Starting phenix.real_space_refine on Wed Jul 30 12:14:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vpn_43411/07_2025/8vpn_43411_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vpn_43411/07_2025/8vpn_43411.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vpn_43411/07_2025/8vpn_43411.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vpn_43411/07_2025/8vpn_43411.map" model { file = "/net/cci-nas-00/data/ceres_data/8vpn_43411/07_2025/8vpn_43411_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vpn_43411/07_2025/8vpn_43411_trim.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.037 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: 6 Type Number sf(0) Gaussians P 9 5.49 5 S 54 5.16 5 Cl 1 4.86 5 C 7771 2.51 5 N 2165 2.21 5 O 2254 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12254 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 896, 6875 Classifications: {'peptide': 896} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 41, 'TRANS': 854} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 176 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 5, 'TPO:plan-1': 2, 'ASP:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 88 Chain: "B" Number of atoms: 5288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 841, 5288 Classifications: {'peptide': 841} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 385} Link IDs: {'PTRANS': 35, 'TRANS': 805} Chain breaks: 2 Unresolved chain link angles: 18 Unresolved non-hydrogen bonds: 1393 Unresolved non-hydrogen angles: 1825 Unresolved non-hydrogen dihedrals: 1192 Unresolved non-hydrogen chiralities: 163 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 12, 'TYR:plan': 18, 'ASN:plan1': 17, 'TRP:plan': 13, 'HIS:plan': 5, 'PHE:plan': 29, 'GLU:plan': 13, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 680 Chain: "A" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'ATP': 1, 'BL1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 9.02, per 1000 atoms: 0.74 Number of scatterers: 12254 At special positions: 0 Unit cell: (91.16, 147.06, 118.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 54 16.00 P 9 15.00 O 2254 8.00 N 2165 7.00 C 7771 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 415 " - pdb=" SG CYS A 420 " distance=2.03 Simple disulfide: pdb=" SG CYS A 429 " - pdb=" SG CYS A 435 " 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: 3.44 Conformation dependent library (CDL) restraints added in 1.6 seconds 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3198 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 2 sheets defined 61.8% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'A' and resid 85 through 90 removed outlier: 3.578A pdb=" N LEU A 89 " --> pdb=" O THR A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 150 Processing helix chain 'A' and resid 152 through 157 Processing helix chain 'A' and resid 157 through 166 Processing helix chain 'A' and resid 166 through 193 removed outlier: 3.857A pdb=" N THR A 193 " --> pdb=" O SER A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 211 removed outlier: 3.551A pdb=" N PHE A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 248 removed outlier: 3.999A pdb=" N SER A 217 " --> pdb=" O GLU A 213 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ALA A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 275 removed outlier: 3.974A pdb=" N ILE A 259 " --> pdb=" O PRO A 255 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG A 260 " --> pdb=" O ILE A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 303 removed outlier: 3.590A pdb=" N GLN A 285 " --> pdb=" O GLU A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 313 Processing helix chain 'A' and resid 320 through 327 Processing helix chain 'A' and resid 338 through 347 Processing helix chain 'A' and resid 348 through 350 No H-bonds generated for 'chain 'A' and resid 348 through 350' Processing helix chain 'A' and resid 356 through 363 removed outlier: 3.618A pdb=" N ILE A 359 " --> pdb=" O GLY A 356 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N GLY A 361 " --> pdb=" O ASN A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 393 Proline residue: A 371 - end of helix Processing helix chain 'A' and resid 403 through 407 removed outlier: 4.095A pdb=" N THR A 407 " --> pdb=" O LEU A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 421 Processing helix chain 'A' and resid 426 through 433 removed outlier: 3.511A pdb=" N THR A 430 " --> pdb=" O PHE A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 450 removed outlier: 3.676A pdb=" N SER A 450 " --> pdb=" O MET A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 485 removed outlier: 4.066A pdb=" N ILE A 456 " --> pdb=" O PHE A 452 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP A 485 " --> pdb=" O CYS A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 494 removed outlier: 3.640A pdb=" N PHE A 493 " --> pdb=" O LEU A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 520 Processing helix chain 'A' and resid 527 through 553 removed outlier: 3.871A pdb=" N ILE A 531 " --> pdb=" O ILE A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 584 removed outlier: 3.796A pdb=" N THR A 584 " --> pdb=" O MET A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 606 Processing helix chain 'A' and resid 613 through 633 removed outlier: 3.609A pdb=" N ALA A 617 " --> pdb=" O SER A 613 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL A 633 " --> pdb=" O GLY A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 640 removed outlier: 4.050A pdb=" N ASN A 639 " --> pdb=" O HIS A 636 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR A 640 " --> pdb=" O ILE A 637 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 636 through 640' Processing helix chain 'A' and resid 654 through 666 removed outlier: 4.009A pdb=" N VAL A 658 " --> pdb=" O ARG A 654 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE A 664 " --> pdb=" O PHE A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 701 removed outlier: 3.673A pdb=" N GLN A 689 " --> pdb=" O MET A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 727 removed outlier: 3.601A pdb=" N GLY A 719 " --> pdb=" O ASP A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 766 removed outlier: 4.094A pdb=" N VAL A 753 " --> pdb=" O HIS A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 823 removed outlier: 3.631A pdb=" N SER A 823 " --> pdb=" O ILE A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 849 removed outlier: 3.538A pdb=" N ILE A 845 " --> pdb=" O LEU A 841 " (cutoff:3.500A) Proline residue: A 846 - end of helix Processing helix chain 'A' and resid 877 through 885 removed outlier: 3.855A pdb=" N LEU A 882 " --> pdb=" O ILE A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 915 removed outlier: 3.764A pdb=" N ARG A 909 " --> pdb=" O GLU A 905 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE A 910 " --> pdb=" O HIS A 906 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N MET A 913 " --> pdb=" O ARG A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 