc_start: 0.9253 (m-80) cc_final: 0.8857 (m-80) REVERT: E 805 ILE cc_start: 0.9783 (pt) cc_final: 0.9449 (tp) REVERT: E 869 MET cc_start: 0.9130 (mtt) cc_final: 0.8721 (mtt) REVERT: E 902 MET cc_start: 0.9656 (mmm) cc_final: 0.9343 (mmt) REVERT: E 934 ILE cc_start: 0.9351 (mm) cc_final: 0.9086 (pt) REVERT: E 964 LYS cc_start: 0.9654 (mmmt) cc_final: 0.9431 (mmmt) REVERT: E 1029 MET cc_start: 0.9345 (tpp) cc_final: 0.8983 (tpp) REVERT: E 1034 LEU cc_start: 0.9599 (mp) cc_final: 0.9390 (mp) outliers start: 1 outliers final: 1 residues processed: 274 average time/residue: 0.1840 time to fit residues: 77.2576 Evaluate side-chains 154 residues out of total 2818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 153 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 2.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 ASN B 394 ASN B 644 GLN B 675 GLN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN B 953 ASN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 HIS D 655 HIS D 762 GLN D 764 ASN D 804 GLN D 935 GLN ** D1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 ASN E 450 ASN E 501 ASN ** E 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 675 GLN ** E 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 784 GLN E 804 GLN E 935 GLN E 953 ASN E 955 ASN E 965 GLN E1119 ASN G 39 GLN I 6 GLN I 79 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.057119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.046060 restraints weight = 254998.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.046642 restraints weight = 118309.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.047350 restraints weight = 66600.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.047598 restraints weight = 40743.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.047647 restraints weight = 31600.493| |-----------------------------------------------------------------------------| r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.134 26195 Z= 0.316 Angle : 0.748 11.361 35698 Z= 0.386 Chirality : 0.045 0.243 4111 Planarity : 0.005 0.086 4571 Dihedral : 6.644 103.412 3949 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.23 % Favored : 95.67 % Rotamer: Outliers : 0.14 % Allowed : 5.46 % Favored : 94.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.32 (0.14), residues: 3190 helix: 1.04 (0.20), residues: 651 sheet: -0.86 (0.17), residues: 786 loop : -1.67 (0.13), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG G 67 TYR 0.027 0.002 TYR G 115 PHE 0.031 0.003 PHE I 98 TRP 0.019 0.003 TRP D 64 HIS 0.011 0.002 HIS E1048 Details of bonding type rmsd covalent geometry : bond 0.00646 (26130) covalent geometry : angle 0.73820 (35551) SS BOND : bond 0.00523 ( 39) SS BOND : angle 1.73496 ( 78) hydrogen bonds : bond 0.04415 ( 1076) hydrogen bonds : angle 5.68221 ( 2979) Misc. bond : bond 0.00335 ( 3) link_NAG-ASN : bond 0.00520 ( 23) link_NAG-ASN : angle 2.35740 ( 69) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 2818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 145 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 406 GLU cc_start: 0.9484 (mm-30) cc_final: 0.8974 (mp0) REVERT: B 869 MET cc_start: 0.9511 (mtm) cc_final: 0.9149 (mtt) REVERT: B 902 MET cc_start: 0.9850 (mmm) cc_final: 0.9424 (mmp) REVERT: B 1018 ILE cc_start: 0.9894 (mm) cc_final: 0.9552 (tt) REVERT: B 1062 PHE cc_start: 0.9693 (m-80) cc_final: 0.9466 (m-10) REVERT: D 277 LEU cc_start: 0.9740 (mp) cc_final: 0.9339 (tt) REVERT: D 731 MET cc_start: 0.9178 (ppp) cc_final: 0.8829 (ppp) REVERT: D 936 ASP cc_start: 0.9149 (m-30) cc_final: 0.8939 (m-30) REVERT: D 1029 MET cc_start: 0.9686 (tpp) cc_final: 0.9467 (tpp) REVERT: E 270 LEU cc_start: 0.9452 (mt) cc_final: 0.9227 (tp) REVERT: E 495 TYR cc_start: 0.5563 (m-10) cc_final: 0.5140 (m-80) REVERT: E 740 MET cc_start: 0.8529 (tpt) cc_final: 0.8187 (tpt) REVERT: E 869 MET cc_start: 0.9488 (mtt) cc_final: 0.9238 (mtt) REVERT: E 902 MET cc_start: 0.9629 (mmm) cc_final: 0.9358 (mmp) REVERT: E 964 LYS cc_start: 0.9735 (mmmt) cc_final: 0.9458 (mmmt) REVERT: E 1001 LEU cc_start: 0.9815 (tp) cc_final: 0.9431 (tp) REVERT: E 1029 MET cc_start: 0.9439 (tpp) cc_final: 0.9084 (tpp) REVERT: E 1034 LEU cc_start: 0.9775 (mp) cc_final: 0.9499 (mt) REVERT: E 1041 ASP cc_start: 0.8782 (t0) cc_final: 0.8415 (t0) REVERT: E 1062 PHE cc_start: 0.9558 (m-80) cc_final: 0.9337 (m-10) REVERT: I 87 TYR cc_start: 0.8032 (m-80) cc_final: 0.7764 (m-10) outliers start: 4 outliers final: 0 residues processed: 147 average time/residue: 0.1654 time to fit residues: 39.0617 Evaluate side-chains 102 residues out of total 2818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 123 optimal weight: 7.9990 chunk 198 optimal weight: 0.3980 chunk 155 optimal weight: 2.9990 chunk 125 optimal weight: 9.9990 chunk 247 optimal weight: 9.9990 chunk 165 optimal weight: 6.9990 chunk 179 optimal weight: 9.9990 chunk 132 optimal weight: 30.0000 chunk 154 optimal weight: 7.9990 chunk 297 optimal weight: 8.9990 chunk 94 optimal weight: 2.9990 overall best weight: 4.