Starting phenix.real_space_refine on Sat Oct 11 06:20:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vpn_43411/10_2025/8vpn_43411_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vpn_43411/10_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 { model { file = "/net/cci-nas-00/data/ceres_data/8vpn_43411/10_2025/8vpn_43411_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vpn_43411/10_2025/8vpn_43411_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vpn_43411/10_2025/8vpn_43411.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vpn_43411/10_2025/8vpn_43411.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.037 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: {'TPO:plan-1': 2, 'GLN:plan1': 5, 'GLU:plan': 3, 'HIS:plan': 1, 'ARG:plan': 5, 'ASN:plan1': 3, 'ASP:plan': 1, 'PHE:plan': 2} 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: {'TRP:plan': 13, 'ARG:plan': 11, 'ASN:plan1': 17, 'TYR:plan': 18, 'GLN:plan1': 11, 'PHE:plan': 29, 'GLU:plan': 13, 'HIS:plan': 5, 'ASP:plan': 12} 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: 3.53, per 1000 atoms: 0.29 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: 1.29 Conformation dependent library (CDL) restraints added in 604.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.46 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: 2.29 Time building geometry restraints manager: 1.63 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: 0.010 Normalize map: mean=0, sd=1: 4.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 13.960 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.320 ------------------------------------------------------------------------------- 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 : 17.35 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.009 0.001 ARG B1001 TYR 0.015 0.002 TYR A 768 PHE 0.014 0.002 PHE A 707 TRP 0.013 0.002 TRP A 171 HIS 0.005 0.001 HIS A 548 Details of bonding type rmsd covalent geometry : bond 0.00695 (12489) covalent geometry : angle 0.82398 (17064) SS BOND : bond 0.00077 ( 2) SS BOND : angle 1.31911 ( 4) hydrogen bonds : bond 0.19050 ( 729) hydrogen bonds : angle 5.97064 ( 2136) *********************** 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 : 0.477 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: 0.5728 time to fit residues: 136.9372 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 : 0.521 ------------------------------------------------------------------------------- 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 98 optimal weight: 20.0000 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 30.0000 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 0.7980 overall best weight: 1.3982 ------------------------------------------------------------------------------- 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 533 ASN 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.163512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.111503 restraints weight = 15384.634| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.27 r_work: 0.3221 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 12491 Z= 0.168 Angle : 0.650 10.949 17068 Z= 0.338 Chirality : 0.044 0.208 1988 Planarity : 0.005 0.071 2209 Dihedral : 8.725 86.320 1962 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.41 % Favored : 93.36 % Rotamer: Outliers : 4.18 % Allowed : 24.20 % Favored : 71.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.21), residues: 1716 helix: 2.01 (0.18), residues: 948 sheet: 0.34 (0.47), residues: 136 loop : -2.60 (0.22), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B1001 TYR 0.020 0.002 TYR A 768 PHE 0.013 0.002 PHE A 288 TRP 0.012 0.002 TRP A 611 HIS 0.011 0.001 HIS A 433 Details of bonding type rmsd covalent geometry : bond 0.00373 (12489) covalent geometry : angle 0.64945 (17064) SS BOND : bond 0.00866 ( 2) SS BOND : angle 2.17375 ( 4) hydrogen bonds : bond 0.07458 ( 729) hydrogen bonds : angle 4.32601 ( 2136) *********************** 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 172 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 