Starting phenix.real_space_refine on Thu Mar 5 21:20:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vhj_31996/03_2026/7vhj_31996.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vhj_31996/03_2026/7vhj_31996.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vhj_31996/03_2026/7vhj_31996.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vhj_31996/03_2026/7vhj_31996.map" model { file = "/net/cci-nas-00/data/ceres_data/7vhj_31996/03_2026/7vhj_31996.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vhj_31996/03_2026/7vhj_31996.cif" } resolution = 4.2 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 16167 2.51 5 N 4220 2.21 5 O 4852 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 127 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: 25353 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 8485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1091, 8485 Classifications: {'peptide': 1091} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 54, 'TRANS': 1036} Chain breaks: 2 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 8457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1087, 8457 Classifications: {'peptide': 1087} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 53, 'TRANS': 1033} Chain breaks: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 8411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1079, 8411 Classifications: {'peptide': 1079} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 52, 'TRANS': 1026} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Time building chain proxies: 5.56, per 1000 atoms: 0.22 Number of scatterers: 25353 At special positions: 0 Unit cell: (154.96, 160.16, 192.4, 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 114 16.00 O 4852 8.00 N 4220 7.00 C 16167 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " 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 731 " - pdb=" SG CYS B 753 " distance=2.03 Simple disulfide: pdb=" SG CYS B 736 " - pdb=" SG CYS B 742 " distance=2.03 Simple disulfide: pdb=" SG CYS B1025 " - pdb=" SG CYS B1036 " distance=2.03 Simple disulfide: pdb=" SG CYS B1075 " - pdb=" SG CYS B1119 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 731 " - pdb=" SG CYS A 753 " distance=2.03 Simple disulfide: pdb=" SG CYS A 736 " - pdb=" SG CYS A 742 " distance=2.02 Simple disulfide: pdb=" SG CYS A1025 " - pdb=" SG CYS A1036 " distance=2.03 Simple disulfide: pdb=" SG CYS A1075 " - pdb=" SG CYS A1119 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 731 " - pdb=" SG CYS C 753 " distance=2.03 Simple disulfide: pdb=" SG CYS C 736 " - pdb=" SG CYS C 742 " distance=2.03 Simple disulfide: pdb=" SG CYS C1025 " - pdb=" SG CYS C1036 " distance=2.03 Simple disulfide: pdb=" SG CYS C1075 " - pdb=" SG CYS C1119 " 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=0, symmetry=0 Time building additional restraints: 1.97 Conformation dependent library (CDL) restraints added in 1.1 seconds 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6090 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 48 sheets defined 22.6% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'B' and resid 294 through 302 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.138A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 730 through 736 removed outlier: 3.813A pdb=" N TYR B 734 " --> pdb=" O ASP B 730 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ILE B 735 " --> pdb=" O CYS B 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 748 removed outlier: 3.760A pdb=" N ASN B 744 " --> pdb=" O THR B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 751 through 775 removed outlier: 3.740A pdb=" N ASN B 757 " --> pdb=" O CYS B 753 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE B 775 " --> pdb=" O THR B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 809 through 819 removed outlier: 3.506A pdb=" N LEU B 814 " --> pdb=" O PHE B 810 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 847 removed outlier: 3.842A pdb=" N LYS B 847 " --> pdb=" O ILE B 843 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 843 through 847' Processing helix chain 'B' and resid 848 through 850 No H-bonds generated for 'chain 'B' and resid 848 through 850' Processing helix chain 'B' and resid 859 through 876 Processing helix chain 'B' and resid 890 through 903 Processing helix chain 'B' and resid 906 through 912 removed outlier: 3.816A pdb=" N TYR B 910 " --> pdb=" O GLN B 906 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 934 removed outlier: 4.289A pdb=" N THR B 934 " --> pdb=" O SER B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 939 through 958 Processing helix chain 'B' and resid 959 through 961 No H-bonds generated for 'chain 'B' and resid 959 through 961' Processing helix chain 'B' and resid 969 through 977 Processing helix chain 'B' and resid 978 through 1026 removed outlier: 4.983A pdb=" N VAL B 984 " --> pdb=" O PRO B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 1133 through 1140 removed outlier: 4.273A pdb=" N GLU B1137 " --> pdb=" O PRO B1133 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N SER B1140 " --> pdb=" O PRO B1136 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 344 Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 383 through 388 removed outlier: 3.917A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 409 removed outlier: 4.006A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.638A pdb=" N GLN A 506 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 624 removed outlier: 4.259A pdb=" N VAL A 622 " --> pdb=" O THR A 618 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ILE A 624 " --> pdb=" O VAL A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 736 Processing helix chain 'A' and resid 739 through 748 Processing helix chain 'A' and resid 751 through 775 removed outlier: 3.898A pdb=" N PHE A 775 " --> pdb=" O THR A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 819 removed outlier: 4.089A pdb=" N LEU A 814 " --> pdb=" O PHE A 810 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU A 815 " --> pdb=" O ILE A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 848 removed outlier: 3.648A pdb=" N PHE A 848 " --> pdb=" O CYS A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 877 Processing helix chain 'A' and resid 879 through 884 Processing helix chain 'A' and resid 890 through 902 Processing helix chain 'A' and resid 905 through 912 removed outlier: 4.184A pdb=" N LEU A 909 " --> pdb=" O THR A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 934 removed outlier: 3.958A pdb=" N THR A 934 " --> pdb=" O SER A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 958 removed outlier: 4.145A pdb=" N GLN A 942 " --> pdb=" O LEU A 938 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 961 No H-bonds generated for 'chain 'A' and resid 959 through 961' Processing helix chain 'A' and resid 969 through 977 removed outlier: 3.868A pdb=" N SER A 975 " --> pdb=" O ASN A 971 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG A 976 " --> pdb=" O ASP A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 1025 removed outlier: 3.613A pdb=" N VAL A 984 " --> pdb=" O PRO