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN B 343 ASN ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 HIS ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1048 HIS E 218 GLN E 501 ASN ** E1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 HIS ** 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 = 0.3428 r_free = 0.3428 target = 0.057082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.046008 restraints weight = 253405.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.046643 restraints weight = 117944.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.047227 restraints weight = 67409.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.047552 restraints weight = 40666.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.047567 restraints weight = 30920.884| |-----------------------------------------------------------------------------| r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 26195 Z= 0.208 Angle : 0.619 9.161 35698 Z= 0.320 Chirality : 0.044 0.200 4111 Planarity : 0.004 0.040 4571 Dihedral : 6.306 76.867 3949 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.36 % Favored : 95.58 % Rotamer: Outliers : 0.11 % Allowed : 3.62 % Favored : 96.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.00 (0.14), residues: 3190 helix: 1.42 (0.21), residues: 651 sheet: -0.76 (0.17), residues: 767 loop : -1.46 (0.14), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 38 TYR 0.022 0.002 TYR E 904 PHE 0.024 0.002 PHE E 759 TRP 0.013 0.002 TRP G 50 HIS 0.023 0.001 HIS I 39 Details of bonding type rmsd covalent geometry : bond 0.00427 (26130) covalent geometry : angle 0.60597 (35551) SS BOND : bond 0.00484 ( 39) SS BOND : angle 1.83999 ( 78) hydrogen bonds : bond 0.03929 ( 1076) hydrogen bonds : angle 5.44506 ( 2979) Misc. bond : bond 0.00096 ( 3) link_NAG-ASN : bond 0.00400 ( 23) link_NAG-ASN : angle 2.24880 ( 69) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 133 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 867 ASP cc_start: 0.9236 (p0) cc_final: 0.8591 (t0) REVERT: B 869 MET cc_start: 0.9579 (mtm) cc_final: 0.9032 (mtp) REVERT: B 902 MET cc_start: 0.9843 (mmm) cc_final: 0.9425 (mmp) REVERT: B 1018 ILE cc_start: 0.9835 (mm) cc_final: 0.9621 (tp) REVERT: B 1062 PHE cc_start: 0.9709 (m-80) cc_final: 0.9500 (m-10) REVERT: D 277 LEU cc_start: 0.9734 (mp) cc_final: 0.9263 (tt) REVERT: D 731 MET cc_start: 0.9271 (ppp) cc_final: 0.8858 (ppp) REVERT: D 1029 MET cc_start: 0.9723 (tpp) cc_final: 0.9395 (tpp) REVERT: E 104 TRP cc_start: 0.8823 (m100) cc_final: 0.8303 (m100) REVERT: E 191 GLU cc_start: 0.8923 (mt-10) cc_final: 0.8678 (pm20) REVERT: E 270 LEU cc_start: 0.9502 (mt) cc_final: 0.9242 (tp) REVERT: E 495 TYR cc_start: 0.5199 (m-10) cc_final: 0.4882 (m-80) REVERT: E 770 ILE cc_start: 0.9775 (mt) cc_final: 0.9397 (mt) REVERT: E 773 GLU cc_start: 0.9282 (pt0) cc_final: 0.8900 (pp20) REVERT: E 869 MET cc_start: 0.9525 (mtt) cc_final: 0.9221 (mtt) REVERT: E 902 MET cc_start: 0.9665 (mmm) cc_final: 0.9370 (mmp) REVERT: E 964 LYS cc_start: 0.9804 (mmmt) cc_final: 0.9503 (mmmt) REVERT: E 1001 LEU cc_start: 0.9842 (tp) cc_final: 0.9507 (tp) REVERT: E 1029 MET cc_start: 0.9435 (tpp) cc_final: 0.9041 (tpp) REVERT: E 1034 LEU cc_start: 0.9828 (mp) cc_final: 0.9537 (mt) REVERT: E 1062 PHE cc_start: 0.9523 (m-80) cc_final: 0.9306 (m-10) REVERT: G 34 MET cc_start: 0.8061 (tpp) cc_final: 0.7834 (tpp) REVERT: I 62 PHE cc_start: 0.6935 (m-10) cc_final: 0.6489 (m-10) REVERT: I 87 TYR cc_start: 0.7723 (m-80) cc_final: 0.7447 (m-10) outliers start: 3 outliers final: 0 residues processed: 136 average time/residue: 0.1642 time to fit residues: 36.3184 Evaluate side-chains 95 residues out of total 2818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 296 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 281 optimal weight: 6.9990 chunk 152 optimal weight: 3.9990 chunk 153 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 299 optimal weight: 8.9990 chunk 203 optimal weight: 6.9990 chunk 286 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 207 HIS E 501 ASN E 965 GLN I 6 GLN ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.056461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.045446 restraints weight = 253573.