129 time to evaluate : 0.547 Fit side-chains REVERT: A 246 GLN cc_start: 0.6663 (tt0) cc_final: 0.6157 (mt0) REVERT: A 344 SER cc_start: 0.8886 (t) cc_final: 0.8626 (m) REVERT: A 422 TYR cc_start: 0.7592 (m-80) cc_final: 0.7136 (m-80) REVERT: A 523 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7711 (tp30) REVERT: A 596 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8402 (tt) REVERT: A 731 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7687 (mtt180) REVERT: A 744 ASN cc_start: 0.7980 (t0) cc_final: 0.7215 (p0) REVERT: A 895 LEU cc_start: 0.5390 (OUTLIER) cc_final: 0.4763 (pp) REVERT: A 899 ASN cc_start: 0.7568 (m-40) cc_final: 0.6749 (p0) REVERT: A 906 HIS cc_start: 0.7340 (m90) cc_final: 0.7050 (m170) REVERT: A 942 ASP cc_start: 0.6642 (t0) cc_final: 0.6371 (m-30) REVERT: B 773 MET cc_start: 0.9055 (ttt) cc_final: 0.8778 (ttt) REVERT: B 943 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7965 (tm-30) REVERT: B 1001 ARG cc_start: 0.5816 (OUTLIER) cc_final: 0.3518 (mtp180) outliers start: 43 outliers final: 16 residues processed: 162 average time/residue: 0.5810 time to fit residues: 102.5876 Evaluate side-chains 132 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.473 ------------------------------------------------------------------------------- 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 427 THR Chi-restraints excluded: chain A residue 447 SER 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 667 ASN 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 167 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 93 optimal weight: 20.0000 chunk 29 optimal weight: 0.8980 chunk 80 optimal weight: 9.9990 chunk 32 optimal weight: 0.0060 chunk 81 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 overall best weight: 1.5802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 GLN A1010 ASN B 725 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.161268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.108587 restraints weight = 15584.648| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.32 r_work: 0.3174 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12491 Z= 0.168 Angle : 0.610 11.150 17068 Z= 0.318 Chirality : 0.043 0.206 1988 Planarity : 0.005 0.063 2209 Dihedral : 8.392 84.118 1941 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.12 % Favored : 93.76 % Rotamer: Outliers : 3.98 % Allowed : 23.71 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.21), residues: 1716 helix: 2.11 (0.17), residues: 956 sheet: 0.75 (0.48), residues: 127 loop : -2.36 (0.21), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 949 TYR 0.017 0.002 TYR A 640 PHE 0.014 0.002 PHE B 664 TRP 0.010 0.001 TRP A 611 HIS 0.004 0.001 HIS A 548 Details of bonding type rmsd covalent geometry : bond 0.00373 (12489) covalent geometry : angle 0.60912 (17064) SS BOND : bond 0.01116 ( 2) SS BOND : angle 2.52997 ( 4) hydrogen bonds : bond 0.07536 ( 729) hydrogen bonds : angle 4.14352 ( 2136) *********************** 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 159 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 118 time to evaluate : 0.460 Fit side-chains REVERT: A 246 GLN cc_start: 0.6601 (tt0) cc_final: 0.6060 (mt0) REVERT: A 300 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7666 (tp) REVERT: A 344 SER cc_start: 0.8815 (t) cc_final: 0.8558 (m) REVERT: A 422 TYR cc_start: 0.7580 (m-80) cc_final: 0.7214 (m-80) REVERT: A 523 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7848 (tp30) REVERT: A 605 LYS cc_start: 0.7125 (tppt) cc_final: 0.6652 (tppp) REVERT: A 731 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.7710 (mtt180) REVERT: A 744 ASN cc_start: 0.8068 (t0) cc_final: 0.7413 (p0) REVERT: A 895 LEU cc_start: 0.5507 (OUTLIER) cc_final: 0.4940 (pp) REVERT: A 899 ASN cc_start: 0.7678 (m-40) cc_final: 0.6857 (p0) REVERT: A 906 HIS cc_start: 0.7335 (m90) cc_final: 0.7020 (m170) REVERT: A 942 ASP cc_start: 0.6764 (t0) cc_final: 0.6452 (m-30) REVERT: B 773 MET cc_start: 0.9107 (ttt) cc_final: 0.8901 (ttt) REVERT: B 911 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.6827 (mm-30) REVERT: B 943 GLU cc_start: 0.8082 (tm-30) cc_final: 0.7851 (tm-30) outliers start: 41 outliers final: 15 residues processed: 148 average time/residue: 0.5443 time to fit residues: 88.4747 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 : 0.515 ------------------------------------------------------------------------------- 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 181 THR Chi-restraints excluded: chain A residue 191 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 300 LEU 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 747 SER 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 911 GLU Chi-restraints excluded: chain B residue 1020 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 9 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 107 optimal weight: 20.0000 chunk 70 optimal weight: 1.9990 chunk 150 optimal weight: 4.9990 chunk 54 optimal weight: 0.1980 chunk 92 optimal weight: 20.0000 chunk 140 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 75 optimal weight: 20.0000 chunk 168 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 ASN A 425 ASN A1010 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 = 0.3927 r_free = 0.3927 target = 0.160783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.108922 restraints weight = 15339.504| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.23 r_work: 0.3186 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12491 Z= 0.153 Angle : 0.584 12.098 17068 Z= 0.303 Chirality : 0.043 0.179 1988 Planarity : 0.004 0.060 2209 Dihedral : 8.241 87.915 1939 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.24 % Favored : 93.65 % Rotamer: Outliers : 4.18 % Allowed : 23.52 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.21), residues: 1716 helix: 2.25 (0.17), residues: 955 sheet: 0.94 (0.49), residues: 127 loop : -2.27 (0.22), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 949 TYR 0.015 0.001 TYR A 640 PHE 0.015 0.001 PHE B 664 TRP 0.010 0.001 TRP A 586 HIS 0.004 0.001 HIS A 548 Details of bonding type rmsd covalent geometry : bond 0.00337 (12489) covalent geometry : angle 0.58038 (17064) SS BOND : bond 0.01011 ( 2) SS BOND : angle 4.21289 ( 4) hydrogen bonds : bond 0.07004 ( 729) hydrogen bonds : angle 3.94297 ( 2136) *********************** 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 157 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 114 time to evaluate : 0.362 Fit side-chains REVERT: A 80 ARG cc_start: 0.6126 (OUTLIER) cc_final: 0.5277 (ttt90) REVERT: A 198 LYS cc_start: 0.9139 (OUTLIER) cc_final: 0.8621 (mtpp) REVERT: A 246 GLN cc_start: 0.6488 (tt0) cc_final: 0.5900 (mt0) REVERT: A 300 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7719 (tp) REVERT: A 344 SER cc_start: 0.8833 (t) cc_final: 0.8568 (m) REVERT: A 422 TYR cc_start: 0.7631 (m-80) cc_final: 0.7351 (m-80) REVERT: A 605 LYS cc_start: 0.7150 (tppt) cc_final: 0.6366 (tmtt) REVERT: A 744 ASN cc_start: 0.8111 (t0) cc_final: 0.7530 (p0) REVERT: A 895 LEU cc_start: 0.5424 (OUTLIER) cc_final: 0.4831 (pp) REVERT: A 899 ASN cc_start: 0.7654 (m-40) cc_final: 0.6804 (p0) REVERT: A 906 HIS cc_start: 0.7191 (m90) cc_final: 0.6908 (m170) REVERT: A 942 ASP cc_start: 0.6796 (t0) cc_final: 0.6492 (m-30) REVERT: B 732 MET cc_start: 0.9089 (mtm) cc_final: 0.8772 (mtm) REVERT: B 773 MET cc_start: 0.9072 (ttt) cc_final: 0.8866 (ttt) REVERT: B 921 ASP cc_start: 0.6378 (t0) cc_final: 0.6135 (t70) REVERT: B 943 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7821 (tm-30) outliers start: 43 outliers final: 18 residues processed: 149 average time/residue: 0.5771 time to fit residues: 93.8971 Evaluate side-chains 124 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.487 ------------------------------------------------------------------------------- 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 181 THR 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 256 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 300 LEU 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 665 THR Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 