A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1109 through 1113 Processing helix chain 'A' and resid 1134 through 1140 removed outlier: 3.717A pdb=" N SER A1140 " --> pdb=" O PRO A1136 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 405 through 408 removed outlier: 3.613A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 405 through 408' Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 730 through 735 Processing helix chain 'C' and resid 739 through 750 removed outlier: 3.643A pdb=" N GLY C 750 " --> pdb=" O LEU C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 751 through 776 Processing helix chain 'C' and resid 809 through 817 removed outlier: 3.956A pdb=" N ASN C 817 " --> pdb=" O ASP C 813 " (cutoff:3.500A) Processing helix chain 'C' and resid 859 through 877 Processing helix chain 'C' and resid 890 through 903 Processing helix chain 'C' and resid 905 through 934 removed outlier: 4.309A pdb=" N LEU C 909 " --> pdb=" O THR C 905 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LYS C 914 " --> pdb=" O TYR C 910 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU C 915 " --> pdb=" O GLU C 911 " (cutoff:3.500A) Processing helix chain 'C' and resid 938 through 958 removed outlier: 4.063A pdb=" N GLN C 942 " --> pdb=" O LEU C 938 " (cutoff:3.500A) Processing helix chain 'C' and resid 969 through 977 removed outlier: 3.529A pdb=" N ILE C 973 " --> pdb=" O VAL C 969 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG C 976 " --> pdb=" O ASP C 972 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 1025 removed outlier: 4.704A pdb=" N VAL C 984 " --> pdb=" O PRO C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1111 No H-bonds generated for 'chain 'C' and resid 1109 through 1111' Processing sheet with id=AA1, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.942A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 55 removed outlier: 4.104A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.759A pdb=" N ARG B 237 " --> pdb=" O GLY B 107 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 152 through 158 removed outlier: 6.477A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 313 through 317 removed outlier: 5.320A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL B 610 " --> pdb=" O ILE B 651 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE B 643 " --> pdb=" O LEU B 650 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 324 through 328 removed outlier: 6.478A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 354 through 358 removed outlier: 5.575A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'B' and resid 654 through 660 removed outlier: 3.741A pdb=" N VAL B 656 " --> pdb=" O ALA B 687 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N THR B 689 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ASN B 658 " --> pdb=" O THR B 689 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 704 through 708 Processing sheet with id=AB2, first strand: chain 'B' and resid 711 through 713 removed outlier: 3.611A pdb=" N MET B1043 " --> pdb=" O VAL B1058 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N TYR B1060 " --> pdb=" O HIS B1041 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N HIS B1041 " --> pdb=" O TYR B1060 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 716 through 720 Processing sheet with id=AB4, first strand: chain 'B' and resid 781 through 783 removed outlier: 5.791A pdb=" N ILE B 781 " --> pdb=" O ASN A 696 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 1113 through 1116 removed outlier: 4.017A pdb=" N CYS B1075 " --> pdb=" O VAL B1126 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 1089 through 1090 Processing sheet with id=AB7, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.543A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.535A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR A 266 " --> pdb=" O ALA A 93 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLY A 89 " --> pdb=" O LEU A 270 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.735A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AC1, first strand: chain 'A' and resid 101 through 103 removed outlier: 6.590A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 118 through 120 removed outlier: 3.671A pdb=" N TYR A 170 " --> pdb=" O ILE A 128 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 142 through 145 removed outlier: 5.823A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 314 through 317 removed outlier: 6.418A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL A 595 " --> pdb=" O SER A 316 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 327 through 328 removed outlier: 3.713A pdb=" N ARG A 328 " --> pdb=" O ASN A 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.771A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 376 through 378 Processing sheet with id=AC8, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AC9, first strand: chain 'A' and resid 551 through 553 removed outlier: 5.623A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.715A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE A 664 " --> pdb=" O ALA A 672 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 704 through 720 removed outlier: 3.525A pdb=" N ILE A 707 " --> pdb=" O LYS A1066 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS A1066 " --> pdb=" O ILE A 707 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLN A1064 " --> pdb=" O THR A 709 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N PHE A 711 " --> pdb=" O PRO A1062 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE A 713 " --> pdb=" O TYR A1060 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N TYR A1060 " --> pdb=" O ILE A 713 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL A 715 " --> pdb=" O VAL A1058 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL A1058 " --> pdb=" O VAL A 715 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR A 717 " --> pdb=" O LEU A1056 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU A1056 " --> pdb=" O THR A 717 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ILE A 719 " --> pdb=" O VAL A1054 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL A1054 " --> pdb=" O ILE A 719 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N MET A1043 " --> pdb=" O VAL A1058 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N TYR A1060 " --> pdb=" O HIS A1041 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N HIS A1041 " --> pdb=" O TYR A1060 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 704 through 720 removed outlier: 3.525A pdb=" N ILE A 707 " --> pdb=" O LYS A1066 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS A1066 " --> pdb=" O ILE A 707 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLN A1064 " --> pdb=" O THR A 709 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N PHE A 711 " --> pdb=" O PRO A1062 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE A 713 " --> pdb=" O TYR A1060 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N TYR A1060 " --> pdb=" O ILE A 713 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL A 715 " --> pdb=" O VAL A1058 