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.046042 restraints weight = 118024.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.046868 restraints weight = 61888.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.046996 restraints weight = 36524.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.047017 restraints weight = 29453.628| |-----------------------------------------------------------------------------| r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 26195 Z= 0.193 Angle : 0.609 10.822 35698 Z= 0.313 Chirality : 0.043 0.209 4111 Planarity : 0.004 0.056 4571 Dihedral : 6.011 57.640 3949 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.73 % Favored : 95.17 % Rotamer: Outliers : 0.04 % Allowed : 3.58 % Favored : 96.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.86 (0.14), residues: 3190 helix: 1.51 (0.21), residues: 644 sheet: -0.71 (0.17), residues: 774 loop : -1.32 (0.14), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 67 TYR 0.019 0.002 TYR G 112 PHE 0.016 0.002 PHE E 759 TRP 0.011 0.001 TRP G 50 HIS 0.007 0.001 HIS I 39 Details of bonding type rmsd covalent geometry : bond 0.00396 (26130) covalent geometry : angle 0.59640 (35551) SS BOND : bond 0.00472 ( 39) SS BOND : angle 1.76031 ( 78) hydrogen bonds : bond 0.03809 ( 1076) hydrogen bonds : angle 5.34958 ( 2979) Misc. bond : bond 0.00078 ( 3) link_NAG-ASN : bond 0.00385 ( 23) link_NAG-ASN : angle 2.31802 ( 69) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 2818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 123 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 867 ASP cc_start: 0.9210 (p0) cc_final: 0.8548 (t0) REVERT: B 869 MET cc_start: 0.9580 (mtm) cc_final: 0.9085 (mtp) REVERT: B 902 MET cc_start: 0.9829 (mmm) cc_final: 0.9432 (mmp) REVERT: B 1018 ILE cc_start: 0.9867 (mm) cc_final: 0.9664 (tp) REVERT: D 277 LEU cc_start: 0.9740 (mp) cc_final: 0.9241 (tt) REVERT: D 387 LEU cc_start: 0.8643 (pp) cc_final: 0.8038 (mt) REVERT: D 731 MET cc_start: 0.9251 (ppp) cc_final: 0.8801 (ppp) REVERT: D 742 ILE cc_start: 0.9773 (mt) cc_final: 0.9552 (tp) REVERT: D 1029 MET cc_start: 0.9724 (tpp) cc_final: 0.9391 (tpp) REVERT: E 104 TRP cc_start: 0.8863 (m100) cc_final: 0.8198 (m100) REVERT: E 191 GLU cc_start: 0.8869 (mt-10) cc_final: 0.8646 (pm20) REVERT: E 270 LEU cc_start: 0.9542 (mt) cc_final: 0.9312 (tp) REVERT: E 697 MET cc_start: 0.7174 (ptp) cc_final: 0.6827 (ptp) REVERT: E 869 MET cc_start: 0.9516 (mtt) cc_final: 0.9239 (mtt) REVERT: E 902 MET cc_start: 0.9658 (mmm) cc_final: 0.9451 (mmm) REVERT: E 1001 LEU cc_start: 0.9852 (tp) cc_final: 0.9519 (tp) REVERT: E 1002 GLN cc_start: 0.9320 (tm-30) cc_final: 0.9046 (tm-30) REVERT: E 1029 MET cc_start: 0.9429 (tpp) cc_final: 0.8980 (tpp) REVERT: E 1034 LEU cc_start: 0.9829 (mp) cc_final: 0.9542 (mm) REVERT: E 1062 PHE cc_start: 0.9538 (m-80) cc_final: 0.9293 (m-10) REVERT: G 34 MET cc_start: 0.8042 (tpp) cc_final: 0.7829 (tpp) REVERT: G 67 ARG cc_start: 0.4357 (tpt170) cc_final: 0.4066 (tpt-90) outliers start: 1 outliers final: 0 residues processed: 124 average time/residue: 0.1564 time to fit residues: 32.6536 Evaluate side-chains 94 residues out of total 2818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 136 optimal weight: 20.0000 chunk 147 optimal weight: 9.9990 chunk 88 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 319 optimal weight: 50.0000 chunk 201 optimal weight: 5.9990 chunk 142 optimal weight: 20.0000 chunk 229 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 255 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN B1048 HIS B1119 ASN D 762 GLN D 965 GLN ** E 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 501 ASN E 751 ASN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.053923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.042701 restraints weight = 259709.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.043585 restraints weight = 122887.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.044181 restraints weight = 66431.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.044413 restraints weight = 40096.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.044469 restraints weight = 32470.639| |-----------------------------------------------------------------------------| r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.4877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.125 26195 Z= 0.277 Angle : 0.701 11.924 35698 Z= 0.364 Chirality : 0.045 0.210 4111 Planarity : 0.005 0.043 4571 Dihedral : 6.309 57.615 3949 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.71 % Favored : 94.23 % Rotamer: Outliers : 0.04 % Allowed : 3.30 % Favored : 96.