918 No H-bonds generated for 'chain 'A' and resid 916 through 918' Processing helix chain 'A' and resid 925 through 933 removed outlier: 4.273A pdb=" N ASN A 930 " --> pdb=" O GLU A 926 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLU A 931 " --> pdb=" O ALA A 927 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N MET A 932 " --> pdb=" O THR A 928 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ARG A 933 " --> pdb=" O VAL A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 948 Processing helix chain 'A' and resid 949 through 966 removed outlier: 3.618A pdb=" N ARG A 954 " --> pdb=" O VAL A 950 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLN A 955 " --> pdb=" O LYS A 951 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N VAL A 956 " --> pdb=" O SER A 952 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE A 961 " --> pdb=" O ARG A 957 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASP A 964 " --> pdb=" O GLU A 960 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR A 965 " --> pdb=" O ILE A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 997 removed outlier: 3.525A pdb=" N LEU A 993 " --> pdb=" O TYR A 989 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU A 994 " --> pdb=" O MET A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1018 removed outlier: 4.225A pdb=" N THR A1016 " --> pdb=" O ASN A1013 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE A1017 " --> pdb=" O VAL A1014 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR A1018 " --> pdb=" O LEU A1015 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1013 through 1018' Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 157 through 166 removed outlier: 3.784A pdb=" N ILE B 161 " --> pdb=" O ARG B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 193 Processing helix chain 'B' and resid 201 through 211 Processing helix chain 'B' and resid 211 through 247 removed outlier: 3.509A pdb=" N GLY B 215 " --> pdb=" O GLY B 211 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N SER B 217 " --> pdb=" O GLU B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 273 Processing helix chain 'B' and resid 274 through 276 No H-bonds generated for 'chain 'B' and resid 274 through 276' Processing helix chain 'B' and resid 278 through 304 removed outlier: 3.941A pdb=" N SER B 282 " --> pdb=" O MET B 278 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LEU B 304 " --> pdb=" O LEU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 315 removed outlier: 3.837A pdb=" N LYS B 314 " --> pdb=" O ASP B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 328 Processing helix chain 'B' and resid 338 through 347 Processing helix chain 'B' and resid 350 through 359 removed outlier: 4.611A pdb=" N LEU B 354 " --> pdb=" O ALA B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 395 Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 426 through 432 Processing helix chain 'B' and resid 445 through 450 Processing helix chain 'B' and resid 452 through 484 Processing helix chain 'B' and resid 504 through 520 Processing helix chain 'B' and resid 523 through 553 Proline residue: B 529 - end of helix Processing helix chain 'B' and resid 565 through 584 removed outlier: 3.518A pdb=" N ALA B 569 " --> pdb=" O ASN B 565 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR B 584 " --> pdb=" O MET B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 601 Processing helix chain 'B' and resid 614 through 630 removed outlier: 3.518A pdb=" N GLY B 618 " --> pdb=" O SER B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 640 Processing helix chain 'B' and resid 654 through 666 removed outlier: 4.150A pdb=" N VAL B 658 " --> pdb=" O ARG B 654 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N PHE B 664 " --> pdb=" O PHE B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 702 removed outlier: 3.789A pdb=" N LEU B 690 " --> pdb=" O PRO B 686 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG B 702 " --> pdb=" O TRP B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 727 Processing helix chain 'B' and resid 749 through 766 removed outlier: 3.712A pdb=" N VAL B 753 " --> pdb=" O HIS B 749 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU B 760 " --> pdb=" O TYR B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 823 removed outlier: 3.686A pdb=" N GLN B 822 " --> pdb=" O THR B 819 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER B 823 " --> pdb=" O ILE B 820 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 819 through 823' Processing helix chain 'B' and resid 840 through 851 Proline residue: B 846 - end of helix Processing helix chain 'B' and resid 870 through 886 removed outlier: 3.958A pdb=" N ALA B 877 " --> pdb=" O GLN B 873 " (cutoff:3.500A) Processing helix chain 'B' and resid 903 through 915 removed outlier: 3.741A pdb=" N LYS B 908 " --> pdb=" O ALA B 904 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG B 909 " --> pdb=" O GLU B 905 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU B 911 " --> pdb=" O THR B 907 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE B 914 " --> pdb=" O PHE B 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 918 No H-bonds generated for 'chain 'B' and resid 916 through 918' Processing helix chain 'B' and resid 925 through 930 removed outlier: 3.552A pdb=" N VAL B 929 " --> pdb=" O GLU B 926 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN B 930 " --> pdb=" O ALA B 927 " (cutoff:3.500A) Processing helix chain 'B' and resid 941 through 948 removed outlier: 3.691A pdb=" N THR B 946 " --> pdb=" O ASP B 942 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS B 947 " --> pdb=" O GLU B 943 " (cutoff:3.500A) Processing helix chain 'B' and resid 948 through 964 removed outlier: 3.798A pdb=" N ASN B 959 " --> pdb=" O GLN B 955 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU B 960 " --> pdb=" O VAL B 956 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP B 964 " --> pdb=" O GLU B 960 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 997 removed outlier: 3.542A pdb=" N LEU B 993 " --> pdb=" O TYR B 989 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU B 994 " --> pdb=" O MET B 990 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR B 995 " --> pdb=" O ALA B 991 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER B 997 " --> pdb=" O LEU B 993 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 707 through 712 removed outlier: 6.572A pdb=" N LEU A 645 " --> pdb=" O VAL A 738 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N GLY A 740 " --> pdb=" O LEU A 645 " (cutoff:3.500A) removed outlier: 8.699A pdb=" N LEU A 647 " --> pdb=" O GLY A 740 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL A 770 " --> pdb=" O ARG A1008 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG A1008 " --> pdb=" O VAL A 770 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N ILE A1005 " --> pdb=" O ALA A 970 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ILE A 972 " --> pdb=" O ILE A1005 