820 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 102 optimal weight: 5.9990 chunk 143 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 141 optimal weight: 0.6980 chunk 148 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 93 optimal weight: 20.0000 chunk 144 optimal weight: 2.9990 chunk 159 optimal weight: 0.8980 chunk 121 optimal weight: 30.0000 chunk 155 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A 358 ASN A 636 HIS A1010 ASN B 893 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.160735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.109583 restraints weight = 15345.660| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.25 r_work: 0.3184 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.3019 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= 0.147 Angle : 0.571 12.245 17068 Z= 0.296 Chirality : 0.042 0.208 1988 Planarity : 0.004 0.060 2209 Dihedral : 8.137 88.336 1937 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.77 % Favored : 94.11 % Rotamer: Outliers : 3.50 % Allowed : 23.91 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.21), residues: 1716 helix: 2.31 (0.17), residues: 963 sheet: 0.97 (0.48), residues: 132 loop : -2.21 (0.22), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 949 TYR 0.015 0.001 TYR A 640 PHE 0.014 0.001 PHE B 664 TRP 0.010 0.001 TRP A 586 HIS 0.003 0.001 HIS A 548 Details of bonding type rmsd covalent geometry : bond 0.00323 (12489) covalent geometry : angle 0.56958 (17064) SS BOND : bond 0.00138 ( 2) SS BOND : angle 2.94544 ( 4) hydrogen bonds : bond 0.06777 ( 729) hydrogen bonds : angle 3.87176 ( 2136) *********************** 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: 36 poor density : 108 time to evaluate : 0.502 Fit side-chains REVERT: A 80 ARG cc_start: 0.6100 (OUTLIER) cc_final: 0.5262 (ttt90) REVERT: A 198 LYS cc_start: 0.9111 (OUTLIER) cc_final: 0.8619 (mtpp) REVERT: A 246 GLN cc_start: 0.6475 (tt0) cc_final: 0.5875 (mt0) REVERT: A 300 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7678 (tp) REVERT: A 344 SER cc_start: 0.8835 (t) cc_final: 0.8585 (m) REVERT: A 422 TYR cc_start: 0.7663 (m-80) cc_final: 0.7183 (m-80) REVERT: A 605 LYS cc_start: 0.7144 (tppt) cc_final: 0.6431 (tmtt) REVERT: A 744 ASN cc_start: 0.8189 (t0) cc_final: 0.7633 (p0) REVERT: A 895 LEU cc_start: 0.5472 (OUTLIER) cc_final: 0.5160 (pp) REVERT: A 899 ASN cc_start: 0.7637 (m-40) cc_final: 0.6734 (p0) REVERT: A 942 ASP cc_start: 0.6758 (t0) cc_final: 0.6442 (m-30) REVERT: B 732 MET cc_start: 0.9092 (mtm) cc_final: 0.8771 (mtm) REVERT: B 921 ASP cc_start: 0.6446 (t0) cc_final: 0.6213 (t70) REVERT: B 943 GLU cc_start: 0.8079 (tm-30) cc_final: 0.7813 (tm-30) outliers start: 36 outliers final: 17 residues processed: 133 average time/residue: 0.5568 time to fit residues: 81.4517 Evaluate side-chains 125 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 0.469 ------------------------------------------------------------------------------- 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 181 THR 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 300 LEU 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 665 THR Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 820 ILE 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 860 ILE Chi-restraints excluded: chain B residue 1020 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 112 optimal weight: 8.9990 chunk 133 optimal weight: 7.9990 chunk 158 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 10 optimal weight: 0.0060 chunk 62 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 overall best weight: 1.