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.13 (0.14), residues: 3190 helix: 1.07 (0.20), residues: 649 sheet: -0.95 (0.18), residues: 741 loop : -1.37 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 357 TYR 0.029 0.002 TYR D 313 PHE 0.024 0.002 PHE B1052 TRP 0.012 0.002 TRP E 886 HIS 0.007 0.002 HIS D1083 Details of bonding type rmsd covalent geometry : bond 0.00566 (26130) covalent geometry : angle 0.68849 (35551) SS BOND : bond 0.00497 ( 39) SS BOND : angle 1.90720 ( 78) hydrogen bonds : bond 0.04212 ( 1076) hydrogen bonds : angle 5.78117 ( 2979) Misc. bond : bond 0.00086 ( 3) link_NAG-ASN : bond 0.00471 ( 23) link_NAG-ASN : angle 2.43664 ( 69) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 120 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 740 MET cc_start: 0.9201 (mtp) cc_final: 0.8940 (mtp) REVERT: B 869 MET cc_start: 0.9590 (mtm) cc_final: 0.9014 (mtp) REVERT: B 902 MET cc_start: 0.9845 (mmm) cc_final: 0.9435 (mmp) REVERT: B 1018 ILE cc_start: 0.9887 (mm) cc_final: 0.9643 (tp) REVERT: D 277 LEU cc_start: 0.9744 (mp) cc_final: 0.9218 (tt) REVERT: D 731 MET cc_start: 0.9287 (ppp) cc_final: 0.8754 (ppp) REVERT: D 742 ILE cc_start: 0.9789 (mt) cc_final: 0.9577 (tp) REVERT: D 1029 MET cc_start: 0.9685 (tpp) cc_final: 0.9352 (tpp) REVERT: E 104 TRP cc_start: 0.9043 (m100) cc_final: 0.8374 (m100) REVERT: E 191 GLU cc_start: 0.8822 (mt-10) cc_final: 0.8548 (pm20) REVERT: E 869 MET cc_start: 0.9542 (mtt) cc_final: 0.9183 (mtt) REVERT: E 902 MET cc_start: 0.9646 (mmm) cc_final: 0.9406 (mmm) REVERT: E 1001 LEU cc_start: 0.9837 (tp) cc_final: 0.9530 (tt) REVERT: E 1029 MET cc_start: 0.9446 (tpp) cc_final: 0.9002 (tpp) REVERT: E 1034 LEU cc_start: 0.9827 (mp) cc_final: 0.9513 (mt) REVERT: E 1062 PHE cc_start: 0.9542 (m-80) cc_final: 0.9281 (m-10) REVERT: G 45 LEU cc_start: 0.5422 (tp) cc_final: 0.5110 (tp) outliers start: 1 outliers final: 0 residues processed: 121 average time/residue: 0.1552 time to fit residues: 31.4043 Evaluate side-chains 93 residues out of total 2818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 106 optimal weight: 8.9990 chunk 14 optimal weight: 0.6980 chunk 261 optimal weight: 20.0000 chunk 32 optimal weight: 0.0570 chunk 117 optimal weight: 6.9990 chunk 78 optimal weight: 0.9980 chunk 197 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 278 optimal weight: 0.9980 chunk 143 optimal weight: 9.9990 overall best weight: 1.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 HIS ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN B 953 ASN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN D1048 HIS ** E 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 501 ASN E 784 GLN ** E1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.057350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.046031 restraints weight = 250514.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.046965 restraints weight = 120846.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.047624 restraints weight = 64846.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.047888 restraints weight = 37481.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.048001 restraints weight = 31002.129| |-----------------------------------------------------------------------------| r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.4722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 26195 Z= 0.123 Angle : 0.579 9.200 35698 Z= 0.296 Chirality : 0.045 0.229 4111 Planarity : 0.004 0.054 4571 Dihedral : 5.854 58.638 3949 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.98 % Favored : 95.96 % Rotamer: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.72 (0.15), residues: 3190 helix: 1.66 (0.21), residues: 653 sheet: -0.65 (0.18), residues: 741 loop : -1.24 (0.14), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 67 TYR 0.020 0.001 TYR G 33 PHE 0.025 0.001 PHE E 759 TRP 0.011 0.001 TRP D 104 HIS 0.005 0.001 HIS D1083 Details of bonding type rmsd covalent geometry : bond 0.00268 (26130) covalent geometry : angle 0.56714 (35551) SS BOND : bond 0.00386 ( 39) SS BOND : angle 1.67881 ( 78) hydrogen bonds : bond 0.03662 ( 1076) hydrogen bonds : angle 5.22785 ( 2979) Misc. bond : bond 0.00037 ( 3) link_NAG-ASN : bond 0.00268 ( 23) link_NAG-ASN : angle 2.07628 ( 69) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 2818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 697 MET cc_start: 0.8637 (ppp) cc_final: 0.8410 (ppp) REVERT: B 731 MET cc_start: 0.9606 (ptp) cc_final: 0.9227 (ptp) REVERT: B 740 MET cc_start: 0.9198 (mtp) cc_final: 0.8909 (mtp) REVERT: B 867 ASP