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ILE A1007 " --> pdb=" O ILE A 972 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE A 974 " --> pdb=" O ILE A1007 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N THR A 829 " --> pdb=" O ALA A 969 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU A 971 " --> pdb=" O THR A 829 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR A 975 " --> pdb=" O TYR A 833 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ILE A 830 " --> pdb=" O ARG A 861 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N PHE A 863 " --> pdb=" O ILE A 830 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE A 832 " --> pdb=" O PHE A 863 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLU A 891 " --> pdb=" O ILE A 860 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL A 862 " --> pdb=" O GLU A 891 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 707 through 713 removed outlier: 4.981A pdb=" N GLY B 740 " --> pdb=" O LEU B 647 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE B 972 " --> pdb=" O ILE B1005 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N ILE B1007 " --> pdb=" O ILE B 972 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE B 974 " --> pdb=" O ILE B1007 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N VAL B 973 " --> pdb=" O THR B 829 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ASP B 831 " --> pdb=" O VAL B 973 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N THR B 975 " --> pdb=" O ASP B 831 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N TYR B 833 " --> pdb=" O THR B 975 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ILE B 830 " --> pdb=" O ARG B 861 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N PHE B 863 " --> pdb=" O ILE B 830 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE B 832 " --> pdb=" O PHE B 863 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N GLY B 865 " --> pdb=" O ILE B 832 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ILE B 860 " --> pdb=" O GLU B 891 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N HIS B 893 " --> pdb=" O ILE B 860 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL B 862 " --> pdb=" O HIS B 893 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N LEU B 895 " --> pdb=" O VAL B 862 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL B 864 " --> pdb=" O LEU B 895 " (cutoff:3.500A) 729 hydrogen bonds defined for protein. 2136 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.02 Time building geometry restraints manager: 3.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.07 - 1.22: 6 1.22 - 1.37: 4204 1.37 - 1.52: 4126 1.52 - 1.66: 4070 1.66 - 1.81: 83 Bond restraints: 12489 Sorted by residual: bond pdb=" CG PRO A 607 " pdb=" CD PRO A 607 " ideal model delta sigma weight residual 1.503 1.075 0.428 3.40e-02 8.65e+02 1.59e+02 bond pdb=" O1A ATP A1102 " pdb=" PA ATP A1102 " ideal model delta sigma weight residual 1.477 1.607 -0.130 1.10e-02 8.26e+03 1.39e+02 bond pdb=" O1A ATP B1101 " pdb=" PA ATP B1101 " ideal model delta sigma weight residual 1.477 1.593 -0.116 1.10e-02 8.26e+03 1.11e+02 bond pdb=" C6 ATP A1102 " pdb=" N6 ATP A1102 " ideal model delta sigma weight residual 1.337 1.443 -0.106 1.10e-02 8.26e+03 9.28e+01 bond pdb=" C6 ATP B1101 " pdb=" N6 ATP B1101 " ideal model delta sigma weight residual 1.337 1.433 -0.096 1.10e-02 8.26e+03 7.66e+01 ... (remaining 12484 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.44: 17021 5.44 - 10.87: 33 10.87 - 16.31: 3 16.31 - 21.74: 4 21.74 - 27.18: 3 Bond angle restraints: 17064 Sorted by residual: angle pdb=" PA ATP B1101 " pdb=" O3A ATP B1101 " pdb=" PB ATP B1101 " ideal model delta sigma weight residual 136.83 111.44 25.39 1.00e+00 1.00e+00 6.45e+02 angle pdb=" PB ATP A1102 " pdb=" O3B ATP A1102 " pdb=" PG ATP A1102 " ideal model delta sigma weight residual 139.87 120.07 19.80 1.00e+00 1.00e+00 3.92e+02 angle pdb=" PB ATP B1101 " pdb=" O3B ATP B1101 " pdb=" PG ATP B1101 " ideal model delta sigma weight residual 139.87 121.17 18.70 1.00e+00 1.00e+00 3.50e+02 angle pdb=" N PRO A 607 " pdb=" CD PRO A 607 " pdb=" CG PRO A 607 " ideal model delta sigma weight residual 103.20 76.02 27.18 1.50e+00 4.44e-01 3.28e+02 angle pdb=" PA ATP A1102 " pdb=" O3A ATP A1102 " pdb=" PB ATP A1102 " ideal model delta sigma weight residual 136.83 120.23 16.60 1.00e+00 1.00e+00 2.76e+02 ... (remaining 17059 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 6372 17.79 - 35.58: 700 35.58 - 53.37: 206 53.37 - 71.16: 60 71.16 - 88.95: 18 Dihedral angle restraints: 7356 sinusoidal: 2383 harmonic: 4973 Sorted by residual: dihedral pdb=" CB CYS A 415 " pdb=" SG CYS A 415 " pdb=" SG CYS A 420 " pdb=" CB CYS A 420 " ideal model delta sinusoidal sigma weight residual 93.00 6.39 86.61 1 1.00e+01 1.00e-02 9.03e+01 dihedral pdb=" CA PRO B1002 " pdb=" C PRO B1002 " pdb=" N PRO B1003 " pdb=" CA PRO B1003 " ideal model delta harmonic sigma weight residual 180.00 141.12 38.88 0 5.00e+00 4.00e-02 6.05e+01 dihedral pdb=" CA ARG B1001 " pdb=" C ARG B1001 " pdb=" N PRO B1002 " pdb=" CA PRO B1002 " ideal model delta harmonic sigma weight residual -180.00 -150.12 -29.88 0 5.00e+00 4.00e-02 3.57e+01 ... (remaining 7353 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1456 0.044 - 0.089: 426 0.089 - 0.133: 99 0.133 - 0.177: 4 0.177 - 0.221: 3 Chirality restraints: 1988 Sorted by residual: chirality pdb=" CA LEU A1015 " pdb=" N LEU A1015 " pdb=" C LEU A1015 " pdb=" CB LEU A1015 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" C3' ATP B1101 " pdb=" C2' ATP B1101 " pdb=" C4' ATP B1101 " pdb=" O3' ATP B1101 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA PHE A 56 " pdb=" N PHE A 56 " pdb=" C PHE A 56 " pdb=" CB PHE A 56 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.99e-01 ... (remaining 1985 not shown) Planarity restraints: 2209 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 250 " 0.085 5.00e-02 4.00e+02 1.19e-01 2.25e+01 pdb=" N PRO A 251 " -0.205 5.00e-02 4.00e+02 pdb=" CA PRO A 251 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO A 251 " 0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 679 " -0.056 5.00e-02 4.00e+02 8.57e-02 1.17e+01 pdb=" N PRO A 680 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO A 680 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 680 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 679 " -0.052 5.00e-02 4.00e+02 7.38e-02 8.70e+00 pdb=" N PRO B 680 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO B 680 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 680 " -0.041 5.00e-02 4.00e+02 ... (remaining 2206 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 122 2.61 - 3.19: 11005 3.19 - 3.76: 17985 3.76 - 4.33: 23270 4.33 - 4.90: 38916 Nonbonded interactions: 91298 Sorted by model distance: nonbonded pdb=" OE1 GLU A 416 " pdb=" OG1 THR A 427 " model vdw 2.042 3.040 nonbonded pdb=" O ARG B1001 " pdb=" NH1 ARG B1001 " model vdw 2.044 3.120 nonbonded pdb=" O ALA B 419 " pdb=" N GLY B 423 " model vdw 2.070 3.120 nonbonded pdb=" NH1 