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL A1058 " --> pdb=" O VAL A 715 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR A 717 " --> pdb=" O LEU A1056 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU A1056 " --> pdb=" O THR A 717 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ILE A 719 " --> pdb=" O VAL A1054 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL A1054 " --> pdb=" O ILE A 719 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N PHE A1088 " --> pdb=" O ALA A1071 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 727 through 729 removed outlier: 3.828A pdb=" N SER A 728 " --> pdb=" O THR A 852 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 1080 through 1081 Processing sheet with id=AD6, first strand: chain 'C' and resid 28 through 30 removed outlier: 5.078A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 48 through 53 removed outlier: 3.560A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD9, first strand: chain 'C' and resid 141 through 145 removed outlier: 6.640A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 317 removed outlier: 3.768A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR C 313 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL C 597 " --> pdb=" O TYR C 313 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR C 315 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 325 through 327 removed outlier: 5.888A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 356 through 358 Processing sheet with id=AE4, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AE5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'C' and resid 551 through 554 Processing sheet with id=AE7, first strand: chain 'C' and resid 655 through 656 removed outlier: 8.040A pdb=" N VAL C 656 " --> pdb=" O ILE C 685 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ALA C 687 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 704 through 713 removed outlier: 6.919A pdb=" N SER C 704 " --> pdb=" O THR C1069 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N THR C1069 " --> pdb=" O SER C 704 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA C 706 " --> pdb=" O ASN C1067 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ASN C1067 " --> pdb=" O ALA C 706 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N GLU C1065 " --> pdb=" O PRO C 708 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ASN C 710 " --> pdb=" O ALA C1063 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 704 through 713 removed outlier: 6.919A pdb=" N SER C 704 " --> pdb=" O THR C1069 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N THR C1069 " --> pdb=" O SER C 704 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA C 706 " --> pdb=" O ASN C1067 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ASN C1067 " --> pdb=" O ALA C 706 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N GLU C1065 " --> pdb=" O PRO C 708 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ASN C 710 " --> pdb=" O ALA C1063 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLY C1052 " --> pdb=" O SER C1048 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N SER C1048 " --> pdb=" O GLY C1052 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL C1054 " --> pdb=" O PRO C1046 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU C1056 " --> pdb=" O SER C1044 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N SER C1044 " --> pdb=" O LEU C1056 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL C1058 " --> pdb=" O LEU C1042 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR C1040 " --> pdb=" O TYR C1060 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1074 through 1075 Processing sheet with id=AF2, first strand: chain 'C' and resid 1082 through 1083 Processing sheet with id=AF3, first strand: chain 'C' and resid 1087 through 1089 868 hydrogen bonds defined for protein. 2403 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.20 Time building geometry restraints manager: 2.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8217 1.34 - 1.46: 6265 1.46 - 1.58: 11324 1.58 - 1.70: 0 1.70 - 1.82: 144 Bond restraints: 25950 Sorted by residual: bond pdb=" C ALA C1071 " pdb=" N PRO C1072 " ideal model delta sigma weight residual 1.337 1.323 0.014 9.80e-03 1.04e+04 2.02e+00 bond pdb=" C THR A 588 " pdb=" O THR A 588 " ideal model delta sigma weight residual 1.249 1.237 0.012 8.50e-03 1.38e+04 1.86e+00 bond pdb=" CB CYS C 525 " pdb=" SG CYS C 525 " ideal model delta sigma weight residual 1.808 1.765 0.043 3.30e-02 9.18e+02 1.71e+00 bond pdb=" C ASP C1132 " pdb=" N PRO C1133 " ideal model delta sigma weight residual 1.336 1.323 0.013 9.80e-03 1.04e+04 1.70e+00 bond pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " ideal model delta sigma weight residual 1.808 1.767 0.041 3.30e-02 9.18e+02 1.56e+00 ... (remaining 25945 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 34359 1.62 - 3.25: 845 3.25 - 4.87: 104 4.87 - 6.49: 31 6.49 - 8.12: 7 Bond angle restraints: 35346 Sorted by residual: angle pdb=" C ILE A 587 " pdb=" N THR A 588 " pdb=" CA THR A 588 " ideal model delta sigma weight residual 122.64 118.86 3.78 1.25e+00 6.40e-01 9.15e+00 angle pdb=" N GLN A 173 " pdb=" CA GLN A 173 " pdb=" C GLN A 173 " ideal model delta sigma weight residual 108.97 114.12 -5.15 1.82e+00 3.02e-01 7.99e+00 angle pdb=" N PRO C 979 " pdb=" CA PRO C 979 " pdb=" C PRO C 979 " ideal model delta sigma weight residual 110.70 113.91 -3.21 1.22e+00 6.72e-01 6.91e+00 angle pdb=" C LYS C 847 " pdb=" N PHE C 848 " pdb=" CA PHE C 848 " ideal model delta sigma weight residual 121.54 126.56 -5.02 1.91e+00 2.74e-01 6.90e+00 angle pdb=" CA TRP B 64 " pdb=" CB TRP B 64 " pdb=" CG TRP B 64 " ideal model delta sigma weight residual 113.60 118.49 -4.89 1.90e+00 2.77e-01 6.62e+00 ... (remaining 35341 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 14004 17.59 - 35.18: 1220 35.18 - 52.77: 163 52.77 - 70.35: 35 70.35 - 87.94: 20 Dihedral angle restraints: 15442 sinusoidal: 5961 harmonic: 9481 Sorted by residual: dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 1.29 -87.29 1 1.00e+01 1.00e-02 9.15e+01 dihedral pdb=" CB CYS A 731 " pdb=" SG CYS A 731 " pdb=" SG CYS A 753 " pdb=" CB CYS A 753 " ideal model delta sinusoidal sigma weight residual -86.00 -6.80 -79.20 1 1.00e+01 1.00e-02 7.80e+01 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -8.34 -77.66 1 1.00e+01 1.00e-02 7.55e+01 ... (remaining 15439 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2871 0.042 - 0.084: 838 0.084 - 0.126: 279 0.126 - 0.168: 18 0.168 - 0.210: 2 Chirality restraints: 4008 Sorted by residual: chirality pdb=" CA CYS A 617 " pdb=" N CYS A 617 " pdb=" C CYS A 617 " pdb=" CB CYS A 617 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CB ILE C 101 " pdb=" CA ILE C 101 " pdb=" CG1 ILE C 101 " pdb=" CG2 ILE C 101 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.28e-01 chirality pdb=" CB ILE C 410 " pdb=" CA ILE C 410 " pdb=" CG1 ILE C 410 " pdb=" CG2 ILE C 410 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.68e-01 ... (remaining 4005 not shown) Planarity restraints: 4596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 560 " -0.028 