cc_start: 0.9167 (p0) cc_final: 0.8536 (t0) REVERT: B 869 MET cc_start: 0.9565 (mtm) cc_final: 0.9138 (mtp) REVERT: B 902 MET cc_start: 0.9828 (mmm) cc_final: 0.9409 (mmp) REVERT: B 1018 ILE cc_start: 0.9839 (mm) cc_final: 0.9526 (tp) REVERT: D 104 TRP cc_start: 0.9150 (m-90) cc_final: 0.8919 (m-90) REVERT: D 277 LEU cc_start: 0.9717 (mp) cc_final: 0.9137 (tt) REVERT: D 387 LEU cc_start: 0.8771 (pp) cc_final: 0.8210 (mt) REVERT: D 731 MET cc_start: 0.9302 (ppp) cc_final: 0.8816 (ppp) REVERT: D 742 ILE cc_start: 0.9787 (mt) cc_final: 0.9535 (tp) REVERT: E 270 LEU cc_start: 0.9568 (mt) cc_final: 0.9355 (tp) REVERT: E 697 MET cc_start: 0.6874 (ptp) cc_final: 0.6485 (ptp) REVERT: E 770 ILE cc_start: 0.9771 (mt) cc_final: 0.9397 (mt) REVERT: E 773 GLU cc_start: 0.9261 (pt0) cc_final: 0.8881 (pp20) REVERT: E 869 MET cc_start: 0.9502 (mtt) cc_final: 0.9230 (mtt) REVERT: E 902 MET cc_start: 0.9644 (mmm) cc_final: 0.9329 (mmp) REVERT: E 1002 GLN cc_start: 0.9368 (tm-30) cc_final: 0.9128 (tm-30) REVERT: E 1062 PHE cc_start: 0.9576 (m-80) cc_final: 0.9300 (m-10) REVERT: I 35 TRP cc_start: 0.6886 (m100) cc_final: 0.6401 (m100) REVERT: I 47 MET cc_start: 0.8316 (mmp) cc_final: 0.8008 (mmm) REVERT: I 48 ILE cc_start: 0.8436 (mt) cc_final: 0.8039 (mt) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.1625 time to fit residues: 35.5680 Evaluate side-chains 94 residues out of total 2818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 140 optimal weight: 6.9990 chunk 321 optimal weight: 20.0000 chunk 94 optimal weight: 0.7980 chunk 120 optimal weight: 3.9990 chunk 30 optimal weight: 20.0000 chunk 74 optimal weight: 5.9990 chunk 101 optimal weight: 6.9990 chunk 36 optimal weight: 20.0000 chunk 102 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 171 optimal weight: 8.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 564 GLN ** D 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1002 GLN E 125 ASN ** E 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 655 HIS E 784 GLN ** E 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.063516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.049933 restraints weight = 237625.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.050870 restraints weight = 140965.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.051526 restraints weight = 97795.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.051963 restraints weight = 74898.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.052317 restraints weight = 61589.669| |-----------------------------------------------------------------------------| r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.5208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 26195 Z= 0.231 Angle : 0.648 9.105 35698 Z= 0.335 Chirality : 0.044 0.205 4111 Planarity : 0.004 0.068 4571 Dihedral : 6.025 58.215 3949 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.67 % Favored : 94.26 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.89 (0.14), residues: 3190 helix: 1.53 (0.20), residues: 647 sheet: -0.77 (0.18), residues: 763 loop : -1.33 (0.14), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 190 TYR 0.026 0.002 TYR D 313 PHE 0.019 0.002 PHE B1052 TRP 0.019 0.002 TRP G 50 HIS 0.017 0.002 HIS E1048 Details of bonding type rmsd covalent geometry : bond 0.00474 (26130) covalent geometry : angle 0.63670 (35551) SS BOND : bond 0.00441 ( 39) SS BOND : angle 1.82649 ( 78) hydrogen bonds : bond 0.03981 ( 1076) hydrogen bonds : angle 5.50696 ( 2979) Misc. bond : bond 0.00085 ( 3) link_NAG-ASN : bond 0.00370 ( 23) link_NAG-ASN : angle 2.11384 ( 69) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 2818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 731 MET cc_start: 0.9675 (ptp) cc_final: 0.9282 (ptp) REVERT: B 867 ASP cc_start: 0.9256 (p0) cc_final: 0.8616 (t0) REVERT: B 869 MET cc_start: 0.9596 (mtm) cc_final: 0.9126 (mtp) REVERT: B 902 MET cc_start: 0.9839 (mmm) cc_final: 0.9418 (mmp) REVERT: B 1018 ILE cc_start: 0.9869 (mm) cc_final: 0.9570 (tp) REVERT: D 277 LEU cc_start: 0.9730 (mp) cc_final: 0.9193 (tt) REVERT: D 387 LEU cc_start: 0.8837 (pp) cc_final: 0.8285 (mt) REVERT: D 731 MET cc_start: 0.9247 (ppp) cc_final: 0.8726 (ppp) REVERT: D 742 ILE cc_start: 0.9823 (mt) cc_final: 0.9566 (tp) REVERT: D 776 LYS cc_start: 0.9872 (tttt) cc_final: 0.9475 (ptmm) REVERT: D 780 GLU cc_start: 0.9528 (mt-10) cc_final: 0.9323 (mm-30) REVERT: E 495 TYR cc_start: 0.5187 (m-10) cc_final: 0.4800 (m-80) REVERT: E 697 MET cc_start: 0.7232 (ptp) cc_final: 0.6915 (ptp) REVERT: E 740 MET cc_start: 0.8842 (tpt) cc_final: 0.8597 (tpp) REVERT: E 869 MET cc_start: 0.9545 (mtt) cc_final: 