ARG B 774 " pdb=" O SER B 997 " model vdw 2.109 3.120 nonbonded pdb=" OD2 ASP A 831 " pdb=" OG SER A 966 " model vdw 2.134 3.040 ... (remaining 91293 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 136 or (resid 137 through 139 and (name N or name CA or na \ me C or name O or name CB )) or resid 140 or (resid 141 through 150 and (name N \ or name CA or name C or name O or name CB )) or resid 151 or (resid 152 through \ 165 and (name N or name CA or name C or name O or name CB )) or resid 166 or (re \ sid 167 through 184 and (name N or name CA or name C or name O or name CB )) or \ resid 185 or (resid 186 through 194 and (name N or name CA or name C or name O o \ r name CB )) or resid 195 or (resid 196 through 199 and (name N or name CA or na \ me C or name O or name CB )) or resid 200 through 201 or (resid 202 through 210 \ and (name N or name CA or name C or name O or name CB )) or resid 211 or (resid \ 212 through 214 and (name N or name CA or name C or name O or name CB )) or resi \ d 215 through 216 or (resid 217 through 218 and (name N or name CA or name C or \ name O or name CB )) or resid 219 or (resid 220 through 228 and (name N or name \ CA or name C or name O or name CB )) or resid 229 or (resid 230 through 235 and \ (name N or name CA or name C or name O or name CB )) or resid 236 or (resid 237 \ through 248 and (name N or name CA or name C or name O or name CB )) or (resid 2 \ 49 through 276 and (name N or name CA or name C or name O or name CB )) or resid \ 277 or (resid 278 through 301 and (name N or name CA or name C or name O or nam \ e CB )) or resid 302 or (resid 303 through 314 and (name N or name CA or name C \ or name O or name CB )) or resid 315 or (resid 316 through 333 and (name N or na \ me CA or name C or name O or name CB )) or resid 334 or (resid 335 through 336 a \ nd (name N or name CA or name C or name O or name CB )) or resid 337 or (resid 3 \ 38 through 340 and (name N or name CA or name C or name O or name CB )) or resid \ 341 or (resid 342 through 351 and (name N or name CA or name C or name O or nam \ e CB )) or resid 352 or (resid 353 through 355 and (name N or name CA or name C \ or name O or name CB )) or (resid 356 through 360 and (name N or name CA or name \ C or name O or name CB )) or resid 361 or (resid 362 through 372 and (name N or \ name CA or name C or name O or name CB )) or resid 373 or (resid 374 through 39 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 393 or (resi \ d 394 through 401 and (name N or name CA or name C or name O or name CB )) or re \ sid 402 or (resid 403 through 410 and (name N or name CA or name C or name O or \ name CB )) or resid 411 or (resid 412 and (name N or name CA or name C or name O \ or name CB )) or (resid 413 through 416 and (name N or name CA or name C or nam \ e O or name CB )) or resid 417 or (resid 418 through 422 and (name N or name CA \ or name C or name O or name CB )) or resid 423 or (resid 424 through 437 and (na \ me N or name CA or name C or name O or name CB )) or resid 438 or (resid 439 thr \ ough 450 and (name N or name CA or name C or name O or name CB )) or resid 451 o \ r (resid 452 through 458 and (name N or name CA or name C or name O or name CB ) \ ) or resid 459 or (resid 460 through 461 and (name N or name CA or name C or nam \ e O or name CB )) or (resid 462 through 485 and (name N or name CA or name C or \ name O or name CB )) or (resid 496 and (name N or name CA or name C or name O or \ name CB )) or resid 497 or (resid 498 and (name N or name CA or name C or name \ O or name CB )) or (resid 499 through 506 and (name N or name CA or name C or na \ me O or name CB )) or resid 507 or (resid 508 through 555 and (name N or name CA \ or name C or name O or name CB )) or resid 556 or (resid 557 through 571 and (n \ ame N or name CA or name C or name O or name CB )) or (resid 572 through 592 and \ (name N or name CA or name C or name O or name CB )) or resid 593 or (resid 594 \ through 606 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 07 or (resid 608 through 610 and (name N or name CA or name C or name O or name \ CB )) or resid 611 through 1019 or resid 1102)) selection = (chain 'B' and (resid 136 through 690 or (resid 691 through 693 and (name N or n \ ame CA or name C or name O or name CB )) or resid 694 through 695 or (resid 696 \ through 697 and (name N or name CA or name C or name O or name CB )) or resid 69 \ 8 through 699 or (resid 700 through 703 and (name N or name CA or name C or name \ O or name CB )) or resid 704 through 863 or (resid 864 and (name N or name CA o \ r name C or name O or name CB )) or resid 865 through 866 or (resid 867 through \ 887 and (name N or name CA or name C or name O or name CB )) or resid 888 or (re \ sid 889 and (name N or name CA or name C or name O or name CB )) or resid 890 th \ rough 1019 or resid 1101)) } 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 individual isotropic 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: 3.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 32.790 Find NCS groups from input model: 1.010 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:14.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.428 12491 Z= 0.343 Angle : 0.824 27.176 17068 Z= 0.541 Chirality : 0.043 0.221 1988 Planarity : 0.006 0.119 2209 Dihedral : 17.803 88.950 4152 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.11 % Favored : 92.72 % Rotamer: Outliers : 4.96 % Allowed : 29.83 % Favored : 65.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.21), residues: 1716 helix: 1.52 (0.18), residues: 914 sheet: -0.16 (0.47), residues: 133 loop : -2.77 (0.21), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 171 HIS 0.005 0.001 HIS A 548 PHE 0.014 0.002 PHE A 707 TYR 0.015 0.002 TYR A 768 ARG 0.009 0.001 ARG B1001 Details of bonding type rmsd hydrogen bonds : bond 0.19050 ( 729) hydrogen bonds : angle 5.97064 ( 2136) SS BOND : bond 0.00077 ( 2) SS BOND : angle 1.31911 ( 4) covalent geometry : bond 0.00695 (12489) covalent geometry : angle 0.82398 (17064) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 180 time to evaluate : 1.393 Fit side-chains REVERT: A 72 ASN cc_start: 0.8180 (t0) cc_final: 0.7937 (t0) REVERT: A 181 THR cc_start: 0.8261 (OUTLIER) cc_final: 0.7846 (p) REVERT: A 246 GLN cc_start: 0.6742 (tt0) cc_final: 0.6445 (mt0) REVERT: A 422 TYR cc_start: 0.7591 (m-80) cc_final: 0.7153 (m-80) REVERT: A 432 GLN cc_start: 0.7657 (tt0) cc_final: 0.7443 (pt0) REVERT: A 744 ASN cc_start: 0.7820 (t0) cc_final: 0.7293 (p0) REVERT: A 899 ASN cc_start: 0.7577 (m-40) cc_final: 0.6988 (p0) REVERT: A 906 HIS cc_start: 0.7137 (m90) cc_final: 0.6913 (m170) REVERT: B 773 MET cc_start: 0.8819 (ttt) cc_final: 0.8499 (ttt) REVERT: B 853 ARG cc_start: 0.7272 (OUTLIER) cc_final: 0.6536 (ppt90) outliers start: 51 outliers final: 17 residues processed: 219 average time/residue: 1.1518 time to fit residues: 275.9916 Evaluate side-chains 145 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain B residue 658 