5.00e-02 4.00e+02 4.27e-02 2.91e+00 pdb=" N PRO C 561 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO C 561 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 561 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 173 " -0.028 5.00e-02 4.00e+02 4.19e-02 2.81e+00 pdb=" N PRO A 174 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 174 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 174 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 520 " 0.028 5.00e-02 4.00e+02 4.18e-02 2.79e+00 pdb=" N PRO B 521 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 521 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 521 " 0.023 5.00e-02 4.00e+02 ... (remaining 4593 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 585 2.67 - 3.23: 26054 3.23 - 3.78: 39097 3.78 - 4.34: 52634 4.34 - 4.90: 84240 Nonbonded interactions: 202610 Sorted by model distance: nonbonded pdb=" O LEU A 959 " pdb=" OG SER A 968 " model vdw 2.109 3.040 nonbonded pdb=" OH TYR C 749 " pdb=" OD1 ASP C 987 " model vdw 2.120 3.040 nonbonded pdb=" OG1 THR B 376 " pdb=" O ALA B 435 " model vdw 2.125 3.040 nonbonded pdb=" O VAL B1033 " pdb=" OG SER C1023 " model vdw 2.154 3.040 nonbonded pdb=" NH1 ARG B 898 " pdb=" O LEU B1042 " model vdw 2.155 3.120 ... (remaining 202605 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 332 or (resid 333 and (name N or name CA or nam \ e C or name O or name CB )) or resid 334 through 465 or (resid 466 and (name N o \ r name CA or name C or name O or name CB )) or resid 467 through 527 or (resid 5 \ 28 through 529 and (name N or name CA or name C or name O or name CB )) or resid \ 530 through 553 or (resid 554 and (name N or name CA or name C or name O or nam \ e CB )) or resid 555 through 582 or (resid 583 and (name N or name CA or name C \ or name O or name CB )) or resid 584 through 621 or resid 640 through 645 or (re \ sid 646 through 647 and (name N or name CA or name C or name O or name CB )) or \ resid 648 through 820 or resid 845 through 1140)) selection = (chain 'B' and (resid 27 through 416 or (resid 417 and (name N or name CA or nam \ e C or name O or name CB )) or resid 418 through 423 or (resid 424 and (name N o \ r name CA or name C or name O or name CB )) or resid 425 through 453 or (resid 4 \ 54 and (name N or name CA or name C or name O or name CB )) or resid 455 through \ 456 or (resid 457 and (name N or name CA or name C or name O or name CB )) or r \ esid 458 through 465 or (resid 466 and (name N or name CA or name C or name O or \ name CB )) or resid 467 through 621 or resid 640 through 645 or (resid 646 thro \ ugh 647 and (name N or name CA or name C or name O or name CB )) or resid 648 th \ rough 820 or resid 845 through 1140)) selection = (chain 'C' and (resid 27 through 332 or (resid 333 and (name N or name CA or nam \ e C or name O or name CB )) or resid 334 through 416 or (resid 417 and (name N o \ r name CA or name C or name O or name CB )) or resid 418 through 423 or (resid 4 \ 24 and (name N or name CA or name C or name O or name CB )) or resid 425 through \ 453 or (resid 454 and (name N or name CA or name C or name O or name CB )) or r \ esid 455 through 456 or (resid 457 and (name N or name CA or name C or name O or \ name CB )) or resid 458 through 527 or (resid 528 through 529 and (name N or na \ me CA or name C or name O or name CB )) or resid 530 through 553 or (resid 554 a \ nd (name N or name CA or name C or name O or name CB )) or resid 555 through 582 \ or (resid 583 and (name N or name CA or name C or name O or name CB )) or resid \ 584 through 621 or resid 640 through 1099 or (resid 1100 and (name N or name CA \ or name C or name O or name CB )) or resid 1101 through 1140)) } 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: 2.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 22.160 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.050 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 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 : 0.004 0.047 25989 Z= 0.186 Angle : 0.651 8.118 35424 Z= 0.361 Chirality : 0.044 0.210 4008 Planarity : 0.004 0.043 4596 Dihedral : 13.111 87.943 9235 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 0.07 % Allowed : 4.64 % Favored : 95.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.85 (0.12), residues: 3239 helix: -1.73 (0.17), residues: 667 sheet: -2.15 (0.19), residues: 634 loop : -3.15 (0.12), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 403 TYR 0.019 0.002 TYR B 351 PHE 0.025 0.002 PHE C 899 TRP 0.017 0.001 TRP A 633 HIS 0.011 0.001 HIS B1041 Details of bonding type rmsd covalent geometry : bond 0.00399 (25950) covalent geometry : angle 0.64581 (35346) SS BOND : bond 0.00336 ( 39) SS BOND : angle 1.88352 ( 78) hydrogen bonds : bond 0.15065 ( 862) hydrogen bonds : angle 7.75380 ( 2403) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 342 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 122 ASN cc_start: 0.6300 (p0) cc_final: 0.5140 (m-40) REVERT: B 135 PHE cc_start: 0.7154 (m-10) cc_final: 0.6280 (m-80) REVERT: B 153 MET cc_start: 0.7837 (mtt) cc_final: 0.6955 (tpp) REVERT: B 374 PHE cc_start: 0.6647 (m-10) cc_final: 0.6368 (m-10) REVERT: B 408 ARG cc_start: 0.8175 (ptt90) cc_final: 0.7954 (ptt-90) REVERT: B 862 MET cc_start: 0.8306 (ptp) cc_final: 0.7836 (ptp) REVERT: B 958 GLN cc_start: 0.8666 (mm-40) cc_final: 0.8395 (tt0) REVERT: B 986 ILE cc_start: 0.9296 (mm) cc_final: 0.9013 (mt) REVERT: A 30 ASN cc_start: 0.7892 (t0) cc_final: 0.7502 (m110) REVERT: A 190 ARG cc_start: 0.5731 (mtt180) cc_final: 0.5527 (mtt180) REVERT: A 195 LYS cc_start: 0.8524 (pttt) cc_final: 0.8283 (pttt) REVERT: A 449 TYR cc_start: 0.5651 (m-80) cc_final: 0.5062 (m-10) REVERT: A 516 GLU cc_start: 0.7437 (pm20) cc_final: 0.6676 (pm20) REVERT: A 569 ILE cc_start: 0.8103 (tt) cc_final: 0.7657 (tp) REVERT: A 733 MET cc_start: 0.8650 (tpp) cc_final: 0.8196 (tpt) REVERT: A 767 GLN cc_start: 0.8668 (mm-40) cc_final: 0.8424 (mt0) REVERT: A 881 PHE cc_start: 0.8160 (p90) cc_final: 0.7887 (p90) REVERT: C 129 LYS cc_start: 0.8656 (pttp) cc_final: 0.8378 (pttp) REVERT: C 141 LEU cc_start: 0.8069 (tp) cc_final: 0.7849 (tp) REVERT: C 402 ILE cc_start: 0.8730 (mm) cc_final: 0.8521 (mm) REVERT: C 995 GLN cc_start: 0.8033 (tt0) cc_final: 0.7824 (tp40) outliers start: 2 outliers final: 1 residues processed: 344 average time/residue: 0.1703 time to fit residues: 91.7098 Evaluate side-chains 176 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 175 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 0.5980 chunk 298 optimal weight: 0.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 HIS ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 245 HIS B 271 GLN B 394 ASN B 474 GLN B 865 GLN ** B 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 921 ASN ** B 948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 962 ASN B1135 GLN A 49 HIS A 66 HIS A 125 ASN ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 ASN A 188 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS A 282 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 894 GLN ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN C 121 ASN ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN C 314 GLN C 414 GLN C 544 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 928 GLN ** C 998 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1057 HIS C1064 GLN C1076 HIS Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.098417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.077593 restraints weight = 85915.