0.9178 (mtt) REVERT: E 902 MET cc_start: 0.9591 (mmm) cc_final: 0.9303 (mmp) REVERT: E 1029 MET cc_start: 0.9566 (ttt) cc_final: 0.9095 (tpp) REVERT: E 1062 PHE cc_start: 0.9473 (m-80) cc_final: 0.9142 (m-10) REVERT: G 67 ARG cc_start: 0.5064 (tpt-90) cc_final: 0.4840 (tpt-90) REVERT: I 35 TRP cc_start: 0.6639 (m100) cc_final: 0.6218 (m100) REVERT: I 48 ILE cc_start: 0.8285 (mt) cc_final: 0.7884 (mt) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.1523 time to fit residues: 28.8333 Evaluate side-chains 89 residues out of total 2818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 316 optimal weight: 40.0000 chunk 302 optimal weight: 9.9990 chunk 172 optimal weight: 1.9990 chunk 227 optimal weight: 20.0000 chunk 230 optimal weight: 20.0000 chunk 293 optimal weight: 9.9990 chunk 118 optimal weight: 4.9990 chunk 312 optimal weight: 30.0000 chunk 61 optimal weight: 8.9990 chunk 6 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1048 HIS ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 207 HIS E 501 ASN ** E 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.052842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.041674 restraints weight = 261114.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.042421 restraints weight = 124447.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.042991 restraints weight = 69244.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.043233 restraints weight = 42587.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.043299 restraints weight = 34412.916| |-----------------------------------------------------------------------------| r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.5988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.126 26195 Z= 0.295 Angle : 0.747 14.633 35698 Z= 0.387 Chirality : 0.046 0.275 4111 Planarity : 0.005 0.057 4571 Dihedral : 6.669 59.457 3949 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 20.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.05 % Favored : 92.88 % Rotamer: Outliers : 0.04 % Allowed : 1.60 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.32 (0.14), residues: 3190 helix: 0.85 (0.20), residues: 659 sheet: -0.99 (0.18), residues: 736 loop : -1.51 (0.14), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 190 TYR 0.033 0.002 TYR D 313 PHE 0.023 0.002 PHE E 342 TRP 0.015 0.002 TRP E 886 HIS 0.011 0.002 HIS E1048 Details of bonding type rmsd covalent geometry : bond 0.00595 (26130) covalent geometry : angle 0.73496 (35551) SS BOND : bond 0.00879 ( 39) SS BOND : angle 1.99177 ( 78) hydrogen bonds : bond 0.04438 ( 1076) hydrogen bonds : angle 6.05454 ( 2979) Misc. bond : bond 0.00102 ( 3) link_NAG-ASN : bond 0.00465 ( 23) link_NAG-ASN : angle 2.36208 ( 69) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 2818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 105 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 697 MET cc_start: 0.8811 (ppp) cc_final: 0.8452 (ppp) REVERT: B 731 MET cc_start: 0.9560 (ptp) cc_final: 0.9217 (ptp) REVERT: B 740 MET cc_start: 0.9166 (mtp) cc_final: 0.8950 (mtp) REVERT: B 869 MET cc_start: 0.9593 (mtm) cc_final: 0.9109 (mtp) REVERT: B 902 MET cc_start: 0.9876 (mmm) cc_final: 0.9470 (mmp) REVERT: B 1062 PHE cc_start: 0.9649 (m-10) cc_final: 0.9426 (m-10) REVERT: D 104 TRP cc_start: 0.9253 (m-90) cc_final: 0.9045 (m-90) REVERT: D 277 LEU cc_start: 0.9694 (mp) cc_final: 0.9147 (tt) REVERT: D 613 GLN cc_start: 0.9450 (mt0) cc_final: 0.9174 (mp10) REVERT: D 731 MET cc_start: 0.9242 (ppp) cc_final: 0.8720 (ppp) REVERT: D 742 ILE cc_start: 0.9792 (mt) cc_final: 0.9565 (tp) REVERT: E 495 TYR cc_start: 0.5003 (m-10) cc_final: 0.4642 (m-80) REVERT: E 740 MET cc_start: 0.8833 (tpt) cc_final: 0.8622 (tpt) REVERT: E 902 MET cc_start: 0.9621 (mmm) cc_final: 0.9374 (mmp) REVERT: E 1029 MET cc_start: 0.9611 (ttt) cc_final: 0.9144 (tpp) REVERT: E 1062 PHE cc_start: 0.9541 (m-80) cc_final: 0.9272 (m-10) REVERT: I 47 MET cc_start: 0.8319 (mmp) cc_final: 0.8087 (mmm) outliers start: 1 outliers final: 0 residues processed: 106 average time/residue: 0.1425 time to fit residues: 26.2156 Evaluate side-chains 77 residues out of total 2818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 61 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 chunk 39 optimal weight: 20.0000 chunk 273 optimal weight: 0.9990 chunk 282 optimal weight: 9.9990 chunk 125 optimal weight: 8.9990 chunk 179 optimal weight: 3.9990 chunk 30 optimal weight: 9.9990 chunk 59 optimal weight: 0.4980 chunk 246 optimal weight: 20.0000 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 HIS ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** D 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 501 ASN ** E 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.055910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.044604 restraints weight = 254106.