VAL Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain B residue 853 ARG Chi-restraints excluded: chain B residue 956 VAL Chi-restraints excluded: chain B residue 974 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 146 optimal weight: 0.9990 chunk 131 optimal weight: 5.9990 chunk 72 optimal weight: 0.0370 chunk 44 optimal weight: 0.7980 chunk 88 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 135 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 157 optimal weight: 1.9990 overall best weight: 0.7662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 GLN A 433 HIS A 616 GLN A 636 HIS A 930 ASN A1010 ASN A1013 ASN B 725 GLN B 825 GLN B 873 GLN B 906 HIS B 920 ASN B1011 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.167033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.115863 restraints weight = 15367.418| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.26 r_work: 0.3281 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 12491 Z= 0.142 Angle : 0.610 9.899 17068 Z= 0.320 Chirality : 0.043 0.169 1988 Planarity : 0.005 0.069 2209 Dihedral : 8.450 87.724 1962 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.71 % Favored : 94.06 % Rotamer: Outliers : 4.37 % Allowed : 23.32 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.21), residues: 1716 helix: 2.15 (0.18), residues: 945 sheet: 0.45 (0.47), residues: 134 loop : -2.54 (0.22), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 992 HIS 0.010 0.001 HIS A 433 PHE 0.012 0.001 PHE B 664 TYR 0.015 0.001 TYR A 768 ARG 0.007 0.001 ARG B1001 Details of bonding type rmsd hydrogen bonds : bond 0.06354 ( 729) hydrogen bonds : angle 4.24815 ( 2136) SS BOND : bond 0.00757 ( 2) SS BOND : angle 2.11486 ( 4) covalent geometry : bond 0.00298 (12489) covalent geometry : angle 0.60938 (17064) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 129 time to evaluate : 1.360 Fit side-chains REVERT: A 181 THR cc_start: 0.8116 (m) cc_final: 0.7545 (p) REVERT: A 246 GLN cc_start: 0.6418 (tt0) cc_final: 0.5919 (mt0) REVERT: A 344 SER cc_start: 0.8883 (t) cc_final: 0.8627 (m) REVERT: A 422 TYR cc_start: 0.7605 (m-80) cc_final: 0.7047 (m-80) REVERT: A 523 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7673 (tp30) REVERT: A 596 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8374 (tt) REVERT: A 731 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.7553 (mtt180) REVERT: A 744 ASN cc_start: 0.7980 (t0) cc_final: 0.7112 (p0) REVERT: A 895 LEU cc_start: 0.5297 (OUTLIER) cc_final: 0.4631 (pp) REVERT: A 899 ASN cc_start: 0.7510 (m-40) cc_final: 0.6754 (p0) REVERT: A 906 HIS cc_start: 0.7339 (m90) cc_final: 0.7005 (m170) REVERT: A 942 ASP cc_start: 0.6607 (t0) cc_final: 0.6351 (m-30) REVERT: B 773 MET cc_start: 0.8996 (OUTLIER) cc_final: 0.8711 (ttt) REVERT: B 943 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7911 (tm-30) REVERT: B 1001 ARG cc_start: 0.5722 (OUTLIER) cc_final: 0.3592 (mtm180) outliers start: 45 outliers final: 13 residues processed: 163 average time/residue: 1.1607 time to fit residues: 207.4487 Evaluate side-chains 129 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 731 ARG Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain B residue 658 VAL Chi-restraints excluded: chain B residue 773 MET Chi-restraints excluded: chain B residue 860 ILE Chi-restraints excluded: chain B residue 1001 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 72 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 chunk 47 optimal weight: 0.3980 chunk 78 optimal weight: 0.0070 chunk 23 optimal weight: 0.9990 chunk 166 optimal weight: 2.9990 chunk 98 optimal weight: 20.0000 chunk 82 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 overall best weight: 0.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1010 ASN B 725 GLN B 893 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.168445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.118121 restraints weight = 15511.347| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.28 r_work: 0.3301 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 12491 Z= 0.116 Angle : 0.523 10.079 17068 Z= 0.273 Chirality : 0.041 0.136 1988 Planarity : 0.004 0.060 2209 Dihedral : 7.649 86.227 1940 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.13 % Favored : 94.76 % Rotamer: Outliers : 3.40 % Allowed : 24.59 % Favored : 72.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.21), residues: 1716 helix: 2.41 (0.17), residues: 959 sheet: 1.06 (0.48), residues: 132 loop : -2.32 (0.22), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 586 HIS 0.003 0.001 HIS A 548 PHE 0.011 0.001 PHE B 664 TYR 0.012 0.001 TYR A 768 ARG 0.007 0.001 ARG B 949 Details of bonding type rmsd hydrogen bonds : bond 0.05217 ( 729) hydrogen bonds : angle 3.84415 ( 2136) SS BOND : bond 0.00107 ( 2) SS BOND : angle 1.90954 ( 4) covalent geometry : bond 0.00241 (12489) covalent geometry : angle 0.52266 (17064) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 119 time to evaluate : 1.278 Fit side-chains REVERT: A 181 THR cc_start: 0.8132 (m) cc_final: 0.7566 (p) REVERT: A 295 SER cc_start: 0.8291 (OUTLIER) cc_final: 0.7914 (p) REVERT: A 344 SER cc_start: 0.8811 (t) cc_final: 0.8561 (m) REVERT: A 422 TYR cc_start: 0.7565 (m-80) cc_final: 0.7038 (m-80) REVERT: A 431 GLN cc_start: 0.8045 (mt0) cc_final: 0.7833 (mt0) REVERT: A 523 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7755 (tp30) REVERT: A 731 ARG cc_start: 0.7805 (OUTLIER) cc_final: 0.7446 (mtt180) REVERT: A 744 ASN cc_start: 0.8046 (t0) cc_final: 0.7209 (p0) REVERT: A 895 LEU cc_start: 0.5398 (OUTLIER) cc_final: 0.4829 (pp) REVERT: A 899 ASN cc_start: 0.7613 (m-40) cc_final: 0.6789 (p0) REVERT: A 906 HIS cc_start: 0.7237 (m90) cc_final: 0.6880 (m170) REVERT: A 942 ASP cc_start: 0.6636 (t0) cc_final: 0.6375 (m-30) REVERT: B 943 GLU cc_start: 0.7727 (tm-30) cc_final: 0.7468 (tm-30) outliers start: 35 outliers final: 11 residues processed: 149 average time/residue: 0.9879 time to fit residues: 163.7853 Evaluate side-chains 118 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 731 ARG Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain B residue 658 VAL Chi-restraints excluded: chain B residue 901 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 21 optimal weight: 6.9990 chunk 75 optimal weight: 20.0000 chunk 82 optimal weight: 2.9990 chunk 96 optimal weight: 30.0000 chunk 55 optimal weight: 2.9990 chunk 165 optimal weight: 0.0470 chunk 95 optimal weight: 20.0000 chunk 9 optimal weight: 0.8980 chunk 167 optimal weight: 4.9990 chunk 150 optimal weight: 0.6980 chunk 164 optimal weight: 0.0370 overall best weight: 0.9358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A1010 ASN B 667 ASN B 725 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.165364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.113325 restraints weight = 15385.847| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.31 r_work: 0.3237 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12491 Z= 0.128 Angle : 0.538 10.879 17068 Z= 0.279 Chirality : 0.041 0.164 1988 Planarity : 0.004 0.058 2209 Dihedral : 7.755 83.955 1938 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.65 % Favored : 94.23 % Rotamer: Outliers : 3.50 % Allowed : 24.30 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.21), residues: 1716 helix: 2.45 (0.17), residues: 965 sheet: 1.16 (0.48), residues: 132 loop : -2.21 (0.22), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 611 HIS 0.003 0.001 HIS A 548 PHE 0.012 0.001 PHE A 664 TYR 0.012 0.001 TYR A 768 ARG 0.003 0.000 ARG B 949 Details of bonding type rmsd hydrogen bonds : bond 0.05918 ( 729) hydrogen bonds : angle 3.76581 ( 2136) SS BOND : bond 0.00660 ( 2) SS BOND : angle 3.58235 ( 4) covalent geometry : bond 0.00272 (12489) covalent geometry : angle 0.53557 (17064) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 117 time to evaluate : 1.445 Fit side-chains REVERT: A 181 THR cc_start: 0.8234 (m) cc_final: 0.7718 (p) REVERT: A 198 LYS cc_start: 0.9003 (OUTLIER) cc_final: 0.8540 (mtpp) REVERT: A 246 GLN cc_start: 0.6163 (tt0) cc_final: 0.5868 (tt0) REVERT: A 344 SER cc_start: 0.8833 (t) cc_final: 0.8577 (m) REVERT: A 420 CYS cc_start: 0.5987 (OUTLIER) cc_final: 0.5669 (m) REVERT: A 422 TYR cc_start: 0.7582 (m-80) cc_final: 0.7155 (m-80) REVERT: A 431 GLN cc_start: 0.8036 (mt0) cc_final: 0.7784 (mt0) REVERT: A 605 LYS cc_start: 0.6840 (tppt) cc_final: 0.6485 (tptp) REVERT: A 744 ASN cc_start: 0.8109 (t0) cc_final: 0.7357 (p0) REVERT: A 895 LEU cc_start: 0.5465 (OUTLIER) cc_final: 0.4950 (pp) REVERT: A 899 ASN cc_start: 0.7656 (m-40) cc_final: 0.6810 (p0) REVERT: A 906 HIS cc_start: 0.7392 (m90) cc_final: 0.7048 (m170) REVERT: B 732 MET cc_start: 0.9074 (mtm) cc_final: 0.8762 (mtm) REVERT: B 773 MET cc_start: 0.9041 (ttt) cc_final: 0.8829 (ttt) REVERT: B 775 MET cc_start: 0.9264 (mtp) cc_final: 0.8986 (ttt) REVERT: B 921 ASP cc_start: 0.6266 (t0) cc_final: 0.5899 (t70) REVERT: B 943 GLU cc_start: 0.7868 (tm-30) cc_final: 0.7618 (tm-30) outliers start: 36 outliers final: 12 residues processed: 141 average time/residue: 1.2360 time to fit residues: 190.6713 Evaluate side-chains 121 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain A residue 945 ILE Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain B residue 658 VAL Chi-restraints excluded: chain B residue 1020 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 20 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 137 optimal weight: 1.9990 chunk 152 optimal weight: 0.0050 chunk 157 optimal weight: 4.9990 chunk 156 optimal weight: 0.0270 chunk 43 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 114 optimal weight: 10.0000 chunk 123 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 overall best weight: 0.7654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A1010 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.166275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.115340 restraints weight = 15322.644| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.27 r_work: 0.3256 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12491 Z= 0.117 Angle : 0.515 10.837 17068 Z= 0.268 Chirality : 0.041 0.178 1988 Planarity : 0.004 0.057 2209 Dihedral : 7.628 84.030 1937 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.95 % Favored : 94.93 % Rotamer: Outliers : 3.11 % Allowed : 24.68 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.21), residues: 1716 helix: 2.58 (0.17), residues: 961 sheet: 1.27 (0.48), residues: 132 loop : -2.13 (0.22), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 586 HIS 0.003 0.001 HIS A 548 PHE 0.011 0.001 PHE B 664 TYR 0.013 0.001 TYR A 640 ARG 0.005 0.000 ARG B1001 Details of bonding type rmsd hydrogen bonds : bond 0.05339 ( 729) hydrogen bonds : angle 3.66346 ( 2136) SS BOND : bond 0.00342 ( 2) SS BOND : angle 3.05590 ( 4) covalent geometry : bond 0.00244 (12489) covalent geometry : angle 0.51259 (17064) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 112 time to evaluate : 1.320 Fit side-chains REVERT: A 181 THR cc_start: 0.8223 (m) cc_final: 0.7711 (p) REVERT: A 198 LYS cc_start: 0.9000 (OUTLIER) cc_final: 0.8527 (mtpp) REVERT: A 295 SER cc_start: 0.8349 (OUTLIER) cc_final: 0.7976 (p) REVERT: A 344 SER cc_start: 0.8829 (t) cc_final: 0.8561 (m) REVERT: A 420 CYS cc_start: 0.5713 (OUTLIER) cc_final: 0.5332 (m) REVERT: A 422 TYR cc_start: 0.7618 (m-80) cc_final: 0.7213 (m-80) REVERT: A 605 LYS cc_start: 0.6830 (tppt) cc_final: 0.6487 (tptp) REVERT: A 744 ASN cc_start: 0.8104 (t0) cc_final: 0.7412 (p0) REVERT: A 895 LEU cc_start: 0.5281 (OUTLIER) cc_final: 0.4731 (pp) REVERT: A 899 ASN cc_start: 0.7690 (m-40) cc_final: 0.6802 (p0) REVERT: A 906 HIS cc_start: 0.7250 (m90) cc_final: 0.6967 (m170) REVERT: B 732 MET cc_start: 0.9052 (mtm) cc_final: 0.8767 (mtm) REVERT: B 773 MET cc_start: 0.9003 (ttt) cc_final: 0.8791 (ttt) REVERT: B 921 ASP cc_start: 0.6257 (t0) cc_final: 0.5976 (t70) REVERT: B 943 GLU cc_start: 0.7697 (tm-30) cc_final: 0.7468 (tm-30) outliers start: 32 outliers final: 11 residues processed: 138 average time/residue: 0.9850 time to fit residues: 151.8011 Evaluate side-chains 122 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain B residue 658 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 166 optimal weight: 0.9980 chunk 155 optimal weight: 0.6980 chunk 75 optimal weight: 20.0000 chunk 78 optimal weight: 0.9990 chunk 161 optimal weight: 0.0570 chunk 91 optimal weight: 3.9990 chunk 126 optimal weight: 20.0000 chunk 141 optimal weight: 0.9990 chunk 138 optimal weight: 0.7980 chunk 147 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A 675 HIS A1010 ASN B 621 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.165500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.115024 restraints weight = 15429.023| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.26 r_work: 0.3259 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12491 Z= 0.113 Angle : 0.509 10.760 17068 Z= 0.263 Chirality : 0.041 0.197 1988 Planarity : 0.004 0.056 2209 Dihedral : 7.584 88.525 1937 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.13 % Favored : 94.81 % Rotamer: Outliers : 2.82 % Allowed : 25.27 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.21), residues: 1716 helix: 2.57 (0.17), residues: 971 sheet: 1.35 (0.48), residues: 132 loop : -2.10 (0.23), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 586 HIS 0.002 0.000 HIS A 548 PHE 0.011 0.001 PHE B 664 TYR 0.010 0.001 TYR A 640 ARG 0.003 0.000 ARG B 949 Details of bonding type rmsd hydrogen bonds : bond 0.05211 ( 729) hydrogen bonds : angle 3.61188 ( 2136) SS BOND : bond 0.00140 ( 2) SS BOND : angle 2.80353 ( 4) covalent geometry : bond 0.00237 (12489) covalent geometry : angle 0.50708 (17064) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 108 time to evaluate : 1.692 Fit side-chains REVERT: A 181 THR cc_start: 0.8208 (m) cc_final: 0.7702 (p) REVERT: A 198 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8532 (mtpp) REVERT: A 295 SER cc_start: 0.8272 (OUTLIER) cc_final: 0.7883 (p) REVERT: A 344 SER cc_start: 0.8834 (t) cc_final: 0.8583 (m) REVERT: A 420 CYS cc_start: 0.5464 (OUTLIER) cc_final: 0.5062 (m) REVERT: A 422 TYR cc_start: 0.7660 (m-80) cc_final: 0.7232 (m-80) REVERT: A 605 LYS cc_start: 0.6846 (tppt) cc_final: 0.6524 (tppp) REVERT: A 744 ASN cc_start: 0.8093 (t0) cc_final: 0.7604 (p0) REVERT: A 773 MET cc_start: 0.8914 (OUTLIER) cc_final: 0.8257 (tpp) REVERT: A 895 LEU cc_start: 0.5347 (OUTLIER) cc_final: 0.5010 (pp) REVERT: A 899 ASN cc_start: 0.7644 (m-40) cc_final: 0.6717 (p0) REVERT: A 906 HIS cc_start: 0.7261 (m90) cc_final: 0.6948 (m170) REVERT: B 732 MET cc_start: 0.9044 (mtm) cc_final: 0.8757 (mtm) REVERT: B 921 ASP cc_start: 0.6297 (t0) cc_final: 0.6080 (t70) REVERT: B 943 GLU cc_start: 0.7651 (tm-30) cc_final: 0.7427 (tm-30) outliers start: 29 outliers final: 11 residues processed: 130 average time/residue: 1.1562 time to fit residues: 167.0639 Evaluate side-chains 124 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 773 MET Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain B residue 658 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 170 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 107 optimal weight: 8.9990 chunk 82 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 chunk 115 optimal weight: 30.0000 chunk 171 optimal weight: 0.4980 chunk 132 optimal weight: 30.0000 chunk 5 optimal weight: 3.9990 chunk 105 optimal weight: 30.0000 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A 257 ASN A 358 ASN A 431 GLN A 533 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.156036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.103497 restraints weight = 15376.346| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.23 r_work: 0.3110 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 12491 Z= 0.290 Angle : 0.742 14.911 17068 Z= 0.382 Chirality : 0.049 0.369 1988 Planarity : 0.005 0.058 2209 Dihedral : 8.766 89.743 1937 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.64 % Favored : 93.30 % Rotamer: Outliers : 3.60 % Allowed : 23.71 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.21), residues: 1716 helix: 2.00 (0.17), residues: 956 sheet: 1.05 (0.49), residues: 127 loop : -2.26 (0.22), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 332 HIS 0.008 0.002 HIS A 675 PHE 0.022 0.002 PHE B1017 TYR 0.020 0.003 TYR A 640 ARG 0.007 0.001 ARG A 774 Details of bonding type rmsd hydrogen bonds : bond 0.09987 ( 729) hydrogen bonds : angle 4.16451 ( 2136) SS BOND : bond 0.00054 ( 2) SS BOND : angle 2.94217 ( 4) covalent geometry : bond 0.00717 (12489) covalent geometry : angle 0.74083 (17064) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 121 time to evaluate : 1.372 Fit side-chains REVERT: A 80 ARG cc_start: 0.6160 (OUTLIER) cc_final: 0.5214 (ttt90) REVERT: A 198 LYS cc_start: 0.9205 (OUTLIER) cc_final: 0.8796 (mtpp) REVERT: A 246 GLN cc_start: 0.6872 (tt0) cc_final: 0.6323 (mt0) REVERT: A 248 TYR cc_start: 0.7095 (m-80) cc_final: 0.6786 (m-80) REVERT: A 344 SER cc_start: 0.8813 (t) cc_final: 0.8569 (m) REVERT: A 406 ASP cc_start: 0.7620 (OUTLIER) cc_final: 0.7028 (t70) REVERT: A 420 CYS cc_start: 0.5675 (OUTLIER) cc_final: 0.5092 (m) REVERT: A 605 LYS cc_start: 0.7505 (tppt) cc_final: 0.6676 (tmtt) REVERT: A 744 ASN cc_start: 0.8169 (t0) cc_final: 0.7545 (p0) REVERT: A 773 MET cc_start: 0.9027 (OUTLIER) cc_final: 0.8451 (tpp) REVERT: A 895 LEU cc_start: 0.5406 (OUTLIER) cc_final: 0.5134 (pp) REVERT: A 899 ASN cc_start: 0.7628 (m-40) cc_final: 0.6757 (p0) REVERT: A 1001 ARG cc_start: 0.8008 (ttm-80) cc_final: 0.7757 (mtp180) REVERT: B 732 MET cc_start: 0.9168 (mtm) cc_final: 0.8848 (mtm) REVERT: B 943 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7998 (tm-30) outliers start: 37 outliers final: 17 residues processed: 145 average time/residue: 1.1506 time to fit residues: 183.0426 Evaluate side-chains 139 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 773 MET Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain A residue 945 ILE Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain B residue 658 VAL Chi-restraints excluded: chain B residue 860 ILE Chi-restraints excluded: chain B residue 1020 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 164 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 84 optimal weight: 0.0970 chunk 137 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 170 optimal weight: 0.9980 chunk 155 optimal weight: 0.9980 chunk 136 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A 636 HIS A1010 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.163194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.111401 restraints weight = 15497.470| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.31 r_work: 0.3224 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12491 Z= 0.122 Angle : 0.536 11.341 17068 Z= 0.278 Chirality : 0.042 0.217 1988 Planarity : 0.004 0.061 2209 Dihedral : 7.948 86.965 1937 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.72 % Favored : 95.22 % Rotamer: Outliers : 2.53 % Allowed : 25.07 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.21), residues: 1716 helix: 2.43 (0.17), residues: 964 sheet: 1.18 (0.47), residues: 132 loop : -2.14 (0.22), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 586 HIS 0.003 0.001 HIS A 548 PHE 0.012 0.001 PHE B 664 TYR 0.011 0.001 TYR A 640 ARG 0.003 0.000 ARG B 774 Details of bonding type rmsd hydrogen bonds : bond 0.05805 ( 729) hydrogen bonds : angle 3.77008 ( 2136) SS BOND : bond 0.00522 ( 2) SS BOND : angle 3.10486 ( 4) covalent geometry : bond 0.00251 (12489) covalent geometry : angle 0.53432 (17064) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 112 time to evaluate : 1.366 Fit side-chains REVERT: A 80 ARG cc_start: 0.6198 (OUTLIER) cc_final: 0.5203 (mtp85) REVERT: A 198 LYS cc_start: 0.9075 (OUTLIER) cc_final: 0.8556 (mtpp) REVERT: A 246 GLN cc_start: 0.6359 (tt0) cc_final: 0.5765 (mt0) REVERT: A 344 SER cc_start: 0.8864 (t) cc_final: 0.8582 (m) REVERT: A 406 ASP cc_start: 0.7475 (OUTLIER) cc_final: 0.6710 (t70) REVERT: A 420 CYS cc_start: 0.5532 (OUTLIER) cc_final: 0.5016 (m) REVERT: A 422 TYR cc_start: 0.7619 (m-80) cc_final: 0.7170 (m-80) REVERT: A 605 LYS cc_start: 0.7005 (tppt) cc_final: 0.6708 (tppp) REVERT: A 744 ASN cc_start: 0.8199 (t0) cc_final: 0.7632 (p0) REVERT: A 773 MET cc_start: 0.8951 (OUTLIER) cc_final: 0.8234 (tpp) REVERT: A 895 LEU cc_start: 0.5427 (OUTLIER) cc_final: 0.5125 (pp) REVERT: A 899 ASN cc_start: 0.7622 (m-40) cc_final: 0.6720 (p0) REVERT: B 943 GLU cc_start: 0.7959 (tm-30) cc_final: 0.7701 (tm-30) outliers start: 26 outliers final: 12 residues processed: 132 average time/residue: 1.1343 time to fit residues: 168.0827 Evaluate side-chains 128 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 773 MET Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain B residue 658 VAL Chi-restraints excluded: chain B residue 923 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 50 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 chunk 164 optimal weight: 0.0770 chunk 122 optimal weight: 7.9990 chunk 151 optimal weight: 0.9980 chunk 153 optimal weight: 4.9990 chunk 162 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.163083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.111257 restraints weight = 15231.925| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.24 r_work: 0.3223 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 12491 Z= 0.129 Angle : 0.560 11.771 17068 Z= 0.289 Chirality : 0.042 0.272 1988 Planarity : 0.004 0.062 2209 Dihedral : 7.869 87.379 1937 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.89 % Favored : 94.06 % Rotamer: Outliers : 2.33 % Allowed : 25.95 % Favored : 71.