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.077488 restraints weight = 69015.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.077935 restraints weight = 52247.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.078355 restraints weight = 43732.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.078472 restraints weight = 39810.734| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 25989 Z= 0.155 Angle : 0.615 8.397 35424 Z= 0.326 Chirality : 0.044 0.178 4008 Planarity : 0.004 0.044 4596 Dihedral : 5.229 24.413 3493 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 0.11 % Allowed : 5.63 % Favored : 94.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.73 (0.13), residues: 3239 helix: -0.19 (0.19), residues: 673 sheet: -1.67 (0.19), residues: 636 loop : -2.59 (0.13), residues: 1930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 102 TYR 0.016 0.002 TYR A 473 PHE 0.021 0.002 PHE C 157 TRP 0.020 0.001 TRP B 64 HIS 0.008 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00350 (25950) covalent geometry : angle 0.60961 (35346) SS BOND : bond 0.00587 ( 39) SS BOND : angle 1.78492 ( 78) hydrogen bonds : bond 0.04522 ( 862) hydrogen bonds : angle 6.15692 ( 2403) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 301 time to evaluate : 0.959 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 153 MET cc_start: 0.7642 (mtt) cc_final: 0.6717 (tpp) REVERT: B 425 LEU cc_start: 0.6565 (mt) cc_final: 0.6102 (mp) REVERT: B 582 LEU cc_start: 0.8230 (mt) cc_final: 0.7806 (pp) REVERT: B 958 GLN cc_start: 0.8646 (mm-40) cc_final: 0.8103 (tp-100) REVERT: B 986 ILE cc_start: 0.9390 (mm) cc_final: 0.9084 (mt) REVERT: A 195 LYS cc_start: 0.8612 (pttt) cc_final: 0.8354 (pttt) REVERT: A 449 TYR cc_start: 0.5616 (m-80) cc_final: 0.4924 (m-10) REVERT: A 451 TYR cc_start: 0.6009 (m-80) cc_final: 0.5765 (m-80) REVERT: A 733 MET cc_start: 0.8733 (tpp) cc_final: 0.8428 (tpt) REVERT: A 807 LYS cc_start: 0.7925 (mmtt) cc_final: 0.6923 (mmmt) REVERT: C 129 LYS cc_start: 0.8600 (pttp) cc_final: 0.8364 (pttp) REVERT: C 402 ILE cc_start: 0.8660 (mm) cc_final: 0.8354 (mm) REVERT: C 514 SER cc_start: 0.8336 (t) cc_final: 0.8080 (m) REVERT: C 995 GLN cc_start: 0.8207 (tt0) cc_final: 0.7981 (tp40) REVERT: C 1020 THR cc_start: 0.8780 (m) cc_final: 0.8577 (m) outliers start: 3 outliers final: 0 residues processed: 304 average time/residue: 0.1558 time to fit residues: 77.5574 Evaluate side-chains 170 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 255 optimal weight: 10.0000 chunk 119 optimal weight: 20.0000 chunk 45 optimal weight: 10.0000 chunk 153 optimal weight: 8.9990 chunk 319 optimal weight: 5.9990 chunk 177 optimal weight: 5.9990 chunk 105 optimal weight: 0.5980 chunk 127 optimal weight: 2.9990 chunk 227 optimal weight: 0.9980 chunk 56 optimal weight: 9.9990 chunk 286 optimal weight: 0.3980 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 921 ASN ** B 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1016 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN A 422 ASN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 ASN ** A 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 894 GLN ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1029 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 958 GLN C 998 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.098369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.077749 restraints weight = 86367.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.077675 restraints weight = 66509.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.078072 restraints weight = 53080.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.078359 restraints weight = 47975.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.078524 restraints weight = 40164.966| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 25989 Z= 0.169 Angle : 0.614 9.163 35424 Z= 0.323 Chirality : 0.044 0.173 4008 Planarity : 0.004 0.045 4596 Dihedral : 5.167 24.948 3493 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.31 (0.14), residues: 3239 helix: 0.26 (0.20), residues: 673 sheet: -1.39 (0.20), residues: 635 loop : -2.36 (0.13), residues: 1931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 988 TYR 0.017 0.001 TYR A 453 PHE 0.034 0.002 PHE B 816 TRP 0.012 0.001 TRP A 104 HIS 0.013 0.002 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00382 (25950) covalent geometry : angle 0.60655 (35346) SS BOND : bond 0.00539 ( 39) SS BOND : angle 2.09932 ( 78) hydrogen bonds : bond 0.04289 ( 862) hydrogen bonds : angle 5.92671 ( 2403) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.7698 (mtt) cc_final: 0.6662 (tpp) REVERT: B 425 LEU cc_start: 0.6639 (mt) cc_final: 0.5958 (mp) REVERT: B 862 MET cc_start: 0.8412 (ptp) cc_final: 0.8209 (ptm) REVERT: B 958 GLN cc_start: 0.8700 (mm-40) cc_final: 0.8070 (tp-100) REVERT: B 986 ILE cc_start: 0.9388 (mm) cc_final: 0.9069 (mt) REVERT: A 449 TYR cc_start: 0.5644 (m-80) cc_final: 0.4909 (m-10) REVERT: A 733 MET cc_start: 0.8561 (tpp) cc_final: 0.8311 (tpt) REVERT: A 807 LYS cc_start: 0.7902 (mmtt) cc_final: 0.6909 (mmmt) REVERT: C 129 LYS cc_start: 0.8636 (pttp) cc_final: 0.8413 (pttp) REVERT: C 153 MET cc_start: 0.7027 (mmm) cc_final: 0.6801 (mmm) REVERT: C 402 ILE cc_start: 0.8598 (mm) cc_final: 0.8330 (mm) REVERT: C 571 ASP cc_start: 0.7325 (t70) cc_final: 0.6967 (t0) REVERT: C 995 GLN cc_start: 0.8165 (tt0) cc_final: 0.7952 (tp40) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.1541 time to fit residues: 67.8289 Evaluate side-chains 165 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 26 optimal weight: 8.9990 chunk 36 optimal weight: 20.0000 chunk 248 optimal weight: 1.9990 chunk 197 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 260 optimal weight: 6.9990 chunk 245 optimal weight: 3.9990 chunk 145 optimal weight: 0.9990 chunk 314 optimal weight: 7.9990 chunk 158 optimal weight: 7.9990 chunk 41 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1029 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.098486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.077973 restraints weight = 85627.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.077349 restraints weight = 70024.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.077838 restraints weight = 55474.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.078151 restraints weight = 45983.