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN B 621 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.160513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.108512 restraints weight = 15285.932| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.24 r_work: 0.3179 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.3193 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= 0.150 Angle : 0.574 12.692 17068 Z= 0.297 Chirality : 0.042 0.193 1988 Planarity : 0.004 0.059 2209 Dihedral : 8.105 84.493 1937 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.29 % Favored : 93.65 % Rotamer: Outliers : 3.79 % Allowed : 23.81 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.21), residues: 1716 helix: 2.34 (0.17), residues: 967 sheet: 1.04 (0.49), residues: 127 loop : -2.14 (0.22), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 949 TYR 0.015 0.001 TYR A 640 PHE 0.013 0.001 PHE B 664 TRP 0.009 0.001 TRP A 586 HIS 0.003 0.001 HIS A 548 Details of bonding type rmsd covalent geometry : bond 0.00331 (12489) covalent geometry : angle 0.57197 (17064) SS BOND : bond 0.00182 ( 2) SS BOND : angle 3.01343 ( 4) hydrogen bonds : bond 0.06891 ( 729) hydrogen bonds : angle 3.85309 ( 2136) *********************** 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 148 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 109 time to evaluate : 0.453 Fit side-chains REVERT: A 62 ASP cc_start: 0.8279 (OUTLIER) cc_final: 0.7826 (m-30) REVERT: A 80 ARG cc_start: 0.6126 (OUTLIER) cc_final: 0.5285 (ttt90) REVERT: A 198 LYS cc_start: 0.9147 (OUTLIER) cc_final: 0.8622 (mtpp) REVERT: A 246 GLN cc_start: 0.6492 (tt0) cc_final: 0.5885 (mt0) REVERT: A 300 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7677 (tp) REVERT: A 344 SER cc_start: 0.8843 (t) cc_final: 0.8594 (m) REVERT: A 422 TYR cc_start: 0.7680 (m-80) cc_final: 0.7234 (m-80) REVERT: A 605 LYS cc_start: 0.7206 (tppt) cc_final: 0.6487 (tmtt) REVERT: A 744 ASN cc_start: 0.8181 (t0) cc_final: 0.7670 (p0) REVERT: A 895 LEU cc_start: 0.5452 (OUTLIER) cc_final: 0.5162 (pp) REVERT: A 899 ASN cc_start: 0.7596 (m-40) cc_final: 0.6700 (p0) REVERT: A 942 ASP cc_start: 0.6694 (t0) cc_final: 0.6427 (m-30) REVERT: B 732 MET cc_start: 0.9092 (mtm) cc_final: 0.8778 (mtm) REVERT: B 775 MET cc_start: 0.9294 (mtp) cc_final: 0.9070 (ttt) REVERT: B 943 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7856 (tm-30) outliers start: 39 outliers final: 18 residues processed: 136 average time/residue: 0.5256 time to fit residues: 78.6246 Evaluate side-chains 129 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASP 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 181 THR 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 256 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 820 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 128 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 127 optimal weight: 7.9990 chunk 117 optimal weight: 30.0000 chunk 98 optimal weight: 10.0000 chunk 87 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.163154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.111569 restraints weight = 15148.617| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.22 r_work: 0.3224 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 12491 Z= 0.126 Angle : 0.546 11.832 17068 Z= 0.284 Chirality : 0.041 0.197 1988 Planarity : 0.004 0.061 2209 Dihedral : 7.811 80.236 1937 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.13 % Favored : 94.81 % Rotamer: Outliers : 2.82 % Allowed : 24.59 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.21), residues: 1716 helix: 2.49 (0.17), residues: 970 sheet: 1.10 (0.48), residues: 132 loop : -2.06 (0.22), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 949 TYR 0.012 0.001 TYR A 640 PHE 0.013 0.001 PHE B 664 TRP 0.011 0.001 TRP A 586 HIS 0.003 0.001 HIS A 548 Details of bonding type rmsd covalent geometry : bond 0.00263 (12489) covalent geometry : angle 0.54100 (17064) SS BOND : bond 0.00491 ( 2) SS BOND : angle 4.92104 ( 4) hydrogen bonds : bond 0.05739 ( 729) hydrogen bonds : angle 3.72436 ( 2136) *********************** 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 144 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 115 time to evaluate : 0.467 Fit side-chains REVERT: A 80 ARG cc_start: 0.6201 (OUTLIER) cc_final: 0.5302 (ttt90) REVERT: A 198 LYS cc_start: 0.9094 (OUTLIER) cc_final: 0.8591 (mtpp) REVERT: A 246 GLN cc_start: 0.6351 (tt0) cc_final: 0.5757 (mt0) REVERT: A 300 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.7441 (tp) REVERT: A 344 SER cc_start: 0.8840 (t) cc_final: 0.8588 (m) REVERT: A 422 TYR cc_start: 0.7651 (m-80) cc_final: 0.7286 (m-80) REVERT: A 605 LYS cc_start: 0.7073 (tppt) cc_final: 0.6772 (tppp) REVERT: A 744 ASN cc_start: 0.8154 (t0) cc_final: 0.7624 (p0) REVERT: A 895 LEU cc_start: 0.5392 (OUTLIER) cc_final: 0.5118 (pp) REVERT: A 899 ASN cc_start: 0.7609 (m-40) cc_final: 0.6684 (p0) REVERT: A 942 ASP cc_start: 0.6604 (t0) cc_final: 0.6379 (m-30) REVERT: B 732 MET cc_start: 0.9058 (mtm) cc_final: 0.8763 (mtm) outliers start: 29 outliers final: 14 residues processed: 138 average time/residue: 0.5433 time to fit residues: 82.6244 Evaluate side-chains 125 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.496 ------------------------------------------------------------------------------- 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 256 ILE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 820 ILE 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 860 ILE Chi-restraints excluded: chain B residue 923 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 60 optimal weight: 8.9990 chunk 138 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 15 optimal weight: 0.9990 chunk 128 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 119 optimal weight: 0.0470 chunk 35 optimal weight: 3.9990 chunk 116 optimal weight: 20.0000 overall best weight: 1.5284 ------------------------------------------------------------------------------- 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 = 0.3916 r_free = 0.3916 target = 0.159898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.108131 restraints weight = 15210.811| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.22 r_work: 0.3173 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12491 Z= 0.157 Angle : 0.582 13.187 17068 Z= 0.300 Chirality : 0.043 0.265 1988 Planarity : 0.004 0.061 2209 Dihedral : 7.981 82.672 1937 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.18 % Favored : 93.76 % Rotamer: Outliers : 3.79 % Allowed : 23.81 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.21), residues: 1716 helix: 2.36 (0.17), residues: 972 sheet: 1.10 (0.48), residues: 127 loop : -2.08 (0.22), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 967 TYR 0.015 0.001 TYR A 640 PHE 0.014 0.001 PHE B1017 TRP 0.008 0.001 TRP A 586 HIS 0.003 0.001 HIS A 433 Details of bonding type rmsd covalent geometry : bond 0.00352 (12489) covalent geometry : angle 0.58062 (17064) SS BOND : bond 0.00417 ( 2) SS BOND : angle 2.68038 ( 4) hydrogen bonds : bond 0.07008 ( 729) hydrogen bonds : angle 3.80458 ( 2136) *********************** 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 148 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 109 time to evaluate : 0.469 Fit side-chains REVERT: A 62 ASP cc_start: 0.8286 (OUTLIER) cc_final: 0.7820 (m-30) REVERT: A 80 ARG cc_start: 0.6224 (OUTLIER) cc_final: 0.5413 (ttt90) REVERT: A 198 LYS cc_start: 0.9140 (OUTLIER) cc_final: 0.8634 (mtpp) REVERT: A 246 GLN cc_start: 0.6495 (tt0) cc_final: 0.5893 (mt0) REVERT: A 300 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7569 (tp) REVERT: A 344 SER cc_start: 0.8847 (t) cc_final: 0.8584 (m) REVERT: A 605 LYS cc_start: 0.7233 (tppt) cc_final: 0.6518 (tmtt) REVERT: A 614 SER cc_start: 0.8778 (OUTLIER) cc_final: 0.8574 (m) REVERT: A 744 ASN cc_start: 0.8167 (t0) cc_final: 0.7657 (p0) REVERT: A 895 LEU cc_start: 0.5466 (OUTLIER) cc_final: 0.4881 (pp) REVERT: A 899 ASN cc_start: 0.7517 (m-40) cc_final: 0.6633 (p0) REVERT: A 942 ASP cc_start: 0.6618 (t0) cc_final: 0.6384 (m-30) REVERT: A 1001 ARG cc_start: 0.7960 (ttm-80) cc_final: 0.7679 (mtp180) REVERT: B 732 MET cc_start: 0.9097 (mtm) cc_final: 0.8797 (mtm) outliers start: 39 outliers final: 24 residues processed: 138 average time/residue: 0.5215 time to fit residues: 79.4777 Evaluate side-chains 139 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 109 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASP 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 181 THR 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 256 