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.21), residues: 1716 helix: 2.49 (0.17), residues: 966 sheet: 1.17 (0.47), residues: 132 loop : -2.09 (0.22), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 586 HIS 0.004 0.001 HIS A 433 PHE 0.012 0.001 PHE B 664 TYR 0.012 0.001 TYR A 640 ARG 0.003 0.000 ARG B 875 Details of bonding type rmsd hydrogen bonds : bond 0.05986 ( 729) hydrogen bonds : angle 3.73000 ( 2136) SS BOND : bond 0.00118 ( 2) SS BOND : angle 4.21092 ( 4) covalent geometry : bond 0.00275 (12489) covalent geometry : angle 0.55683 (17064) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 1.793 Fit side-chains REVERT: A 80 ARG cc_start: 0.6202 (OUTLIER) cc_final: 0.5197 (mtp85) REVERT: A 198 LYS cc_start: 0.9102 (OUTLIER) cc_final: 0.8566 (mtpp) REVERT: A 246 GLN cc_start: 0.6349 (tt0) cc_final: 0.5766 (mt0) REVERT: A 344 SER cc_start: 0.8856 (t) cc_final: 0.8590 (m) REVERT: A 406 ASP cc_start: 0.7498 (OUTLIER) cc_final: 0.6738 (t70) REVERT: A 420 CYS cc_start: 0.5551 (OUTLIER) cc_final: 0.5053 (m) REVERT: A 422 TYR cc_start: 0.7656 (m-80) cc_final: 0.7224 (m-80) REVERT: A 605 LYS cc_start: 0.7076 (tppt) cc_final: 0.6792 (tppp) REVERT: A 744 ASN cc_start: 0.8171 (t0) cc_final: 0.7625 (p0) REVERT: A 773 MET cc_start: 0.8958 (OUTLIER) cc_final: 0.8277 (tpp) REVERT: A 895 LEU cc_start: 0.5364 (OUTLIER) cc_final: 0.5125 (pp) REVERT: A 899 ASN cc_start: 0.7616 (m-40) cc_final: 0.6696 (p0) REVERT: B 732 MET cc_start: 0.9065 (mtm) cc_final: 0.8773 (mtm) REVERT: B 943 GLU cc_start: 0.7912 (tm-30) cc_final: 0.7712 (tm-30) outliers start: 24 outliers final: 13 residues processed: 129 average time/residue: 1.3229 time to fit residues: 188.8210 Evaluate side-chains 128 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 773 MET Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain B residue 658 VAL Chi-restraints excluded: chain B residue 923 PHE Chi-restraints excluded: chain B residue 967 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 26 optimal weight: 5.9990 chunk 151 optimal weight: 0.7980 chunk 92 optimal weight: 20.0000 chunk 39 optimal weight: 0.9980 chunk 169 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 112 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 82 optimal weight: 10.0000 chunk 161 optimal weight: 2.9990 chunk 122 optimal weight: 9.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.164043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.114273 restraints weight = 15583.627| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.23 r_work: 0.3250 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12491 Z= 0.149 Angle : 0.577 12.780 17068 Z= 0.298 Chirality : 0.043 0.283 1988 Planarity : 0.004 0.061 2209 Dihedral : 8.020 85.452 1937 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.00 % Favored : 93.94 % Rotamer: Outliers : 2.33 % Allowed : 25.85 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.21), residues: 1716 helix: 2.38 (0.17), residues: 972 sheet: 1.12 (0.47), residues: 132 loop : -2.09 (0.22), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 611 HIS 0.004 0.001 HIS A 548 PHE 0.013 0.001 PHE B1017 TYR 0.015 0.001 TYR A 640 ARG 0.003 0.000 ARG B 774 Details of bonding type rmsd hydrogen bonds : bond 0.06858 ( 729) hydrogen bonds : angle 3.82776 ( 2136) SS BOND : bond 0.01178 ( 2) SS BOND : angle 2.62895 ( 4) covalent geometry : bond 0.00328 (12489) covalent geometry : angle 0.57609 (17064) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 113 time to evaluate : 1.372 Fit side-chains REVERT: A 80 ARG cc_start: 0.6164 (OUTLIER) cc_final: 0.5135 (mtp85) REVERT: A 198 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8462 (mtpp) REVERT: A 246 GLN cc_start: 0.6337 (tt0) cc_final: 0.5743 (mt0) REVERT: A 344 SER cc_start: 0.8655 (t) cc_final: 0.8369 (m) REVERT: A 406 ASP cc_start: 0.7560 (OUTLIER) cc_final: 0.6859 (t70) REVERT: A 420 CYS cc_start: 0.5420 (OUTLIER) cc_final: 0.4814 (m) REVERT: A 422 TYR cc_start: 0.7582 (m-80) cc_final: 0.7216 (m-80) REVERT: A 605 LYS cc_start: 0.6917 (tppt) cc_final: 0.6643 (tppp) REVERT: A 744 ASN cc_start: 0.8089 (t0) cc_final: 0.7457 (p0) REVERT: A 773 MET cc_start: 0.8997 (OUTLIER) cc_final: 0.8378 (tpp) REVERT: A 899 ASN cc_start: 0.7553 (m-40) cc_final: 0.6573 (p0) REVERT: B 732 MET cc_start: 0.9031 (mtm) cc_final: 0.8740 (mtm) REVERT: B 943 GLU cc_start: 0.7925 (tm-30) cc_final: 0.7675 (tm-30) outliers start: 24 outliers final: 14 residues processed: 131 average time/residue: 1.0833 time to fit residues: 157.5289 Evaluate side-chains 129 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 773 MET Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain B residue 658 VAL Chi-restraints excluded: chain B residue 923 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 120 optimal weight: 30.0000 chunk 118 optimal weight: 6.9990 chunk 160 optimal weight: 3.9990 chunk 172 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 90 optimal weight: 20.0000 chunk 152 optimal weight: 6.9990 chunk 159 optimal weight: 0.6980 chunk 155 optimal weight: 0.7980 chunk 110 optimal weight: 8.9990 chunk 104 optimal weight: 30.0000 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A1010 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.160838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.111105 restraints weight = 15696.035| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.20 r_work: 0.3211 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 12491 Z= 0.207 Angle : 0.652 14.157 17068 Z= 0.336 Chirality : 0.045 0.319 1988 Planarity : 0.005 0.063 2209 Dihedral : 8.284 80.764 1937 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.53 % Favored : 93.41 % Rotamer: Outliers : 2.53 % Allowed : 25.75 % Favored : 71.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.21), residues: 1716 helix: 2.21 (0.17), residues: 967 sheet: 1.03 (0.47), residues: 127 loop : -2.18 (0.22), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 745 HIS 0.005 0.001 HIS A 675 PHE 0.019 0.002 PHE B1017 TYR 0.018 0.002 TYR A 640 ARG 0.005 0.001 ARG B 875 Details of bonding type rmsd hydrogen bonds : bond 0.08471 ( 729) hydrogen bonds : angle 3.94675 ( 2136) SS BOND : bond 0.00235 ( 2) SS BOND : angle 2.95058 ( 4) covalent geometry : bond 0.00488 (12489) covalent geometry : angle 0.65060 (17064) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10350.72 seconds wall clock time: 178 minutes 20.22 seconds (10700.22 seconds total)