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.078317 restraints weight = 42734.896| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 25989 Z= 0.166 Angle : 0.599 8.309 35424 Z= 0.316 Chirality : 0.044 0.173 4008 Planarity : 0.004 0.051 4596 Dihedral : 5.095 24.769 3493 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.14), residues: 3239 helix: 0.61 (0.20), residues: 665 sheet: -1.24 (0.20), residues: 643 loop : -2.24 (0.13), residues: 1931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 758 TYR 0.015 0.001 TYR B 265 PHE 0.027 0.001 PHE B 374 TRP 0.016 0.001 TRP B 64 HIS 0.010 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00375 (25950) covalent geometry : angle 0.59242 (35346) SS BOND : bond 0.00456 ( 39) SS BOND : angle 1.92936 ( 78) hydrogen bonds : bond 0.04184 ( 862) hydrogen bonds : angle 5.82486 ( 2403) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.7311 (mtt) cc_final: 0.6958 (tpp) REVERT: B 237 ARG cc_start: 0.6830 (mtm180) cc_final: 0.6606 (mtm-85) REVERT: B 425 LEU cc_start: 0.6620 (mt) cc_final: 0.6292 (mp) REVERT: B 958 GLN cc_start: 0.8718 (mm-40) cc_final: 0.8037 (tp-100) REVERT: A 177 MET cc_start: 0.6205 (mmm) cc_final: 0.5975 (mmm) REVERT: A 195 LYS cc_start: 0.8482 (pttt) cc_final: 0.8261 (pttt) REVERT: A 449 TYR cc_start: 0.5893 (m-80) cc_final: 0.5107 (m-10) REVERT: A 516 GLU cc_start: 0.7115 (pm20) cc_final: 0.6567 (pm20) REVERT: A 807 LYS cc_start: 0.7873 (mmtt) cc_final: 0.6874 (mmmt) REVERT: C 129 LYS cc_start: 0.8643 (pttp) cc_final: 0.8389 (pttp) REVERT: C 153 MET cc_start: 0.7190 (mmm) cc_final: 0.6952 (mmm) REVERT: C 402 ILE cc_start: 0.8633 (mm) cc_final: 0.8392 (mm) REVERT: C 571 ASP cc_start: 0.7379 (t70) cc_final: 0.6996 (t0) outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 0.1530 time to fit residues: 67.5852 Evaluate side-chains 160 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 172 optimal weight: 0.2980 chunk 232 optimal weight: 20.0000 chunk 9 optimal weight: 6.9990 chunk 162 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 44 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 309 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 188 optimal weight: 6.9990 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 928 GLN ** B 948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 52 GLN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1029 GLN ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1112 ASN ** 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 = 0.3701 r_free = 0.3701 target = 0.097373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.076658 restraints weight = 86593.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.076282 restraints weight = 69834.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.076837 restraints weight = 54775.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.077135 restraints weight = 45477.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.077271 restraints weight = 41651.739| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 25989 Z= 0.209 Angle : 0.638 9.222 35424 Z= 0.336 Chirality : 0.044 0.210 4008 Planarity : 0.004 0.080 4596 Dihedral : 5.203 24.971 3493 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.14), residues: 3239 helix: 0.60 (0.20), residues: 665 sheet: -1.23 (0.20), residues: 634 loop : -2.23 (0.13), residues: 1940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B1032 TYR 0.021 0.002 TYR C 897 PHE 0.024 0.002 PHE B 275 TRP 0.019 0.001 TRP A 104 HIS 0.010 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00467 (25950) covalent geometry : angle 0.63080 (35346) SS BOND : bond 0.00526 ( 39) SS BOND : angle 2.09569 ( 78) hydrogen bonds : bond 0.04356 ( 862) hydrogen bonds : angle 5.85809 ( 2403) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.7493 (mtt) cc_final: 0.7007 (tpp) REVERT: B 237 ARG cc_start: 0.6837 (mtm180) cc_final: 0.6597 (mtm-85) REVERT: B 374 PHE cc_start: 0.6716 (m-10) cc_final: 0.6274 (m-10) REVERT: B 425 LEU cc_start: 0.6613 (mt) cc_final: 0.5836 (mp) REVERT: B 958 GLN cc_start: 0.8722 (mm-40) cc_final: 0.8074 (tp-100) REVERT: A 195 LYS cc_start: 0.8448 (pttt) cc_final: 0.8173 (pttt) REVERT: A 516 GLU cc_start: 0.7060 (pm20) cc_final: 0.6733 (pm20) REVERT: A 807 LYS cc_start: 0.7860 (mmtt) cc_final: 0.6897 (mmmt) REVERT: A 895 MET cc_start: 0.8405 (mmp) cc_final: 0.8024 (mmp) REVERT: C 129 LYS cc_start: 0.8650 (pttp) cc_final: 0.8424 (pttp) REVERT: C 571 ASP cc_start: 0.7418 (t70) cc_final: 0.6999 (t0) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.1452 time to fit residues: 58.8252 Evaluate side-chains 151 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 169 optimal weight: 9.9990 chunk 200 optimal weight: 5.9990 chunk 102 optimal weight: 9.9990 chunk 306 optimal weight: 3.9990 chunk 308 optimal weight: 1.9990 chunk 14 optimal weight: 20.0000 chunk 163 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.098581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.077872 restraints weight = 86199.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.077504 restraints weight = 69978.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.078033 restraints weight = 55123.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.078462 restraints weight = 45261.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.078564 restraints weight = 40779.589| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25989 Z= 0.153 Angle : 0.598 8.611 35424 Z= 0.313 Chirality : 0.044 0.210 4008 Planarity : 0.004 0.069 4596 Dihedral : 5.050 25.066 3493 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.14), residues: 3239 helix: 0.79 (0.20), residues: 672 sheet: -1.08 (0.20), residues: 680 loop : -2.10 (0.14), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 102 TYR 0.020 0.001 TYR B 897 PHE 0.027 0.001 PHE C 157 TRP 0.017 0.001 TRP A 104 HIS 0.009 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00346 (25950) covalent geometry : angle 0.59060 (35346) SS BOND : bond 0.00456 ( 39) SS BOND : angle 2.03712 ( 78) hydrogen bonds : bond 0.04068 ( 862) hydrogen bonds : angle 5.66980 ( 2403) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.7540 (mtt) cc_final: 0.6932 (tpp) REVERT: B 237 ARG cc_start: 0.6846 (mtm180) cc_final: 0.6612 (mtm-85) REVERT: B 425 LEU cc_start: 0.6748 (mt) cc_final: 0.6278 (mp) REVERT: A 177 MET cc_start: 0.5513 (mmm) cc_final: 0.5150 (mmm) REVERT: A 195 LYS cc_start: 0.8292 (pttt) cc_final: 0.7898 (pttm) REVERT: A 449 TYR cc_start: 0.5723 (m-80) cc_final: 0.4826 (m-10) REVERT: A 516 GLU cc_start: 0.7044 (pm20) cc_final: 0.6799 (pm20) REVERT: A 807 LYS cc_start: 0.7853 (mmtt) cc_final: 0.6885 (mmmt) REVERT: A 895 MET cc_start: 0.8467 (mmp) cc_final: 0.8163 (mmp) REVERT: A 966 ILE cc_start: 0.8185 (mm) cc_final: 0.7977 (mm) REVERT: A 987 ASP cc_start: 0.8467 (m-30) cc_final: 0.8186 (m-30) REVERT: C 129 LYS cc_start: 0.8585 (pttp) cc_final: 0.8311 (pttp) REVERT: C 402 ILE cc_start: 0.8720 (mm) cc_final: 0.8484 (mm) REVERT: C 571 ASP cc_start: 0.7369 (t70) cc_final: 0.6975 (t0) REVERT: C 754 THR cc_start: 0.8096 (p) cc_final: 0.7737 (t) REVERT: C 1043 MET cc_start: 0.8459 (ptp) cc_final: 0.8244 (ptp) outliers start: 0 outliers final: 0 residues processed: 253 average time/residue: 0.1479 time to fit residues: 63.2623 Evaluate side-chains 167 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 182 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 260 optimal weight: 5.9990 chunk 137 optimal weight: 0.4980 chunk 247 optimal weight: 20.0000 chunk 228 optimal weight: 0.5980 chunk 198 optimal weight: 1.9990 chunk 101 optimal weight: 0.0050 chunk 289 optimal weight: 6.9990 chunk 89 optimal weight: 6.9990 chunk 175 optimal weight: 0.6980 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 958 GLN ** B1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 ASN A 865 GLN ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 998 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1016 ASN C 173 GLN C 207 HIS C 563 GLN ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.100771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.081086 restraints weight = 85349.