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.045531 restraints weight = 118753.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.046078 restraints weight = 64011.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.046328 restraints weight = 38717.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.046406 restraints weight = 31913.220| |-----------------------------------------------------------------------------| r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.5783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 26195 Z= 0.138 Angle : 0.608 9.873 35698 Z= 0.314 Chirality : 0.045 0.221 4111 Planarity : 0.004 0.058 4571 Dihedral : 6.157 59.565 3949 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.83 % Favored : 95.11 % Rotamer: Outliers : 0.04 % Allowed : 0.46 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.93 (0.15), residues: 3190 helix: 1.35 (0.20), residues: 662 sheet: -0.81 (0.17), residues: 779 loop : -1.32 (0.15), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B1014 TYR 0.031 0.002 TYR G 60 PHE 0.038 0.001 PHE B 970 TRP 0.012 0.001 TRP D 104 HIS 0.009 0.001 HIS E 207 Details of bonding type rmsd covalent geometry : bond 0.00301 (26130) covalent geometry : angle 0.59684 (35551) SS BOND : bond 0.00402 ( 39) SS BOND : angle 1.79234 ( 78) hydrogen bonds : bond 0.03888 ( 1076) hydrogen bonds : angle 5.50264 ( 2979) Misc. bond : bond 0.00055 ( 3) link_NAG-ASN : bond 0.00258 ( 23) link_NAG-ASN : angle 1.96184 ( 69) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 2818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 117 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 740 MET cc_start: 0.9144 (mtp) cc_final: 0.8874 (mtp) REVERT: B 867 ASP cc_start: 0.9123 (p0) cc_final: 0.8524 (t0) REVERT: B 869 MET cc_start: 0.9519 (mtm) cc_final: 0.9080 (mtp) REVERT: B 902 MET cc_start: 0.9830 (mmm) cc_final: 0.9419 (mmp) REVERT: B 1018 ILE cc_start: 0.9907 (mm) cc_final: 0.9591 (tp) REVERT: D 104 TRP cc_start: 0.9253 (m-90) cc_final: 0.9002 (m-90) REVERT: D 277 LEU cc_start: 0.9709 (mp) cc_final: 0.9123 (tt) REVERT: D 387 LEU cc_start: 0.8930 (pp) cc_final: 0.8214 (mt) REVERT: D 613 GLN cc_start: 0.9369 (mt0) cc_final: 0.9122 (mp10) REVERT: D 731 MET cc_start: 0.9275 (ppp) cc_final: 0.8793 (ppp) REVERT: D 742 ILE cc_start: 0.9768 (mt) cc_final: 0.9499 (tp) REVERT: D 776 LYS cc_start: 0.9861 (tttt) cc_final: 0.9552 (ptmm) REVERT: E 118 LEU cc_start: 0.9672 (tp) cc_final: 0.9460 (mp) REVERT: E 495 TYR cc_start: 0.4907 (m-10) cc_final: 0.4637 (m-80) REVERT: E 697 MET cc_start: 0.6948 (ptp) cc_final: 0.6599 (ptp) REVERT: E 740 MET cc_start: 0.8818 (tpt) cc_final: 0.8495 (tpp) REVERT: E 770 ILE cc_start: 0.9767 (mt) cc_final: 0.9377 (mt) REVERT: E 773 GLU cc_start: 0.9217 (pt0) cc_final: 0.8837 (pp20) REVERT: E 869 MET cc_start: 0.9492 (mtm) cc_final: 0.9252 (mtt) REVERT: E 902 MET cc_start: 0.9618 (mmm) cc_final: 0.9322 (mmp) REVERT: E 1029 MET cc_start: 0.9561 (ttt) cc_final: 0.9236 (tpp) REVERT: G 67 ARG cc_start: 0.4868 (tpt-90) cc_final: 0.4543 (tpt-90) outliers start: 1 outliers final: 0 residues processed: 118 average time/residue: 0.1481 time to fit residues: 30.0822 Evaluate side-chains 92 residues out of total 2818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 188 optimal weight: 6.9990 chunk 246 optimal weight: 0.9990 chunk 253 optimal weight: 4.9990 chunk 166 optimal weight: 8.9990 chunk 316 optimal weight: 0.7980 chunk 151 optimal weight: 0.6980 chunk 214 optimal weight: 6.9990 chunk 104 optimal weight: 9.9990 chunk 185 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 182 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 501 ASN E 751 ASN E 784 GLN E 901 GLN ** E 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.057049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.045690 restraints weight = 251532.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.046609 restraints weight = 119787.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.047238 restraints weight = 65682.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.047504 restraints weight = 38223.