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 820 ILE 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 A residue 1010 ASN Chi-restraints excluded: chain B residue 658 VAL Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain B residue 860 ILE Chi-restraints excluded: chain B residue 901 ASN Chi-restraints excluded: chain B residue 923 PHE Chi-restraints excluded: chain B residue 1020 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 17 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 111 optimal weight: 9.9990 chunk 118 optimal weight: 20.0000 chunk 136 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 141 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A 432 GLN A1010 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.163945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.114042 restraints weight = 15512.331| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.22 r_work: 0.3213 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12491 Z= 0.145 Angle : 0.580 12.725 17068 Z= 0.299 Chirality : 0.043 0.260 1988 Planarity : 0.004 0.065 2209 Dihedral : 7.858 82.096 1937 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.48 % Favored : 94.46 % Rotamer: Outliers : 3.30 % Allowed : 24.88 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.21), residues: 1716 helix: 2.42 (0.17), residues: 970 sheet: 1.05 (0.47), residues: 132 loop : -2.08 (0.22), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 967 TYR 0.015 0.001 TYR A 422 PHE 0.013 0.001 PHE B 664 TRP 0.010 0.001 TRP A 586 HIS 0.003 0.001 HIS A 548 Details of bonding type rmsd covalent geometry : bond 0.00321 (12489) covalent geometry : angle 0.57680 (17064) SS BOND : bond 0.00369 ( 2) SS BOND : angle 3.97607 ( 4) hydrogen bonds : bond 0.06637 ( 729) hydrogen bonds : angle 3.78214 ( 2136) *********************** 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 143 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 109 time to evaluate : 0.496 Fit side-chains REVERT: A 62 ASP cc_start: 0.8197 (OUTLIER) cc_final: 0.7783 (m-30) REVERT: A 80 ARG cc_start: 0.6198 (OUTLIER) cc_final: 0.5382 (ttt90) REVERT: A 198 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8533 (mtpp) REVERT: A 246 GLN cc_start: 0.6415 (tt0) cc_final: 0.5809 (mt0) REVERT: A 300 LEU cc_start: 0.7557 (OUTLIER) cc_final: 0.7343 (tp) REVERT: A 344 SER cc_start: 0.8714 (t) cc_final: 0.8442 (m) REVERT: A 420 CYS cc_start: 0.5562 (OUTLIER) cc_final: 0.4951 (m) REVERT: A 422 TYR cc_start: 0.7543 (m-80) cc_final: 0.7190 (m-80) REVERT: A 605 LYS cc_start: 0.6999 (tppt) cc_final: 0.6694 (tppp) REVERT: A 744 ASN cc_start: 0.8049 (t0) cc_final: 0.7475 (p0) REVERT: A 899 ASN cc_start: 0.7537 (m-40) cc_final: 0.6577 (p0) REVERT: A 942 ASP cc_start: 0.6526 (t0) cc_final: 0.6310 (m-30) REVERT: B 732 MET cc_start: 0.9038 (mtm) cc_final: 0.8771 (mtm) outliers start: 34 outliers final: 22 residues processed: 134 average time/residue: 0.5182 time to fit residues: 76.5311 Evaluate side-chains 135 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 108 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASP 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 181 THR 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 256 ILE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain A residue 432 GLN Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 820 ILE 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 820 ILE Chi-restraints excluded: chain B residue 860 ILE Chi-restraints excluded: chain B residue 901 ASN 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 47 optimal weight: 0.1980 chunk 76 optimal weight: 3.9990 chunk 157 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 24 optimal weight: 0.2980 chunk 45 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 163 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A 431 GLN A 432 GLN A1010 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.163908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.114056 restraints weight = 15695.328| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.23 r_work: 0.3212 