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.080866 restraints weight = 59335.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.081087 restraints weight = 48381.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.081326 restraints weight = 43552.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.081471 restraints weight = 40647.168| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 25989 Z= 0.108 Angle : 0.563 8.886 35424 Z= 0.295 Chirality : 0.043 0.174 4008 Planarity : 0.004 0.058 4596 Dihedral : 4.733 26.524 3493 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 0.04 % Allowed : 1.56 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.15), residues: 3239 helix: 1.17 (0.21), residues: 661 sheet: -0.97 (0.20), residues: 668 loop : -2.02 (0.13), residues: 1910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 898 TYR 0.015 0.001 TYR C 265 PHE 0.032 0.001 PHE C 392 TRP 0.036 0.001 TRP C 436 HIS 0.009 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00242 (25950) covalent geometry : angle 0.55778 (35346) SS BOND : bond 0.00433 ( 39) SS BOND : angle 1.78334 ( 78) hydrogen bonds : bond 0.03745 ( 862) hydrogen bonds : angle 5.42783 ( 2403) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 281 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.7604 (mtt) cc_final: 0.6958 (tpp) REVERT: B 228 ASP cc_start: 0.7234 (t0) cc_final: 0.6916 (t0) REVERT: B 425 LEU cc_start: 0.6731 (mt) cc_final: 0.6462 (tp) REVERT: B 958 GLN cc_start: 0.8737 (mm110) cc_final: 0.7891 (tp-100) REVERT: B 1070 THR cc_start: 0.8246 (t) cc_final: 0.7697 (t) REVERT: A 177 MET cc_start: 0.5605 (mmm) cc_final: 0.5161 (mmm) REVERT: A 195 LYS cc_start: 0.8227 (pttt) cc_final: 0.7403 (pttt) REVERT: A 394 ASN cc_start: 0.8244 (m-40) cc_final: 0.7693 (m-40) REVERT: A 449 TYR cc_start: 0.5765 (m-80) cc_final: 0.4872 (m-10) REVERT: A 516 GLU cc_start: 0.7003 (pm20) cc_final: 0.6781 (pm20) REVERT: A 807 LYS cc_start: 0.7770 (mmtt) cc_final: 0.6814 (mmmt) REVERT: A 888 GLN cc_start: 0.8272 (mp10) cc_final: 0.7901 (mp10) REVERT: A 895 MET cc_start: 0.8388 (mmp) cc_final: 0.8063 (mmp) REVERT: A 966 ILE cc_start: 0.7925 (mm) cc_final: 0.7701 (mm) REVERT: C 129 LYS cc_start: 0.8628 (pttp) cc_final: 0.8371 (pttp) REVERT: C 571 ASP cc_start: 0.7289 (t70) cc_final: 0.6952 (t0) REVERT: C 754 THR cc_start: 0.8056 (p) cc_final: 0.7735 (t) REVERT: C 767 GLN cc_start: 0.8804 (mm-40) cc_final: 0.8413 (mm-40) outliers start: 1 outliers final: 0 residues processed: 282 average time/residue: 0.1411 time to fit residues: 67.4571 Evaluate side-chains 181 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 315 optimal weight: 3.9990 chunk 216 optimal weight: 1.9990 chunk 218 optimal weight: 7.9990 chunk 132 optimal weight: 20.0000 chunk 44 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 268 optimal weight: 4.9990 chunk 254 optimal weight: 7.9990 chunk 248 optimal weight: 0.0170 chunk 160 optimal weight: 0.9980 chunk 220 optimal weight: 7.9990 overall best weight: 2.0024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN C 564 GLN C 894 GLN ** C 958 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1112 ASN ** 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 = 0.3735 r_free = 0.3735 target = 0.099212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.078851 restraints weight = 86168.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.078429 restraints weight = 75515.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.079112 restraints weight = 58179.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.079519 restraints weight = 46214.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.079614 restraints weight = 41522.088| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 25989 Z= 0.157 Angle : 0.590 9.082 35424 Z= 0.310 Chirality : 0.044 0.223 4008 Planarity : 0.004 0.061 4596 Dihedral : 4.803 27.381 3493 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 0.04 % Allowed : 1.27 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.15), residues: 3239 helix: 1.12 (0.21), residues: 663 sheet: -0.82 (0.20), residues: 660 loop : -1.97 (0.14), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 976 TYR 0.019 0.001 TYR B 897 PHE 0.035 0.002 PHE A 275 TRP 0.020 0.001 TRP C 436 HIS 0.014 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00359 (25950) covalent geometry : angle 0.58163 (35346) SS BOND : bond 0.00394 ( 39) SS BOND : angle 2.20739 ( 78) hydrogen bonds : bond 0.03924 ( 862) hydrogen bonds : angle 5.50479 ( 2403) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 256 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.7534 (mtt) cc_final: 0.6880 (tpp) REVERT: B 425 LEU cc_start: 0.6647 (mt) cc_final: 0.6393 (tp) REVERT: B 893 MET cc_start: 0.8411 (mmm) cc_final: 0.7819 (mmm) REVERT: B 958 GLN cc_start: 0.8679 (tp40) cc_final: 0.7778 (tp-100) REVERT: A 176 LEU cc_start: 0.8320 (mt) cc_final: 0.8030 (mt) REVERT: A 177 MET cc_start: 0.5750 (mmm) cc_final: 0.5305 (mmm) REVERT: A 195 LYS cc_start: 0.8416 (pttt) cc_final: 0.8008 (pttm) REVERT: A 394 ASN cc_start: 0.8182 (m-40) cc_final: 0.7752 (m-40) REVERT: A 807 LYS cc_start: 0.7755 (mmtt) cc_final: 0.6825 (mmmt) REVERT: A 888 GLN cc_start: 0.8364 (mp10) cc_final: 0.7987 (mp10) REVERT: A 895 MET cc_start: 0.8439 (mmp) cc_final: 0.8062 (mmp) REVERT: A 987 ASP cc_start: 0.8403 (m-30) cc_final: 0.8190 (m-30) REVERT: C 571 ASP cc_start: 0.7359 (t70) cc_final: 0.6997 (t0) REVERT: C 754 THR cc_start: 0.8164 (p) cc_final: 0.7831 (t) REVERT: C 767 GLN cc_start: 0.8800 (mm-40) cc_final: 0.8378 (mm-40) REVERT: C 1043 MET cc_start: 0.8537 (ptp) cc_final: 0.8292 (ptp) outliers start: 1 outliers final: 0 residues processed: 256 average time/residue: 0.1410 time to fit residues: 61.3998 Evaluate side-chains 170 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 158 optimal weight: 9.9990 chunk 1 optimal weight: 0.6980 chunk 25 optimal weight: 9.9990 chunk 263 optimal weight: 4.9990 chunk 235 optimal weight: 20.0000 chunk 113 optimal weight: 30.0000 chunk 84 optimal weight: 0.9980 chunk 210 optimal weight: 0.9980 chunk 81 optimal weight: 6.9990 chunk 130 optimal weight: 9.9990 chunk 241 optimal weight: 10.0000 overall best weight: 2.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 958 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.097783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.077368 restraints weight = 87166.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.076744 restraints weight = 74629.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.077283 restraints weight = 56708.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.077552 restraints weight = 47819.