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.047626 restraints weight = 31235.386| |-----------------------------------------------------------------------------| r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.5682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 26195 Z= 0.113 Angle : 0.580 9.458 35698 Z= 0.298 Chirality : 0.045 0.253 4111 Planarity : 0.004 0.056 4571 Dihedral : 5.753 58.299 3949 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.70 % Favored : 95.24 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.73 (0.15), residues: 3190 helix: 1.54 (0.21), residues: 667 sheet: -0.70 (0.17), residues: 798 loop : -1.21 (0.15), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E1039 TYR 0.025 0.001 TYR D 313 PHE 0.024 0.001 PHE B 970 TRP 0.013 0.001 TRP D 104 HIS 0.006 0.001 HIS I 39 Details of bonding type rmsd covalent geometry : bond 0.00246 (26130) covalent geometry : angle 0.57116 (35551) SS BOND : bond 0.00320 ( 39) SS BOND : angle 1.57761 ( 78) hydrogen bonds : bond 0.03668 ( 1076) hydrogen bonds : angle 5.21218 ( 2979) Misc. bond : bond 0.00042 ( 3) link_NAG-ASN : bond 0.00223 ( 23) link_NAG-ASN : angle 1.75378 ( 69) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 2818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 697 MET cc_start: 0.8704 (ppp) cc_final: 0.8483 (ppp) REVERT: B 740 MET cc_start: 0.9173 (mtp) cc_final: 0.8896 (mtp) REVERT: B 867 ASP cc_start: 0.9128 (p0) cc_final: 0.8511 (t0) REVERT: B 869 MET cc_start: 0.9503 (mtm) cc_final: 0.8979 (mtp) REVERT: B 902 MET cc_start: 0.9805 (mmm) cc_final: 0.9378 (mmp) REVERT: B 1018 ILE cc_start: 0.9908 (mm) cc_final: 0.9590 (tp) REVERT: D 104 TRP cc_start: 0.9177 (m-90) cc_final: 0.8953 (m-90) REVERT: D 277 LEU cc_start: 0.9722 (mp) cc_final: 0.9104 (tt) REVERT: D 387 LEU cc_start: 0.8888 (pp) cc_final: 0.8201 (mt) REVERT: D 731 MET cc_start: 0.9197 (ppp) cc_final: 0.8740 (ppp) REVERT: D 742 ILE cc_start: 0.9773 (mt) cc_final: 0.9493 (tp) REVERT: D 776 LYS cc_start: 0.9851 (tttt) cc_final: 0.9529 (ptmm) REVERT: E 118 LEU cc_start: 0.9655 (tp) cc_final: 0.9454 (mp) REVERT: E 495 TYR cc_start: 0.5038 (m-10) cc_final: 0.4721 (m-80) REVERT: E 740 MET cc_start: 0.8795 (tpt) cc_final: 0.8507 (tpp) REVERT: E 770 ILE cc_start: 0.9750 (mt) cc_final: 0.9362 (mm) REVERT: E 773 GLU cc_start: 0.9194 (pt0) cc_final: 0.8819 (pp20) REVERT: E 869 MET cc_start: 0.9463 (mtm) cc_final: 0.9201 (mtt) REVERT: E 902 MET cc_start: 0.9621 (mmm) cc_final: 0.9313 (mmp) REVERT: E 1029 MET cc_start: 0.9540 (ttt) cc_final: 0.9274 (tpp) REVERT: G 67 ARG cc_start: 0.4672 (tpt-90) cc_final: 0.4442 (tpt-90) REVERT: I 47 MET cc_start: 0.8288 (mmp) cc_final: 0.7974 (mmm) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.1553 time to fit residues: 32.3427 Evaluate side-chains 97 residues out of total 2818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 165 optimal weight: 8.9990 chunk 99 optimal weight: 2.9990 chunk 186 optimal weight: 0.9980 chunk 104 optimal weight: 10.0000 chunk 206 optimal weight: 0.3980 chunk 292 optimal weight: 6.9990 chunk 62 optimal weight: 8.9990 chunk 211 optimal weight: 9.9990 chunk 98 optimal weight: 6.9990 chunk 109 optimal weight: 20.0000 chunk 268 optimal weight: 5.9990 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.055110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.043984 restraints weight = 253499.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.044778 restraints weight = 109331.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.045309 restraints weight = 63890.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.045496 restraints weight = 40559.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.045639 restraints weight = 33323.415| |-----------------------------------------------------------------------------| r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.5914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 26195 Z= 0.177 Angle : 0.609 10.933 35698 Z= 0.315 Chirality : 0.044 0.215 4111 Planarity : 0.004 0.057 4571 Dihedral : 5.836 57.666 3949 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.92 % Favored : 94.01 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.76 (0.15), residues: 3190 helix: 1.51 (0.21), residues: 667 sheet: -0.66 (0.18), residues: 769 loop : -1.25 (0.15), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 408 TYR 0.024 0.002 TYR D 313 PHE 0.021 0.002 PHE B 970 TRP 0.012 0.002 TRP I 35 HIS 0.006 0.001 HIS E1048 Details of bonding type rmsd covalent geometry : bond 0.00370 (26130) covalent geometry : angle 0.60029 (35551) SS BOND : bond 0.00375 ( 39) SS BOND : angle 1.68386 ( 78) hydrogen bonds : bond 0.03801 ( 1076) hydrogen bonds : angle 5.35441 ( 2979) Misc. bond : bond 0.00072 ( 3) link_NAG-ASN : bond 0.00271 ( 23) link_NAG-ASN : angle 1.78650 ( 69) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3656.51 seconds wall clock time: 64 minutes 38.58 seconds (3878.58 seconds total)