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.3471 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= 0.143 Angle : 0.569 12.591 17068 Z= 0.293 Chirality : 0.042 0.285 1988 Planarity : 0.004 0.067 2209 Dihedral : 7.770 81.892 1937 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.77 % Favored : 94.17 % Rotamer: Outliers : 3.01 % Allowed : 24.88 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.21), residues: 1716 helix: 2.42 (0.17), residues: 970 sheet: 1.06 (0.47), residues: 132 loop : -2.07 (0.22), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 967 TYR 0.014 0.001 TYR A 640 PHE 0.013 0.001 PHE B 664 TRP 0.010 0.001 TRP A 586 HIS 0.005 0.001 HIS A 433 Details of bonding type rmsd covalent geometry : bond 0.00314 (12489) covalent geometry : angle 0.56796 (17064) SS BOND : bond 0.00356 ( 2) SS BOND : angle 2.79009 ( 4) hydrogen bonds : bond 0.06607 ( 729) hydrogen bonds : angle 3.79143 ( 2136) ********************** 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 138 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 107 time to evaluate : 0.487 Fit side-chains REVERT: A 62 ASP cc_start: 0.8191 (OUTLIER) cc_final: 0.7781 (m-30) REVERT: A 80 ARG cc_start: 0.6196 (OUTLIER) cc_final: 0.5307 (ttt90) REVERT: A 198 LYS cc_start: 0.9035 (OUTLIER) cc_final: 0.8538 (mtpp) REVERT: A 246 GLN cc_start: 0.6424 (tt0) cc_final: 0.5815 (mt0) REVERT: A 300 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7346 (tp) REVERT: A 344 SER cc_start: 0.8711 (t) cc_final: 0.8439 (m) REVERT: A 422 TYR cc_start: 0.7547 (m-80) cc_final: 0.7199 (m-80) REVERT: A 605 LYS cc_start: 0.7030 (tppt) cc_final: 0.6721 (tppp) REVERT: A 744 ASN cc_start: 0.8052 (t0) cc_final: 0.7486 (p0) REVERT: A 899 ASN cc_start: 0.7517 (m-40) cc_final: 0.6548 (p0) REVERT: A 942 ASP cc_start: 0.6534 (t0) cc_final: 0.6314 (m-30) REVERT: B 732 MET cc_start: 0.9041 (mtm) cc_final: 0.8771 (mtm) outliers start: 31 outliers final: 23 residues processed: 131 average time/residue: 0.5201 time to fit residues: 75.1186 Evaluate side-chains 134 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 107 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASP 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 256 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 432 GLN Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 820 ILE 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 860 ILE Chi-restraints excluded: chain B residue 901 ASN Chi-restraints excluded: chain B residue 923 PHE Chi-restraints excluded: chain B residue 1020 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 129 optimal weight: 10.0000 chunk 161 optimal weight: 5.9990 chunk 131 optimal weight: 8.9990 chunk 106 optimal weight: 30.0000 chunk 68 optimal weight: 0.7980 chunk 21 optimal weight: 7.9990 chunk 87 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A 431 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.165627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.115968 restraints weight = 15564.168| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.22 r_work: 0.3227 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12491 Z= 0.125 Angle : 0.549 11.845 17068 Z= 0.284 Chirality : 0.042 0.265 1988 Planarity : 0.004 0.064 2209 Dihedral : 7.559 80.002 1937 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.07 % Favored : 94.87 % Rotamer: Outliers : 2.92 % Allowed : 25.07 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.21), residues: 1716 helix: 2.52 (0.17), residues: 972 sheet: 1.14 (0.47), residues: 132 loop : -2.00 (0.23), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 774 TYR 0.013 0.001 TYR A 422 PHE 0.013 0.001 PHE B 664 TRP 0.011 0.001 TRP A 586 HIS 0.004 0.001 HIS A 433 Details of bonding type rmsd covalent geometry : bond 0.00262 (12489) covalent geometry : angle 0.54696 (17064) SS BOND : bond 0.00204 ( 2) SS BOND : angle 2.81480 ( 4) hydrogen bonds : bond 0.05878 ( 729) hydrogen bonds : angle 3.68720 ( 2136) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5211.66 seconds wall clock time: 89 minutes 6.94 seconds (5346.94 seconds total)