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.077694 restraints weight = 44029.806| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 25989 Z= 0.203 Angle : 0.640 8.761 35424 Z= 0.336 Chirality : 0.045 0.228 4008 Planarity : 0.004 0.062 4596 Dihedral : 5.043 26.086 3493 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.15), residues: 3239 helix: 0.90 (0.21), residues: 668 sheet: -0.92 (0.20), residues: 649 loop : -1.97 (0.14), residues: 1922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 976 TYR 0.020 0.002 TYR A 866 PHE 0.034 0.002 PHE A 275 TRP 0.019 0.001 TRP C 436 HIS 0.029 0.002 HIS B1041 Details of bonding type rmsd covalent geometry : bond 0.00456 (25950) covalent geometry : angle 0.63103 (35346) SS BOND : bond 0.00423 ( 39) SS BOND : angle 2.31449 ( 78) hydrogen bonds : bond 0.04212 ( 862) hydrogen bonds : angle 5.66758 ( 2403) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.7591 (mtt) cc_final: 0.6911 (tpp) REVERT: B 425 LEU cc_start: 0.6791 (mt) cc_final: 0.6470 (tp) REVERT: B 958 GLN cc_start: 0.8690 (tp40) cc_final: 0.7799 (tp-100) REVERT: A 176 LEU cc_start: 0.8500 (mt) cc_final: 0.8276 (mt) REVERT: A 195 LYS cc_start: 0.8469 (pttt) cc_final: 0.7948 (pttm) REVERT: A 807 LYS cc_start: 0.7806 (mmtt) cc_final: 0.6802 (mmmt) REVERT: A 888 GLN cc_start: 0.8491 (mp10) cc_final: 0.8119 (mp10) REVERT: C 571 ASP cc_start: 0.7487 (t70) cc_final: 0.7043 (t0) REVERT: C 754 THR cc_start: 0.8218 (p) cc_final: 0.7875 (t) REVERT: C 770 ASN cc_start: 0.9153 (m-40) cc_final: 0.8885 (m-40) REVERT: C 894 GLN cc_start: 0.8364 (tt0) cc_final: 0.8150 (tp40) REVERT: C 1043 MET cc_start: 0.8584 (ptp) cc_final: 0.8369 (ptp) outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.1478 time to fit residues: 60.9426 Evaluate side-chains 163 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 58 optimal weight: 0.5980 chunk 244 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 166 optimal weight: 0.0050 chunk 178 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 287 optimal weight: 4.9990 chunk 152 optimal weight: 7.9990 chunk 89 optimal weight: 0.8980 chunk 302 optimal weight: 5.9990 overall best weight: 1.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 948 ASN ** B1041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 958 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1029 GLN C 317 ASN C 894 GLN ** C1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1112 ASN ** 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 = 0.3733 r_free = 0.3733 target = 0.099183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.078670 restraints weight = 85997.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.078449 restraints weight = 71050.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.078930 restraints weight = 54168.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.079275 restraints weight = 45188.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.079387 restraints weight = 40462.430| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 25989 Z= 0.138 Angle : 0.606 8.817 35424 Z= 0.316 Chirality : 0.044 0.209 4008 Planarity : 0.004 0.054 4596 Dihedral : 4.878 25.177 3493 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 0.04 % Allowed : 0.32 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.15), residues: 3239 helix: 1.01 (0.21), residues: 662 sheet: -0.81 (0.21), residues: 634 loop : -1.91 (0.14), residues: 1943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 976 TYR 0.016 0.001 TYR A 866 PHE 0.027 0.001 PHE B 816 TRP 0.022 0.001 TRP C 436 HIS 0.025 0.001 HIS B1041 Details of bonding type rmsd covalent geometry : bond 0.00317 (25950) covalent geometry : angle 0.59830 (35346) SS BOND : bond 0.00365 ( 39) SS BOND : angle 2.15858 ( 78) hydrogen bonds : bond 0.03963 ( 862) hydrogen bonds : angle 5.52895 ( 2403) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 254 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.7596 (mtt) cc_final: 0.6905 (tpp) REVERT: B 425 LEU cc_start: 0.6716 (mt) cc_final: 0.6398 (tp) REVERT: B 911 GLU cc_start: 0.8320 (pp20) cc_final: 0.7822 (pp20) REVERT: B 958 GLN cc_start: 0.8646 (tp40) cc_final: 0.7772 (tp-100) REVERT: A 176 LEU cc_start: 0.8369 (mt) cc_final: 0.8070 (mt) REVERT: A 177 MET cc_start: 0.5664 (mmm) cc_final: 0.5438 (tpp) REVERT: A 195 LYS cc_start: 0.8487 (pttt) cc_final: 0.8227 (pttt) REVERT: A 233 ILE cc_start: 0.7609 (tt) cc_final: 0.6992 (mt) REVERT: A 807 LYS cc_start: 0.7759 (mmtt) cc_final: 0.6777 (mmmt) REVERT: A 888 GLN cc_start: 0.8408 (mp10) cc_final: 0.8015 (mp10) REVERT: A 895 MET cc_start: 0.8493 (mmp) cc_final: 0.8164 (mmp) REVERT: A 987 ASP cc_start: 0.8462 (m-30) cc_final: 0.8253 (m-30) REVERT: C 405 ASP cc_start: 0.7332 (t0) cc_final: 0.7019 (p0) REVERT: C 571 ASP cc_start: 0.7357 (t70) cc_final: 0.6969 (t0) REVERT: C 754 THR cc_start: 0.8109 (p) cc_final: 0.7769 (t) REVERT: C 767 GLN cc_start: 0.8819 (mm-40) cc_final: 0.8430 (mm-40) outliers start: 1 outliers final: 0 residues processed: 254 average time/residue: 0.1421 time to fit residues: 61.4576 Evaluate side-chains 175 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 60 optimal weight: 4.9990 chunk 244 optimal weight: 0.8980 chunk 256 optimal weight: 5.9990 chunk 219 optimal weight: 9.9990 chunk 242 optimal weight: 5.9990 chunk 291 optimal weight: 0.8980 chunk 164 optimal weight: 3.9990 chunk 32 optimal weight: 10.0000 chunk 209 optimal weight: 0.5980 chunk 184 optimal weight: 0.0000 chunk 298 optimal weight: 7.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN B 948 ASN ** B1041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN C 894 GLN ** C1112 ASN ** 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 = 0.3738 r_free = 0.3738 target = 0.099484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.079023 restraints weight = 85740.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.078857 restraints weight = 67117.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.079236 restraints weight = 53914.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.079594 restraints weight = 44717.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.079698 restraints weight = 40860.633| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25989 Z= 0.130 Angle : 0.593 9.094 35424 Z= 0.310 Chirality : 0.043 0.208 4008 Planarity : 0.004 0.056 4596 Dihedral : 4.789 24.981 3493 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.07 % Allowed : 0.28 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.15), residues: 3239 helix: 1.03 (0.21), residues: 669 sheet: -0.78 (0.20), residues: 642 loop : -1.87 (0.14), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 976 TYR 0.021 0.001 TYR B 866 PHE 0.030 0.001 PHE C 157 TRP 0.019 0.001 TRP C 436 HIS 0.021 0.001 HIS B1041 Details of bonding type rmsd covalent geometry : bond 0.00299 (25950) covalent geometry : angle 0.58508 (35346) SS BOND : bond 0.00385 ( 39) SS BOND : angle 2.11739 ( 78) hydrogen bonds : bond 0.03885 ( 862) hydrogen bonds : angle 5.45656 ( 2403) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3492.16 seconds wall clock time: 61 minutes 36.25 seconds (3696.25 seconds total)